Protein synthesis evolution

Biological systems depend on specific detailed recognition of molecules that distinguish between chiral forms. The translation machinery for protein synthesis has evolved to utilize only one of the chiral forms of amino acids, the L-form. All amino acids that occur in proteins therefore have the L-form. There is, however, no obvious reason why the L-form was chosen during evolution and not the D-form... 

Molecular complexation is a precondition for receptor functions such as substrate selection, substrate transportation, isomeric differentiation, and stereoselective catalysis. Although the investigation of such functions with synthetically derived compounds is a relatively new development in chemistry, they are well known and extensively studied functions in the biological domain. Evolution, gene expression, cell division, DNA replication, protein synthesis, immunological response, hormonal control, ion transportation, and enzymic catalysis are only some of the many examples where molecular complexation is a prerequisite for observing a biological process. 

Some time after the evolution of this primitive protein-synthesizing system, there was a further development DNA molecules with sequences complementary to the self-replicating RNA molecules took over the function of conserving the genetic information, and RNA molecules evolved to play roles in protein synthesis. (We explain in Chapter 8 why DNA is a more stable molecule than RNA and thus a better repository of inheritable information.) Proteins proved to be versatile catalysts and, over time, took over that function. Lipidlike compounds in the primordial soup formed relatively impermeable layers around self-replicating collections of molecules. The concentration of proteins and nucleic acids within these lipid enclosures favored the molecular interactions required in self-replication. 

Protein synthesis is a central function in cellular physiology and is the primary target of many naturally occurring antibiotics and toxins. Except as noted, these antibiotics inhibit protein synthesis in bacteria. The differences between bacterial and eukaryotic protein synthesis, though in some cases subtle, are sufficient that most of the compounds discussed below are relatively harmless to eukaryotic cells. Natural selection has favored the evolution of compounds that exploit minor differences in order to affect bacterial systems selectively, such that these biochemical weapons are synthesized by some microorganisms and are extremely toxic to others. Because nearly every step in protein synthesis can be specifically inhibited by one antibiotic or another, antibiotics have become valuable tools in the study of protein biosynthesis. 

The second difference enables errors in DNA replication to be corrected with relative ease. During protein synthesis, the growing end of the polypeptide chain is activated and transferred to the next amino acid in the sequence (Figure 13.5). There is no means of removing an incorrectly added residue and reactivating the polypeptide. Error correction has to be made before polymerization. But in the synthesis of DNA, the monomeric nucleotide is activated and added to the unactivated growing chain. This has enabled the evolution of a mechanism for the editing of errors after polymerization has occurred. 

E. coli maintains all of its genes in a state where they can be turned on or turned off on short notice. The short messenger lifetime makes it possible to control gene expression from the transcription level. The lack of separate compartments for RNA and protein synthesis has fostered mechanisms where translation actually exerts a direct role on transcription. These are some of the special features that have influenced the evolution of regulatory systems in E. coli. 

Gerbi, S.A. (1 996) Expansion segments regions of variable size that interrupt the universal core secondary structure of ribosomal RNA. In Dahlberg, A.E. and Zimmermann, R.A. (eds) Ribosomal RNA Structure, Evolution, Processing and Function in Protein Synthesis. CRC Press, Boca Raton, Florida, pp. 71-87. 

The dynamic process is akin to the error checking mechanisms employed in protein synthesis each reaction is reversible until the correct product has formed. In any evolutionary chemical system it is important to ensure copying fidelity and the success of dynamic combinatorial libraries indicates that concepts associate with supramolecular chemistry can be valuable in advancing chemical evolution. 

Synthesis of molecular chaperones may be constitutive or stress-induced. Several size classes of molecular chaperones are synthesized constitutively to facilitate the housekeeping functions associated with protein synthesis and maturation. All organisms contain constitutively expressed chaperones, and the ubiquitous occurrence of these proteins is strong reason to believe that they appeared very early in evolution. Orthologs of some classes of molecular chaperones are found in prokaryotes and all eukaryotes. 

At this point, however, we cannot ignore the fact that the evolution of protein synthesis started before the origin of the first cells, in systems which could not have cell walls, cytoskeleton filaments or sodium pumps, for the very good reason that all these structures require well-developed proteins. How could precellular systems have high potassium concentrations, and low sodium levels, without any of the molecular mechanisms that cells employ to this end The most plausible answer is that those concentrations did not have to be produced in prebiotic systems because they already existed in the environment of the primitive seas. The ribotype world, in short, was also a potassium world. 

Aminoacyl-tRNA synthetases (aaRSs) compose a family of essential enzymes that attach amino acids covalently to tRNA molecules during protein synthesis. Some aaRSs possess a hydrolytic amino acid editing function to ensure the fidelity of protein synthesis. In addition, aminoacylation can occur by indirect pathways that rely on mischarged tRNA intermediates and enzymes other than aaRSs. Throughout evolution, structural and functional divergence of aaRSs has yielded diverse secondary roles. 

Another motif recurs in this activation reaction. The enzyme-hound acyl-adenylate intermediate is not unique to the synthesis of acyl CoA. Acyl adenylates are frequently formed when carboxyl groups are activated in biochemical reactions. Amino acids are activated for protein synthesis hy a similar mechanism (Section 29.2.1). although the enzymes that catalyze this process are not homologous to acyl CoA synthetase. Thus, activation by adenylation recurs in part because of convergent evolution. 

The basics of protein synthesis are the same across all kingdoms of life, attesting to the fact that the protein-synthesis system arose very early in evolution. A protein is synthesized in the amino-to-carboxyl direction by the sequential addition of amino acids to the carboxyl end of the growing peptide chain (Figure 29,2). The amino acids arrive at the... 

Kondoh Y, Kaneshiro KY, Kimura K, Yamamoto D (2003) Evolution of sexual dimorphism in the olfactory brain of Hawaiian Drosophila. Proc R Soc Lond B 270 1005-1013 Krashes MJ, Keene AC, Leung B, Armstrong JD, Waddell S (2007) Sequential use of mushroom body neuron subsets during Drosophila odor memory processing. Neuron 53 103-115 Krashes MJ, Waddell S (2008) Rapid consolidation to a radish and protein synthesis-dependent long-term memory after single-session appetitive olfactory conditioning in Drosophila. J NeuroSci. 28 3103-3113... 

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