Cellular Machines Coming to Light

51; As imaging techniques improve, cells are yielding up their secrets.  Scientists are getting closer to watching the processes in cellular factories in real time.

1. Dynein:  PhysOrg reported, “Biologists capture cell’s elusive ‘motor’ on videotape, solving the mystery of its deployment.”  The article began, “Their experiments can be likened to restoring never-before-seen footage to a classic film.”  Researchers at the University of Massachusetts Amherst are discovering “How dynein, the cell’s two-part, nano-scale ‘mitotic motor,’ positions itself to direct the [cell] dividing process.”  They described their delight at watching “a complete surprise and a eureka moment for us to witness a hypothesis supported by direct evidence for the first time.”
2. Myosin:  Another motor machine in the cell is myosin.  PhysOrg described how scientists on the east coast have found a way to turn the motor on and off with light.  “Molecular ‘motors’ are at the root of most biological movement,” the press release stated.  “They propel cell components, whole cells, and even our muscles on command.”  The team’s paper claimed “this should make it possible to follow cellular processes that involve myosin in real time.”
3. DNA structure:  Scientists at the University of Amsterdam have measured the force holding DNA together, and found that a small force can make it separate like a zipper.  PhysOrg told how the strands re-join when the tension is relaxed.  With this research, they “can now have a better understanding of how DNA in cells is locally opened so genes can be turned ‘on’ or ‘off’.”
4. DNA packaging  Penn State researchers have discovered more about how DNA is packaged into chromosomes.  They have achieved a milestone in the goal of assembling a chromosome from its component parts by adding histones to purified yeast DNA and watching it wrap into nucleosomes – building blocks of the supercoils that form chromosomes.  To get the wrapping started, they had to add ATP, which they likened to the leaven that makes bread rise.  Enzymes used the ATP to wrap the DNA neatly into the nucleosomes.  Some 60,000 nucleosomes make up a yeast chromosome.
       According to PhysOrg, their work “overturns three previous theories of the genome-packaging process and opens the door to a new era of genome-wide biochemistry research.”  It is hoped that research like this will yield insights leading to therapies for genetic disorders.
5. Photosynthesis:  Argonne National Laboratory “has worked for fifty years to understand photosynthesis—one of the most mysterious and wonderful chemical processes in the world,” an article on PhysOrg began.  “Photosynthesis built a green Earth out of the bare, meteor-blistered planet which had sat empty for a billion years; it tipped the composition of the atmosphere towards oxygen, allowing all kinds of life to blossom, including us.”
       The team is applying what they are learning for human benefit.  “Basically, we’ve been reverse-engineering photosynthesis,” one of the researchers said.  “If we understand how Nature does it, we can tweak the process to produce hydrogen” that would lead to efficient solar cells.
6. Photosynthesis reactor:  Speaking of photosynthesis, Japanese scientists have achieved the imaging of the “Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9?Å,”  zooming in almost twice as far as previous studies.  Their paper, published in Nature,¹ spoke of the reactor as “indispensable for sustaining life on Earth.”  It includes detailed drawings of the 20 subunits involved with numerous molecular contacts.
       The particular part of the reactor that splits water molecules and combines oxygen atoms into the O2 gas we breathe they said is “one of nature’s most fascinating and important reactions.”  Understanding Photosystem II may help humans to mimic plants’ ability to split water efficiently at ambient temperatures, leading to renewable energy for a multitude of applications.  The ability lives all around us if we can tap into its secrets.
7. Ribosome:  Biochemists from five US universities have witnessed a key reaction in the ribosomes, the elaborate structures that translate messenger RNA [mRNA] into proteins.  Reporting in Science,² they described how the ribosome, the transfer RNA [tRNA] molecules and other elements form moving parts and machinery:
   

   During protein synthesis, the ribosome controls the movement of tRNA and mRNA by means of large-scale structural rearrangements.  We describe structures of the intact bacterial ribosome from Escherichia coli that reveal how the ribosome binds tRNA in two functionally distinct states, determined to a resolution of ~3.2 angstroms by means of x-ray crystallography.  One state positions tRNA in the peptidyl-tRNA binding site.  The second, a fully rotated state, is stabilized by ribosome recycling factor and binds tRNA in a highly bent conformation in a hybrid peptidyl/exit site.  The structures help to explain how the ratchet-like motion of the two ribosomal subunits contributes to the mechanisms of translocation, termination, and ribosome recycling.

   Drawings in the paper show the moving parts with rotations of up to 70°.  In their concluding paragraph, they described what they saw: “Because simple mRNAs can be translated in the absence of exogenous factors like EF-G (44), the ribosome itself serves as a Brownian ratchet, with tRNA substrates probably serving as the ‘teeth.’,” they said.  “A notable feature of the ratcheting mechanism is the use of RNA secondary structural elements to control large-scale conformational rearrangements in the ribosome.”  They went on to compare the moving parts to bridges, swivels, springs, pawls, and hinges.

8. Ribosome information:  Information is a profound concept that presupposes purpose and design.  It is being joined to biology.  Two researchers at the University of Maryland titled a paper, “An Extensive Network of Information Flow through the B1b/c Intersubunit Bridge of the Yeast Ribosome.”  Writing in PLoS One,³ they described “an extensive network of information exchange between distinct regions of the large and small subunits” of the ribosome.  Mutations, they found, “had wide-ranging effects on cellular viability and translational fidelity” and mentioned some of the diseases they cause.
       They discussed two subunits in particular that “work together to communicate information pertaining to the tRNA occupancy status of the P-site and the B1b/c bridge.”  In fact, “These shared changes in rRNA chemical protection patterns suggest that, while spatially remote, all of these different regions of the ribosome are connected through specific ‘informational nodes’ comprised of specific bases of 25S rRNA.”  The words information and translational fidelity were key terms in this paper.

1.  Umena, Kawakami, Shen, and Kamiya, “Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9?Å,” Nature 473 (05 May 2011), pp. 55?60, doi:10.1038/nature09913.
2.  Dunkle, Wang et al, “Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding,” Science 20 May 2011: Vol. 332 no. 6032 pp. 981-984, DOI: 10.1126/science.1202692.
3.  Rhodin and Dinman, “An Extensive Network of Information Flow through the B1b/c Intersubunit Bridge of the Yeast Ribosome,” PLoS One 6(5): e20048, May 19, 2011; doi:10.1371/journal.pone.0020048.

None of these articles even attempted to explain how these complex systems evolved (“oxygen-evolving photosystem II” doesn’t count – that’s a different meaning of the word).  Only one (the Science paper) mentioned evolution at all, and only on the periphery, as if needing to acknowledge an irrelevant faith in evolution to fulfill some kind of obligation.  These articles need Darwin like a swimmer needs a barbell.
    Stephen C. Meyer, author of Signature in the Cell, has this quote on his website.  It suffices as commentary.  “In the 21st century, the information age has finally come to biology.  We now know that biology at its root is comprised of information rich systems, such as the complex digital code encoded in DNA.  Groundbreaking discoveries of the past decade are revealing the information bearing properties of biological systems.”