FUNCTIONAL, SELF-REFERENTIAL GENETIC CODING
ROMEU CARDOSO GUIMARÃES Dept. Biologia Geral, Inst. Ciências Biológicas, Univ. Federal Minas Gerais, Belo Horizonte MG 31270-901 Brasil;
[email protected] CARLOS HENRIQUE COSTA MOREIRA Dept. Matemática, Inst. Ciências Exatas, Univ. Federal Minas Gerais, Belo Horizonte MG 30123-970 Brasil;
[email protected]
Abstract. A model for the genetic code structure and organization is presented. It is self-referential due to starting without an mRNA to be translated. Recruitment of tRNAs occurs in pairs, one fishing the other, their anticodons being simultaneously codons for each other. Genes – mRNAs – arise in the process of formation of the code. It is also functional, depicting various consistent correlations with protein properties. First attributions – Gly, Pro, Ser – are the outliers from the hydropathy correlation, proteinstabilizing and RNA-binding amino acids. These properties allow formation of a stable RNP system, the source-product relationship being established. The succession of entries also obeys the following criteria: (a) synthetases class II to class I; (b) protein conformations from aperiodic to helices and then strands; (c) ordering of protein sequences with heads and tails, respectively, stable and unstable, called a non-specific punctuation system, in the second stage; (d) DNA-binding amino acids in the third stage; (e) late development of the specific punctuation system, that of initiation defining the stop signs, and (f) of the hexacodonic expansions of Leu and Arg.
1. Introduction A model for the structure of the genetic code is presented, describing how the matrix was formed and organized. This work had a first presentation in Guimarães (1996) and a description of the first stages in Guimarães and Moreira (2002). A concise account of the full model (Guimarães and Moreira, 2004) is shown here.
2. Self-reference and function The model is based on successive recruitment of pairs of anticodons of the palindromic type – with the same bases at the extremities (TABLE I).
It is indicated that the triplets AGA : UCU fished each other while Ser was octacodonic, before concession of YCU to Arg, and that the coherence of synthetases class I for Gln and Val was established after concession of YUG to Gln.
TABLE I. Anticodon pairs and synthetase class couples. pDiN underlined, stages numbered with letter indices, classes in Roman numerals.
AAA Phe UUU Lys 2b II : II (both atypic)
AGA Ser UCU Ser 1b II : II
ACA Cys UGU Thr 3c I : II
AUA Tyr UAU Ile 4a I:I
GAG Leu CUC Glu 2a I:I
GGG Pro CCC Gly 1a II : II
GCG Arg CGC Ala 3a I : II
GUG His CAC Val 3b I:I (Gln)
In Stage 1 the system is entirely self-referential – anticodons in a pair are simultaneously codons for each other – and there is no need for an mRNA to be translated. In Stage 2, mRNAs are formed and structured, with heads and tails (non-specific punctuation; Guimarães, 2001). So, genes (mRNAs) are formed and defined concomitantly with formation of the coding system, when the proteins (now ´products´) feed back upon the RNAs, through binding to them and stabilizing the nucleoproteins. Thereafter, the system developed auto-catalytic features. The model is also functional, due to the consistency with various other protein properties. Stage 3 contains the amino acids most characteristic of DNA-binding motifs. The specific punctuation system and the hexacodonic expansions of Leu and Arg are placed in Stage 4. Besides the characters specified, note the trajectories: from the GC-rich core to the periphery of the matrix; from synthetases class II to I, and the consistency with amino acid biosynthesis derivations. Sectors of pDiN are self-contained, the only cross-sector attribution being the hexacodonic Arg (FIGURE 1).
3. Stages Stage 1: (1 a) Gly +CC : +GG (Gly) Pro, (1 b) Ser +GA : +CU Ser. The sector of Ho pDiN (quadrants: +RR : +YY) starts being filled. Amino acids are protein-stabilizers, RNA-binders and characteristic of coils and turns of proteins. Attributions are the outliers of the hydropathy correlation. All synthetases are class II.
Gly may have preceded Pro in the +GG box, since Pro is derived biosynthetically from Glu. Stage 2: (2 a) Asp then Glu +UC : +AG Leu, (2 b) Asn then Lys +UU : +AA Phe. The hydropathy correlation is established. Synthetases make one couple of class I and the atypical couple: Lys class II, but class I in some organisms; Phe class II, but acylating in the class I mode. Non-specific punctuation and mRNA structure are formed: amino acids of Stage 1 become heads of proteins, those of Stage 2 added as tails. Enter 3/8 of the amino acids of the set of protein helix-forming, 1/7 of the strand-forming.
FIGURE 1. Formation of the genetic anticode. Bases in hydrophilicity A-G-C-U order. Sectors of principal dinucleotide (pDiN) types: mixed (Mx; quadrants +RY : +YR) and homogeneous (Ho, bold; +RR : +YY); +, the 5´ bases. Stages numbered with letter indices, in parenthesis. The amino acids in parenthesis are indicated to be previous occupiers of the respective boxes. Further explanations in the text.
+AA Phe
(2 b) +GA Ser
Leu +AG Leu
(4 c) (2 a) +GG Pro (Gly) (3 b) +GC Ala
+AC Val +AU Ile Met fMet
(4 a) (4 b)
+GU Thr
(1 b)
(3 c)
+UA Tyr
(4 a)
(4 b) (3 a)
(3 c)
+CU Ser
(1 b)
X +UG His Gln +UC Asp Glu +UU Asn Lys
(4 b) (3 b)
(3 a)
+CA Cys Trp X +CG Arg (Ala) +CC Gly
Arg
(4 c)
(1 a)
(1 a)
(2 a) (2 b)
Stage 3: (3 a) Ala +GC : +CG (Ala) Arg, (3 b) His then Gln +UG : +AC Val, (3 c) Thr +GU : +CA Cys then Trp. Start the sector of mixed pDiN (quadrants: +RY : +YR). Amino acids are characteristic of DNA-binding motifs. Synthetases make one class I couple (Gln / Val) and the two couples of different classes – among the 8 pairs of boxes. Ala may have preceded Arg in the +CG box, which is a simpler alternative to other proposals for the predecessor to Arg. Stage 4: (4 a) Ile then Met +AU : +UA Tyr. All synthetases are class I. (4 b) The specific punctuation system is formed: fMet with slipped pDiN CAU and codons +UG ; X anticodons UCA and YUA, pairing with the initiation codon, thereby competing with fMet, are deleted. (4 c) The hexacodonic expansions of Leu and Arg synthetases class I, respectively, into YAA and YCU, are formed, driven by codon usage.
Acknowledgments Support from CNPq and FAPEMIG to Romeu Cardoso Guimarães.
4. References Guimarães, R.C. (1996) Anticomplementary order in the genetic coding system, Abstracts of the International Conference on the Origin of Life, ISSOL, Orléans, 11: 100. Guimarães, R.C. (2001) Two punctuation systems in the genetic code, in J. Chela-Flores, T. Owen and F. Raulin (eds.), First Steps in the Origin of Life in the Universe, Kluwer, Dordrecht, pp. 91-94. Guimarães, R.C. and Moreira, C.H.C. (2002) Genetic code structure and evolution: aminoacyl-tRNA synthetases and principal dinucleotides, in G. Pályi, C. Zucchi and L. Caglioti (eds.), Fundamentals of Life, Elsevier, Paris, pp. 249-276. Guimarães, R.C. and Moreira, C.H.C. (2004) The functional and self-referential genetic code, in G. Pályi, C. Zucchi and L. Caglioti (eds.), Progress in Biological Chirality, Elsevier, Oxford, in press.
GUIMARÃES Romeu Cardoso and MOREIRA Carlos Henrique Costa. Functional, selfreferential genetic coding. In: Joseph Seckbach, Julian Chela-Flores, Tobias Owen, Francois Raulin (Org.). Life in the universe - from the Miller experiment to the search for life on other worlds. 1ed. Dordrecht, Kluwer Academic Publishers, 2004, v. 1, p. 89-91
