How could prebiotic molecules make the code and how all this is related to proteins?: Reply to comments on “A colorful origin to the genetic code” by H. Takagi, K. Kaneko and R. Wallace
✍ Scribed by Tsvi Tlusty
- Publisher
- Elsevier Science
- Year
- 2010
- Tongue
- English
- Weight
- 83 KB
- Volume
- 7
- Category
- Article
- ISSN
- 1571-0645
No coin nor oath required. For personal study only.
✦ Synopsis
I am grateful to the commentators for bringing up two fundamental questions that are in fact related. Takagi and Kaneko look into a concrete molecular mechanism that could lead to the emergence of the genetic code [1], while Wallace takes the rate-distortion paradigm to the realm of proteins and asks about possible implications of my information-theoretic view [2].
Let us start from the first-principles model of the Takagi, Kaneko and Yomo (TKY) [3] for the emergence of genetic codes via bifurcation of attractors in biochemical dynamical systems [4]. My rate-distortion approach [5,6] assumes a priori the existence of molecular machinery that can facilitate the back-and-forth mapping between amino-acids and codons, formally defined by the decoder and the encoder matrices [7]. The TKY paper constructs a concrete biochemical network that could in principle facilitate such a mapping. The network includes tRNAs, aminoacyl tRNA synthetases, codons and amino-acids, together with other enzymes and metabolites that are required for power up the transcription-translation pathway and the rest of metabolism.
Via elaborate simulations, the model suggests that fluctuations in metabolic states can lead to differentiation of synthetases, which imply bifurcation of the molecular code. TKY augment this mechanism with population dynamics of competition and selection of optimal codes that is far from the 'frozen accident' view [8,9]. Of course, this bifurcation [10] is a manifestation at a molecular level of the coding phase transition described in the information-theoretic model [7,11]. Feedback loops are pivotal in the emergence of a coding machinery that synthesis itself [12]. I believe that this self-referential feature of the emergent code is also linked to the universality of the coding phase transition and to its generic topological features [13][14][15], including the 'magic number' of 20 amino-acids [16,17]. Concrete models, such as the TKY dynamical system [3] will allow stringent testing of the topological coding transition.
An essential ingredient of any concrete molecular model is a genotype-phenotype map that specifies the stability and functionality of a given protein basing on the DNA sequence of its gene [18] and on the genetic code map that translates the gene into an amino-acid chain. Such gene-protein map is necessary to close the feedback loops between mutations of aminoacyl-tRNA synthetases and the effect on the genetic code which in turn changes the synthetases,