Biomolecular Machines

Ribosomal Quality Control

2009-01-19T11:15:00.000-08:00

In order to demonstrate the validity of viewing cells as computers that are able to manipulate information, consider the following finding.

The Ribosome: Perfectionist Protein-maker Trashes Errors

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ScienceDaily (Jan. 9, 2009) — The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist.

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It turns out, the Johns Hopkins researchers say, that the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products which, as workhorses of the cell, carry out the very business of life.

"What we now know is that in the event of miscoding, the ribosome cuts the bond and aborts the protein-in-progress, end of story," says Rachel Green, a Howard Hughes Medical Institute investigator and professor of molecular biology and genetics in the Johns Hopkins University School of Medicine. "There's no second chance." Previously, Green says, molecular biologists thought the ribosome tightly managed its actions only prior to the actual incorporation of the next building block by being super-selective about which chemical ingredients it allows to enter the process.

Because a protein's chemical "shape" dictates its function, mistakes in translating assembly codes can be toxic to cells, resulting in the misfolding of proteins often associated with neurodegenerative conditions. Working with bacterial ribosomes, Green and her team watched them react to lab-induced chemical errors and were surprised to see that the protein-manufacturing process didn't proceed as usual, getting past the error and continuing its "walk" along the DNA's protein-encoding genetic messages.

"We thought that once the mistake was made, it would have just gone on to make the next bond and the next," Green says. "But instead, we noticed that one mistake on the ribosomal assembly line begets another, and it's this compounding of errors that leads to the partially finished protein being tossed into the cellular trash," she adds.

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So what is being monitored by the ribosome? Information. Material representations (amino acid sequence vs DNA sequence) of information. But, it does not only monitor it, it manipulates it as a means to an end... fidelity.

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To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis.

"These are not subtle numbers," she says, noting that there's a clear biological cost for this ribosomal editing and jettisoning of errors, but a necessary expense.

"The cell is a wasteful system in that it makes something and then says, forget it, throw it out," Green concedes. "But it's evidently worth the waste to increase fidelity. There are places in life where fidelity matters."

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The ribosome is optimized to manipulate information for fidelity.

Preaching bad design: An argument from ignorance?

2009-01-04T08:37:00.000-08:00

Over the years many people have come with arguments that systems in nature are sub-optimal, or sub-par. These arguments were used as a means to point out that they are "dumb" designs if it was the product of mind.

An example of such an argument is given by Richard Dawkins. Take his article:
The Information Challenge

Quote:

Genomes are littered with nonfunctional pseudogenes, faulty duplicates of functional genes that do nothing, while their functional cousins (the word doesn't even need scare quotes) get on with their business in a different part of the same genome. And there's lots more DNA that doesn't even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, "tandem repeats", and other nonsense which may be useful for forensic detectives but which doesn't seem to be used in the body itself.

Luckily science moves forward and these arguments from ignorance get left behind and the proponents of these arguments fade into history as proponents of ignorance trying to sell meaningless metaphysics.

Junk DNA is a myth.
Examples abound of research finding fascinating functions for these previously thought non-functional parts of the genome (out of ignorance and bad metaphysics-- Dawkins: "And there's lots more DNA that doesn't even deserve the name pseudogene.").

Model unravels rules that govern how genes are switched on and off

Quote:

"Since the discovery of DNA's double helical structure more than a half century ago, scientists have focused much of their attention on understanding the 2 percent of the genome that is made up of classic genes, which code for the production of proteins.

However, the instructions for turning these genes on or off are generally not in the genes themselves. Rather, they are buried in the 98 percent of the genome that was once cast aside as little more than genetic "junk."

Scientists at CSHL uncover new RNA processing mechanism and a class of previously unknown small RNAs

Quote:

A very small fraction of our genetic material--about 2%-- performs the crucial task scientists once thought was the sole purpose of the genome: to serve as a blueprint for the production of proteins, the molecules that make cells work and sustain life. This 2% of human DNA is converted into intermediary molecules called RNAs, which in turn carry instructions within cells for protein manufacture.
"And what of the other 98% of the genome? It has been assumed by many to be genetic junk, a massive accumulation of “code” that evolution has rendered superfluous. Now, however, scientists are discovering that the vast bulk of the DNA in our genomes, while it does not “code” for the specific RNA molecules that serve as templates for protein synthesis, do nevertheless perform various kinds of work."

'Junk' DNA May Have Important Role In Gene Regulation

Quote:

ScienceDaily (Oct. 20, 2008) — For about 15 years, scientists have known that certain "junk" DNA -- repetitive DNA segments previously thought to have no function -- could evolve into exons, which are the building blocks for protein-coding genes in higher organisms like animals and plants. Now, a University of Iowa study has found evidence that a significant number of exons created from junk DNA seem to play a role in gene regulation.

Well, it is not only supposedly "junk DNA" that was used for these kind of arguments. The vertebrate eye has been preached to be a bad design. Why? Why is it a bad design?

The human eye contain bona fide optical fibers to conduct light and here is a nice illustration. Besides the design arose 40-60 times during evolution, like evolution was biased (converged on an optimal design) towards such a structure. So why is it sub optimal? Are proponents of these arguments going to suggest a better design with all the blueprints? Thought not, arguments from ignorance are short on design.

Why was it suggested that the appendix is useless and functionless, instead of just admitting "we are still looking into it".
A few articles discussing its function:
1) Dasso JF. Howell MD. 1997. "Neonatal appendectomy impairs mucosal immunity in rabbits." Cellular Immunology. 182(1):29-37.
2) Dasso JF. Obiakor H. Bach H. Anderson AO. Mage RG. 2000. "A morphological and immunohistological study of the human and rabbit appendix for comparison with the avian bursa." Developmental & Comparative Immunology. 24:8:797-814.
3) Fisher, RE. 2000. "The primate appendix: a reassessment." The Anatomical Record (New Anatomist) 261:228-236.
4) Weinstein PD. Mage RG. Anderson AO. 1994. "The appendix functions as a mammalian bursal equivalent in the developing rabbit." Advances in Experimental Medicine & Biology. 355:249-53.
5) A more detailed survey of the evidence, with numerous references to other technical literature, showing that the appendix is not a vestigial organ can be found in J.W. Glover, The Human Vermiform Appendix—a General Surgeon’s Reflections, CEN Technical Journal, 3:31–38, 1988.

In short:
The appendix contains a high concentration of very specialized structures called lymphoid follicles (also found throughout the GIT). Lymphoid follicles in the appendix produce cells that produce antibodies that control which essential bacteria come to reside in the caecum and colon in neonatal life. The "strategic" placement of the appendix is important during the development of neonatal life in the setup of healthy intestinal flora therefore neonatal appendectomy will impair mucosal immunity.

"The appendix's job is to reboot the digestive system..." and "acts as a good safe house for bacteria,".

It might not be that important in later life and it can be removed, but so can your one kidney, your stomach, an eye, small intestines, reproductive organs etc. Are these bad designs then as well? See... these arguments have no force. Empty arguments from ignorance...

And the cilium? Until the 1990s, the prevailing view of the primary cilium was that it was merely a vestigial organelle, without important function (wiki). Seems like pretty high-tech structures to me?

Primary Cilium As Cellular 'GPS System' Crucial To Wound Repair

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ScienceDaily (Dec. 25, 2008) — The primary cilium, the solitary, antenna-like structure that studs the outer surfaces of virtually all human cells, orient cells to move in the right direction and at the speed needed to heal wounds, much like a Global Positioning System helps ships navigate to their destinations.

Quote:

What we are dealing with is a physiological analogy to the GPS system with a coupled autopilot that coordinates air traffic or tankers on open sea," says Soren T. Christensen, describing his recent research findings on the primary cilium, the GPS-like cell structure, at the American Society for Cell Biology (ASCB) 48th Annual Meeting, Dec. 13-17, 2008 in San Francisco.

Christensen and his colleagues at the University of Copenhagen in Denmark and the Albert Einstein School of Medicine in the Bronx studied the primary cilia in lab cultures of mice fibroblasts, the cells that along with related connective tissues sculpt the bulk of the mammalian body.

So we think we have designed GPS systems?

Quote:

"The really important discovery is that the primary cilium detects signals, which tell the cells to engage their compass reading and move in the right direction to close the wound," Christensen explains.

Purposefully communicating information as a means to an end... wound healing.

Quote:

The researchers suspect this cellular GPS system plays roles other than wound healing. The primary cilia could serve as a fail-safe device against uncontrolled cell movement, says Christensen. Without chemical stimulation, the primary cilia would restrain cell migration, preventing the dangerous displacement of cells that is associated with invasive cancers and fibrosis, the scientists explain. On the other hand, defective primary cilia might fail to provide correct directional instructions during cell differentiation. This failure could be another link connecting primary cilia to severe developmental disorders, the researchers suggest.

Protruding through the cell membrane, primary cilia occur on almost every non-dividing cell in the body. Once written off as a vestigial organelle discarded in the evolutionary dust, primary cilia in the last decade have risen to prominence as a vital cellular sensor at the root of a wide range of health disorders, from polycystic kidney disease to cancer to left-right anatomical abnormalities.

Demonstrating the vacuity of preaching sub-optimal design... an idea from faulty Darwinian reasoning?

And taking clues from original design (cellular machinery) to design our own optimal nanotechnology? Does that make the original design optimal/above par/good?

Clockwork That Drives Powerful Virus Nanomotor Discovered

Quote:
Because of the motor's strength--to scale, twice that of an automobile--the new findings could inspire engineers designing sophisticated nanomachines. In addition, because a number of virus types may possess a similar motor, including the virus that causes herpes, the results may also assist pharmaceutical companies developing methods to sabotage virus machinery.

One has to wonder were the next spate of these arguments are going to come from? Perhaps the low optimality of the genetic code? Perhaps not... Maybe the inefficiency of biomolecular machines? Maybe not...

Arguments from bad design should be taken with a pinch of salt as they are often made out of ignorance with hidden meaningless and mindless metaphysical propositions.

Computers Making Computers?

2009-01-01T06:20:00.000-08:00

An interesting article authored by Antoine Danchin from the Pasteur Institut was recently published and is sure to bring forth much discussion.
Bacteria as computers making computers

Various efforts to integrate biological knowledge into networks of interactions have produced a lively microbial systems biology. Putting molecular biology and computer sciences in perspective, we review another trend in systems biology, in which recursivity and information replace the usual concepts of differential equations, feedback and feedforward loops and the like. Noting that the processes of gene expression separate the genome from the cell machinery, we analyse the role of the separation between machine and program in computers. However, computers do not make computers. For cells to make cells requires a specific organization of the genetic program, which we investigate using available knowledge. Microbial genomes are organized into a paleome (the name emphasizes the role of the corresponding functions from the time of the origin of life), comprising a constructor and a replicator, and a cenome (emphasizing community-relevant genes), made up of genes that permit life in a particular context. The cell duplication process supposes rejuvenation of the machine and replication of the program. The paleome also possesses genes that enable information to accumulate in a ratchet-like process down the generations. The systems biology must include the dynamics of information creation in its future developments.

The quantum teleportation experiments have demonstrated that information can be viewed as a fundamental irreducible property of physics (informationalism). Systems biology is moving in that same direction, as viewing cells as computers with machinery and software makes it possible to view information as a fundamental category of nature and all future developments of systems biology can include this concept when looking at cells.

There are many interesting passages in this article. A few of these are going to be highlighted for discussion.

Historically, systems biology follows on from molecular biology, a science based on many concepts more closely linked to arithmetic and computation than to classical physics or chemistry. Molecular biology relies heavily on concepts such as ‘control’, ‘coding’ or ‘information’, which are at the heart of arithmetic and computation. To accept the cell as a computer conjecture first requires an exploration of the concept of information, in relation to the concept of genetic program.

Cellular processes are exquisitely controlled and carried out by remarkable biomolecular machines. The software needed to coordinate these processes is located in a fairly optimal genetic code that is optimized for evolution and maintains its own functional integrity.

The Austrian mathematician Kurt Godel showed that arithmetic (the science of whole numbers) can make statements about itself. To substantiate this remarkable claim, which implies that just manipulating whole numbers with the rules of arithmetic can generate novel information, G¨odel used a simple trick. He coded the words used in Number Theory as integers (e.g. four, which is quatre in French, vier in German and tessera in Greek, can be coded by 4) and used the corresponding code to translate propositions of arithmetic. This generated a large whole number, which could be manipulated by the rules of arithmetic, and after a sequence of operations, this manipulation generated another whole number. The latter could be decoded using the initial code. Godel’s trick was to drive the sequence of operations modifying the initial statement, to lead to a very particular conclusion. When decoded, the manipulated sequence translated into a particular proposition, which, briefly, stated: ‘I am impossible to prove’. In other words, arithmetic is incomplete, i.e. some propositions of arithmetic can be understood as valid; yet they cannot be proven within the frame of arithmetic. But this ‘incompleteness’ can also be seen as a positive feature; it is what allows the creation of new information – in Godel’s case, the statement of a fact of which the world was previously unaware. In his book, Hofstadter showed that the genetic code, which enables the world of nucleic acids to be translated into the world of proteins, which in turn manipulate nucleic acids, behaves exactly as Godel’s code does. This implies that manipulating strings of symbols, via a process that uses a code, can generate novel information. Of course, in the case of nucleic acids and proteins, there is no Godel to drive the process, and no need for one: while Godel knew what he was aiming at, living systems will accumulate information through recursivity, without any design being required. We only perceive a design because the end result is familiar to us, and thus seems more ‘right’ than any other possible result. But what we commonly term the ‘genetic program’ because it unfolds through time in a consistent manner is not a programme with an aim – it is merely there, and functions because it cannot do otherwise.

Why can't the function of the program be to actively manipulate information as a means to an end... self-replication and preservation. Later in the article something similar to this is actually suggested:

The reluctance of investigators to regard information as an authentic category of Nature suggests that, at this point in the present review of the literature, it may still be difficult for the reader to accept that a cell could behave as a computer. Indeed, what would the role of computation be in the process of evolution? We have already provided some elements of the answer to the question: Turing showed that the consequence of the process of computation along the lines he outlined is that his machine would be able to perform any conceivable operation of logic or computation by reading and writing on a data/program tape. Stated otherwise, and in a way that is easier to relate to biology, the machine manipulates information and, because arithmetic is incomplete [as illustrated in the introduction above (Hofstadter, 1979)], it is able to create information. The machine is therefore in essence unpredictable (Turing, 1936–1937), but not in a random way – quite the contrary, in a very interesting way, as lack of prediction is not due to lack of determinism, but due to a creative action that results in novel information. If the image is correct, then it shows that living organisms are those material systems that are able to manipulate information so as to produce unexpected solutions that enable them to survive in an unpredictable future (Danchin, 2003, 2008a).

There we go, organisms can be viewed as entities that are able to manipulate information as a means to an end. Why would it be difficult to accept that cells to behave like computers? Yet, cells are capable of more than computers, e.g. self-replication and autonomous manipulation of information.

A form of endogenous adaptive mutagenesis (EAM) is also being alluded to in the article:
Living organisms are, therefore, infinitely far removed from the clockwork mechanicism that superficial opponents of molecular biology associate with the widespread analytical stance they call ‘reductionism’ (Lewontin, 1993). It is important to emphasize here that, in the Turing machine, the machine is not only allowed to read the program but also to write on it. If, then, the conjecture of the cell as a Turing machine is valid, apparent paradoxes such as the controversial ‘adaptive mutations’ that enable the cell to invent novel metabolic pathways should not be unexpected (Cairns et al., 1988; Danchin, 1988b).

There is also room for drawing parallels between evolution, memetic algorithms and designed molecular docking programs.

Finally, we must note that the algorithmic approach, presented when considering the genetic program as an authentic program in a Turing machine (Danchin, 2003), identifies two completely different levels: the level of the program and the level of the machine.

The article continues to discuss at length the parallels between our own created information processing systems (computers) and molecular processes fundamental to life. The article is sure to provide information for many more interesting blog discussions.

The Kinesin Motor Machine.

2008-12-05T23:43:00.000-08:00

How Tiny Cell Proteins Generate Force To 'Walk'

Quote:

ScienceDaily (Dec. 4, 2008) — MIT researchers have shown how a cell motor protein exerts the force to move, enabling functions such as cell division.

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Kinesin, a motor protein that also carries neurotransmitters, "walks" along cellular beams known as microtubules. For the first time, the MIT team has shown at a molecular level how kinesin generates the force needed to step along the microtubules.

Microtubules, quantum physics, and consciousness ? Microtubules form tracks for neurotransmitters to be transported and can possibly act as quantum computational structures.

Quote:

The researchers, led by Matthew Lang, associate professor of biological and mechanical engineering, report their findings in the Nov. 24 online early issue of the Proceedings of the National Academy of Sciences.

Because kinesin is involved in organizing the machinery of cell division, understanding how it works could one day be useful in developing therapies for diseases involving out-of-control cell division, such as cancer.

The protein consists of two "heads," which walk along the microtubule, and a long "tail," which carries cargo. The heads take turns stepping along the microtubule, at a rate of up to 100 steps (800 nanometers) per second.

In the PNAS paper, Lang and his colleagues offer experimental evidence for a model they reported in January in the journal Structure. Their model suggests — and the new experiments confirm — that a small region of the protein, part of which joins the head and tail is responsible for generating the force needed to make kinesin walk. Two protein subunits, known as the N-terminal cover strand and neck linker, line up next to each other to form a sheet, forming the cover-neck bundle that drives the kinesin head forward.

"This is the kinesin power stroke," said Lang.

Next, Lang's team plans to investigate how the two kinesin heads communicate with each other to coordinate their steps.

Lead author of the PNAS paper is Ahmad Khalil, graduate student in mechanical engineering. Other MIT authors of the paper are David Appleyard, a graduate student in biological engineering; Anna Labno, a recent MIT graduate; Adrien Georges, a visiting student in Lang's lab; and Angela Belcher, the Germehausen Professor of Materials Science and Engineering and Biological Engineering. This work is a close collaboration with authors Martin Karplus of Harvard and Wonmuk Hwang of Texas A&M.

The research was funded by the National Institutes of Health and the Army Research Office Institute of Collaborative Biotechnologies.

Few videos describing the motor:
Kinesin Transport Protein
Kinesin Explanation

Mice with a few kinesin mutations? Look like there is something wrong with their neurphysiology, almost like they are not interacting with the environment in the correct way?
Kinesin mutations in mice

Ever wondered how cellular machinery causes replication of cells?
Awesome video:
Inside the cell
And it does not even remotely cover the intricate mechanisms controllong the process.

Another video of mitosis:
Mitosis
Active cyclinB/cdc2 plays a part in nuclear envelope breakdown, and destruction of cyclinB and abolition of cdc2 activity allows nuclear envelope formation.

In real life it looks something like this:

Idle Control Units and Metabolomics

2008-12-05T21:30:00.000-08:00

Well designed cars have well designed idle control units that spontaneously kick in to maintain the speed of the crankshaft within a pre-set range (usually >200rpm). An interesting study has demonstrated that 4 single celled organisms in two domains of life (bacteria and eukaryotes) uses the same number of biochemical reactions when optimizing growth.

Spontaneous Reaction Silencing in Metabolic Optimization
From the article:

Performing numerical optimization in glucose minimal media (Materials and Methods), we find that the number of active reactions in such optimal states is reduced by 21%–50% compared to typical non-optimal states, as indicated in the middle bars of Figure 2. Interestingly, the absolute number of active reactions under maximum growth is, 300 and appears to be fairly independent of the organism and network size for the cases analyzed. We observe that the minimum number of reactions required merely to sustain positive growth [7,8] is only a few reactions smaller than the number of reactions used in growth-maximizing states (bottom bars, Figure 2). This implies that surprisingly small metabolic adjustment or genetic modification is sufficient for an optimally growing organism to stop growing completely, which reveals a robust-yet-subtle tendency in cellular metabolism: while the large number of inactive reactions offers tremendous mutational and environmental robustness Papp:2004dn, the system is very sensitive if limited only to the set of reactions optimally active. The flip side of this prediction is that significant increase in growth can result from very few mutations, as observed recently in adaptive evolution experiments.

Reaction irreversibility and spontaneous cascading (article) of inactivity are described as built-in mechanisms that mediate these metabolic adjustments. The authors also point out that 638 out of the 931 reactions in the E. coli glucose metabolic network can be removed whilst maintaining a maximum growth rate in glucose. The mutational robustness as a result of inactive reactions under maximum growth thus act as a sort of preadaptation whereby different pathways can be spontaneously activated under shifting environmental conditions.

The tremendous robustness of these systems raises an interesting question regarding the origins of these non-essential pathways under maximum growth rates. The authors provide a testable hypothesis:

An alternative explanation would be that in variable environments, which is a natural selective pressure likely to be more important than considered in standard laboratory experiments, the apparently dispensable pathways may play a significant role in suboptimal states induced by environmental changes. This alternative is based on the hypothesis that latent pathways provide intermediate states necessary to facilitate adaptation, therefore conferring competitive advantage even if the pathways are not active in any single fixed environmental condition.

This alternative is based on the hypothesis that latent pathways provide intermediate states necessary to facilitate adaptation, therefore conferring competitive advantage even if the pathways are not active in any single fixed environmental condition. In light of our results, this hypothesis can be tested experimentally in medium-perturbation assays by measuring the change in growth or other phenotype caused by deleting the predicted latent pathways in advance to a medium change.

Even more intriguing is the fact that metabolic adjustments are also controlled by anticipatory transcriptional reprogramming in response to environmental changes. It is posited to be as result an “associative learning” paradigm.

Looking at the motor industry again, anticipatory systems and structures have been designed in order to optimize the structure stiffness for a particular crash scenario. Pre-crash sensing is used to adjust structural stiffness and crumple zones in response to a particular deceleration scenario in order to maximize the crash worthiness of the vehicle. It seems this kind of anticipatory programming is an ancient invention, a few billion years old.

Using this information, another core element can be added to an initial state: Robust metabolic networks with tremendous adaptability that "idle" under maximum growth conditions.

Figure 1: An initial state. Reverse engineer ubiquitous core components of various life forms at present. Will it repeatedly produce similar endpoints after evolutionary processes, irrespective of its origin?

Protein folding, Nanotubes and Engineering

2008-11-25T07:04:00.000-08:00

More on protein folding:
Many proteins have intricate folds and one of these fold types include the figure eight knot fold. A team of researchers tried to figure out how these proteins are folded. At present, it is only known that the knot is formed quickly soon after polypeptide chain formation, with an unknown mechanism. The researchers tentatively propose:
"an early threading event may be the defining feature of a polypeptide-knotting with the ensuing folding occurring in a similar fashion to unknotted proteins; the folding of a knotted protein differs only with an initial knotting event in a denatured-like state."

Perhaps an an as of yet undiscovered knot-folding machine?
Article: Exploring knotting mechanisms in protein folding

And nanotubes? Bah, old news... a few hundred million years old...
Tunnelling nanotubes: Life's secret network

Quote:

The closest animal equivalents to plasmodesmata were thought to be gap junctions, which are like hollow rivets joining the membranes of adjacent cells. A channel through the middle of each gap junction directly connects the cell interiors, but the channel is very narrow - just 0.5 to 2 nanometres wide - and so only allows ions and small molecules to pass from one cell to another.

Nanotubes are something different. They are 50 to 200 nanometres thick, which is more than wide enough to allow proteins to pass through. What's more, they can span distances of several cell diameters, wiggling around obstacles to connect the insides of two cells some distance apart. "This gives the organism a new way to communicate very selectively over long range," says Gerdes. It is a previously unknown way in which cells can communicate over a distance

Soon after they first saw nanotubes in rat cells, he and Rustom saw them forming between human kidney cells too. Using video microscopy, they watched adjacent cells reach out to each other with antenna-like projections, establish contact and then build the tubular connections. The connections were not just between pairs of cells. Cells can send out several nanotubes, forming an intricate and transient network of linked cells lasting anything from minutes to hours. Using fluorescent proteins, the team also discovered that relatively large cellular structures, or organelles, could move from one cell to another through the nanotubes

Quote:

Their work, published in May, shows that nanotubes are not just an artefact of the methods used to grow cells in culture, as some have suggested. And what they have seen is spectacular: some of the longest tunnelling nanotubes ever observed, more than 300 micrometres long, connecting dendritic cells in the cornea (The Journal of Immunology, vol 180, p 5779). "We can see them their whole course, spindling all the way through the cornea," says McMenamin. "It's fantastic."

"I'll bet you that within weeks to months, people will start noticing them in other tissues. It's just a case of how you look," he adds. "You've got to know what you are looking for. It's a bit like being a good bird-watcher. A hundred people will see a flock of seagulls, and it's only a very good bird-watcher who will spot this one tern flying in that flock."

Gerdes, meanwhile, continues to marvel at what is unravelling before his very eyes. "Whatever one can think of has been done by nature," he says. "It is unbelievable what the cell is able to do."

One striking feature that makes us different from other primates is our innate ability to develop a theory of mind at around 4-6 years. We start to develop the remarkable ability to simulate what other people are thinking and understand their thoughts through our own thinking. We also create our own model of the world in our own minds that leads to understanding of concepts.

Attempting to unravel nature's mysteries by trying to look at it from another engineering Mind's eye seems to make sense when one marvels at the engineering feats in cells. Why not?

Replication Machinery and Transcription Factories

2008-11-25T07:03:00.000-08:00

How DNA Is Unwound So That Its Code Can Be Read

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ScienceDaily (Nov. 24, 2008) — Researchers at The Scripps Research Institute have figured out how a macromolecular machine is able to unwind the long and twisted tangles of DNA within a cell's nucleus so that genetic information can be "read" and used to direct the synthesis of proteins, which have many specific functions in the body.

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"This is a fundamental processes that takes place countless times inside each of our cells every day, but how it happens had not been understood." says the study's lead investigator, Francisco Asturias, Ph.D., associate professor in the Department of Cell Biology at Scripps Research. "The structure we have solved provides important clues into one of the first steps in gene expression regulation."

Anybody interested in some of the 3D-structure, go to rcsb.org.

Quote:

"Remarkable Unpacking and Repacking"

To understand the complexity of the process, it is important to know that if the DNA in each cell were stretched out, it would be more than three feet long—and given the trillions of cells within a human body, it has been calculated that a single individual's DNA could stretch to cover the distance to the sun and back many times over.

So DNA must be packaged into tidy little chromosomes. The DNA in each gene first assembles into what looks like a string of beads: the string is the DNA and to compact its length, it is wrapped two times around a spool-like bead of histone protein, to form a nucleosome. But there is so much DNA in a single gene that each gene is packed into a necklace of nucleosomes on a DNA string. These beads then become further compressed into twisted ropes that eventually form chromatin, in which DNA is compacted about 10,000 times from its extended length.

What the Scripps Research scientists set out to do is to understand how the RSC complex unwinds DNA from the many histone beads within a gene so that other molecular machines can read the genetic code.

RSC is a huge complex of 13 different proteins and the scientists first found that it holds an individual nucleosome in what looks like a vise grip. They then found that RSC creates a little bulge in the DNA that can be propagated around the nucleosome and make possible translocation of the DNA with respect to the histones, exposing the DNA so that it can be read.

"Imagine a rubber band wrapped twice around a water glass. The easiest way to move the band is to pull a little of it away from the glass and then slide it" Asturias says. "By using energy from an external source (ATP hydrolysis) RSC can repeatedly pull DNA away from the histones and eventually expose all of the DNA."

The researchers believe that by translocating a nucleosome along the DNA, RSC eventually slides into the next adjoining nucleosome, causing the histones to be ejected and exposing the DNA. "Interestingly, although its DNA is gradually exposed, the nucleosome to which RSC is bound remains intact," Asturias says.

The structure RSC interacting with a nucleosome explains how previously observed DNA bulges formed by chromatin remodeling complexes are formed, and why a single intact nucleosome appears to be left on a fully activated gene before other cellular machinery scoop up the histones and repack the DNA until it needs to be read again.

"Every time your cell expresses a gene, it goes through this remarkable unpacking and repacking," he says. "We are happy to have provided some clarity to the process."

Published article:
Structure of a RSC–nucleosome complex and insights into chromatin remodeling

Nice video showing DNA wrapping.

An interesting blog entry (and an interesting blog worth a read) describes how the transcription machinery is assembled and disassembled in a few sites in cells.

Yet another twist in the world of gene expression - transcription factories

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First of all I will ask you, did you know that transcription only happened at a few sites within the nucleus? In mouse cells from the animal there are between 100-300 of these but in cultured cells such as HeLa cells there are many more. Transcription factories also known as RNAPII foci are where most, if not all mRNA is produced. This amazed me and raises the obvious questions of why and how. The why may be obvious. It is a good idea to keep the nucleus as I see it ‘tidy’ but in more technical terms it is a way of keeps gene expression organised and regulating it (see below). The how this work I don’t think has been addressed! All I can say is watch this space.

There is more there.

Biomolecular machines utilizing thermal fluctuations

2008-11-25T07:02:00.000-08:00

Article related to the unique operations of biological molecular machines
Fluctuation as a tool of biological molecular machines
Abstract:

Quote:

The mechanism for biological molecular machines is different from that of man-made ones. Recently single molecule measurements and other
experiments have revealed unique operations where biological molecular machines exploit thermal fluctuation in response to small inputs of energy
or signals to achieve their function. Understanding and applying this mechanism to engineering offers new artificial machine designs.

The article continues:

Quote:

Biological machines are different from man-made artificial ones in many ways. One primary difference is the amount of energy supplied. For example, a supercomputer playing chess with a champion uses much larger amounts of energy than its adversary. A computer unit element, or IC chip, uses energy much larger than thermal energy (500 times greater) to avoid the disturbance caused from thermal noises whereas biological machines use the energy released from the hydrolysis of ATP, which is only approximately 10 times greater than thermal energy. Large excess energy inputs in computers result in far less efficiency at converting their energy inputs although they are more precise at their task than biological machines. Computers err once per 1060 trials, while basic biochemical reactions underlying biological machines err as often as once per 103 trials. For this reason, computers are in some respects superior to one of nature’s greatest machines, the human brain. Computers make calculations much faster as IC chips work on the order of nanoseconds (10−9 s), while the time scale for basic biochemical reactions in biological machines is milliseconds (10−3 s). They also have superior memory capacity and data transfer rate. The computer rate is on the order of 109 bites/s while in brain it is estimated to be only 400 bites/s. However, biological machines are more flexible, readily responding to changes in their environment. In contrast, man-made machines are designed to maintain their. function regardless of environmental changes. Therefore, the fundamental mechanisms between the two machines are different. Biomolecules and their assemblies, biomolecular machines, are in the order of nanometer in size meaning the effects of thermal noises are large. Nevertheless, biomolecules and molecular machines execute their roles despite these noises. But how? Recent experimental data suggest that biological molecular machines harness thermal fluctuation to achieve their functions. Thus, thermal fluctuation seems to play an important role from the molecular level to cellular and organism level. We have developed measurement systems that trace these thermal fluctuations in biomolecular machines when eliminating measurement noise.

Our model biomolecular machine of choice is the molecular motor. Molecular motors are composed of a motor protein, which move using the chemical energy of ATP, and protein tracks, which the motors move along. Molecular motors and protein tracks share unique characteristic properties such as enzymatic activity, molecular recognition, energy conversion and self-organization with other typical molecular machines. Thus the results obtained for molecular motors may be extended to other systems.

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Thermal fluctuation is involved in function at different hierarchies of biological systems (Fig. 3). In the mechanism for molecular motor motility, it has been shown that thermal fluctuation is involved and biased to generate directional movement. In live cells, a mechanism that utilizes thermal fluctuation is also likely.

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Lastly, in addition to the stochastic nature at the molecular and cellular levels, visual perception has shown stochastic dynamics. Visual perception processes are explained by equations similar to formulae that govern the behavior of biomolecules (Murata et al., 2003). Thus the mechanisms obtained at molecular and cellular levels likely apply at even higher levels. These mechanisms offer blueprints to engineer artificial machines that utilize fluctuations.

Again, showing the carbon based nanotechnology in cells can be utilized and adopted by our engineers for our own designs seeing that these machines are able to harness even thermal fluctuations.

Efficiency of enzymes

2008-11-25T06:59:00.000-08:00

How long will a reaction take to complete without enzymes?
Well, some reactions will only complete in about 2.3 billion years without them...
Without Enzyme, Biological Reaction Essential To Life Takes 2.3 Billion Years

But enzymes don't just pop into existence, not even under the BEST pre-biotic synthesis scenarios. Enzymes are produced and folded into the correct conformation by.... other enzymes... controlled by.... biomolecular machines and a genetic code..

More about the efficiency of enzymes:
Biochemistry: Enzymes under the nanoscope

Quote:

Small-scale interactions of substrates with an enzyme's active site — over distances smaller than the length of a chemical bond — can make big differences to the enzyme's catalytic efficiency.

When Richard Feynman died in 1988, he left behind the following words on his blackboard: "What I cannot create, I do not understand." His message certainly resonates with protein engineers.

Enzymes are guided into their correct 3D configuration by other enzyme complexes known as chaperones (part of the heat-shock protein family). What happens if the configurations are not right? Scientists determined that some enzymes, as in the case of ketosteroid isomerase, are so precisely folded for their particular ligand/substrate that if it the 3d conformation was off by even 10 picometers (10^12 meters) it would lose its efficiency. Firstly, the conformation has to be just right to tightly bind the ligand into the pocket of the protein, then another mechanism (built in property of the enzyme) is responsible the transfer of electrons in order to catalyze and complete the enzymatic reaction. Our current best efforts at designing artificial enzymes are (from the article) “still tens of billions of times smaller than those of many enzymes.”

The ribosome is a super complex of enzymes, a molecular machine responsible for the building of polypeptide chains which in turn are folded into active proteins by chaperone complexes.
Problems do occur, but checks and balances are present. For example:
Side-chain recognition and gating in the ribosome exit tunnel
At the exit tunnel of the ribosome, it is hypothesized that there are gate and latch mechanisms with active valves controlling the exit of polypeptides. The researchers conclude that these mechanisms play a role in the regulation of "nascent chain exit and ion flux". Sort-off like a final checkpoint.

As already seen, without enzymes, reactions that are crucial to life might take billions of years to complete. Small changes (10 picometers) in the 3D structure of an enzyme can also negatively affect the function of an enzyme.
So how are enzymes folded into their active conformation?

Chaperonins: Two-stroke, two-speed, protein machines

Article:
Setting the chaperonin timer: A two-stroke, two-speed, protein machine
From the article:

Quote:

Protein machines and their man-made, macroscopic counterparts share several common attributes, e.g., concerted, coordinated movements, cyclical operation, and energy transduction. These machines are seldom reversible because each cycle generally involves at least one irreversible step, e.g., the consumption of fuel. Often these machines operate at variable speed, a plethora of timing devices adjusting the cycle speed in response to demand.

An exemplary bipartite protein machine is the chaperonin system, typified by GroEL and GroES from Escherichia coli. GroEL is composed of 2 heptameric rings, stacked back to back, which, in the presence of GroES, operate out of phase with one another in the manner of a 2-stroke, reciprocating motor (1, 2). Driven by the hydrolysis of ATP, the chaperonin proteins function as a biological simulated annealing machine (3, 4), optimizing the folding of their substrate proteins (SPs) whose passage to biologically functional conformations is thus assured.

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The picture of the chaperonins that emerges from our work is that of a machine equipped with a timer, the trans ring, poised to respond to the appearance of SP [substrate protein inside the cavity] but otherwise idling in a quiescent state. We note that Nature’s design of this 2-speed protein machine minimizes the hydrolysis of ATP in the absence of SP. However, it maximizes the number of turnovers and minimizes the residence time available to the encapsulated SP to reach the native state, design principles well suited to the operation of an iterative annealing device.

Partial part and dynamics of the system.
Nice video of how it operates

Machines folding machines into place. Beautiful...

Trash Removal

2008-11-25T06:58:00.000-08:00

How Cells Take Out The Trash To Prevent Disease

Quote:

ScienceDaily (Nov. 10, 2008) — Garbage collectors are important for removing trash; without them waste accumulates and can quickly become a health hazard. Similarly, individual cells that make up such biological organisms as humans also have sophisticated methods for managing waste.

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The researchers, including postdoctoral fellows Jason MacGurn and Chris Stefan, identified nine related proteins in yeast, which they named the "arrestin-related trafficking" adaptors or ARTs. Each of these proteins identifies and binds to a different set of membrane proteins. Once bound, the ART protein links to an enzyme that attaches a chemical tag for that protein's removal. The ARTs are found in both yeast and humans, suggesting the fundamental nature of their function.

Once the protein is tagged, the piece of membrane with the targeted protein forms a packet, called a vesicle, that enters the cell's cytoplasm. There, the vesicle enters a larger membrane body called an endosome, which in turn dumps it into another compartment called the lysosome, where special enzymes break apart big molecules to their core units: proteins to amino acids, membranes to fatty acids, carbohydrates to sugars and nucleic acids to nucleotides, and those basic materials are then reused.

The paper in Developmental Cell, co-authored by Emr with postdoctoral fellows David Teis and Suraj Saksena, describes for the first time how a set of four proteins assemble into a highly ordered complex. This complex encircles membrane proteins that must be disposed of in the lysosome. Emr's lab was the first to identify and characterize these protein complexes (known as ESCRTs). The Developmental Cell paper describes the order of events in which the ESCRT complexes encircle and deliver "waste" proteins into vesicles destined for recycling in the lysosome.

Lysosomal, autophagic, chaperone mediated autophagy processes...etc. taking out the trash: All highly regulated, exquisitely controlled processes carried out by biomolecular machines. And these same processes are so ancient... present in yeast...

Gene activation governed by machines

2008-11-25T06:56:00.000-08:00

How 'molecular machines' kick start gene activation revealed

Quote:

How 'molecular machines' inside cells swing into action to activate genes at different times in a cell's life is revealed today (6 November) in new research published in Molecular Cell. Genes are made of double stranded DNA molecules containing the coded information an organism's cells need to produce proteins. The DNA double strands need to be 'melted out' and separated in order for the code to be accessed. Once accessed, the genetic codes are converted to messenger RNAs (mRNA) which are used to make proteins. Cells need to produce particular proteins at different times in their lives, to help them respond and adapt to changes in their environment.

The "melting out" process is carried out by helicases which is part of the replisome. Exquisitely controlled.
Helicases are also known to be ring-shaped motor proteins, typically hexamers and separate double-stranded DNA into single-stranded templates for the replication machinery. Replication occurs at about 1000 base pairs per second due to the highly efficient combination of sliding clamps and the polymerases. Thus, helicases need to unwind DNA at at least that speed. Unwinding DNA too slowly and the replication machinery might break down . Unwind the DNA too fast or untimely and harmful mutations might occur as single-stranded DNA is prone to degradation and cytosine deamination. The speed at which helicase unwinds DNA is no accident though, as it is intrinsically controlled. As helicase is bound to the lagging strand, it unwinds the leading strand in a separate direction. Applying a pulling force on the leading strand leads to a 7-fold increase in the speed of DNA unwinding by helicase. The highly efficient DNA polymerase/sliding clamp combination provides this controlling force on the leading strand. This forms a robust unwinding/polymerization interaction whereby polymerization controls and prevents unwanted DNA unwinding.

Quote:

The new study outlines exactly how a molecular machine called RNA polymerase, which reads the DNA code and synthesizes mRNA, is kickstarted by specialised activator proteins. The scientists have discovered that RNA polymerase uses a tightly regulated internal blocking system that prevents genes from being activated when they are not needed.

Using electron microscopy to look at the inner workings of bacterial cells, the researchers discovered that the DNA strand-separating process is kickstarted when RNA polymerase is modified by an activator protein, which the cell sends to the site of the gene that needs to be switched on.

This activator protein jump-starts the RNA polymerase machine by removing a plug which blocks the DNA's entrance to the machine. The activator protein also causes the DNA strands to shift position so that the DNA lines up with the entrance to the RNA polymerase. Once these two movements have occurred and the DNA strands are in position, the RNA polymerase machine gets to work melting them out, so that the information they contain can be processed to produce mRNA, and ultimately allow production of proteins.

Professor Xiaodong Zhang, lead author of the paper from the Department of Life Sciences at Imperial College London, explains the significance of the team's findings, saying:

"Understanding how the RNA polymerase gene transcription 'machine' is activated, and how it is stalled from working when it is not needed, gives us a better insight than ever before into the inner workings of cells, and the complex processes that occur to facilitate the carefully regulated production of proteins."

Professor Martin Buck, Head of Imperial's Division of Biology and one of the paper's co-authors, adds that understanding how this process works in bacteria cells is of particular interest, because it is this gene transcription and protein production process which allows bacterial cells to adapt, respond and thrive despite changes in their environment:

"In other words, this is the process that occurs inside bacteria that makes them so good at survival. Many bacteria cause infection and disease in humans, and are hard to defeat. Bacterial RNA polymerase is a proven target for antibiotics such as rifampicin, against which many bacteria have become resistant. Insights gained form our research will now provide opportunities and strategies for the design of novel antibacterial compounds," he concludes

So machines govern the activity of gene expression, and machines are governed by gene expression through a reasonably optimal genetic code mmmm....

RNA Splicing

2008-11-25T06:55:00.000-08:00

A little about RNA splicing machinery: Possibly the most complex macromolecular machine in the cell

What is RNA splicing?

Many human genes (+-94%) contain exons (the DNA sequences that code for amino acids). These exons can be spliced together to form different types of proteins from a single gene.

How is it controlled?

Extensively and exquisitely controlled.

How common is it in humans?

Human Genes: Alternative Splicing Far More Common Than Thought

Quote:

ScienceDaily (Nov. 4, 2008) — Scientists have long known that it's possible for one gene to produce slightly different forms of the same protein by skipping or including certain sequences from the messenger RNA. Now, an MIT team has shown that this phenomenon, known as alternative splicing, is both far more prevalent and varies more between tissues than was previously believed.

Quote:

Two different forms of the same protein, known as isoforms, can have different, even completely opposite functions. For example, one protein may activate cell death pathways while its close relative promotes cell survival.

The researchers found that the type of isoform produced is often highly tissue-dependent. Certain protein isoforms that are common in heart tissue, for example, might be very rare in brain tissue, so that the alternative exon functions like a molecular switch. Scientists who study splicing have a general idea of how tissue-specificity may be achieved, but they have much less understanding of why isoforms display such tissue specificity, Burge said.

Thus, the same gene can result in different functions, depending on the functionality and control of the RNA splicing machinery.

Is it important?

Humans And Chimps Differ At Level Of Gene Splicing
Not only do we differ genetically, but the way the genes are processed differ.

What happens if the machinery malfunctions?

Quality control systems are in place.
RNA Biology Finding Makes Waves By Challenging Current Thinking

Quote:

ScienceDaily (Jan. 23, 2008) — Case Western Reserve University School of Medicine researcher Kristian E. Baker, Ph.D. challenges molecular biology's established body of evidence and widely-accepted model for nonsense-mediated messenger ribonucleic acid (mRNA) decay with a new study. With her collaborator, Ambro van Hoof, Ph.D. of The University of Texas Health Sciences Center, Baker directly tested the "faux 3' UTR" model and proved it could not explain how cells recognize and destroy deviant mRNA. This landmark discovery will redirect mRNA research and expand opportunities for new discoveries in understanding the cells' ability to protect itself from these potential errors.

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In all cells, including human, mRNA is a copy of the information carried by a gene on the DNA. Occasionally, mRNA contains errors that can make the information it carries unusable. Cells posses a remarkable mechanism to detect these aberrant mRNAs and eliminate them from the cell -- this process represents a very important quality control system for gene expression. "A significant amount of past research in this area of RNA biology has collected data to support the 'faux 3' UTR' model for mRNA quality control, and, as a result, has shaped present research directions in the field," said Baker. "Our recent findings preclude this explanation and will, undoubtedly, result in a rethinking by many as to how to experimentally approach this important cellular process."

For decades researchers have been puzzled by cells' ability to differentiate between "normal" mRNA and those carrying certain types of mutations. mRNA transports DNA's genetic coding information to the sites of protein synthesis: ribosomes. Cells are able to identify mRNA carrying a mutation and prevent it from reaching the protein synthesis phase. Once identified, the cell destroys the abnormal, mutated mRNA. This naturally occurring process ensures malfunctioning proteins are not produced.

Using a yeast model system, Baker's research offers a better understanding of this mRNA quality control process which closely mimics the process in human cells.

Present in yeast, primitive organisms.

But how prevalent is this kind of machinery?

Visualizing The Machinery Of mRNA Splicing

Quote:

ScienceDaily (Apr. 8, 2008) — Recent research at Yale provided a glimpse of the ancient mechanism that helped diversify our genomes; it illuminated a relationship between gene processing in humans and the most primitive organisms by creating the first crystal structure of a crucial self-splicing region of RNA.

Quote:

This work, published in Science, highlights a 16-year quest by Anna Marie Pyle, the William Edward Gilbert Professor of Molecular Biophysics & Biochemistry at Yale, and her research team into the nature of "group II" introns, a particular type of intron within gene transcripts that catalyzes its own removal during the maturation of RNA.

Group II introns are found throughout nature, in all forms of living organisms. Although much has been learned about their structure and how they work through biochemical and computational analysis, until now there have been no high-resolution crystal structures available. The resulting images have provided both confirmation of the earlier work and new information on the three-dimensional structure of RNA and the mechanism of splicing.

"One of the most exciting aspects of this work was that we did not need to do anything disruptive to these molecules to prepare them for structural analysis," said Pyle. "The molecules showed us their structure, their active site and their activity -- all in a natural state. We were even able to visualize their associated ions."

According to Pyle, the crystal structure revealed some unexpected features -- showing two sections that were most implicated as key elements of the active site and strengthening a theory that the process of splicing in humans "shares a close evolutionary heritage" with ancient forms of bacteria.

Forms of this machinery present all the way down to bacteria.

Here is a video describing the process.

Rewinding Motors

2008-11-25T06:54:00.000-08:00

More on the nanomachinery that governs DNA processing.
Biologists Discover Motor Protein That Rewinds DNA

Quote:

ScienceDaily (Nov. 2, 2008) — Two biologists at the University of California, San Diego have discovered the first of a new class of cellular motor proteins that “rewind” sections of the double-stranded DNA molecule that become unwound, like the tangled ribbons from a cassette tape, in “bubbles” that prevent critical genes from being expressed.

Quote:

“When your DNA gets stuck in the unwound position, your cells are in big trouble, and in humans, that ultimately leads to death” said Jim Kadonaga, a professor of biology at UCSD who headed the study. “What we discovered is the enzyme that fixes this problem.”

The discovery represents the first time scientists have identified a motor protein specifically designed to prevent the accumulation of bubbles of unwound DNA, which occurs when DNA strands become improperly unwound in certain locations along the molecule.

Quote:

“We knew this particular protein caused this disease before we started the study,” said Kadonaga. “That’s why we investigated it. We just didn’t know what it did.”

What this protein, called HARP for HepA-related protein, did astounded Kadonaga and Timur Yusufzai, a postdoctoral fellow working in his laboratory. The two molecular biologists initially discovered that this motor protein burns energy in the same way as enzymes called helicases and, like helicases, attached to the dividing sections of DNA. But while helicases use their energy to separate two annealed nucleic acid strands—such as two strands of DNA, two strands of RNA or the strands of a RNA-DNA hybrid— the scientists found to their surprise that this protein did the opposite; that is, it rewinds sections of defective DNA and thus seals the two strands together again.

As a consequence, the UCSD biologists termed their new enzyme activity an “annealing helicase.”

“We didn’t even consider the idea of annealing helicases before this study started,” said Kadonaga. “It didn’t occur to us that such enzymes even existed. In fact, we never knew until now what happened to DNA when it got stuck in the unwound position.”

Clocks, motors, nanomachines etc. Superbly intelligent biomolecular machinery making life possible.

Paley’s Watch?

2008-11-25T06:53:00.000-08:00

Cyanobacteria are one of the organisms with the deepest history, with evidence of their remains dating back possibly to about 3.5 billion years ago. So, what is found in some of these simple cells? CLOCKWORK...

A cyanobacterial circadian clockwork.

Quote:

Cyanobacteria have become a major model system for analyzing circadian rhythms. The temporal program in this organism enhances fitness in rhythmic environments and is truly global--essentially all genes are regulated by the circadian system. The topology of the chromosome also oscillates and possibly regulates the rhythm of gene expression. The underlying circadian mechanism appears to consist of both a post-translational oscillator (PTO) and a transcriptional/translational feedback loop (TTFL). The PTO can be reconstituted in vitro with three purified proteins (KaiA, KaiB, and KaiC) and ATP. These three core oscillator proteins have been crystallized and structurally determined, the only full-length circadian proteins to be so characterized. The timing of cell division is gated by a circadian checkpoint, but the circadian pacemaker is not influenced by the status of the cell division cycle. This imperturbability may be due to the presence of the PTO that persists under conditions in which metabolism is repressed. Recent biochemical, biophysical, and structural discoveries have brought the cyanobacterial circadian system to the brink of explaining heretofore unexplainable biochemical characteristics of a circadian oscillator: the long time constant, precision, and temperature compensation.

On the structure of:
Structural Insights into a Circadian Oscillator

Quote:

An endogenous circadian system in cyanobacteria exerts pervasive control over cellular processes, including global gene expression. Indeed, the entire chromosome undergoes daily cycles of topological changes and compaction. The biochemical machinery underlying a circadian oscillator can be reconstituted in vitro with just three cyanobacterial proteins, KaiA, KaiB, and KaiC. These proteins interact to promote conformational changes and phosphorylation events that determine the phase of the in vitro oscillation. The high-resolution structures of these proteins suggest a ratcheting mechanism by which the KaiABC oscillator ticks unidirectionally. This posttranslational oscillator may interact with transcriptional and translational feedback loops to generate the emergent circadian behavior in vivo. The conjunction of structural, biophysical, and biochemical approaches to this system reveals molecular mechanisms of biological timekeeping.

A biological clock with all the cogs and gears. The KaiABC clock is a bona fide dynamically oscillating nanomachine that precess unidirectionally and robustly. Present in one of the most primitive, simple organisms...

Compasses, Translational Machinery and a little epigenetics

2008-11-25T06:51:00.000-08:00

A few more agents and biomolecular machines .
Protein Compass Guides Amoebas Toward Their Prey

Quote:

ScienceDaily (Oct. 26, 2008) — Amoebas glide toward their prey with the help of a protein switch that controls a molecular compass, biologists at the University of California, San Diego have discovered.

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Their finding, recently detailed in the journal Current Biology, is important because the same molecular switch is shared by humans and other vertebrates to help immune cells locate the sites of infections.

The amoeba Dictyostelium finds bacteria by scent and moves toward its meal by assembling a molecular motor on its leading edge. The active form of a protein called Ras sets off a cascade of signals to start up that motor, but what controlled Ras was unknown.

Richard Firtel, professor of biology along with graduate student Sheng Zhang and postdoctoral fellow Pascale Charest tested seven suspect proteins by disrupting their genes. One called NF1, which matches a human protein, proved critical to chemical navigation.

NF1 turns Ras off. Without this switch mutant amoebas extended false feet called pseudopodia in all directions and wandered aimlessly as Ras flickered on and off at random points on their surfaces. “You have to orient Ras in order to drive your cell in the right direction,” Firtel said.

In contrast, normal amoebas with working versions of NF1 elongate in a single direction and head straight for the most intense concentration of bacterial chemicals, the team reports.

The biochemical components of the system match those found in vertebrate immune cells called neutrophils that hunt down bacterial invaders, suggesting that the switch might be a key navigational control for many types of cells, Firtel said. “The pathway and responses are very similar and so are the molecules.”

The US Public Health Service funded this work.

Agents assemble their equipment in order to hunt down their prey. An intentional plan laid out purposefully in order to manipulate the environment as a means to an end... food.

More equipment capable of manipulating the environment as a means to an end....
New Light Shed On Molecular Machinery Required For Translation Of Histone Crosstalk

Quote:

ScienceDaily (Dec. 14, 2007) — The Stowers Institute's Shilatifard Lab has published findings that shed light on the molecular machinery required for the translation of histone crosstalk, or communication between histones.

Quote:

Histones are important components of chromatin, the packing material surrounding chromosomal DNA. Also, histones play an important role in the regulation of gene expression. Histone H3 can be modified by methylation and this modification is an essential part of gene expression.

Several years ago, the Shilatifard Lab identified the first histone H3 lysine 4 (H3K4) methyltransferase, known as COMPASS, in yeast. Soon thereafter, it was established that the MLL protein in humans also existed in a COMPASS-like complex capable of methylating H3K4. In 2002, the Shilatifard Lab reported the existence of the first histone crosstalk between histone H2B monoubiquitination for the regulation of histone methylation by COMPASS.

"We now know that this mode of histone crosstalk is highly conserved from yeast to humans, but until now, its molecular mechanism of action was poorly understood. Jung-Shin Lee, a Postdoctoral Research Associate in my laboratory, was able to demonstrate the molecular machinery required for the translation of this histone crosstalk," said Ali Shilatifard, Ph.D., Investigator and senior author on the paper.

This work demonstrated that the Cps35 subunit of COMPASS is required to translate the crosstalk between H2B monoubiquitination and H3 methylation by COMPASS.

"Given the importance of histone methylation by the MLL complex and leukemia pathogenesis, defining the molecular machinery involved in this process could be highly useful," said Dr. Shilatifard.

Microfluidics

2008-11-25T06:50:00.000-08:00

The inner life of mesoorganisms

Quote:

Some of the most ingenious ideas for designing microfluidic systems come from observing plants and animals. A study that quantifies the protein-driven helical flow of liquid in large plant cells, for instance, may well inspire micron-scale liquid mixers and sensors.

Quote:

This brings us back to the issue of biomimetic strategies that borrow nature’s designs to engineer useful devices. Strategies to increase mass transport rates in microchannels, for example, will be essential for rapid sensing of extremely dilute systems [7]. In microfluidics, the “staggered herringbone mixer” [8] incorporates ridges along the walls to drive counter-rotating, helical flows to enhance mixing across the channel, while reducing dispersion along the channel. The mesoorganisms studied by van de Meent et al. illustrate a case where nature, faced with a similar problem, found a similar solution. Hundreds of millions of years later, in developing new microfluidic technologies, humans have found solutions that are not so far from those evolved in nature. Even though the methods for driving the flows are different (pressure-driven vs “cargo-driven,” and chaotic vs regular), the resulting double-helical flows share much in common.

While much of biophysics has been devoted to single-molecule and molecular-level studies, many mysteries remain on larger scales, at the cell level and above, where perceptive questions and keen physical insight reveal many surprises and useful insight into nature’s bag of tricks. van de Meent et al. nicely highlight the interesting and potentially important implications of cyclosis, and more generally the seemingly endless supply of fascinating physical processes at work in biological systems of all scales.

Once again borrowing from design motifs in cells to support our own design initiative.

Metals and Protein Folding

2008-11-25T06:49:00.000-08:00

Molecular factories:
Scientists Unwrap The Elements Of Life

Quote:

ScienceDaily (Oct. 22, 2008) — Researchers at Newcastle University have taken a step forward in our understanding of how the fundamental building blocks of life are put together.

Quote:

The researchers have shown that the way the metals attach is identical for a protein that binds manganese to one that binds copper. In both cases the metals bind inside protein barrels with the same type of metal-attractions.

Carrying out the work in a blue-green algae, a cyanobacterium, the team has been able to show that a protein requiring copper transports to the periplasm, the outer area of the cell, where it then folds around the available metal, which is copper.

Conversely, manganese but not copper atoms are found in the cytosol, in the middle of the cell. The team has demonstrated that a protein requiring manganese folds in the cytosol. The manganese protein is then transported to the periplasm having first trapped its manganese.

Quote:

Once folded, the manganese site is buried, the metal trapped inside the protein, and so the manganese protein can subsequently co-exist with the copper protein because its' metal becomes impervious to replacement by metals further up the Irving-Williams series.

The work exemplifies a cell overcoming the metal binding preferences of proteins.

The new discipline of synthetic biology aims to engineer cells to carry out useful tasks, for example to generate valuable compounds. Because metals are the catalysts for so much of biology, knowing how to engineer a supply of the right metals to the right proteins will be important to the success of these ventures.

Mmmm, reverse engineering the efficiency of intracellular biomolecular machinery and making use of it to design and synthesize valuable compounds. Sounds like a good strategy.

Development: Robust and precise

2008-11-25T06:48:00.001-08:00

Ever wondered how an embryo develops?
Read up on the "fifth DNA molecule" or epigenetics. Read a little on genomic imprinting and X-inactivation. Also, totipotential cells and pluropotency.

During development a genetic program governs the developmental process. Primordial germ cells (PGC) are prevented from entering the somatic program (somatic differentiation) and are demethylated (genome-wide erasure of existing epigenetic modifications/remocal of a methyl group from cytosine). Then the gametes are imprinted (targeted DNA methylation/addition of methyl group to cytosine) during gametogenesis, only to be demethylated again after fertilization. Then during development, DNA is methylated again, causing totipotential cells to become pluripotent. These genomic reprogramming events are strictly controlled.

And now:
Scientists trace molecular origin of proportional development.

Quote:

CINCINNATI – When it comes to embryo formation in the lowly fruit fly, a little molecular messiness actually leads to enhanced developmental precision, according to a study in the Oct. 14 Developmental Cell from Cincinnati Children's Hospital Medical Center.

While the fundamentals of this tiny bug's reproductive biology may seem insignificant, one day they could matter quite a bit to humans. That's because the study provides new information about how cells choose their own fates, especially in maintaining the size relationship and proportionality of body parts during embryonic development, said Jun Ma, Ph.D., a researcher in the divisions of Biomedical Informatics and Developmental Biology at Cincinnati Children's and the study's corresponding author.

"We used the fruit fly in our study to trace the molecular origin of where body proportionality comes from, directly affecting how we think about precision control mechanisms during development," Dr. Ma said. "This new information is a basic, but very important, step. Although humans are far more complex, this could one day help us understand how two different-sized babies – with different mothers providing varied environmental and genetic influences – are born alike, with properly sized heads and limbs."

Besides discovering a scientific platform that will advance studies into precise, or normal, development, Dr. Ma and colleagues hope their knowledge will facilitate research into abnormal development, like certain types of birth defects.

Although fruit flies have miniscule brains and dine on rotten fruit, genetically the species has quite a bit in common with humans – a concept known as evolutionary conservation. This relationship has long made the insect a model for studying body patterning in animals.

Dr. Ma's team probed how a gene transcription regulatory protein called Bicoid turns on another gene, known as Hunchback. Hunchback instructs the embryo's anterior to begin formation of proportional body parts in the fruit fly's head and thoracic regions. Hunchback is switched on in the anterior half of the embryo, where the level of Bicoid is high. In normal (wild-type) embryos, the process begins when Bicoid diffuses from the anterior toward the posterior end, a principal already established in existing research literature. Bicoid, which comes from the mother, then forms a gradient along this body axis.

Dr. Ma and his colleagues discovered the amount of Bicoid in early embryos depends on the size of the egg. Larger embryos in the study showed higher Bicoid levels in the anterior region, while smaller embryos showed lower levels. This relationship between embryo size and Bicoid amount helps Bicoid establish a gradient scaled precisely according to each embryo's length, which is necessary for Hunchback to respond precisely, they said.

One area of messiness in the system is that the precision levels of Bicoid and Hunchback are different. The research team reported that imaging analyses of 28 wild-type embryos showed even a precise Bicoid gradient still has positional errors that go beyond the boundaries set up by its target Hunchback. Dr. Ma's team suggests that Bicoid can self correct its positional errors through a coupling that develops between Bicoid's forming gradient and the protein's activation of target genes. The correction essentially fine tunes the mechanism to achieve further developmental precision.

Other studies have suggested Bicoid level differences among individual embryos play little or no role in the precision of fruit fly embryo development. Bicoid gradient, they say, is inherently so precise at switching on its target genes that it approaches the limits set by basic physical principles. While offering important new insights into how Bicoid establishes a precise gradient along the embryo's length, Dr. Ma said the previous research also begged the questions: What then makes the Bicoid gradient so precise, or is it really so precise?

"Instead of discounting the variability of the Bicoid gradient among different embryos, we found this noise to be an advantage of the system," said Dr. Ma, also a professor of pediatrics at the University of Cincinnati College of Medicine. "The amount of Bicoid going to small and large embryos all self corrects, so the system is built to be very robust and precise so different cells can be told to become part of the head, or part of something else, in a proportionate manner."

Besides conducting staining and imaging tests on normal wild-type embryos to test their hypothesis, Dr.Ma's team also studied Bicoid and Hunchback expression in embryos from genetically altered, mutant (staufen) female fruit flies. They found Bicoid could not form a precise and scaled gradient in embryos from these mutant females, which, they concluded, contributed to additional Hunchback variations and disproportionate development.

Internal control of developmental processes whereby cells "choose" their own fate. Precise and robust control in a "messy system".

Channel hopping nanomachines

2008-11-25T06:46:00.000-08:00

Newly discovered mechanics of a molecular machine that transports proteins.

Channel hopping: protein translocation through the SecA–SecY complex

Quote:

Newly synthesized proteins are translocated across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane through an evolutionarily conserved protein conducting channel or translocon known as Sec61 in eukaryotes and SecY in prokaryotes. In bacteria, the SecA ATPase is thought to be the motor for translocation through the SecY channel. Two papers by Tom Rapoport and colleagues report the long-awaited structure of the SecA–SecY complex from bacteria. The structure, reveals major conformational changes between both partners and suggests that SecA uses a two-helix finger to push translocating proteins into SecY's cytoplasmic funnel. Crosslinking studies provide further experimental support for this mechanism. In a third paper, Osamu Nureki and colleagues present a crystal structure of SecY bound to an anti-SecY Fab fragment revealing a pre-open state of the channel. Together these three papers provide novel insights into the path taken by a translocating protein. In News and Views, Anastassios Economou takes stock of where this work leaves current knowledge of this 'astonishing cellular nanomachine'

Research articles:
Structure of a complex of the ATPase SecA and the protein-translocation channel
A role for the two-helix finger of the SecA ATPase in protein translocation
Conformational transition of Sec machinery inferred from bacterial SecYE structures

Quote:

Over 30% of proteins are secreted across or integrated into membranes. Their newly synthesized forms contain either cleavable signal sequences or non-cleavable membrane anchor sequences, which direct them to the evolutionarily conserved Sec translocon (SecYEG in prokaryotes and Sec61, comprising alpha-, bold gamma- and bold beta-subunits, in eukaryotes). The translocon then functions as a protein-conducting channel1. These processes of protein localization occur either at or after translation. In bacteria, the SecA ATPase2, 3 drives post-translational translocation. The only high-resolution structure of a translocon available so far is that for SecYEbold beta from the archaeon Methanococcus jannaschii 4, which lacks SecA. Here we present the 3.2-Å-resolution crystal structure of the SecYE translocon from a SecA-containing organism, Thermus thermophilus. The structure, solved as a complex with an anti-SecY Fab fragment, revealed a 'pre-open' state of SecYE, in which several transmembrane helices are shifted, as compared to the previous SecYEbold beta structure4, to create a hydrophobic crack open to the cytoplasm. Fab and SecA bind to a common site at the tip of the cytoplasmic domain of SecY. Molecular dynamics and disulphide mapping analyses suggest that the pre-open state might represent a SecYE conformational transition that is inducible by SecA binding. Moreover, we identified a SecA–SecYE interface that comprises SecA residues originally buried inside the protein, indicating that both the channel and the motor components of the Sec machinery undergo cooperative conformational changes on formation of the functional complex.

Exquisite control of biomolecular processes with the aid of nanomachines all the way down to the simplest organisms .

Plants and nervous systems

2008-11-25T06:42:00.000-08:00

When under attack, plants can signal microbial friends for help

Quote:

11:39 a.m., Oct. 17, 2008----Researchers at the University of Delaware have discovered that when the leaf of a plant is under attack by a pathogen, it can send out an S.O.S. to the roots for help, and the roots will respond by secreting an acid that brings beneficial bacteria to the rescue.
The finding quashes the misperception that plants are “sitting ducks”--at the mercy of passing pathogens--and sheds new light on a sophisticated signaling system inside plants that rivals the nervous system in humans and animals.

Seems like The Happening is not too far fetched... ?

Agents all around us.

Female Plant 'Communicates' Rejection Or Acceptance Of Male

Quote:

ScienceDaily (Oct. 23, 2008) — Without eyes or ears, plants must rely on the interaction of molecules to determine appropriate mating partners and avoid inbreeding. In a new study, University of Missouri researchers have identified pollen proteins that may contribute to the signaling processes that determine if a plant accepts or rejects individual pollen grains for reproduction.

Quote:

Like humans, the mating game isn’t always easy for plants. Plants rely on external factors such as wind and animals to bring them potential mates in the form of pollen grains. When pollen grains arrive, an introduction occurs through a “conversation” between the pollen (the male part of the flower) and the pistil (the female part of the flower). In this conversation, molecules take the place of words and allow the pollen to identify itself to the pistil. Listening in on this molecular conversation may provide ways to control the spread of transgenes from genetically-modified crops to wild relatives, offer better ways to control fertilization between cross species, and lead to a more efficient way of growing fruit trees.

“Unlike an animal’s visual cues about mate selection, a plant’s mate recognition takes place on a molecular level,” said Bruce McClure, associate director of the Christopher S. Bond Life Sciences Center and researcher in the MU Interdisciplinary Plant Group and Division of Biochemistry. “The pollen must, in some way, announce to the pistil its identity, and the pistil must interpret this identity. To do this, proteins from the pollen and proteins from the pistil interact; this determines the acceptance or rejection of individual pollen grains.”

In the study, researchers used two specific pistil proteins, NaTTS and 120K, as “bait” to see what pollen proteins would bind to them. These two pistil proteins were used because they directly influence the growth of pollen down the pistil to the ovary where fertilization takes place.

First the finding that signaling systems in plants rivals the nervous system of animals , now plant communication through interaction, interpretation, acceptance, rejection and control. Inbreeding is bad for the future, agents plan for the future through intelligence

Cell movement

2008-11-25T06:41:00.000-08:00

Cells Coordinate Gene Activity With FM Bursts, Scientists Find

Quote:

Proteins Have Controlled Motions, Researcher Shows[/url][/b]
ScienceDaily (Oct. 2, 2008) — How a cell achieves the coordinated control of a number of genes at the same time, a process that's necessary for it to regulate its own behavior and development, has long puzzled scientists.

Quote:

Michael Elowitz, an assistant professor of biology and applied physics at the California Institute of Technology (Caltech), along with Long Cai, a postdoctoral research scholar at Caltech, and graduate student Chiraj Dalal, have discovered a surprising answer. Just as human engineers control devices ranging from dimmer switches to retrorockets using pulsed -- or frequency modulated (FM) -- signals, cells tune the expression of groups of genes using discrete bursts of activation.

Elowitz, who is also a Bren Scholar and an investigator with the Howard Hughes Medical Institute, and his colleagues discovered this process by combining mathematical and computational modeling with experiments on individual living cells. The scientists looked specifically at the molecular changes within simple baker's yeast (Saccharomyces cerevisiae) cells after exposure to excess calcium, which increases in concentration in cells in response to stressful conditions such as high salt levels, alkaline pH, and cell wall damage.

The scientists tracked that response using a protein called Crz1 labeled with a green fluorescent tag. Crz1 is stimulated in response to high calcium levels and activates genes that help protect the cell. The glowing of the fluorescent marker allowed Elowitz and colleagues to visualize the movement of Crz1 as it travelled within the cell from the cytoplasm into the cell nucleus and out again into the cytoplasm. Using time-lapse microscopy, they created "movies" of that movement.

Landmark Discovery Of 'Engine' That Drives Cell Movement

Quote:

ScienceDaily (Oct. 7, 2008) — How a cell assembles its internal machinery required for cell movement has been revealed for the first time.

Quote:

The researchers discovered a complex of three proteins that directly regulates the myosin network within a cell, thus generating traction force to propel the cell forward. (Myosin is the most common protein found in muscle cells, and is responsible for the elastic and contractile properties of muscle. A different form of myosin is involved in cell movement.)

This action of the tripartite protein complex may be likened to a spring in a toy motorcar – when the protein complex assembles and moves backwards within the cell, it resembles the wound up "engine" of the toy car that has been pulled backwards.

Subsequent disassembling of the protein complex and the resultant forward movement of the cell can be likened to the released spring which unleashes the earlier stored potential energy to propel the car forward.

Michael Sheetz, Ph.D., who is William R Kenan Jr Professor of Cell Biology at the Department of Biological Sciences, Columbia University, and also Distinguished Visiting Professor at the National University of Singapore, said, "This is an exciting paper because Leung's group has discovered an unexpected step in cell migration and contractility — a complex of three proteins including a form of myosin, that is responsible for assembling most of the other myosin components involved in motile processes. The assembly mechanism has been a major mystery and is critical in a variety of diseases from cardiovascular to aging. Now we have a new tool to understand the bases of these critical processes."

Of the three proteins MRCK, LRAP35a and MYO18A, MRCK was discovered by the GSK-IMCB group 10 years ago, while the other two had hitherto unknown functions. Dr. Leung of IMCB said, "The success of the work relies on the commitment and perseverance of the team. A major contributor, Dr. Ivan Tan, is a home-grown scientist who has been working on this project for many years and he has had several clues as to how the system functions for some time, but it was only recently that the jigsaw puzzle was put together. The system has the potential to unravel other as yet undiscovered mechanisms that coordinate the different 'engines' for proper cell migration."

Emphasis mine.
Hard work with spectacular results

Protein Motion

2008-11-25T06:38:00.000-08:00

Proteins Have Controlled Motions, Researcher Shows

Quote:

Iowa State University researcher Robert Jernigan believes that his research shows proteins have controlled motions.

Quote:

Most biochemists traditionally believe proteins have many random, uncontrolled movements.

Research conducted by Jernigan, director of the L.H. Baker Center for Bioinformatics and Biological Statistics together with Guang Song, an assistant professor in computer science and graduate student Lei Yang, over a 10-year period shows that not only are protein motions more restricted, but also that these restricted, controlled motions are part of the function of the proteins.

The group's findings were recently published in the journal "Structure"

Using as an example a protein from HIV virus, Jernigan conducted his research using a simple model and tested to see how the proteins moved. The large number of reported structures show exactly the motions that are required for their function, and exactly the same motions as computed by Jernigan's model.

"This is one experimental case that is indicative, but there are many others," he said.

Jernigan believes this research is the first step to better understanding proteins and cell behaviors.

"There is the possibility of creating designer drugs with this newly discovered information," he said.

"These are models that conform to the point of view that the structures have been designed to exert very strong control of their motions," he said. "Those motions correspond closely to the motions needed for their function."

For instance, HIV virus protein structures that Jer****n studied did not move randomly, but actually opened and closed to allow access to other structures.

There is a binding site that must open to permit access to the protein and then close again to allow the protein to function, he said.

Because the protein structure opens and closes as part of it function, Jernigan believes that the motion is controlled and part of the function of the protein.

Jernigan's studies used the HIV virus, but he believes that the results are relevant to many other protein structures.

So much control, all the way down to protein motion.

Sonic hedgehog

2008-11-25T06:33:00.000-08:00

Here is a gene with a funny name with an awesome array of signaling capabilities:
Sonic-hedgehog

Also plays a role in brain development:
Tiny Cellular Antennae Trigger Neural Stem Cells

Quote:

ale University scientists today reported evidence suggesting that the tiny cilia found on brain cells of mammals, thought to be vestiges of a primeval past, actually play a critical role in relaying molecular signals that spur creation of neurons in an area of the brain involved in mood, learning and memory.

Quote:

The cilia found on brain cells of mammals until recently had been viewed as a mysterious remnant of a distant evolutionary past, when the tiny hair-like structures were used by single-celled organisms to navigate a primordial world.

“Many neuroscientists are shocked to learn that cells in the brain have cilia. Thus it was even more exciting to show that cilia have a key function in regulating the birth of new neurons in the brain,” said Matthew Sarkisian, post doctoral fellow in the department of neurobiology and co-first author on the study.

In the past decade, scientists have discovered primary cilia may have important functions in many animals. For instance, in 2000, Yale University scientists discovered defects in these cilia could lead to rare type of kidney disease. Researchers have been finding new functions for primary cilia ever since.

In the present study, researchers discovered that in mice, primary cilia act like antennae to receive and coordinate signals that spur creation of new brain cells. These cilia receive signals from a key protein required in development called “sonic hedgehog.” When the Yale team deleted genes needed to form primary cilia, they discovered that mice developed significant brain abnormalities including hydrocephalus. They also found that the absence of primary cilia on neural stem cells disrupted the ability of sonic hedgehog to signal neural stem cells to initiate creation of new neurons in the brain.

Furthermore, this group also observed cilia on dividing brain tumor cells. Postdoctoral fellow and co-first author Joshua Breunig said, “Considering sonic hedgehog is also heavily implicated in brain tumor formation, our study places the primary cilium at the crossroads of both regenerative neurobiology and neuro-oncology.”

An interesting take on the evolution of sonic-hedghog.

White blood cells, catapults, DNA repair and junk DNAnomore

2008-11-25T06:28:00.000-08:00

White Blood Cell Uses DNA 'Catapult' To Fight Infection

Quote:

U.S. and Swiss scientists have made a breakthrough in understanding how a type of white blood cell called the eosinophil may help the body to fight bacterial infections in the digestive tract, according to research published online in Nature Medicine.

Quote:

Hans-Uwe Simon, from the University of Bern, Switzerland, Gerald J.Gleich, M.D., from the University of Utah School of Medicine, and their colleagues discovered that bacteria can activate eosinophils to release mitochondrial DNA in a catapult-like fashion to create a net that captures and kills bacteria.

Dang, how cool is that. Like catching fish (bacteria) with a DNA net.

Quote:

"This is a fascinating finding," says Gleich, professor of dermatology and internal medicine at the University of Utah and a co-author of the study. "The DNA is released out of the cell in less than a second."

Eosiniphils, which comprise only 1 to 3 percent of human white blood cells, are known to be useful in the body's defense mechanisms against parasites. But their exact role in the immune system is not clear. Unlike other white blood cells, which are distributed throughout the body, eosinophils are found only in selected areas, including the digestive tract. Mitochondria – often referred to as the power plants of the cell – are components within cells that are thought to descend from ancient bacteria. Although most cellular DNA is contained in the nucleus, mitochondria have their own DNA.

Quote:

The researchers hope to learn more about how eosiniphils expel mitochondrial DNA. They speculate that the explosive mechanism might rely on stored energy, similar to the way plants release pollen into the air. "We don't know how eosinophils are capable of catapulting mitochondrial DNA so quickly," says Gleich.

Future investigation may focus on how this energy is generated and how this new knowledge can be applied to the treatment of bacterial infections and inflammatory diseases related to eosinophils.

More functions for previously thought Darwinian junk DNA.
How DNA Repairs Can Reshape Genome, Spawn New Species

Quote:

Researchers at Duke University Medical Center and at the National Institute of Environmental Health Sciences (NIEHS) have shown how broken sections of chromosomes can recombine to change genomes and spawn new species.

Quote:

"People have discovered high levels of repeated sequences in the genomes of most higher species and spun theories about why there are so many repeats," said Lucas Argueso, Ph.D., a research scholar in Duke's Department of Molecular Genetics and Microbiology. "We have been able to show with yeast that these repeated sequences allow the formation of new types of chromosomes (chromosome aberrations), and represent one important way of diversifying the genome."

The scientists used X-rays to break yeast chromosomes, and then studied how the damage was repaired. Most of the chromosome aberrations they identified resulted from interactions between repeated DNA sequences located on different chromosomes rather than from a simple re-joining of the broken ends on the same chromosome.

Chromosome aberrations are a change in the normal chromosome complement because of deletion, duplication, or rearrangement of genetic material. On rare occasions, the development of one of these new chromosome structures is beneficial, but more often DNA changes can be detrimental, leading to problems like tumors.

"Every so often the rearrangements may be advantageous," Argueso said. "Those particular differences may prove to be more successful in natural selection and eventually you may get a new species.

Repeat sequences aid in chromosome aberration repair and contributes to introduction of variability.

Look at all that Darwinian junk in the genome, honestly, who would make such a useless genome.
But, but, but....
'Junk' DNA May Have Important Role In Gene Regulation

Quote:

ScienceDaily (Oct. 20, 2008) — For about 15 years, scientists have known that certain "junk" DNA -- repetitive DNA segments previously thought to have no function -- could evolve into exons, which are the building blocks for protein-coding genes in higher organisms like animals and plants. Now, a University of Iowa study has found evidence that a significant number of exons created from junk DNA seem to play a role in gene regulation.

Quote:

"Hundreds of exons in the human genome were created from Alu elements. The whole-genome exon microarray allowed us to quickly identify exons that most likely contribute to the regulation of gene expression and function," said Lan Lin, Ph.D., University of Iowa postdoctoral fellow in internal medicine and the lead author of this study.

Analysis of one human gene, SEPN1, which is known to be involved in a type of muscular dystrophy, along with comparative data from chimpanzee and macaque tissues, suggested that the presence of a muscle-specific Alu-derived exon resulted from a human-specific change that occurred after humans and chimpanzees diverged evolutionarily.

"In this case, this exon is only expressed at a high level in the human muscle but not in any other human or non-human primate tissue, so this implies that the exon plays a functional role in muscle, and this role is human-specific," said Xing, who is also affiliated with University of Iowa Center for Bioinformatics and Computational Biology.

... you forget about cellular intelligence capable of harnessing random variation and selection.

Photosynthesis

2008-11-25T06:02:00.000-08:00

Very nice article about the photosynthesis photosystem II mechanism and how design principles of the system can be used to engineer similar systems to produce solar fuel.
Solar water-splitting into H2 and O2: design principles of photosystem II and hydrogenases

2.6 Summary: Principles of photosynthetic water-splitting

From the above text the following seven principles of photosynthetic water splitting can be extracted:

1. The components of the primary photo-reactions as well as the Mn4OxCa cluster are supported by protective components and, once destroyed, automatically replaced by the organism by a specific repair mechanism.
2. A multimeric transition metal complex (Mn4OxCa cluster) is employed to couple the very fast one–electron photochemistry with several orders of magnitude slower four electron water-splitting chemistry.
3. The water-splitting catalyst is located in a sequestered environment; channels exist for substrate entry and product release.
4. The matrix (protein) around the Mn4OxCa cluster is highly important for the coupling of proton and electron transfer reactions. This feature is essential for achieving about equal redox potentials for all oxidation steps that match the oxidizing potential of the light-generated primary oxidant.
5. Point 4 leads to a decoupling of the release of the two products O2 and H+ from the catalytic site.
6. The substrate water molecules are stepwise prepared for O–O bond formation by binding to the Mn4OxCa cluster and by (partial) deprotonation. The concerted oxidation of the activated substrate occurs then either in two 2 e− or one concerted 4 e− reaction step(s). This avoids high energy intermediates.
7. The Mn4OxCa cluster undergoes several structural changes during the Kok cycle, which are probably significant for the mechanism. The surrounding matrix therefore needs to be flexible enough to support such changes.

3.6 Design principles of hydrogenases

For a better understanding of the design principles of native hydrogenases a comparison of the two major hydrogenases is useful.

The two groups of hydrogenases have a completely different genetic background. Whereas the [NiFe] group is widely distributed in prokaryotes (mostly sulfur reducing bacteria), the [FeFe] group is less widely distributed but occurs in both prokaryots and eukaryots (algae, yeast). In fact, the genetic signature of the H-cluster is found in many higher organisms, even in homo sapiens. The [FeFe] hydrogenases are, in general, most active in H2 production while [NiFe] hydrogenases are more tuned to H2 oxidation. Both types are however bidirectional. Organisms employing [NiFe] hydrogenases are found in regions with higher oxygen levels than those using [FeFe] hydrogenase. This is because [FeFe] hydrogenases are extremely oxygen sensitive and will be inhibited irreversibly under O2. [NiFe] hydrogenases are, in general, more oxygen tolerant and some enzymes even evolve H2 under O2.

On the other hand, there are many similarities between the basic structures of the active site in both enzymes:

1. Both enzymes employ a bimetallic center where the chemistry is taking place.
2. Both active sites have a butterfly-shaped core in which the two metals are bridged by SR-ligands.
3. Only one of these metal atoms is redox active (Ni in [NiFe] and Fed in [FeFe] hydrogenase) and they both have a d7 configuration (Ni(III) and Fe(I), respectively) in their active states.
4. In both catalytic sites the Fe atom is kept at a low valence by the strongly donating ligands CN− and CO.
5. The metal-metal distance in both structures is short (2.5–2.9 ), indicating a metal–metal bond.
6. One metal with an open coordination site can be identified in both active states. This is the site where H2 is believed to bind or is being released.
7. The H/D-isotope effect shows that in both cases the H2 splitting is heterolytic
8. In both active sites a sulfur or nitrogen/oxygen ligand probably acts as base to accept or donate the H+.
9. For both enzymes the catalytic activity is often inhibited by O2 and CO.

These features can serve as guidelines for the construction of biomimetic hydrogenase models.

Emphasis mine.

Also, the photosystem II mechanism makes use of quantum mechanical computing principles, leading to an excellent quantum efficiency for water-splitting.

From Nature;Vol 446;12 April 2007: Quantum path to photosynthesis

Elsewhere in this issue, Engel et al. (page 782) take a close look at how nature, in the form of the green sulphur bacterium Chlorobium tepidum, manages to transfer and trap light’s energy so effectively. The key might be a clever quantum computation built into the photosynthetic algorithm.

The process is analogous to Grover’s algorithm in quantum computing, which has been proved to provide the fastest possible search of an unsorted information database.

And in the same issue: Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems

When viewed in this way, the system is essentially performing a single quantum computation, sensing many states simultaneously and selecting the correct answer, as indicated by the efficiency of the energy transfer.

A glimpse into the future of our own designs.

Robustness and back-up systems

2008-11-25T05:45:00.000-08:00

New Evidence On The Robustness Of Metabolic Networks

Biological systems are constantly evolving in ways that increase their fitness for survival amidst environmental fluctuations and internal errors. Now, in a study of cell metabolism, a Northwestern University research team has found new evidence that evolution has produced cell metabolisms that are especially well suited to handle potentially harmful changes like gene deletions and mutations.

You Can Be Replaced: Immune Cells Compensate For Defective DNA Repair Factor

Genetic instability can lead to multiple problems, including cell death and many forms of cancer. Therefore, it is absolutely critical for cells to have both the means to constantly survey genes for damage and the mechanisms to repair broken DNA. Currently, there are six well characterized classical non-homologous end-joining (C-NHEJ) factors that repair double strand breaks (DSBs) in mammalian cells.Lymphocytes, a type of immune cell, use a kind of genetic shuffling called variable, diversity, joining V(D)J recombination. This gene shuffling occurs during lymphocyte development and helps to produce diverse immune system cells that can recognize all sorts of different foreign substances, called antigens, that might pose a threat to the organism. Previous work in mice has shown that deficiency of C-NHEJ factors results in a severely compromised immune system, because of incomplete V(D)J recombination, along with increased sensitivity to cellular ionizing radiation (IR) and genomic instability.

Nice to know cell intelligence and evolution from a front-loaded state provide for robust systems with back-up. Preadaptation is good for the future.

Putting cytosine deamination to work

2008-11-25T05:44:00.000-08:00

The effect of cytosine deamination on a random pool of amino acids and how it might facilitate evolution has been described. Cytosine deamination also does not result in any stop codon formation. Bollenbach et al. (2007) briefly describes a few more optimal features of the genetic code as discussed in more detail by Itzkovitz and Alon (2007).

These include:
1) Quote:

They (Itzkovitz and Alon) compared the actual genetic code with an ensemble of all other codes that are equally optimized with respect to mistranslation or mutation (for more on this statistical approach, see also Alff-Steinberger 1969; Haig and Hurst 1991; Freeland and Hurst 1998). Assuming that the usage frequencies of the different amino acids are fixed, while their codon assignments vary in the ensemble, they find that the actual code is far better than other possible codes in minimizing the number of amino acids incorporated until translation is interrupted after a frameshift error occurred. This new observation by Itzkovitz and Alon could therefore be seen as reviving the basis for Crick’s theory of a comma-less code, modified by the constraints imposed on the code by the need to be robust to other kinds of translation errors and mutations. Another possible interpretation of their result is that the amino acid usage has adjusted to reduce the effects of frameshift errors; alternative genetic codes would have had a different amino acid usage coadapted to them. It has been shown previously that amino acid usage is rather malleable, and, for example, influenced by GC content (Knight et al. 2001b).

2) Quote:

Itzkovitz and Alon suggest another, quite unanticipated, type of optimality: the code is highly optimal for encoding arbitrary additional information, i.e., information other than the amino acid sequence in protein-coding sequences. Optimality for encoding additional information is particularly important and relevant given the known signals contained in the nucleotide sequence of coding regions. These include RNA splicing signals, which are encoded in the nucleotide sequence together with the amino acid sequence of the prospective protein (Cartegni et al. 2002), as well as signals recognized by the translation apparatus.

Bollenbach et al. (2007) also briefly mentions how the code could have evolved:
1) Quote:

(1) the code has evolved under selection pressure to optimize certain functions such as minimization of the impact of mutations (Sonneborn 1965) or translation errors (Woese 1965a); Random mutation is a source of variability, yet selection pressure is believed to have selected for a system to put constraints on variability. Why?

2) Quote:

(2) the number of amino acids in the code has increased over evolutionary time according to evolution of the pathways for amino acid biosynthesis (Wong 1975)

Why was selection so strong in removing the other variants with fewer codons? Is there evidence of organisms using only 5, 6, 9, 13, 18 etc. amino acid codons? Bollenbach et al. (2007) also points out the following:
Quote:

The discovery of variant codes (Barrell et al. 1979; Fox 1987; Knight et al. 2001a) made the connection between evolvability and universality even more puzzling. On one hand, they prove that the genetic codes can evolve; on the other hand, if they could easily evolve, why are all variations minor? It was recently proposed that extensive horizontal gene transfer during early evolution can account for both evolution toward optimality and the near universality of the genetic code (Vetsigian et al. 2006).

3) Quote:

(3) direct chemical interactions between amino acids and short nucleic acid sequences originally led to corresponding assignments in the genetic code (Woese et al. 1966b).

Bollenbach et al. (2007) concludes with the following:
Quote:

As we learn more about the functions of the genetic code, it becomes ever clearer that the degeneracy in the genetic code is not exploited in such a way as to optimize one function, but rather to optimize a combination of several different functions simultaneously. Looking deeper into the structure of the code, we wonder what other remarkable properties it may bear. While our understanding of the genetic code has increased substantially over the last decades, it seems that exciting discoveries are waiting to be made.

The vertebrate immune system exploits these optimal features of the genetic code by "putting cytosine deamination to work". Antibody diversification is crucial in limiting the frequency of environmentally acquired infections and thereby increasing the fitness of the organism. Initial diversification of antibodies is achieved by assembling variable (V), diversity (D) and joining (J) gene segments (V(D)J recombination) by non-homologous recombination. Further diversification is carried out by somatic hypermutation (SHM) and Class Switch Recombination. Central to the initiation to these diversification processes is the activation-induced cytosine deaminase (AID) protein. AID deaminates cytosine to uracil in single stranded DNA (ssDNA - arising during gene transcription) and is dependent on active gene transcription of the various antibody genes. The induced mutation is resolved by at least 4 pathways (Figure 4):
1) Copying of the base by high-fidelity polymerases during DNA replication.
2) Short-Patch Base Excision Repair (SP-BER) by uracil-DNA glycosylase removal and subsequent repair of the base.
3) Long-Patch Base Excision Repair (LP-BER)
4) Mismatch repair (MMR)

Figure 1: Activation induced cytosine deamination and the pathways involved in resolving the induced mutation. 1) Normal DNA replication results in a C:G→T:A transition. 2) Successful SP-BER resolves the mutation, however the recruitment of error-prone translesion polymerases results (e.g. REV1) in transversions (REV1; C:G→G:C) and transition. 3) LP-BER can also resolve the mutation, however recruitment of low-fidelity polymerases (e.g. Pol n) also causes transition and transversion mutations. 4) MMR repair can also resolve the mutation, however the recruitment of low-fidelity polymerases through this pathway is a major cause of A:T transitions.

AID causes somatic hypermutation and its activity is limited to the certain genetic regions of the immune system. When the system runs unchecked, mutations might be introduced into proto-oncogenes, resulting in possible cancerous growth. The system is controlled (Figure 2). The activity and gene expression of AID is controlled. The type of error-repair pathway and the subsequent recruitment of various low-fidelity polymerases determine the type of mutations after the repair process and these also seem to be controlled. Current research focuses on the mechanisms of control of downstream repair pathways and why this system is selectively targeted to the small region of antibody genes.

Figure 2: Controlled variability of somatic hypermutation.

Thus, the immune system exploits the properties the genetic code for the purpose of controlled variability. Is the system limited to vertabrates or can similar systems be found in other organisms. Cytosine deamninases are found in bacteria as well. Error-prone repair systems are also present. Will we discover an active system in bacteria that exploits the properties of the genetic code for the purpose of controlled variability under selective pressure? Will RecA
and LexA play a part?

References:
Peled JU, Kuang FL, Iglesias-Ussel MD, Roa S, Kalis SL, Goodman MF et al. The biochemistry of somatic hypermutation. Annu Rev Immunol. 2008;26:481-511.

Teng G, Papavasiliou FN. Immunoglobulin somatic hypermutation. Annu Rev Genet. 2007;41:107-20.

Goodman MF, Scharff MD, Romesberg FE. Abstract AID-initiated purposeful mutations in immunoglobulin genes. Adv Immunol. 2007;94:127-55.

Basu U, Chaudhuri J, Phan RT, Datta A, Alt FW. Regulation of activation induced deaminase via phosphorylation. Adv Exp Med Biol. 2007;596:129-37

Cell cycle signaling network

2008-11-25T05:41:00.001-08:00

DNA replication, DNA repair, cell division signaling and programmed cell death

The cell cycle is a highly regulated process and "takes micromanagement to the extreme". Various positive- and negative-feedback systems ensure that cells divide in a controlled manner. The process consists of a sequence of events by which a growing cell duplicates all its components and divides into two daughter cells, each with sufficient machinery to repeat the process. In eukaryotic cells, one round of cell division consists of two “gap” phases termed G₁- and G₂-, an S-phase during which duplication of all DNA happen, and an M-phase where proper segregation of duplicated chromosomes and chromatid separation occur. During each of these phases, regulatory signaling pathways monitor the successful completion of events in each phase before proceeding to the next phase. These regulatory pathways are commonly referred to as cell cycle checkpoints. Cell cycle checkpoints are activated in response the following (Figure 1):

Cellular damage
Exogenous cellular stress signals
Lack of availability of nutrients, hormones and essential growth factors.

During the G₁ phase many signals intervene to influence cell division and the deployment of a cell’s developmental program (Figure 1). Crucial "decisions" are made to pass the G₁ restriction point as commitment to replicate DNA and divide is irreversible until the next G₁ phase. Failure to meet the correct conditions results in a failed attempt to divide. Signaling events converge to affect the phosphorylation status of the retinoblastoma protein (pRB) family (pRB, p107, and p130). Cyclin dependent kinases (CDKs) play a crucial role in pRB phosphorylation status and their activity is in turn controlled by cell stress and growth inhibitory signaling pathways. Sufficient phosphorylation (hyper-phosphorylation) of pRB causes it to dissociate from the elongation factor 2 (e2F) family of transcription factors. Dissociated e2F transcription factors mediate the transcription and activity of genes required for DNA replication during the S-phase.

As soon as the restriction point (G₁/S transition checkpoint) is passed, initiation of DNA replication takes place at multiple sites on the chromosomes, called the origins of replication. The origin recognition complex (ORC) marks the position of replication origins in the genome and serves as the landing pad for the assembly of a multiprotein, pre-replicative complex (pre-RC) at the origins, consisting of ORC, cell division cycle 6 (Cdc6), Cdc10-dependent transcript (Cdt1), mini-chromosome maintenance (MCM) proteins, clamp-loaders, sliding clamps, helicases, DNA polymerases etc. The MCM proteins serve as key participants in the mechanism that limits eukaryotic DNA replication to once-per-cell-cycle and its binding to the chromatin marks the final step of pre-RC formation. Once the replisome is assembled, the transition to DNA replication is irreversibly completed and the cell enters the S-phase.

After successful completion of DNA replication the mitosis promoting factor (MPF) complex forms and plays a crucial role in nuclear envelope breakdown, centrosome separation, spindle assembly, chromosome condensation and Golgi fragmentation during mitosis. Cells only enter mitosis (G₂/M transition) after the completion of the above events.

When a cell is unable to address the above circumstances, cell division is permanently halted and the cell either enters senescence or programmed cell death is activated (Figure 1). Programmed cell death (particularly apoptosis) removes potentially hazardous cells from a population of cells, resulting in the controlled destruction of the cells designated for destruction. Two checkpoints during the cell cycle exist.

The DNA structure checkpoint
The spindle checkpoint

The DNA structure checkpoint operates between the G₁/S transition, the S-phase and the G₂/M transition (Figure 1). The DNA structure checkpoint during the G₁/S and G₂/M transitions ensure that DNA damage is minimal while the S-phase DNA structure checkpoint also recognizes and deals with replication intermediates, stalled replication forks and unreplicated DNA. Whenever the criteria are not met during a checkpoint, a cell will not proceed to the next phase. Various signaling networks are activated and operate to ensure these criteria are met. DNA structure checkpoint signaling has the same pattern during any phase of the cell cycle (Figure 1):

Detection: Sensor proteins include proliferating cell nuclear antigen (PCNA)-like and replication factor C (RFC)-like protein complexes (see Sliding clamps, clamp-loaders and helicases), which are able to bind to damaged DNA to form a scaffold for downstream repair proteins. The Rad50/Mre11/NBS1 complex is also loaded onto damaged DNA sites and mediates downstream checkpoint and repair proteins.
Signal transduction: Activated sensor proteins in turn activate several signaling proteins which in turn activates DNA repair mechanisms and downstream effector proteins that controls cell cycle checkpoint signal transduction and programmed cell death signaling. Some examples include, ataxia telangiectasia mutated (ATM), ataxia telangiectasia and Rad3 related (ATR) p53 binding protein (53bp), the topoisomerase binding protein TopBP1, mediator of DNA damage checkpoint (MDC1), breast cancer 1 (BRCA 1) etc.
Effect: Downstream of the signal transducers include the the effector serine/threonine protein kinases CHK1 and CHK2. CHK’s transfer the signal of DNA damage to the phosphotyrosine phosphatases and cell division cycle proteins Cdc25A, Cdc25B, and Cdc25C as well the tumor-suppressor p53. Cdc25A controls the G₁/S and S-phase transition (prevents pRB dissociation through dephosphorylation of pRB proteins) while Cdc25B and Cdc25C control the G₂/M transition (both upregulating Wee1 and Myt1 by phosphorylation, which together control Cdc2/CyclinB activity). Tumor supressor p53 protein activity links DNA damage to programmed cell death.

Figure 1: Dynamic control of cell cycle events through cell signaling, checkpoints, nutrient availability and extracellular stress.

The spindle assembly checkpoint is a molecular system that ensures accurate segregation of mitotic chromosomes and functions during the M-phase of cell division. The spindle checkpoint depends on the activity of two systems.

The 26S proteasome (APC/C-cdc20 complex) for the degradation of cyclin B.
The anaphase promoting complex/cyclosome (APC/C-cdh1 complex) for the degradation of cyclins and securin

How are these for provocative sounding titles:
Voges D, Zwickl P, Baumeister W. The 26S proteasome: a molecular machine designed for controlled proteolysis. Annu Rev Biochem. 1999;68:1015-68.
Peters JM. The anaphase promoting complex/cyclosome: a machine designed to destroy. Nat Rev Mol Cell Biol. 2006 Sep;7(9):644-56.

Cyclin B is ubiquitinylated and degraded by the the 26S proteasome (APC/C-cdc20 complex) which in turn results in the activation of the APC/C-cdh1 complex. The APC/C-cdc20 complex is controlled by the mitotic checkpoint complex (MCC) which detects tubulin and kinetochore integrity. The APC/C-cdh1 complex mediates the degradation of securin resulting in chromosome segregation.

There is a considerable amount of cross-talk between DNA repair mechanisms, programmed cell cycle signaling pathways, cell death pathways (autophagy, apoptosis, mitotic catastrophe etc.) and other cell stress signaling pathways. All these intricately interwoven pathways serve to ensure accurate cell division and removal of faulty cells from a population through programmed cell death. The problem comes when one of the checkpoints or programmed cell death pathways become corrupted and causes uncontrolled cell division in multicellular organisms. Cancer is one of the outcomes of abrogated cell death signaling and uncontrolled cell division. Programmed cell death is however not limited to multicellular organisms as bacteria also contain the necessary pathways to self destruct.

E.g.:
Engelberg-Kulka H, Amitai S, Kolodkin-Gal I, Hazan R. Bacterial programmed cell death and multicellular behavior in bacteria. PLoS Genet. 2006 Oct;2(10):e135.

Rice KC, Bayles KW. Molecular control of bacterial death and lysis. Microbiol Mol Biol Rev. 2008 Mar;72(1):85-109.

Chaperones

2008-11-25T05:38:00.000-08:00

One of the most intriguing group of proteins is a group of proteins that assist in the folding and unfolding of macromolecular structures into the correct 3D-architecture, prevents protein clumping and transport damaged or improperly made proteins to be recycled. The chaperones (a lot of them are also known as heat-shock proteins)

Great video

New Insights Into Hidden World Of Protein Folding

Quote:

"Folding is one of the key steps for the health of the cell," Frydman said.

Virtually all proteins have to be folded-some in complex configurations-in order to function properly, and many are known to require a molecule called a chaperone to fold them. Frydman estimates that perhaps 10 percent of the proteins needing chaperones must have one that, like TRiC, is part of the subset called chaperonins. Other work done in Frydman's lab has shown that proteins that have very complex folds seem to require chaperonins.

"Many of the proteins that have these complex folds are the most important ones for life," Frydman said. "The proteins that control the cell cycle, tumor suppressers and the proteins that control the shape of the cell are dependent on chaperonins to get to the folded state.

"If the chaperones don't work well, then all these proteins that have been made become toxic," she said.

Protein 'Shocks' Evolution Into Action

Quote:

“One of the great mysteries of biology is how life could have evolved so rapidly,” says Lindquist. “This research gives at least one plausible explanation for the speed of evolution and for the evolution of complex traits affected by several genes.”

Quote:

“One stressful event can affect many traits and allow previously unseen genetic variation to be expressed,” says Sangster. “We don’t know yet what is going on at the molecular level—why the HSP90-dependent traits are expressed when the plants are mildly stressed.”

Seeing that the structure and functionality of sliding clamps and clamp loaders (not an isolated case btw) are conserved across the three domains of life with very little sequence similarity it seems reasonable that chaperones played a part in conserving the structure and functionality of selected proteins over deep time while retaining flexibility and allowing sequence variability.
This ties in nicely with the robust Universal Optimal codon Code that allows for variation but also buffers against the effects of mutation.

The bc1-complex for electron transfer from dihydroubiquinone to cytochrome c through the Q-cycle.

2008-11-25T05:36:00.000-08:00

The bc1-like complexes (Complex III in mitochondria) play a central role in the electron transport chains of respiratory and photosynthetic machinery.

Their function is to carry out a sequence of electron and proton transfer reactions to generate a trans-membrane proton motive force that supplies the energy for ATP synthesizing utilizing the ATP synthase (excellent video, funny clip) machinery. Protons and electrons are supplied by dihydroubiquinone which in turn is generated by complexes I and II of the electron transport chain.

How do the bc1-like complexes carry out their function?
First the structure:

Figure 1: Bc1-complex

The cyt bc1-complex contains two separate redox chains; High potential and low potential.
The high-potential chain connects the Qo-binding site with the cyt c1 through the Rieske Iron-sulphur-protein (RISP). The RISP is situated on a rotateable arm that is able to connect the cyt c1 component with the Qo-binging site.
The low potential chain connects the Qo-site with the Q1-site through the cyt BL and Cyt BH complexes.

Now the mechanism. A bifurcated electron transfer mechanism:

Figure 2: Bifurcated electron transfer the Qo-site of the bc1-complex.

1) The lipid-soluble dihydroubiquinone molecule binds at the Qo-site and liberates one proton into the intermembrane space and in the process forms a semiubiquinone radical.
2) The RISP swings around to receives an electron from the semiubiquinone and donates it to cyt c1 which in turn donates it to cytochrome c. Cytochrome c plays its part in energy transfer to complex IV of the electron transfer chain.
3) A second proton is liberates into the intermembrane space and an electron is donated to the low potential chain, resulting in the formation of ubiquinone
4) At the Q1-site the electron is donated to ubiquinone to form semiubiquinone, while a proton is donated from the mitochondrial matrix.
5) In order for the formation of dihydroubiquinone at the Q1-site, two dihydroubiquinones must bins at the Qo-site.
6) Thus the end result is the formation of 1 dihydroubiquinone, 2 quinones, 4 intermembrane protons and 2 ferrocyrochrome c proteins and loss of 2 mitochondrial matrix molecules after the binding of 2 dihydroubiquinones at the Qo-site.

That is the basic general mechanism, however research is ongoing into how bypass reactions are avoided.
For example:
Why do the electrons flow in only one direction in the low electron transport chains?
Why aren't both electrons donated to the high-potential chain in the first place?
Radical hypotheses have been proposed including (From Cape et al. 2006 Trends Plant Sci. 2006 Jan;11(1):46-55.):

Quote:

(i) A complex that can either stabilize the intermediate semiubiquinone, rendering it inert and invisible through some unknown mechanism, or that can use the unprecedented tactic of destabilizing its reactive intermediates.
(ii) A kinetic ‘water-park’ that tunes reaction activation enthalpies or entropies to route ‘water’ (electron) flow into productive channels.
(iii) A nano-machine that gates the electron and proton transfer reactions of semiubiquinone according to its recognition of the different redox and/or conformational states of the complex.
(iv) An extraordinary, and unprecedented, double concerted oxidation of dihydroubiquinone that simultaneously distributes two electrons and at least one proton between at least three different acceptors.

Options II and III do not exclude the possibility of quantum mechanics and coulombic interactions playing a role.

All-in-all a brilliant solution for a bifurcated electron transfer mechanism in order to generate a proton motive force from dihydroubiquinone.

Interestingly, the intermediate (semiubiquinone) generated at the Qo-site is believed to be a major contributor to the formation of reactive oxygen species by donating it's free electron to oxygen and thereby resulting in the formation of superoxide. Superoxide formation causes damage to various molecules including DNA, RNA, proteins and lipids.

Figure 3: Semiubiquinone

Paradoxically though, reactive oxygen specie generation at the Qo-site as a result of semiubiquinone formation is increased during periods of hypoxia (low oxygen). Hypoxia is a major initiator of cancerous growth because it activates various pro-growth signaling pathways. Hypoxia in cells usually occur as a result of poor circulation and delivery of oxygen. Obesity, lack of exercise and poor diet all contribute to these circumstances.

Thus, the bc1-complexes connects bad health choices with higher incidences of cancers and other mitochondrially related diseases through reactive oxygen species formation as a result of hypoxic conditions within various systems of the body.

Exercising and eating right are good for oiling your biomolecular machines. :)

Sliding clamps, clamp-loaders and helicases.

2008-11-25T05:34:00.001-08:00

Sliding clamps, clamp-loaders and helicases.

Sliding clamps are ring-shaped proteins that some refer to as the “guardians” of the genome or others name them as the “ringmasters” of the genome.
Interestingly these clamps are structurally and functionally conserved in all branches of life and crystallographic studies have shown that they have almost superimposable three-dimensional structures, yet these components have very little sequence similarity (Figure 1) [1].

Figure 1: Sliding clamps eukaryotes, bacteria, phages and archaea.

What do they do?

The picture below is taken from the Molecular Biology Visualization of DNA video (2:14) from the freesciencelectures.com site (Figure 2).

Great video!
Figure 2: Replication machinery.

The following components can be seen.
Sliding clamps (PCNA in eukaryotes): Green circular shaped
Clamp loader (RFC in eukaryotes): Blue-white component in the middle
Helicase: Blue
DNA polymerase: Dark-blue components attached to the sliding clamps
Primase: Green component attached to helicase
Leading strand: Spinning off to the right
Lagging strand: Spinning off to the top

They are not ringmasters for nothing. Sliding clamps participate and control events that orchestrate DNA replication events in the following ways:

Enhancement of DNA polymerase activity.
Coordinate Okazaki fragment processing.
Prevention of rereplication
Translesion synthesis
Prevents sister-chromatid recombination and also coordinates sister-chromatid cohesion
Crucial role in mismatch repair, base excision repair, nucleotide excision repair
Participates in chromatin assembly

Other functions include:

Epigenetic inheritance
Chromatin remodeling
Controls cell cycle and cell death signaling

The true ringmasters.

Clamp loaders are another group of interesting proteins (see video and figures 3-4).

Figure 3: Structures of Proliferating Cell Nuclear Antigen connected to
Replication factor C (Front).

Figure 4: Structures of Proliferating Cell Nuclear Antigen connected
to Replication factor C (Side).

Interestingly again, their functional and structural architecture are conserved across the three domains of life with low-level sequence similarity [2]. At the replication fork during replication, they load the sliding clamps many times onto the lagging strand (after DNA priming) and only once onto the leading strand. They also act as a bridge to connect the leading and lagging strand polymerases and the helicase. Which brings us to another interesting group of proteins; the helicases.

Helicases are also known to be ring-shaped motor proteins, typically hexamers (see figure 5) and separate double-stranded DNA into single-stranded templates for the replication machinery.

Figure 5: Helicase

Replication occurs at about 1000 base pairs per second due to the highly efficient combination of sliding clamps and the polymerases. Thus, helicases need to unwind DNA at at least that speed. Unwinding DNA too slowly and the replication machinery might break down . Unwind the DNA too fast or untimely and harmful mutations might occur as single-stranded DNA is prone to degradation and cytosine deamination.

The speed at which helicase unwinds DNA is no accident though, as it is intrinsically controlled. As helicase is bound to the lagging strand, it unwinds the leading strand in a separate direction. Applying a pulling force on the leading strand leads to a 7-fold increase in the speed of DNA unwinding by helicase [3, 4]. The highly efficient DNA polymerase/sliding clamp combination provides this controlling force on the leading strand. This forms a robust unwinding/polymerization interaction whereby polymerization controls and prevents unwanted DNA unwinding.

Altogether, the replisome machinery provides a robust way for DNA replication to prevent unnecessary DNA damage and mutation.

References
1. Vivona JB, Kelman Z. The diverse spectrum of sliding clamp interacting proteins. FEBS Lett. 2003 Jul 10;546(2-3):167-72.
2. Jeruzalmi D, O'Donnell M, Kuriyan J. Clamp loaders and sliding clamps. Curr Opin Struct Biol. 2002 Apr;12(2):217-24.
3. Ha T. Need for speed: mechanical regulation of a replicative helicase. Cell. 2007 Jun 29;129(7):1249-50.
4. Johnson DS, Bai L, Smith BY, Patel SS, Wang MD. Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase. Cell. 2007 Jun 29;129(7):1299-309.

Introduction

2008-11-25T05:07:00.000-08:00

A blog dedicated to the inner workings of cells.