Saturday, May 2, 2009

The ribosome as ancient relic

The ribosome is a fascinating and enormous vestige of the RNA world

One little problem of biology is its ultimate origin. Darwinian biology traces back to something called the "last common ancestor" (LCA for short)- a bacterium-like species from which all life appears to have diversified, containing DNA, proteins, and a membrane. But what came before the LCA? Much of the machinery of the LCA descended from a lengthy process of prior evolution, partly chemical in nature, which is to say that heritability of traits might have been due more to replication of the individual parts of the proto-cell (e.g., by natural expansion of its membrane with like-structured compounds), than by a segregated informational molecule that encoded everything else. For membranes, this is still the case. There is no gene that "encodes the membrane", though there are now plenty of genes that encode proteins that manage membranes and synthesize their components.

One way-station on the path to the LCA, prior to the appearance of DNA, appears to have been a period called the RNA world. RNA (ribonucleic acid) is not as chemically stable as DNA, and is also not as physically rigid as DNA. Being chemically stable is great for DNA (by virtue of a single oxygen subtraction from RNA, thus the "deoxy"), but having chemical reactivity and flexibility is an interesting property of RNA, making it capable of catalyzing reactions as well as carrying information. Thus was born the idea that RNA embodies in one molecule two of the key parts of the original aspects of life- metabolism and heritable information, though quite inefficiently for each.

Scientists now fall over each other to create clever catalytic schemes using RNA, which can cleave other molecules and ligate RNAs, depending on its sequence and shape. A nobel prize has been awarded in this field, and quite a bit of in-vitro evolution has been done to optimize what are called "ribozymes". A quasi- self-reproducing system has recently been devised whose input is short fragments of RNA, which get ligated together by their large products, leading to amplification of the catalytic RNAs, as well as selection and diversification.

But the main evidence for the RNA world comes not from the proof-of-principle experiments, but from the many vestiges that remain in modern cells, first and foremost of which is the translation system. Translation is the process of making proteins from the genetic code- currently DNA. DNA is copied into "messenger" RNA, the mRNA is spliced (by an RNA-based "spliceosome"), capped, and transported out of the nucleus, where it docks to ribosomes which synthesize the encoded protein by reading off three-nucleotide codons.

The ribosome is a huge scaffold (~3,000 kDaltons, or about 20 times the size of an average protein) composed of RNA and proteins that holds the participants and synthesizes the protein, but it does not actually do the codon reading- that part is done by yet another RNA species, the transfer RNAs, which are small L-shaped RNAs that expose an "anti-codon" at the top of the stem of the "L" which hybridize with and "read" codons on the mRNA, and which on their other end carry a single amino acid. Once the ribosome has the right tRNA docked to the mRNA codon, it then spends a little energy to add that tRNA's amino acid to the protein chain it is synthesizing.

Schematic of the translation cycle, with tRNAs pictured in blue,
mRNA in green, and the ribosome in gray.

The key observation, proven only in the last decade, is that the core catalytic activity of polymerizing proteins is in the RNA part of the ribosome, not the protein parts. Indeed, deduced structures of the ribosome show an RNA core decorated with numerous peripheral proteins, as one would imagine if the core were the ancient site of catalytic action, which was later enhanced with various proteins that help efficiency, stability, and regulation. And this RNA is also extremely ancient and well-conserved, recognizably similar in its sequence between all organisms, no matter how distant.

So to recount, translation of proteins involves RNA at every stage- the message/template, the critical bridging function (tRNA) between information code unit and amino acid unit, and lastly the catalytic activity to put them together. I have not even mentioned the RNA catalysis involved in splicing and processing the mRNA, and the RNA core (SRP) involved in docking ribosomes to membranes when making membrane proteins, nor the incredibly ornate pathways of RNA synthesis and modification involved in making ribosomes themselves.

Detailed structure of the inner face of half of a ribosome,
showing key portions of RNA (in red) that interact with the
complementary half. Proteins are in purple.

"There is now strong evidence indicating that an RNA World did indeed exist on the early earth. The smoking gun is seen in the structure of the contemporary ribosome (Ban et al. 2000; Whimberly et al. 2000; Yusupov et al. 2001). The active site for peptide bond formation lies deep within a central core of RNA, whereas proteins decorate the outside of this RNA core and insert narrow fingers into it. No amino acid side chain comes within 18 Å of the active site (Nissen et al. 2000)." - Joyce and Orgel, The RNA world, 2005

Taking the long view, the ribosome is absurdly large and inefficient. DNA and RNA polymerases typically clock in at ~500 kDa, or a fifth the size of ribosomes. The cell spends a huge part of its mass and effort on these little machines. The E. coli cell devotes between 15% to 45% of its dry mass to ribosomes. A rational designer would base the whole mechanism on proteins, which are much better catalysts, and make it far smaller, replacing tRNAs with much smaller protein-based bridging units as well. But no. This is a classic case of sunk costs, of path-dependent development, of sclerotic infrastucture. Cells can not just redesign their most critical function- their method of translation, so we appear to have a luxuriant and wasteful remnant of what we began with- a world where efficiency might not have been the top priority, given the difficulty of making anything work reliably.

So what came before this putative RNA world? Did RNA arise out of the chemistry of early earth spontaneously (highly unlikely), or did it have precursors in the form of crystalline minerals that aided stereo-specific polymerization other organic chemicals? There are plenty of theories, and growing knowledge of the environmental and chemical conditions, which seem to have been propitious, but evidence is extremely thin, if one wishes to stick to evidence.

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