Protein folding, Nanotubes and Engineering

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

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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

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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

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.

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"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

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

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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:

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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

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

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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:

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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

How Cells Take Out The Trash To Prevent Disease

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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

How 'molecular machines' kick start gene activation revealed

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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.

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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

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

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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.

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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

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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

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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.

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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

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

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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.

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“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.

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“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?

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.

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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

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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

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

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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

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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.

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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

The inner life of mesoorganisms

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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.

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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

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.

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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

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

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

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.

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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

Cells Coordinate Gene Activity With FM Bursts, Scientists Find

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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.

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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

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

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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

Proteins Have Controlled Motions, Researcher Shows

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

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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

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.

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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

White Blood Cell Uses DNA 'Catapult' To Fight Infection

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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.

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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

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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.

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"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

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.