Pre-History of Life: Elegantly Simple Organizing Principles Seen in Ribosomes

http://www.sciencedaily.com/releases/2010/04/100412151823.htm

All forms of life rely on the same genetic code which specifies the amino acid composition of proteins. Still subject to speculation is how individual amino acids were assigned to specific three-letter combinations or codons during the evolution of the genetic code. Through research with modern cells at the Salk Institute for Biological Studies concluded that after two waves of “matching” and some minute fiddling, all 20 commonly used amino acids were firmly linked with their respective codons, thus setting the stage for the emergence of proteins with unique, defined sequences and properties. These finding are the first in vio data shediing light on the origin and evolution of the genetic code.

"Although different algorithms, or codes, were likely tested during a long period of chemical evolution, the modern code proved so robust that, once it was established, it gave birth to the entire tree of life," says the study's lead author Lei Wang, Ph.D., an assistant professor in the Chemical Biology and Proteomics Laboratory.

"But the universality of the code makes it very hard for researchers to study its formation since there are no organisms using a primitive or intermediate genetic code that we could analyze for comparison," he explains.

All life forms on earth use the same 20 common amino acids with few exceptions. Each of the 20 amino acids is matched to its own carrier molecule known as transfer RNA (tRNA). During protein synthesis, which is coordinated by so-called ribosomes, amino acids are brought out one by one by their respective tRNAs and inserted in the growing protein chain according to the instructions spelled out in the universal language of life -- the genetic code. The code is "read" with the help of anticodons embedded in each tRNA, which pair up with their codon-counterparts.

Several hypotheses have been put forward to explain why codons are selectively assigned to specific amino acids. "One of the theories, the stereochemical hypothesis, gained some traction when researchers could show that short codon- or anticodon-containing polynucleotide molecules like to interact with their respective amino acids," says graduate student and first author David B. F. Johnson.

According to Johnson if chemical or physical interactions between amino acids and nucleotide drove the formation of the genetic code, then he reasoned that he should be able to find the relics of this mutual affinity in modern cells. He then zoomed in on ribosomes which are large complexes that are consist of some 50 proteins interacting closely with ribosomal RNA’s.

"Also, the ribosome emerged from an early evolutionary stage of life to help with the translation of the genetic code before the last universal common ancestor," explains Wang, "and therefore is more likely to serve as a molecular fossil that preserved biological evidence."

When Wang and Johnson probed bacterial ribosomes for imprints of the genetic code, they found evidence that direct interactions between amino acids and nucleotide triplet anticodons helped establish matching pairs. "We now believe that the genetic code was established in two different stages," says Johnson.

The data that was collected did not shed much light onto the early code, consisting of prebiotically available amino acids. The kind generated in the “zap” experiment of Stanley Miller. When some primitive translational mechanisms were established , he then added new amino acids to the mix and started infiltrating the genetic code based on specific amino acid or anticodon interactions.

"We found evidence that a few amino acids were reassigned to a different codon but once the code was in place it took over," says Johnson. "It might not have been the best possible solution but the only one that was viable at the time."