Archive: Cell Trends Too

[bob b]

Fatty Acid Synthesis: A Machine with “High Degree of Architectural Complexity” 04/19/2007
As Bruce Alberts said in 1998, the biology of the future was going to be the study of molecular machines: “the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.”1 One of those machines is like a mini-factory in itself. It’s called fatty acid synthase (FAS). Three Yale researchers just published the most detailed description of this machine in the journal Cell.2 (cf. last year’s headline, 03/06/2006). They remarked that its most striking feature is the “high degree of architectural complexity” – some 48 active sites, complete with moving parts, in a particle 27 billionths of a meter high and 23 billionths of a meter wide.
Despite our aversion to fat, fatty acids are essential to life. It’s when fat production goes awry that you can become fat. The authors explain:

“Fatty acids are key components of the cell, and their synthesis is essential for all organisms except archaea. They are major constituents of cellular membranes and are used for posttranslational protein modifications that are functionally important. Saturated fatty acids are the main stores of chemical energy in organisms. Deregulation of fatty acid synthesis affects many cellular functions and may result in aberrant mitosis, cancer, and obesity.”

The chemical steps for building fatty acids appear in the simplest cells and remain essentially unchanged up to the most complex organisms, although the machinery differs widely between plants, animals and bacteria. In plants, for instance, the steps are performed by separate enzymes. In animals, a two-part machine does the work. Which organism has one of the most elaborate fatty-acid machines of all? The surprising answer: fungi. The researchers imaged the fatty acid synthase enzymes of yeast and, despite their academic restraint, were clearly excited as the details came into focus:

“Perhaps the most striking feature of fungal FAS is its high degree of architectural complexity, in which 48 functional centers exist in a single ... particle. Detailed structural information is essential for delineating how this complex particle coordinates the reactions involved in many steps of synthesis of fatty acids.... The six alpha subunits form a central wheel in the assembly, and the beta subunits form domes on the top and bottom of the wheel, creating six reaction chambers within which each ACP can reach the six active sites through surprisingly modest movements. This structure now provides a complete framework for understanding the structural basis of this macromolecular machine’s important function. “

Calling it an “elegant mechanism,” they proudly unveiled a new model that tells the secret inside: a swinging arm delivers parts to eight different reaction centers in a precise sequence.
Their dazzling color diagrams are, unfortunately, copyrighted inside a technical journal, but a Google image search shows one reasonable facsimile of the overall shape at a Swiss website: click here. Some of the protein parts provide structural support for the delicate moving parts inside. Taking the structure apart, it looks something like a wagon wheel with tetrahedron-shaped hubcaps above and below. Picture a horizontal wagon wheel with three spokes, bisecting the equator of the structure. Now put the hubcaps over the top and bottom axles. The interior gets divided up into six compartments (“reaction chambers”) where the magic takes place.
In each reaction chamber, eight active sites are positioned on the walls at widely separated angles from the center. Spaced nearly equidistant between them all is a pivot point, and attached to it by a hinge is a lever arm. This lever arm, called ACP, is just the right length to reach all of the reaction sites. From a tunnel on the exterior, the first component arrives and is fastened to the ACP arm (priming). The arm then swings over to another active site to pick up the next part, then cycles through the next six reaction sites that each do their part to add ingredients to the growing fatty acid chain (elongation). The machine cycles through the elongation step multiple times, adding carbons to the growing fatty acid. When the chain reaches its proper length (16-18 carbons, depending on the fatty acid needed), it is sent to a final active site that stops the cycle (termination) and delivers the product through an exit channel to the cytoplasm.
The ACP hinged arm, then, is the key to the system. Imagine a life-size automated factory with a roughly spherical interior. Its task is to build a chain of parts in a precise order. The first ingredient comes through a shaft and is attached to the robotic arm in the center. The arm then follows a pre-programmed sequence that holds out the product to eight different machines on the walls that add their part to the product. The final operation of the arm delivers the product to an exit channel. In a cell, though, how does this arm actually move? The answer: electricity.
Yes, folks, yeast cells contain actual electrical machines. Don’t visualize wires of flowing current; instead, picture active sites with concentrations of positive and negative charges in precise amounts. How does the lever arm use this electrical system? Owing to the specific kinds of amino acids used, each active site has a net positive charge, while the ACP lever arm has a negative charge. Each time a part is added to the product, it changes the overall charge distribution and makes the arm swing over to the next position. Thus, a blind structure made out of amino acids follows a cyclic pattern that builds up a specific product molecule one carbon at a time, and automatically delivers it when complete. After delivery, the system is automatically reset for the next round. Clearly, the precision of charge on each active site is critical to the function of the machine.3, 4
Now that we have described one reaction chamber, step back and see that the yeast FAS machine has six such chambers working independently and simultaneously. Another surprise is that the lever arm inside must be activated from the outside during assembly of the machine by a structure (PPT) on the exterior wall before it can work. There’s a reason for this, too:

“The crystal structure of yeast FAS reveals that this large, macromolecular assembly functions as a six-chambered reactor for fatty acid synthesis. Each of the six chambers functions independently and has in its chamber wall all of the catalytic units required for fatty acid priming, elongation, and termination, while one substrate-shuttling component, ACP, is located inside each chamber and functions like a swinging arm. Surprisingly, however, the step at which the reactor is activated must occur before the complete assembly of the particle since the PPT domain that attaches the pantetheine arm to ACP lies outside the assembly, inaccessible to ACP that lies inside. Remarkably, the architectural complexity of the FAS particle results in the simplicity of the reaction mechanisms for fatty acid synthesis in fungi.”

Maybe the activation step is a quality-control step, to ensure the system doesn’t cause trouble in the cytoplasm before the machinery is completely assembled.
The authors did not mention how fast the synthesis takes place. But if it’s anything like the other machinery in the cell, you can bet the FAS machine cranks out its products swiftly and efficiently, and life goes on, one molecule at a time. Baking a cake with yeast will never seem the same again.
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1Alberts, Bruce (President, National Academy of Sciences ) “The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists”, ScienceDirect, Available online 29 September 2000.
2Lomakin, Xiong and Steitz, “The Crystal Structure of Yeast Fatty Acid Synthase, a Cellular Machine with Eight Active Sites Working Together,” Cell, Volume 129, Issue 2, 20 April 2007, Pages 319-332.
3In addition to electrical charges, some amino acids have side chains that attract or repel water. These hydrophilic and hydrophobic side chains also contribute to the force fields that cause the conformational changes in the enzyme.
4The diagrams in the paper show the details of each active site. To the uninitiated, enzyme models appear like random balls of putty stuck together, but humans should not impose their propensity for straight lines and angles on the world of molecules. The shape and folds of the structure are critical to the function because they control the charge distribution in the vicinity. The active sites are recessed within tunnels. The ACP lever arm tip is guided by charge into these tunnels where ingredients are “snapped on” to the molecule through precise chemical reactions. Each reaction changes the charge distribution, leading to the next stage of the cycle.

More “Candy” Found in Junk DNA 04/24/2007
Powerful regulators that play a crucial role – this is how non-coding sections of DNA are now being described. A story in Science Daily says that these regions of “junk DNA” once dismissed as “gene deserts” actually orchestrate the expression of genes during development.
In a related paper in PNAS,1 researchers found regulatory roles for many conserved noncoding elements (CNEs). “We identify nearly 15,000 conserved sites that likely serve as insulators, and we show that nearby genes separated by predicted CTCF sites2 show markedly reduced correlation in gene expression,” they said. “These sites may thus partition the human genome into domains of expression.” They found one family that might have a “broad role” for gene expression, and other “striking examples of novel functional elements.”
This realization is opening eyes to a new realm of genetic marvels. “Right now it’s like being a kid in a candy warehouse,” said one geneticist. Others who looked at transposons and jumping genes as nuisances that were “messing things up” now see them as useful. Evolutionists are invoking the E word in various ways. Transposons might be a “major vehicle for evolutionary novelty,” said one, while another remarked about emerging new view of junk DNA, “It’s funny how quickly the field is now evolving.”
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1Xie et al, “Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0701811104, published online before print April 18, 2007.
2From the above paper, “CTCF, a protein containing 11 zinc-finger domains, is a major factor implicated in vertebrate insulator activities. An insulator is a DNA sequence element that prevents a regulatory protein binding to the control region of one gene from influencing the transcription of neighboring genes. When placed between an enhancer and a promoter, an insulator can block the interaction between the two. Several dozen insulator sites have been characterized, and almost all have been shown to contain CTCF binding sites. In some cases, the CTCF site has been directly shown to be both necessary and sufficient for enhancer blocking activities in heterologous settings. The known CTCF sites show considerable sequence variation, and no clear consensus sequence has been derived.”

It’s not funny. For decades, Darwinian preconceptions have held back a promising field of genetic research with their falsified notion that most of the genome is composed of evolutionary leftovers. Now that we see the design that was there all along, can we get on with what science should have been doing? Away with this new plot line that junk DNA is a source of “evolutionary novelty.” Darwinians, you have been exposed as usurpers. Get out of the way. The field is not evolving. Intelligent design is taking back its rights.

 

[bob b]

Details of Photosynthesis Coming to Light 05/09/2007
New tools of science are unveiling the secrets of what was long a “black box” in biology: photosynthesis. A paper in Nature last week1 described the structure of the plant PhotoSystem I complex (PSI) in near-atomic resolution. Next day, a paper in Science2 described some of the protein interactions that occur when plants turn light into energy for work. Both papers praised the exceptional efficiency of “the most efficient nano-photochemical machine in nature.”
As is common in the scientific literature, the paper in Nature used engineering language when discussing photosynthesis. It referred to the “reaction centre” as a “light-harvesting complex” and to certain parts as “antennas.” The authors used the root efficient eight times in the paper: for example, “This highly efficient nano-photoelectric machine is expected to interact with other proteins in a regulated and efficient manner” – there are two instances in the same sentence. The paper ended:

“The complexity of PSI belies its efficiency: almost every photon absorbed by the PSI complex is used to drive electron transport. It is remarkable that PSI exhibits a quantum yield of nearly 1 (refs 47, 48), and every captured photon is eventually trapped and results in electron translocation. The structural information on the proteins, the cofactors and their interactions that is described in this work provides a step towards understanding how the unprecedented high quantum-yield of PSI in light capturing and electron transfer is achieved.”

The authors only referred to evolution once: “The two principal subunits of the reaction centre, PsaA and PsaB, share similarities in their amino acid sequences and constitute a pseudosymmetric structure that evolved from an ancient homodimeric assembly.” Yet this was stated dogmatically without any explanation of how that could have occurred.
The paper in Science explored photosynthesis from the protein’s perspective. The authors of this paper also spoke of the “efficient transfer of electrons across biomembranes” and the “high efficiency of the reaction (an electron is transferred for each photon absorbed)” – i.e., there is no loss or waste of input.
The authors discussed how certain protein parts physically move in response to their inputs. These movements among the chlorophylls and other parts modulate the speed of the downstream reactions. Rather than quote their jargon about biomechanics and biomolecular dynamics, let’s attempt an analogy that suggested itself from one of the illustrations: it’s like catching eggs dropping out of the sky into a soft, gentle net, where they can be safely transported to the kitchen. Those who prefer the original jargon can see the footnote.4

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1Amuntz, Drory and Nelson, “The structure of a plant photosystem I supercomplex at 3.4-angstrom resolution,” Nature 447, 58-63 (3 May 2007) | doi:10.1038/nature05687.
2Skourtis and Beratan, “Photosynthesis from the Protein’s Perspective,” Science, 4 May 2007: Vol. 316. no. 5825, pp. 703-704, doi: 10.1126/science.1142330.
3The second paper also spoke of the efficient use of quantum mechanical properties of light: “The experimental data reported by Wang et al. also encourage renewed theoretical attention to the early events in photosynthesis. Models that include quantized nuclear dynamics seem particularly important, because high-frequency quantum modes influence fast electron transfer, producing nonexponential kinetics and unusual temperature dependence.”
4“Wang et al. suggest that the slow protein dynamics discussed above may help to overcome reaction barriers produced by membrane potentials or by environmental factors that perturb the photosynthetic reaction center and potentially slow down the electron-transfer rate. Thus, protein motion could overcome reaction barriers produced by cellular factors that might otherwise perturb the electron-transfer kinetics.”

Molecular Motors Move You 05/30/2007
The realization that cells are filled with molecules that move like machines fascinates many people. Students who grew up thinking of chemistry as bouncing molecules that did little more than link up and separate have a whole new paradigm to consider: molecules that walk, fold and unfold, spin and operate like ratchets, robots, wrenches and motors. Here are a few recent developments in the world of molecular machines:

1. Brownian walk: Researchers in Science1 reported that myosin, a molecular “walking” motor used in muscle, harnesses the random force of Brownian motion to keep on track. Brownian motion is the random shuddering action of small molecules due to thermal motion in the environment. Like sails in the wind, myosin motors are built in such a way that they can make use of the vector component corresponding to the direction they need to go. “The leading neck swings unidirectionally forward, whereas the trailing neck, once lifted, undergoes extensive Brownian rotation in all directions before landing on a site ahead of the leading head,” said Shiroguchi and Kinosita. “The neck-neck joint is essentially free, and the neck motion supports a mechanism where the active swing of the leading neck biases the random motion of the lifted head to let it eventually land on a forward site.” This way they get a push for free. The authors did not discuss how this mechanism might have evolved.

2. Gut-level machinery: Speaking of myosin, did you know it aids digestion? Your digestive tract is lined with microvilli, tiny projections that vastly increase the surface area of the intestinal membrane that absorbs nutrients. Now, scientists have found there’s a lot more going on in the tips of these projections. Science Daily reported on work at Vanderbilt that showed myosin is concentrated in the tips and appears actively involved in shedding membrane material at the tips. This process of vesicle formation and detachment may inject metabolic enzymes into the passing food material, as well as protect the lining of the intestine from invaders. It’s all done with motors: myosin 1a, “a protein with the potential to generate force and move cargo around in cells.” Matthew Tyska figured that there must be a reason these force-generating motors are concentrated in the microvilli, and sure enough, he found them at work: “It’s a little machine that can shed membrane from the tips,” he said. This could give a whole new dimension to the term bowel movement. Now his group is seeing if a similar mechanism operates in other cellular projections, like the hair cells of the inner ear. See also EurekAlert.

3. Clockworks: A paper in Nature discussed the latest research into the molecular mechanisms behind biological clocks.2 There is not one clock molecule involved, but a host of proteins that form feedback loops in cycles that express and repress certain genes in response to environmental cues. One of the proteins is even nicknamed CLOCK. The article payed particular attention to PGC-1-alpha, a protein that appears intimately linked to both the circadian rhythm and metabolism, affecting the production of glucose, fatty acids and haem (iron-containing molecules). Many questions remain, however. This is clearly a work in progress.

4. Splice and dice: Another paper in Nature used the word “machinery” six times, speaking of the spliceosome.3 “A complex macromolecular machinery in the nucleus of eukaryotic cells is responsible for pre-mRNA splicing,” said Blencowe and Khanna. They described how alternative splicing “is a remarkably efficient mechanism for a cell to increase the structural and functional diversity of its proteins, and it plays many roles in gene regulation” (see 05/20/2007). The way alternative splicing is controlled is by RNA “riboswitches,” including messenger-RNA transcripts that can regulate their own expression with feedback and feed-forward loops. These riboswitches can actually change shape in response to cues, and the shape determines how the gene will be expressed. The authors used the word switch 18 times.
Earlier, riboswitches were thought to exist only in bacteria and fungi, but now it appears they may be common in higher animals and in plants. The authors speculated about evolution’s place in this: “It seems plausible that splicing-regulatory riboswitches represent a system that has evolved to coordinately regulate multiple genes in the same biochemical pathway using feedback and, in some cases, feed-forward mechanisms,” they asserted. “Presumably, the rapid kinetics and energy-saving advantages afforded by bypassing protein-mediated regulation explain why riboswitch aptamers have persisted during evolution and function at many levels of regulation of gene expression.” Yet this seems to assume what needs to be proved. They used the presence of these switches, and the advantages they appear to confer, as evidence they evolved, yet provided no details on how that could have occurred by natural selection. By contrast, the evidence they did provide shows the opposite of evolution: between very distant organisms, like fungi and higher plants, the genes involved are “evolutionarily conserved” (i.e., unevolved).

5. Machine language: Two scientists publishing in PNAS sounded like factory planners, but were talking about cells.4 “Experimental and theoretical studies of proteins, acting as motors, ion pumps, or channels, and enzymes, show that their operation involves functional conformational motions,” they said. A few sentences later, the machine talk continued: “Generally, a machine is a mechanical device that performs ordered internal motions that are robust against external perturbations.” They were discussing how molecular machines in the cell, particularly myosin and ATP synthase, are examples of such robustness. “In conclusion,” they said in the final discussion section, “we have shown that motor proteins possess unique dynamical properties, intrinsically related to their functioning as machines.” This recalls a line Scott Minnich said in the film Unlocking the Mystery of Life: “It’s not convenient that we give them these [machine] names; it’s truly their function.”
Part of the title read, “design principles of molecular machines.” Yet the authors attributed this design to undirected chance processes of evolution in this statement: “Actual proteins with specific architectures allowing robust machine operation may have developed through a natural biological evolution, with the selection favoring such special dynamical properties.” They ran a simulation of an “evolutionary computer optimization process” and achieved a “artificial elastic network architectures possessing machine-like properties,” but this statement blurs the line between intelligently-selected outcomes and chance.

“Machine” language is quite common in the scientific literature. One often finds matter-of-fact discussion of proteins and enzymes as machines. They use energy and perform physical work according to tight specifications. The evolutionary conundrum is: how could functioning machines arise from non-functional matter in motion? Authors of scientific papers typically either ignore the question, or assume evolution did the design work.
A more fruitful approach was offered by a biophysicist who wrote Nature last week, suggesting that we “Look at biological systems through an engineer’s eye.”5 R. S. Eisenberg said that when approaching a black box, whether an amplifier in a sound system or an unknown mechanism in a living cell, we should identify the inputs and outputs, the power supply and the device equation. Looking at biological devices with the eyes of an engineer, he said, can lead to fruitful experiments:

“Complex systems – for example, with many internal nonlinear connections like the integrated circuit modules of digital computers or, perhaps, the central nervous system – may not be easily analysed as devices, no matter how many experimental data are available. But it seems clear, at least to a physiologist, that productive research is catalysed by assuming that most biological systems are devices. Thinking today of your biological preparation as a device tells you what experiments to do tomorrow.
Asking the questions in this way leads to the design of useful experiments that may eventually lead to the device description or equation, if it exists. If no device description emerges after extensive investigation of a biological system, one can look for other, more subtle descriptions of nature’s machines.”

An intelligent design scientist might feel vindicated. No evolutionary theorizing is needed in this approach. Assuming design in the device, and asking engineering questions, can stimulate a fruitful experimental program.
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1Shiroguchi and Kinosita, “Myosin V Walks by Lever Action and Brownian Motion,” Science, 25 May 2007: Vol. 316. no. 5828, pp. 1208-1212, DOI: 10.1126/science.1140468.
2Grimaldi and Sassone-Corsi, “Circadian rhythms: Metabolic clockwork,” Nature 447, 386-387 (24 May 2007) | doi:10.1038/447386a.
3Blencowe and Khanna, “Molecular biology: RNA in control,” Nature 47, 391-393 (24 May 2007) | doi:10.1038/447391a.
4Togashi and Mikhailov, “Nonlinear relaxation dynamics in elastic networks and design principles of molecular machines,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0702950104, published online before print May 16, 2007.
5R. S. Eisenberg, “Look at biological systems through an engineer’s eye,” Correspondence, Nature 447, 376 (24 May 2007) | doi:10.1038/447376a.

Did Sponges Invent Nerves? 06/06/2007
Scientists didn’t expect to find working neurons in a sea sponge, among the simplest of multicellular organisms. Sponges lack internal organs and a nervous system. Yet there they were, according to Science Daily, with synapses and apparent means of communication across them.
“This pushes back the origins of these genetic components of the nervous system to at or before the first animals — much earlier than scientists had previously suspected,” said Todd Oakley of UC Santa Barbara. It represents a gap of 600 million years from the time sea sponges are assumed to have arrived and the arrival of the first animal with a rudimentary nervous system.
The article quotes Ken Kocik, also of UCSB, using this surprise finding to elucidate evolutionary theory: “We found this mysterious unknown structure in the sponge, and it is clear that evolution was able to take this entire structure, and, with small modifications, direct its use toward a new function. Evolution can take these ‘off the shelf’ components and put them together in new and interesting ways.”
Yet this is not the way classical Darwinism works. David Berlinski, a Darwin critic, in an earlier article, insisted that the law of natural selection must be strictly enforced to be Darwinian at all.

“A mechanism that requires a discerning human agent cannot be Darwinian. The Darwinian mechanism neither anticipates nor remembers. It gives no direction and makes no choices. What is unacceptable in evolutionary theory, what is strictly forbidden, is the appearance of a force with the power to survey time, a force that conserves a force or a property because it will be useful. Such a force is no longer Darwinian. How would a blind force know such a thing? And by what means could future usefulness be transmitted to the present?
If life is, as evolutionary biologists so often say, a matter merely of blind thrusting and throbbing, any definition of natural selection must plainly meet what I have elsewhere called a rule against deferred success.
It is a rule that cannot be violated with impunity; if evolutionary theory is to retain its intellectual integrity, it cannot be violated at all. But the rule is widely violated, the violations so frequent as to amount to a formal fallacy.”

 

[bob b]

News at Princeton Thursday, July 19, 2007

Fruit fly research may 'clean up' conventional impressions of biology
The metamorphosis of biology into a science offering numerically precise descriptions of nature has taken a leap forward with a Princeton team's elucidation of a key step in the development of fruit fly embryos -- discoveries that could change how scientists think not just about flies, but about life in general.

While biologists have long known that the structure of adult animals follows a blueprint laid out in the early stages of embryonic development, classical biological experiments have provided only isolated "snapshots" of the development process, denying scientists a complete "movie" of it unfolding. Now, by combining experimental methods from physics and molecular biology, the team has replaced these snapshots with the movie, allowing them to see the first steps of blueprint formation in the fly embryo literally live and in color. The first of two papers in the July 13 issue of the scientific journal Cell describes the sophisticated techniques required to make these movies, techniques that could help scientists investigate a wide variety of biological systems.

In the second paper, the group poses a new question, never before asked by scientists studying embryos: How precisely can cells in the embryo read the blueprint? So precisely, the paper suggests, that a precious few molecules signaling a change can make a decisive difference.

"I think the prevailing view has been that cells accomplish all their functions using a complicated combination of mechanisms, each one of which is rather sloppy or noisy," said team member William Bialek, the John Archibald Wheeler/Battelle Professor in Physics. "This research, however, indicates that in the initial hours of a fly embryo's development, cells make decisions to become one part of the body or another by a process so precise that they must be close to counting every available signaling molecule they receive from the mother.”

 

[bob b]

More Cell Codes and Authentication Mechanisms 11/13/2007
Here are more “cool cell tricks” that ensure a smoothly-functioning system inside the cell that can adapt to changes while protecting assets.

1. Ribosome code: Why don’t all ribosomes look alike? Perhaps they know a secret code. Another possible coding mechanism has been found in ribosomes, those important organelles in the cytoplasm that translate messenger RNA into proteins. You might recall that in chromosomes, a “histone code” appears to oversee the genetic code, regulating what genes get translated (07/26/2006, 07/28/2004). Now, researchers at Harvard Medical School reported in Cell¹ that a similar mechanism might be at work in the ribosomes:

This data supports a model in which there are many different forms of functionally distinct ribosomes in yeast, where the functional specificity is determined by the combination of duplicated ribosomal proteins present. However, protein composition is not the only source of ribosomal heterogeneity. Many fungi express different forms of 5S rRNA... Moreover, ribosomal proteins are subject to a variety of posttranslational modifications....; such modifications impact the translational activity of the protein.... Indeed, as previously posited..., there is a wealth of evidence for heterogeneity among ribosomes regulating the translational activity of their targets.
This model of translational regulation bears a striking resemblance to the canonical model for transcriptional regulation.... In sum, the transcription state of a given region of chromatin is determined by specific combinations of histone proteins, posttranslational modifications of histones, and DNA modifications; this complex relationship has been called the “histone code” (Jenuwein and Allis, 2001). Our data support a similar level of complexity for the process of translation in which different combinations of ribosomal protein paralogs, posttranslational modifications of ribosomal proteins, different forms of rRNA, and modifications to the rRNA allow calibrated translation of specific mRNAs. As with the histone code, this “ribosome code” would provide a new level of complexity in the regulation of gene expression.

2.Token authentication: Here’s a design challenge for the engineer in you. A round door needs to be open to the environment, but keep interlopers out. Valid users, coming in a wide variety of sizes, need to be allowed access by an automatic authentication system that will usher them in quickly. Once inside, they should not be able to drift back out. The nuclear pore complex appears to use a most elegant solution to this problem of “selective gating.” It was reported in Science October 26 by researchers in Switzerland and Singapore.²
To spare our readers the technical nomenclature, we’ll substitute a sci-fi analogy for what happens at the 40-nanometer scale. Imagine a spaceship with a highly-sensitive computer center at its core. Objects and spacemen drift by in this weightless environment. The doors to the computer center must remain open at all times, but entry must be protected from enemies and from those who have no business being in there. Anchored to the rims of these doors are chains that extend outward, drifting about like spaghetti in a breeze tied at one end. The ends of these chains contain crystals that emit a force-field, collectively creating an invisible dome of force around the door, preventing accidental or malicious entry.
You, as a valid user, approach the door with a secret crystal in your hand that acts like an authentication token. When you extend it toward the chains, they sense it, and rapidly collapse backwards, pulling you in and forming a kind of tunnel around you. The more distant chains are not affected; they continue to stand guard and keep the force field up. Once you are inside, a robotic device removes your token and secures it in a protective chamber so that it cannot open the door behind you. Meanwhile, the collapsed chains quickly extend outward again, re-establishing the force field to keep out anything or anybody not having the special token.
Want the details? Read footnote 3 for the technical description of the nuclear pore complex authentication mechanism as described by the researchers.³

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1. Komili, Farny, Roth and Silver, “Functional Specificity among Ribosomal Proteins Regulates Gene Expression,” Cell, Volume 131, Issue 3, 2 November 2007, pages 557-571.
2. Lim, Fahrenkrog, Koser, Schwarz-Herion, Deng, and Aebi, “Nanomechanical Basis of Selective Gating by the Nuclear Pore Complex,” Science, 26 October 2007: Vol. 318. no. 5850, pp. 640-643; DOI: 10.1126/science.1145980.
3. Ibid, “The nuclear pore complex regulates cargo transport between the cytoplasm and the nucleus. We set out to correlate the governing biochemical interactions to the nanoscopic responses of the phenylalanineglycine (FG)–rich nucleoporin domains, which are involved in attenuating or promoting cargo translocation. We found that binding interactions with the transport receptor karyopherin-[Beta]1 caused the FG domains of the human nucleoporin Nup153 to collapse into compact molecular conformations. This effect was reversed by the action of Ran guanosine triphosphate, which returned the FG domains into a polymer brush-like, entropic barrier conformation. Similar effects were observed in Xenopus oocyte nuclei in situ. Thus, the reversible collapse of the FG domains may play an important role in regulating nucleocytoplasmic transport.”

 

[bob b]

Cell Gatekeepers: Diverse, Complex, Accurate 12/02/2007
Cargo moves around rapidly and ceaselessly in every cell. Some moves in and out of the external membrane, and some moves in and out of organelles and the nucleus. In a system of protected domains surrounded by impermeable membranes, how does the cell control what should pass? Details of the amazing gatekeeping mechanisms embedded in cell membranes have been coming to light for years now. Some recent articles have reported the latest findings.

Protective sleeve: One method of getting valid cargo through the membrane gate is to wrap it in a protective sleeve that the gate recognizes. PhysOrg has an illustration from the work of a team at Purdue showing how this works. What comes to mind is a personal subway capsule that shuttles you to an escalator that transfers you safely into a shopping mall without any intruders getting past.

Electronic gating: Ions are electrically-charged atoms whose concentration in the cell must be strictly controlled. Compared to the large molecules of the cell, ions of potassium, chlorine and sodium are tiny. Special voltage-sensing gates exist just for them. We reported here on early results from work by Roderick MacKinnon into the structure and function of these ionic gates (see 01/17/2002, 05/29/2002, 05/01/2003, 08/05/2005).
The November issue of The Scientist describes ongoing discoveries about one of these voltage-gated channels, the Kv potassium channel. This electronic mechanism contains a pore, a gate and a voltage sensor. In particular, a key helix protein component called S4 undergoes a conformational change to open the gate for the potassium ion. People who enjoy exercise may want to reflect that all nerve and muscle activity depends on the proper control of these ions.

Nuclear power plant security: For those wanting to follow up on news about the nucleus, and how it controls the cargo going in and out (see last month’s entry, 11/13/2007, bullet #2), the crew of your nuclear power plant made the cover of Science this week. Laura Trinkle-Mulcahy and Angus I. Lamond reviewed the latest work to get high-resolution images of the complex structures and functions of the nuclear membrane, especially the gates of the nuclear pore complex (NPC).1
Four other articles in the 11/30 issue describe the latest findings about the cell nucleus. A paper by 3 Vanderbilt University scientists specifically addresses the factors involved in crossing the nuclear envelope through the NPC gates.2 For those wanting more information about the sensing mechanism, their article contained color diagrams of the structures. The scientists explained how the gates are regulated at multiple levels – a philosophy common in national security and computer security, too. The “dynamic and diverse” mechanisms control what passes at the gate level, the transport receptor level, and the cargo level. In computer parlance, this might translate to requiring a fingerprint, a secure computer, and secure software before you are allowed to login.
Another paper in the same issue of Science describes science’s growing realization that the nuclear membrane does far more than let things in and out.3 It is actively involved in cell division, structuring the cytoskeleton, and signaling other processes in the cell. The nuclear envelope is also connected to the endoplasmic reticulum, a structure essential for post-translational modification of proteins. The authors did not mention how these elaborate mechanisms might have evolved, except to say twice that they raise “intriguing questions” and “fundamental questions” about “evolutionary relations” between the parts. The other two papers did not mention evolution at all.

ER: emergency room or endoplasmic reticulum: Speaking of the endoplasmic reticulum (a kind of subway system within the cell), Nature reported studies about the transport channels in that organelle.4 “A decisive step in the biosynthesis of many proteins is their partial or complete translocation across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane,” began Tom Rapoport (Howard Hughes Medical Institute, Harvard). “Most of these proteins are translocated through a protein-conducting channel that is formed by a conserved, heterotrimeric membrane-protein complex, the Sec61 or SecY complex.”
Polypeptides are the pre-protein strings of amino acids emerging from ribosomes, where the translation from RNA occurs. Getting a wobbly chain of molecules through a pore is somewhat akin to threading a needle. Depending on what the cargo binds to, it may get in by one of several ways: the ribosome may simply attach to and inject the nascent polypeptide into the channel, an ER chaperone might pump it in by a ratcheting mechanism, or a molecular machine running on ATP might push the polypeptide through. These are all regulated by a host of assisting proteins that keep in touch through signaling mechanisms. There’s even a plug that closes the channel after the polypeptide is inside.
Rapoport provided a diagram of the complicated-looking translocation channel, which is made up of three different protein parts. He called it conserved (unevolved) between all three kingdoms of life, but did not say anything else about evolution – certainly, not anything about how it arose in the first place.

Light sensitive: Imagine a receptor on a cell membrane that can respond to one photon of light, and send a signal into the interior. You don’t have to imagine it: it already exists. Rama Ranganathan in Science described the family of G-protein coupled receptors (GPCR) that “occur in nearly every eukaryotic cell and can sense photons, cations, small molecules, peptides, and proteins.”5 How do they do it? The structures of these receptors are just beginning to come to light, and basic models are being formulated. Stay tuned.

Most of the articles above said nothing about how these complex transportation systems might have evolved. A review in Nature,6 however, proposed that “the plethora of transport factors found in modern eukaryotes may have also evolved by duplication events, keeping pace with the evolutionary duplication and diverging specialization of the FG nucleoporins in the NPC’s [nuclear pore complex’s] modules.” Noting some similarities in the NPC to clathrin-coated endocytosis, the team of a dozen UK and American scientists suggested that gene duplication was the method of evolution: “the NPC is another example of how a complicated structure can evolve from the duplication, divergence and elaboration of simple ancestral modules,” they claimed. They also downplayed the complexity of the NPC by pointing out some of the proteins are used in a modular fashion. A summary and diagram was posted by PhysOrg.
Their evolutionary explanation, however, was based entirely on circumstantial evidence of similarity, not on a chain of plausible steps for how diverse mechanisms, despite some structural similarities, achieved their high levels of functional accuracy.

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1. Laura Trinkle-Mulcahy and Angus I. Lamond, “Toward a High-Resolution View of Nuclear Dynamics,” Science, 30 November 2007: Vol. 318. no. 5855, pp. 1402-1407, DOI: 10.1126/science.1142033.
2. Laura J. Terry, Eric B. Shows, Susan R. Wente, “Crossing the Nuclear Envelope: Hierarchical Regulation of Nucleocytoplasmic Transport,” Science, 30 November 2007: Vol. 318. no. 5855, pp. 1412-1416, DOI: 10.1126/science.1142204.
3. Colin L. Stewart, Kyle J. Roux, Brian Burke, “Blurring the Boundary: The Nuclear Envelope Extends Its Reach,” Science, 30 November 2007: Vol. 318. no. 5855, pp. 1408-1412, DOI: 10.1126/science.1142034.
4. Tom O. Rapoport, “Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes,” Nature 450, 663-669 (29 November 2007) | doi:10.1038/nature06384.
5. Rama Ranganathan, “Signaling Across the Cell Membrane,” Science, 23 November 2007: Vol. 318. no. 5854, pp. 1253-1254, DOI: 10.1126/science.1151656.
6. Alber et al, “The molecular architecture of the nuclear pore complex,” Nature 450, 695-701 (29 November 2007) | doi:10.1038/nature06405.

 

[bob b]

DNA Translation Has Codes Upon Codes 12/17/2007
The DNA code is protected by another code, and is read with a machine that reads a third code. This is an emerging picture from ongoing research into DNA translation, as reported in Science.1
In the 1950s, scientists were astonished to find a code at the genetic basis of life. DNA’s four-letter alphabet, arranged into triplet codons, providing 64 combinations that could code for the 20 amino acids and “punctuation” in various ways, seemed simple and elegant (see description in our online book). Now it seems, remarkable as this mechanism is, it is way too simple. Other factors must control when and how particular genes are to be translated. Biochemists have also been cataloguing a huge number of post-translational modifications that take place, from the moment messenger-RNA is formed to after the protein chain is assembled. What controls the regulators?
Additional codes involved in regulating gene expression have been coming to light. One was the histone code attached to DNA (11/13/2007) which may be as complex and as important as the DNA code itself (04/12/2003). Now, Science published two papers on another code attached directly to the translator, RNA Polymerase II. This “CTD code” is composed of tandem repeats of seven amino acids forming a tail called the carboxy-terminal domain (CTD). New work expands the previously-known number of phosphorylation states from four to eight. Since each of these amino acids can be modified by phosphorylation, patterns emerge that resemble a hexadecimal system. Because the tandem repeats vary from 17 to 52 sets on a CTD, if each phosphorylation pattern had a functional meaning, there are potentially 852 different CTD patterns – over 900 trillion trillion trillion trillion.
Such a number is probably degenerate – i.e., vastly greater than the number of states that are actually needed for functional meaning. Still, the potential is there for a huge array of states that can direct the behavior of RNA Polymerase II. Experiments have shown that some distinct phosphorylation patterns do indeed change the expression of the gene. Jeffry Corden [Johns Hopkins U] wrote in the review article on the two papers,

"The biological role of CTD phosphorylation remains to be fully elucidated, but the emerging picture is that the pattern of CTD phosphorylation changes during RNA synthesis, allowing dynamic modification of the DNA template and processing of the nascent RNA transcript. The studies by Chapman et al.2 and by Egloff et al.3 provide both the tools to fully document CTD phosphorylation patterns and the best evidence to date that these patterns constitute a code that intersects, at the most fundamental level, with the regulation of different classes of eukaryotic genes."

It appears that both DNA and its translator have codes, completely independent from the DNA code, affixed to them. Are they passwords forming an authentication scheme? Are they messages telling the machinery what to do? If so, what sends the messages, and what recognizes them? How is the password validated? More work into this fascinating area will surely be needed. For now, Corden said, “Together, the papers show that CTD phosphorylation is more complicated than previously thought and link, for the first time, expression of specific genes with a distinct CTD phosphorylation pattern.”
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1. Jeffry L. Corden, “Seven Ups the Code,” Science, 14 December 2007: Vol. 318. no. 5857, pp. 1735-1736, DOI: 10.1126/science.1152624.
2. Chapman et al, “Transcribing RNA Polymerase II Is Phosphorylated at CTD Residue Serine-7,” Science, 14 December 2007: Vol. 318. no. 5857, pp. 1780-1782, DOI: 10.1126/science.1145977.
3. Egloff et al, “Serine-7 of the RNA Polymerase II CTD Is Specifically Required for snRNA Gene Expression,” Science, 14 December 2007: Vol. 318. no. 5857, pp. 1777-1779, DOI: 10.1126/science.1145989.
The situation just keeps getting worse for the evolutionists. None of the three papers even mentioned evolution. Who would dare?

 

[bob b]

Quality Control Ensures Accurate Cell Division 12/28/2007
Cell division (mitosis) is a very complex process in which every part must be accurately duplicated and sent to the proper destination. Picture a marching band where each flute player or tuba player is able to clone itself. The players congregate at the center in two lines, divide, and move apart, forming two marching bands that can each play independently or as part of a parade of bands. A more realistic picture might require imagining the whole school – library, shop, offices and all – splitting into two identical copies in a matter of hours or minutes.
How does the cell make sure that each copy is identical? Accurate copying is essential, or else errors would accumulate and bring the species to an end. Scientists continue to uncover some of the quality-control policies and procedural tricks that cells follow.

1. A nine in time saves stitch: Centrosomes control the orientation of chromosomes before the split. They create a spindle of microtubules that line the pairs up at the midplane, then pull them apart. Within the centrosomes are two motors called centrioles, oriented perpendicular to one another, that look for all the world like turbines. The blades of the turbine are microtubules with spokes, forming a cylinder that looks like a pie with exactly nine slices. Why nine, and only nine?
Wallace Marshall (UC San Francisco) reviewed experiments into the mechanical basis for nine-ness in centrioles, and published a report in Current Biology.1 Experiments with mutants show that the number is controlled by the length of the spokes that emanate from each slice. This sets the overall diameter of the centriole, and thus the number of pie slices that will fit in the cylinder.
“This study provides an interesting geometrical mechanism by which a length can control a number,” Marshall said. Why was the research worthwhile? “Understanding centriole assembly is likely to reveal many more engineering-design principles that cells use to build complex structures.”
Herding the chromosomes: When a chromosome pair lines up on the spindle midplane right before splitting up, it contains a structure at the waistband called a centromere. This belt of protein contains two attachment points, called kinetochores, used by microtubules to pull them into their respective daughter cells. Our 03/04/2004 entry used the analogy of cowboys lassoing pairs of cattle and pulling them into separate corrals. The yoke holding each pair of cows together is the centromere, and the kinetochores are like saddle horns the ropes can latch onto. Opposing cowboys lasso the horns and start pulling in opposite directions. When all pairs are lined up and accounted for, a foreman named aurora B kinase breaks the yokes, and the cowboys haul in their herds.
The geometry of the centromere is essential for keeping this process error-free, a team from New York and Moscow reported in Nature last month.2 Once in awhile, two cowboys on the same side lasso the same pair (this is called syntelic attachment). Unless corrected, one cell would get both chromosomes and the other would get neither; this “non-disjunction” fault could lead to genetic disorders or cancer. Scientists had previously thought that detaching one rope (microtubule) would make the saddle horn (kinetochore) automatically spring back into position for a rope from the other side. It’s apparently not as simple as that. More quality-control mechanisms are involved. “Achieving chromosome bi-orientation depends on a complex interplay between mechanisms intrinsic to the centromere and those that act externally,” they said. After cross-attachment fibers are released, and after the lassos are disconnected, there are intrinsic properties of the centromere that come into play. “Our findings imply that mechanical properties and the shape of the centromere play an important part in the fidelity of chromosome segregation.” Unless everything works, the operation usually aborts. Security engineers might call this an example of the principle of defense in depth.

2. Pinch me: Perhaps you’ve watched movies of dividing cells, and noticed how they pinch off from each other, as if someone tied a string around a soft balloon and pulled it tight. Since no person is around at the cell level to do this task manually, there must be an automatic molecular mechanism that makes it work. What forms the “contractile ring” and reels it in?
An article in Science Daily described work by scientists from Yale, Columbia and Lehigh to figure out what happens. Cells employ the same molecular motors, actin and myosin, that make muscles work. Actin filaments with attached myosin motors assemble along the inner cell membrane at the dividing plane, and go through a “search, capture, pull and release” operation. Being blind, molecules “feel” their way to neighboring molecules by putting out filaments in random directions. A myosin motor on the neighbor captures the actin filament and pulls on it. Surprisingly, it lets go after about 20 seconds. Why? “The assembly involves many episodes of attractions between pairs of nodes proceeding in parallel,” the article explains. “Eventually the nodes form into a condensed contractile ring around the equator, ready to pinch the mother into two daughters at a later stage.”
The repeating rounds of “release and capture” appear essential to the assembly process of the contractile ring, they said. Like pulling on a purse string, the circle tightens till the cells are pinched off and go their separate ways.
The scientists figured this out by comparing models with observations in an iterative fashion. The work was done on “simple” yeast cells. “Future work will involve testing the concepts learned from fission yeast in other cells to learn if the mechanism is universal,” said Thomas Pollard [Yale]. “Since other cells, including human cells, depend on similar proteins for cytokinesis, it is entirely possible that they use the same strategy.” An abstract of the work appears on Science Express in advance of publication.

3. Plant protection and bearing walls: Dividing plant cells have a different problem. They have cell walls. What determines the exact point at where the wall between two newly-divided cells will form? Shrink yourself down to the size of a plant cell in your imagination, and you can see the difficulty. If you were the foreman of a group of construction workers making a house divide in two, how do you remember where the new wall between them is supposed to go?
Clive Lloyd and Henrik Buschmann (Department of Cell and Developmental Biology, John Innes Centre, Norwich UK) wrote about this predicament in Current Biology.3 What was mysterious is that a structure of microtubules known to form at the dividing plane apparently disassembles right before cell division. How does the cell “memorize” the position of the plane where the future cell wall will form? The trick is somewhat like using a chalk line. The microtubules attract special proteins that adhere to the exact spot, forming a ring around the perimeter. The microtubule scaffolding, no longer needed, is then dismantled. After the chromosomes migrate and cell division completes, a plate of cell-wall proteins grows outward toward the chalk ring. If you can imagine wallboard that grows into position from the center of the room, attracted to the chalk line, you get the idea. The result is a neat, flat, parallel wall, subdividing the daughter cells into their own rooms.
Without these memory proteins, the scientists found, cell walls grew at abnormal positions. Stay tuned, because this doesn’t explain everything about how plants determine the division plane. It’s just an intriguing start. “The search now continues for other components of the division ring and insights into the attractive influence they exert over the leading edge of the cytokinetic apparatus,” they said.

One other recent cell biology paper, not directly about mitosis, is worthy of note. All proteins in the cell need to fold properly before going into service. Many of them use a “dressing room” called GroEL-GroES to avoid the hustle and bustle of the cytoplasm (05/05/2003, 06/07/2006). A team of biochemists from Yale, Howard Hughes, U of Pennsylvania and Scripps, publishing in PNAS,4 asked why one particular protein really needs the dressing room when it can fold outside.
During the folding process, the amino acid chain seeks its “native” or correct fold. If it works the first time or two, all is well; if it cannot fold in time, the chain can degenerate into a glob or “aggregate” that is either useless or dangerous and must be destroyed. The team found that the GroEL “chaperone” is more likely to prevent aggregation if the chain goes down the wrong folding pathway. In the safe, barrel-shaped chamber of the chaperone, the chain can more easily unfold and try again. Outside, bad folds are less likely to get another chance.
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1. Wallace F. Marshall, “Centriole Assembly: The Origin of Nine-ness,” Current Biology, Volume 17, Issue 24, 18 December 2007, Pages R1057-R1059.
2. Loncaronarek et al, “The centromere geometry essential for keeping mitosis error free is controlled by spindle forces,” Nature 450, 745-749 (29 November 2007) | doi:10.1038/nature06344.
3. Clive Lloyd and Henrik Buschmann, “Plant Division: Remembering Where to Build the Wall,” Current Biology, Volume 17, Issue 24, 18 December 2007, Pages R1053-R1055.
4. Horst, Fenton, Englander, Wuthrich and Horwich, “Folding trajectories of human dihydrofolate reductase inside the GroEL-GroES chaperonin cavity and free in solution,” Proceedings of the National Academy of Sciences USA, published online before print December 19, 2007, 10.1073/pnas.0710042105.

 

[bob b]

Bacteria to the Future 01/14/2008

Bacteria used to be considered so boring, they were passed over by scientists eager to look where the action was: eukaryotic cells. That was then. Now, Nature reported,1 the little rods and spheres and spirals have lots of tricks up their sleeves worth investigating. “Long dismissed as featureless, disorganized sacks, bacteria are now revealing a multitude of elegant internal structures.” These include spiral skeletons (“sophisticated internal structures that give them shape, and help them grow and divide”) and actin-like motors that control magnetosomes (iron-containing structures) that give bacteria a sense of direction.
Until recently, bacteria appeared to have featureless interiors, even when viewed through electron microscopes. New techniques, particularly cryo-electron tomography, are disclosing wonders that were previously invisible. The discovery by Jeff Errington in 2001 that bacteria do indeed have a cytoskeleton was “one of those few times in a scientific career when you do an experiment that completely changes your way of thinking.” Errington imaged filaments of tubulin wrapped around the inner wall of the cell like the stripes on a barber pole. One theory is that the scaffolding “tells the cell wall’s enzyme contractors outside the cytoplasm where to lay new bricks” (see 01/16/2003). The filaments and associated proteins are also involved in quality control during cell division, and help organize the magnetosomes into sensory organs.
Eukaryotic cells themselves were assumed by 19th century biologists to be featureless blobs of protoplasm. That view, of course, changed dramatically throughout the second half of the 20th century. History seems to be repeating itself with respect to the tinier cells that comprise the most numerous life forms on earth: “For more than a century, cell biology had been practised on ‘proper’ cells – those of the eukaryotes (a category that includes animals, plants, protists and fungi),” Ewen Callaway wrote. “....Hundreds to thousands of times smaller than their eukaryotic cousins, and seemingly featureless, bacteria were rarely invited to the cell biology party.” These discoveries about “simple” bacteria are helping to change that. “We know very little,” said Dyche Mullins [UC San Francisco]. The discovery of the cytoskeleton proved that “There was a lot of organization in bacterial cells we were just missing.” The field is just now opening up after decades of neglect. “There’s a lot of unexplored biology,” he said – and this article didn’t even touch on the subject of the bacterial flagellum.
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1. Ewen Callaway, “Cell biology: Bacteria’s new bones,” Nature 9 January 2008 | Nature 451, 124-126 (2008) | doi:10.1038/451124a. Also published on News@Nature.