Evolution genetic code

Mukai, T., Yanagisawa, T., Ohtake, K., Wakamori, M. et al. (2011) Genetic-code evolution for protein synthesis with non-natural amino acids. Biochem. Biophys. Res. Commun., 411, 757-761. 

Fig. 1.5 Schematic representation of the evolution of life from its precursors, on the basis of the definition of life given by the authors. If bioenergetic mechanisms have developed via autonomous systems, the thermodynamic basis for the beginning of the archiving of information, and thus for a one-polymer world such as the RNA world , has been set up. Several models for this transition have been discussed. This phase of development is possibly the starting point for the process of Darwinian evolution (with reproduction, variation and heredity), but still without any separation between genotype and phenotype. According to the authors definition, life begins in exactly that moment when the genetic code comes into play, i.e., in the transition from a one-polymer world to a two-polymer world . The last phase, open-ended evolution, then follows. After Ruiz-Mirazo et al. (2004)...

In 1994, a conference with the title Aminoacyl-tRNA Synthetases and the Evolution of the Genetic Code was held in Berkeley, California its patron was the Institute of Advanced Studies in Biology. The conference dealt with the development of the synthetases and that of the genetic code (see Sect. 8.2), i.e., the assignment of the various amino acids to the corresponding base triplets of the nucleic acids. 

The close connection of this enzyme family with the transfer of genetic information has made it a popular object of study when dealing with questions regarding the formation and evolution of the genetic code (see Sect. 8.1). It is now agreed that the aminoacyl-tRNA synthetases are a very ancient enzyme species which do not, however, arise from one single primeval enzyme, but from at least two, corresponding to the synthetase classes. 

Table 8.2 According to the co-evolution theory proposed by Wong, the biosynthetic routes to amino acids from their precursors could perhaps provide information on the evolution of the genetic code (Wong, 1975)...

An important factor in the evolution of the genetic code is certainly provided by the aminoacyl-tRNA synthetases (see Sect. 5.3.2). It is clear that the two synthetase classes are not randomly distributed across the matrix of the amino acid assignment of the genetic code. For example, with one exception, all XUX codons code for class 1 synthetases, while all XCX codons code for class 2 aminoacyl-tRNA synthetases. A possible explanation could be that the synthetases and the genetic code evolved simultaneously. However, it is more likely that these enzymes evolved when the genetic code had already been established (Wetzel, 1995). 

One important question is that of the order in which the basic mechanisms of evolution processes, leading eventually to the emergence of life, occurred. As far as the development of the genetic code is concerned, it is not clear whether the code evolved prior to the aminoacylation process, i.e., whether aminoacyl-tRNA synthetases evolved before or after the code. A tRNA species which is aminoacy-lated by two different synthetases was studied if this tRNA had important identity elements such as the discriminator base and the three anticodon bases for the two synthetases, this would be evidence that the aminoacyl-tRNA synthetases had developed after the genetic code. Dieter Soil s group, which is experienced in working with this family of enzymes, came to the conclusion that the universal genetic code must have developed before the evolution of the aminoacylation system (Hohn et al, 2006). 

A further (mathematical) model for the evolution of the genetic code was devised by Carl Woese and co-workers. This dynamic theory provides information on the evolvability and universality of the genetic code. One conceptual difficulty was due to the fact that it had been overlooked that the genetic code was highly communal... 

A detailed treatment of the evolution of the genetic code requires modelling physical components of the translational process this includes the dynamic processes of the tRNAs and the aminoacyl-tRNA synthetases (Vetsigian et al., 2006). Thus, in spite of considerable advances in the search for the roots of the genetic code, there is still much to do ... 

The interpenetration of these phenomena, mediated by HGT, is also likely to be of great importance for evolution. According to the authors, the genetic code, which plays a key role in all forms of life, leads to the prediction that the first steps of the process of the emergence of life evolved in a Lamarckian manner, with vertical descent driven back by powerful early forms of HGT. 

There are many potential molecules and possible routes to the synthesis of biomolecules that might form the basis of a primitive metabolism but thus far we have not addressed the question of information propagation or Darwinian evolution. Information storage must be contained within a sequence, such as words in a sentence or the base sequences within the genetic code, and that requires a polymerisation reaction, which is preferably autocatalytic to reproduce the information accurately. Peptides and nucleotides have this property, although the condensation reaction joining them together needs to be activated. 

Berenbaum MR (1983) Coumarins and caterpillars a case for coevolution. Evolution 37 163-179 Berenbaum MR (1991) Coumarins. In Rosenthal G, Berenbaum MR (eds) Herbivores their interactions with secondary plant metabolites. Academic, New York, pp 221-249 Berenbaum MR (2002) Postgenomic chemical ecology from genetic code to ecological interactions. J Chem Ecol 28 873-896... 

The physiological functions of carboxylesterases are still partly obscure but these enzymes are probably essential, since their genetic codes have been preserved throughout evolution [84] [96], There is some evidence that microsomal carboxylesterases play an important role in lipid metabolism in the endoplasmic reticulum. Indeed, they are able to hydrolyze acylcamitines, pal-mitoyl-CoA, and mono- and diacylglycerols [74a] [77] [97]. It has been speculated that these hydrolytic activities may facilitate the transfer of fatty acids across the endoplasmic reticulum and/or prevent the accumulation of mem-branolytic natural detergents such as carnitine esters and lysophospholipids. Plasma esterases are possibly also involved in fat absorption. In the rat, an increase in dietary fats was associated with a pronounced increase in the activity of ESI. In the mouse, the infusion of lipids into the duodenum decreased ESI levels in both lymph and serum, whereas an increase in ES2 levels was observed. In the lymph, the levels of ES2 paralleled triglyceride concentrations [92] [98],... 

Universality The genetic code is virtually universal, that is, the specificity of the genetic code has been conserved from very early stages of evolution, with only slight differences in the manner in which the code is translated. [Note An exception occurs in mitochondria, in which a few codons have different meanings than those shown in Figure 31.2.]... 

Bessho, Y., Ohama, T. and Osawa, S. (1 992) Planarian mitochondria, ii. The unique genetic code as deduced from cytochrome c oxidase subunit 1 gene sequences. journal of Molecular Evolution 34, 331-335. 

Ohama, T., Osawa, S., Watanabe, K. and Jukes, T.H. (1990) Evolution of the mitochondrial genetic code. IV. AAA as an asparagine codon in some animal mitochondria. Journal of Molecular Evolution 30, 329-332. 

Woese CR, Dugre DH, Dugre SA et al. On the fundamental nature and evolution of the genetic code. Cold Spring Harbor Symposia on Quantitative Biology 1966 31 723. 

---