Neutral adaptation of the genetic code to double-strand coding

Konecny, Jaromir; Eckert, Michael; Schöniger, Michael; Hofacker, G. L.

doi:10.1007/bf02406718

Cited by 24 publications

(12 citation statements)

References 46 publications

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“…Compared to randomized codes, by being less sensitive to mutations in flanking, 1 st vs. 3 rd ,codon positions, the real code actually favors the SAS coding until one of the complementarily encoded proteins gains a decisive function(s) making further parallel improvements very difficult (if at all possible) to accomplish (Konechny et al, 1993: Rodin and Rodin, 2006a,b). …”

Section: The Hypothesis Of Ancient Sense-antisense Coding: the (Domentioning

confidence: 99%

On Primordial Sense–Antisense Coding

Rodin

Carter

2009

J Mol Evol

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The genetic code is implemented by aminoacyl-tRNA synthetases (aaRS). These twenty enzymes are divided into two classes that, despite performing same functions, have nothing common in structure. The mystery of this striking partition of aaRSs might have been concealed in their sterically complementary modes of tRNA recognition that, as we have found recently, protect the tRNAs with complementary anticodons from confusion in translation. This finding implies that, in the beginning, life increased its coding repertoire by the pairs of complementary codons (rather than one-by-one) and used both complementary strands of genes as templates for translation. The class I and class II aaRSs may represent one of the most important examples of such primordial sence-antisence (SAS) coding (Rodin and Ohno, 1995). In this report, we address the issue of SAS coding in a wider scope. We suggest a variety of advantages that such coding would have had in exploring a wider sequence space before translation became highly specific. In particular, we confirm that in Achylia klebsiana a single gene might have originally coded for an HSP70 chaperonin (class II aaRS homolog) and an NAD-specific GDH-like enzyme (class I aaRS homolog) via its sense and antisense strands. Thus, in contrast to the conclusions in (Williams et al., 2009), this could indeed be a “Rosetta stone” (eroded somewhat, though) gene for the SAS origin of the two aaRS classes (Carter and Duax, 2002).

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Section: The Hypothesis Of Ancient Sense-antisense Coding: the (Domentioning

confidence: 99%

On Primordial Sense–Antisense Coding

Rodin

Carter

2009

J Mol Evol

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“…(Gray, 1992), and in the viral genome (Ziff, 1980). The concept of proteins coded by complementary strands has also been investigated for properties between amino acids and codons and for rules of the two complementary strands of DNA (Zull and Smith, 1990;Konecny et al, 1993;Béland and Allen, 1994;Konecny et al, 1995).…”

Section: Biological Consequences Which Could Be Associated With the Pmentioning

confidence: 99%

A code in the protein coding genes

Arquès

Michel

1997

Biosystems

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A statistical analysis with 12 288 autocorrelation functions applied in protein (coding) genes of prokaryotes and eukaryotes identifies three subsets of trinucleotides in their three frames: T 0 = X 0 @ {AAA, TTT} with X 0 = {AAC, AAT, ACC, ATC, ATT, CAG, CTC, CTG, GAA, GAC, GAG, GAT, GCC, GGC, GGT, GTA, GTC, GTT, TAC, TTC} in frame 0 (the reading frame established by the ATG start trinucleotide), T 1 = X 1 @ {CCC} in frame 1 and T 2 = X 2 @{GGG} in frame 2 (the frames 1 and 2 being the frame 0 shifted by one and two nucleotides, respectively, to the right). These three subsets are identical in these two gene populations and have five important properties: (i) the property of maximal (20 trinucleotides) circular code for X 0 (resp. X 1 , X 2 ) allowing to retrieve automatically the frame 0 (resp. 1, 2) in any region of the gene without start codon; (ii) the DNA complementarity property C (e.g. C(AAC)= GTT): C(T 0 )=T 0 , C(T 1 )=T 2 and C(T 2 )=T 1 allowing the two paired reading frames of a DNA double helix simultaneously to code for amino acids; (iii) the circular permutation property P (e.g. P(AAC)= ACA): P(X 0 )=X 1 and P(X 1 )=X 2 implying that the two subsets X 1 and X 2 can be deduced from X 0 ; (iv) the rarity property with an occurrence probability of X 0 =6×10 − 8 ; and (v) the concatenation properties in favour of an evolutionary code: a high frequency (27.5%) of misplaced trinucleotides in the shifted frames, a maximum (13 nucleotides) length of the minimal window to retrieve automatically the frame and an occurrence of the four types of nucleotides in the three trinucleotide sites. In Discussion, a simulation based on an independent mixing of the trinucleotides of T 0 allows to retrieve the two subsets T 1 and T 2 . Then, the identified subsets T 0 , T 1 and T 2 replaced in the 2-letter genetic alphabet {R, Y} (R =purine= A or G, Y=pyrimidine= C or T) allow to retrieve the RNY model (N=R or Y) and to explain previous works in the alphabet {R, Y}. Then, these three subsets are related to the genetic code. The trinucleotides of T 0 code for 13 amino acids: Ala, Asn, Asp, Gln, Glu, Gly, Ile, Leu, Lys, Phe, Thr, Tyr and Val. Finally, a strong correlation between the usage of the trinucleotides of T 0 in protein genes and the amino acid frequencies in proteins is observed as six among seven amino acids not coded by T 0 , have as expected the lowest frequencies in proteins of both prokaryotes and eukaryotes.

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“…Recently, Yomo and Urabe (1994) have generalized these arguments, taking into account the observation that the frequencies of individual codons in sense strands are often similar to their frequencies in the antisense strands (when read in the same phase and with the correct polarity; Alff-Steinberger 1984, 1987Yomo and Ohno 1989). Others have suggested that the genetic code may initially have evolved to favor the simultaneous emergence of sense and antisense peptides (AlffSteinberger 1984;Zull and Smith 1990;Konecny et al 1993),…”

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confidence: 99%

Sense in antisense?

Forsdyke

1995

J Mol Evol

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A correspondence between open reading frames in sense and antisense strands is expected from the hypothesis that the prototypic triplet code was of general form RNY, where R is a purine base, N is any base, and Y is a pyrimidine. A deficit of stop codons in the antisense strand (and thus long open reading frames) is predicted for organisms with high G + C percentages; however, two bacteria (Azotobacter vinelandii, Rhodobacter capsulatum) have larger average antisense strand open reading frames than predicted from (G + C)%. The similar codon frequencies found in sense and antisense strands can be attributed to the wide distribution of inverted repeats (stem-loop potential) in natural DNA sequences.

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Neutral adaptation of the genetic code to double-strand coding

Cited by 24 publications

References 46 publications

On Primordial Sense–Antisense Coding

On Primordial Sense–Antisense Coding

A code in the protein coding genes

Sense in antisense?

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