Cell Operations Amaze, Inspire

A student's view of a cell under a light microscope is misleading.  It reveals only a tiny fraction of what is really going on.  Within that package of life, invisible to the student's gaze, complex machines work together in cellular factories.  Signals pass back and forth in complex networks.  Libraries of code are transcribed and translated into machine parts.  Security guards open and close gates, and emergency response teams repair damage.  Even a simple bacterial cell has the equivalent of a city council, library, fire department, police department, industrial center, transportation infrastructure, disposal and recycling center, civil defense system and much more.  Here are just a few snippets from recent scientific papers that zoom in past the microscope lens to reveal wonders unimagined just a few decades ago.

1. Electric cells:  You’ve heard of electric eels; how about electric bacteria?  Researchers at Harvard, publishing in Science, were curious about the electrical properties of cells:

Bacterial membrane potential provides a major component of the driving force for oxidative phosphorylation, membrane transport, and flagellar motion. Yet this voltage is inaccessible to techniques of conventional electrophysiology, owing to the small size of bacteria and the presence of a cell wall. Little is known about the electrophysiology of bacteria at the level of single cells.

So they checked.  They observed E. coli bacteria producing electrical spikes at a rate of about one per second.  The electrical charge is generated by ion channels in the membrane that create electrical gradients, working against the natural tendency of charges to cancel out.  “Spiking was sensitive to chemical and physical perturbations and coincided with rapid efflux of a small-molecule fluorophore,” they said, “suggesting that bacterial efflux machinery may be electrically regulated.”  In other words, they were not observing a stochastic effect, but a coordinated action of many ion channels that must organize their active transport mechanisms as a unit.  They speculated that the spiking represents a stress response by the organism.  Coordinated electrical response is known in higher organisms, like electric eels and humans, but “These simple estimates show that some of the tenets of neuronal electrophysiology may need rethinking in the context of bacteria.”

2. Antenna tower construction crew:  Cilia are complex organelles in the cell membrane that protrude into the intercellular medium, where they can sense the surroundings and perform other functions.  Some are motile, like the cilia in the human respiratory tract that sweep foreign matter out with coordinated strokes.  Cells build cilia using molecular ore-carts powered by kinesin-2 motors in a process called intra-flagellar transport (IFT), in which components are hoisted up into the cilium on trackways.  Scientists suspected that additional factors regulate the construction of cilia.  Now, two American molecular biologists publishing in Current Biology identified one such member of the construction crew, named KLP6, that moves independently of kinesin-2 and acts to reduce its velocity.  Note: they found this in a particular kind of cell in a roundworm.
3. Gatekeeper dance:  Ion channels play many vital roles in our bodies.  According to Science Daily, they are “essential for the regulation of important biological processes such as smooth muscle tone and neuronal excitability.”  One such channel, named BK, performs large conductance of potassium ions in the presence of calcium ions.  Scientists had thought that all ion channels followed a unified theory of activation.  Researchers at the University of Texas at Austin have found that BK channels are not that simple. 

Halfway down in the activation channel, a certain amino acid residue M314 in one of the transmembrane proteins does a little dance, “rotating its side chain from a position in the closed state not exposed to the hydrophilic pore to one that is so exposed in the open state.”  This conformational change is part of a larger validation process that ensures only the right ions make it through the selectivity filter.  M314 “might not actually form the part of the activation gate that blocks ion passage, but that motions in the deep pore may be required for blocking ion passage elsewhere in the channel,”  the article explained.  So much for unified theories; “Importantly, they say, the study demonstrates that BK channel activation is not an open-and-shut case as previously suspected.”

4. Salt of the cell:  If you enjoy having a healthy heart, brain and pancreas, thank your sodium channels.  Like the BK potassium channels, sodium channels regulate a wide range of physiological activities.  According to Science Daily, “Mutations in voltage-gated sodium channels underlie inherited forms of epilepsy, migraine headaches, heart rhythm disturbances, periodic paralysis, and some pain syndromes.”  When the dentist numbs your gums, he is effectively blocking the local sodium channels from doing their job – sending pain messages to the brain. 

The Science Daily article reported that a team at Howard Hughes Medical Institute produced the highest-resolution diagram ever of a sodium channel .  In this excerpt, you can sense the fascination as the team looked down the channel for the first time in such detail:

“We hope to gain insight into why they selectively let in sodium ions and nothing else,” the researchers said, “and how they respond to changes in the cell membrane voltage, how they open and close, and how they generate electrical signals.”  The researchers have already spotted intriguing molecular movement, such as rolling motions of some functional parts of the sodium channel molecule and their connectors….

5. DNA orchestra:  An article on PhysOrg about DNA translation begins, “Just like orchestra musicians waiting for their cue, RNA polymerase II molecules are poised at the start site of many developmentally controlled genes, waiting for the ‘Go!’-signal to read their part of the genomic symphony.”  Researchers at Stowers Institute for Medical Research found that Super Elongation Complex (SEC), an assembly of some 10 transcription elongation factors, conveys the downbeat to the translation machine and “helps paused RNA polymerases to come online and start transcribing the gene ahead”.  This quick-start device “reduces the number of steps required for productive transcription and allows cells to respond quickly to internal and external signals,” one of the researchers explained.  Continuing the orchestra metaphor, the article said, “Transcriptional control by RNA polymerase II (Pol II) is a tightly orchestrated, multistep process that requires the concerted action of a large number of players to successfully transcribe the full length of genes.”
6. Quality control inspectors:  At the exit gate of the ribosome, where new proteins have just been assembled, molecular machines called chaperones stand at the ready to help them fold properly.  A Stanford team studied two of these, the Signal Recognition Particle (SNP) and Nascent Chain associated Complex (NAC), which have the remarkable ability to work on a wide variety of proteins, helping them fold properly.  Publishing in PLoS Biology, they said,

Our results provide new insights into SRP selectivity and reveal that NAC is a general cotranslational chaperone. We found surprising differential substrate specificity for the three subunits of NAC, which appear to recognize distinct features within nascent chains. Our results also revealed a partial overlap between the sets of nascent polypeptides that interact with NAC and SRP, respectively, and showed that NAC modulates SRP specificity and fidelity in vivo. These findings give us new insight into the dynamic interplay of chaperones acting on nascent chains.

7. RNA linemen:  We've all watched in the movies how rescue workers toss a line over a wall or pole so that they can climb up.  Something like that happens with some machines that unwind RNA.  In PNAS, a team of researchers described a helicase with the awful name “mitochondrial DEAD-box protein Mss116p” that acts as a general RNA chaperone.  (They really should give these machines better names, like the Chuck Norris Hammerlock Clamp.)  Not only does the machine clamp down on the RNA, it first latches onto it by means of a couple of tails that fasten onto the RNA, tethering the machine to its target:

An analysis of complexes with large chimeric oligonucleotides shows that the basic tails of both proteins are attached flexibly, enabling them to bind rigid duplex DNA segments extending from the core in different directions. Our results indicate that the basic tails of DEAD-box proteins contribute to RNA-chaperone activity by binding nonspecifically to large RNA substrates and flexibly tethering the core for the unwinding of neighboring duplexes.

8. Dirigible doughboys:  Sometimes cells build dirigible-like “transport vesicles” out of parts of the cell membrane, to float large cargo molecules to other organelles in the cell.  This complex process involves many players, including proteins that coat the vesicle, and dockers that hold the dirigible when it comes in for landing; in the case of the cell, though, the dirigible’s coat fuses with the target organelle, so that the contents can enter safely through a membrane tunnel.  Elizabeth Conibear [U of British Columbia] introduced some of the complexity of this process, called endocytosis, in Current Biology, saying, “When a coated transport vesicle docks with its target membrane, the coat proteins and docking machinery must be released before the membranes can fuse. A recent paper shows how this disassembly is triggered at precisely the right time.”  The first paragraph of her review article described just a fraction of what goes on in these operations:

Transport vesicles are created when coat proteins assemble on a flat membrane, select cargo, and deform the membrane into a bud. The budded vesicle is then carried to its target organelle, where it docks by means of ‘tethers’ before undergoing membrane fusion. The vesicle coat was once thought to fall off as soon as budding was complete, but we now know the coat is important for binding the tethering factors that help the vesicle identify the correct organelle. Coat proteins and tethers must be removed before fusion can take place, but what triggers their disassembly has always been a mystery. A paper recently published in Nature now shows that, when one kind of transport vesicle docks with its target membrane, it encounters a kinase that breaks the bond between the coat proteins and the tethers, kick-starting the disassembly process.

The problem she was considering was how the steps are coordinated: “how can a vesicle hang onto its coat long enough to reach its target, but shed it once it arrives?”  Part of the answer appears to be in good management.  Though not yet fully understood, “These results paint a picture of Sec23 as a master regulator of budding and fusion, participating in successive interactions that are regulated by phosphorylation.”  She added, though, that “While this is an attractive model, it may not be the whole story.”  Other protein machines interact in vital ways with Sec23.  Her diagram illustrates several pieces locking together like Lego blocks, arriving and releasing at precise times in a process reminiscent of a space shuttle docking with the space station. 

This complexity undermines a claim on PhysOrg that “Endocytosis is simpler than expected.”  There, researchers in the Netherlands found a simpler model for the way the coat molecules (clathrin) rearrange from flat to spherical during the process of vesicle formation.  That’s only a minor aspect of a much larger multi-stage process involving many protein parts, and as this animation shows, the geodesic-style clathrin molecules are pretty clever little building blocks.

9. Stereo amplifier:  Researchers at Notre Dame and Virginia Tech found that an important signaling enzyme named Pin1 is stereoselective.  “Pin1 is a modular enzyme that accelerates the cis-trans isomerization of phosphorylated-Ser/Thr-Pro (pS/T-P) motifs found in numerous signaling proteins regulating cell growth and neuronal survival,” they wrote in PNAS, showing that conduit response differs if the enzyme binds on one channel instead of the other.  Here’s the scoop for bio-geeks:

We further show interactions between the peptidyl-prolyl isomerase and Trp-Trp (WW) domains amplify the conduit response, and alter binding properties at the remote peptidyl-prolyl isomerase active site. These results suggest that specific input conformations can gate dynamic changes that support intraprotein communication.  Such gating may help control the propagation of chemical signals by Pin1, and other modular signaling proteins.

10. Rubber baby copper pumper:  In “Structural biology: A platform for copper pumps,” Nigel Robinson, writing in Nature, said, “Copper is vital to most cells, but too much is lethal. The structure of a protein that pumps copper ions out of the cytosol provides insight into both the pumping mechanism and how certain mutations in the protein cause disease.”  His diagram shows a molecular machine called LpCopA, comprised of at least 5 protein domains, that safely pumps copper ions out of the cell.  First, the ions have to be delivered to the pump with special chaperone molecules that know how to handle it safely.  Inside the pump are three binding sites that deliver the ion to an L-shaped platform that gently holds the ion while undergoing conformational changes like a lever arm, ejecting the ion safely to the outside.  Then the platform resets for the next round.  Serious brain diseases can occur when these pumps are damaged by mutations.

Readers may wish to investigate these additional papers published this month with intriguing titles:

• “The ribosome uses two active mechanisms to unwind messenger RNA during translation.” (Nature)
•  “Crystal structures of [lambda] exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity.” (PNAS)
• “Mechanism of activation gating in the full-length KcsA K+ channel.” (PNAS)

Time does not permit referencing all these papers; click on the links to go to the abstracts.  These represent part of the backlog of papers on cellular wonders.  Each of them deserve a complete discussion.  Many of them talk about how parts are “highly conserved [i.e., unevolved] from bacteria to humans,” and none of them attempt even a minimally-plausible account of how they might have emerged by chance. 

In these exciting days of opening the cellular black box, we should be standing in awe of the design (and the Designer), not ascribing the machinery inside to mindless, purposeless nothingness.  The record speaks for itself.  Researchers need Darwin like alcoholics need wine (Dar-wine).  It turns them into WINOs, Wesearchers In Name Only (to be pronounced with a drunken drawl).