Nucleotide-amino acid interactions and their relation to the genetic code

Summary The apparent dissociation constants of the complexes of AMP with the methyl esters of amino acids in aqueous solution exhibit good correlations with features of the genetic code and with the frequencies of occurrence of amino acid residues in proteins. Thus it is likely that chemically selective nucleotide-amino acid interactions were involved in the processes of chemical evolution that have led to the emergence of the genetic code. Based on these correlations a storage device for the information regarding nucleotide-amino acid interactions is proposed. It involves processes of simultaneous polymerization to polynucleotides and polypeptides.     

The arbitrariness of the genetic code

The genetic code has been regarded as arbitrary in the sense that the codon-amino acid assignments could be different than they actually are. This general idea has been spelled out differently by previous, often rather implicit accounts of arbitrariness. They have drawn on the frozen accident theory, on evolutionary contingency, on alternative causal pathways, and on the absence of direct stereochemical interactions between codons and amino acids. It has also been suggested that the arbitrariness of the genetic code justifies attributing semantic information to macromolecules, notably to DNA. I argue that these accounts of arbitrariness are unsatisfactory. I propose that the code is arbitrary in the sense of Jacques Monod's concept of chemical arbitrariness: the genetic code is arbitrary in that any codon requires certain chemical and structural properties to specify a particular amino acid, but these properties are not required in virtue of a principle of chemistry. This notion of arbitrariness is compatible with several recent hypotheses about code evolution. I maintain that the code's chemical arbitrariness is neither sufficient nor necessary for attributing semantic information to nucleic acids.     

The analysis of hidden electrophoretic variation: Interspecific electrophoretic differentiation and amino acid divergence

Summary In a study of 25 human variants and 23 evolutionary alleles of hemoglobin we show that intraspecific and interspecific patterns of electrophoretic variability are not comparable. Significant deviation from the predicted electrophoretic differentiation between evolutionary alleles is normally found only when amino acid sequence divergence exceeds 10%. When two sequences had diverged at less than 30 out of 287 amino acid residues sites, only 7% of comparisons showed significant deviations from the expected difference of electrophoretic mobility, while significant deviation was shown by 57% of comparisons involving 30–40 residue differences, by 79% in the case of 51–60 differences and by all of the comparisons involving more than 60 differences. In contrast, human variants, which differ by only one or two amino acid residues (less than 1% difference), had significant deviations in 58% of comparisons. Those mutations that appear as fixed differences in the evolutionary material probably represent only a subset of the mutations which can appear within the species. The results suggest that statistical comparisons such as genetic distance may not measure the same process within a species as between species. This is due not to inherent problems with the statistic, but rather to inherent differences in the nature of molecular changes that are detectable by electrophoresis at different stages of population divergence.     

Examples of the effect of genetic variation on competing species

An ordinary differential equation model for two competing populations with genetic variation in one population is presented. The degree of frequency dependence needed to produce various configurations of stable equilibria is discussed. For example, if the fitnesses are frequency independent then there may exist stable polymorphism although the genetically varying population becomes extinct in each fixation plane. Stable polymorphism where the genetically invariant population becomes extinct in each fixation plane requires frequency dependence in the fitness of the genetically invariant population.     

A computer-assisted examination of the storage protein genetic variation in 841 accessions of Triticum dicoccoides

Summary Triticum turgidum L. var. dicoccoides (wild emmer) is an important genetic resource for increasing the protein content of common wheat (Triticum aestivum L.). Many studies have shown that the presence or absence of bands in sodium dodecyl sulfate polyacrylamide (SDS-PAGE) electrophoregrams of wheat storage proteins to be of a purely genetic character. A total protein extraction and SDS-PAGE technique was used to estimate the storage protein genetic variability among 841 accessions of wild emmer collected from various ecological regions in the Middle East. In addition, a computer data bank was developed, recording the onedimension electrophoregram bands for each accession by molecular weight (MW) and relative Coomassie Blue staining intensity as determined from densitometer scans. Analyses of this information are being used to identify specific accessions for further study by two dimension electrofocusing-electrophoresis and breeding and genetic analyses. The computer-assisted analyses indicated that the greatest genetic variability occurs for proteins in the high MW region (above 70,000 MW) followed by those in the medium range (70,000 to 33,300 MW). Comparatively little variability was revealed for protein subunits of below 33,300 MW.Scientific Paper No. 6591. College of Agriculture Research Center, Washington State University, Pullman, Project No. 1568. This work was supported in part by the U.S.-Israel Binational Agricultural Research and Development Fund (BARD)     

The regularities of the changes of amino acid physico-chemical properties within the genetic code

Summary All the codons of the genetic code can be arranged into the closed one-step mutation ring, containing three periods of the same sequence of mutations (2,3,3,3,1,3,3,3,1,3,3,3,1,3,3,3,2,3,3,3). The codons of Gly play a role of the connecting element between the end of the third, and the beginning of the first period of the genetic code. The reactivity of amino acids, expressed by the reaction rates of aminolysis reaction of N-hydroxysuccinimide esters of protected amino acids with p-anisidine, changes periodically with the respect to the mutation periods of the genetic code. Chou-Fasman P as well as P conformational parameters of amino acids, and also the compositional frequencies of amino acids in proteins, demonstrate the pseudosymmetry pattern with respect to the center of one-step mutation ring, which is situated between Thr ACY and ACR codons.     

Specificity in the genetic code. The role of nucleotide base-amino acid interaction

The mechanism of the unique and specific association of a given amino acid to its t-RNA is investigated by theoretical methods. Several possible schemes are proposed to explain specificity. The physical forces which act within these mechanisms are illustrated by the computer simulation of probable interactions between glycine and nucleotide bases and base pairs. It is demonstrated that glycine has direct and selective affinities for the nucleotide bases and that these interactions are principally determined by the polar groups. Energies have been calculated for the interaction of glycine with several base pairs. From these, the possibility that specificity arises through direct complexing of an amino acid with its anticodon is evaluated.     

Decreased genetic variation in metabolic variables of Litopenaeus vannamei shrimp after exposure to acute hypoxia

Concentration of proteins, carbohydrates, lactate, total lipids, acylglycerides, and carotenoids in shrimp were evaluated for their changes under acute hypoxia, and for their genetic variation under normoxic and hypoxic conditions. Proteins and lactate concentrations in muscle and hepatopancreas were significantly higher and carbohydrates in hepatopancreas were decreased in the hypoxic group. Family variances were significantly different only for proteins and carbohydrates in hepatopancreas in the normoxic group, indicating the existence of genetic variation for these traits. When family variances for each biochemical component were compared between normoxic and hypoxic groups, it was seen that most decreased. However, total variance was not significantly changed in response to hypoxia except for lactate (increased) and carotenoids (decreased) in hepatopancreas. The decrease in genetic variance without an increase in phenotypic variances in an acute response to hypoxia might be related to the known suppression of metabolic pathways that either use or produce ATP, which could result in a decreased expression of additive genes.     

Polymorphism in beta-cyclodextrin-benzoic acid inclusion complex: a kinetically controlled crystal growth according to the Ostwald's rule

Crystal form II of the beta-cyclodextrin-benzoic acid (beta-CD-BA) inclusion complex was obtained from the 1.5-year stored aqueous EtOH solution of beta-CD and BA as 2beta-CD.1.5BA.0.7EtOH.21H(2)O in the monoclinic space group C2 with unit cell constants: a=19.413(3), b=24.306(4), c=32.975(1)A, beta=104.41(1) degrees . By contrast, the desired crystal form I in the triclinic space group P1 that ever grew up from the fresh solution as 2beta-CD.2BA.0.7EtOH.20.65H(2)O was not reproducible any more [Aree, T.; Chaichit, N. Carbohydr. Res.2003, 338, 439-446]. In the two crystal forms, beta-CDs are isostructural with a 'round' conformation stabilized by intramolecular O-3(n)cdots, three dots, centeredO-2(n+1) hydrogen bonds. The BA inclusion geometries are similar with a preferred orientation, that is, BAs are situated above the O-4 plane, point their COOH groups to the beta-CD O-6 side, incline 52 degrees with respect to the O-4 plane and are mainly maintained in positions by hydrogen bonding with the surrounding water molecules. beta-CDs form dimers as structural motif of different packing modes: the screw-channel type in form II and the average of intermediate and tetrad types in form I. Polymorphism in the beta-CD-BA inclusion complex is a kinetically controlled crystal growth following the Ostwald's rule: the less stable crystal form I grew up first within one week from the fresh solution, whereas the more stable crystal form II appeared after 1.5-year storage.     

The contribution of additive genetic variation to personality variation: heritability of personality

Individual animals frequently exhibit repeatable differences from other members of their population, differences now commonly referred to as ‘animal personality’. Personality differences can arise, for example, from differences in permanent environmental effects―including parental and epigenetic contributors―and the effect of additive genetic variation. Although several studies have evaluated the heritability of behaviour, less is known about general patterns of heritability and additive genetic variation in animal personality. As overall variation in behaviour includes both the among-individual differences that reflect different personalities and temporary environmental effects, it is possible for personality to be largely genetically influenced even when heritability of behaviour per se is quite low. The relative contribution of additive genetic variation to personality variation can be estimated whenever both repeatability and heritability are estimated for the same data. Using published estimates to address this issue, we found that approximately 52% of animal personality variation was attributable to additive genetic variation. Thus, while the heritability of behaviour is often moderate or low, the heritability of personality is much higher. Our results therefore (i) demonstrate that genetic differences are likely to be a major contributor to variation in animal personality and (ii) support the phenotypic gambit: that evolutionary inferences drawn from repeatability estimates may often be justified.     

The fourfold way of the genetic code

We describe a compact representation of the genetic code that factorizes the table in quartets. It represents a “least grammar” for the genetic language. It is justified by the Klein-4 group structure of RNA bases and codon doublets. The matrix of the outer product between the column-vector of bases and the corresponding row-vector V^T = (C G U A), considered as signal vectors, has a block structure consisting of the four cosets of the K × K group of base transformations acting on doublet AA. This matrix, translated into weak/strong (W/S) and purine/pyrimidine (R/Y) nucleotide classes, leads to a code table with mixed and unmixed families in separate regions. A basic difference between them is the non-commuting (R/Y) doublets: AC/CA, GU/UG. We describe the degeneracy in the canonical code and the systematic changes in deviant codes in terms of the divisors of 24, employing modulo multiplication groups. We illustrate binary sub-codes characterizing mutations in the quartets. We introduce a decision-tree to predict the mode of tRNA recognition corresponding to each codon, and compare our result with related findings by Jestin and Soulé [Jestin, J.-L., Soulé, C., 2007. Symmetries by base substitutions in the genetic code predict 2′ or 3′ aminoacylation of tRNAs. J. Theor. Biol. 247, 391–394], and the rearrangements of the table by Delarue [Delarue, M., 2007. An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices. RNA 13, 161–169] and Rodin and Rodin [Rodin, S.N., Rodin, A.S., 2008. On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases. Heredity 100, 341–355], respectively.     

A concept of amino acid archaeorelation: Origin of life and the genetic code

Using certain assumptions, an attempt has been made to obtain a quantitative evaluation of the similarity of the bulk amino acid compositions of various organisms and of the quantitative ratios of amino acids in the products of the presumable prebiological ructions and in the natural proteins. The results of comparison between the molar ratios of amino acids in synthesized products and in natural proteins and the quantitative distribution of triplets among amino acids in the existing genetic code are given. Proceeding from the correlations found and the data reported in literature, a concept has been suggested amounting, in essence, to the assertion that the structure of the genetic code (the quantitative distribution of the triplets) is in a certain way determined by the pre-existing, primary ratio (archaeorelation) of amino acids.     

Contributions of tryptophan side chains to the far-ultraviolet circular dichroism of proteins

It has often been assumed that the role of aromatic side chains in the far-ultraviolet region of protein circular dichroism (CD) is negligible. However, some proteins have positive CD bands in the 220–230 nm region which are almost certainly due to aromatic side chains. The contributions to the CD of interactions between tryptophan side chains and the nearest neighbor peptide groups have been studied, focusing on the indole B_b transition which occurs near 220 nm. Calculations on idealized peptide conformations show that the CD depends strongly on both backbone and side-chain conformation. Because of the low symmetry of indole, rotation about the CC bond (dihedral angle ₂) by 180° generally leads to large changes in the CD, often causing the B_b band to reverse sign. When side-chain conformational preferences are taken into account, there is no strong bias for either positive or negative B_b rotational strengths. The observation that simple tryptophan derivatives such as N-acetyl-L-tryptophan methylamide have positive CD near 220 nm implies either that these derivatives prefer the _R region over the region, or that there is little preference for ₂ < 180° over ₂ > 180°. Nearest-neighbor-only calculations on individual tryptophans in 15 globular proteins also reveal a small bias toward positive B_b bands. Rotational strengths of the B_b transition for some conformations can be as large as 1.0 Debye-Bohr magnetons in magnitude, corresponding to maximum molar ellipticities greater than 10⁵ degcm²/dmol. Although a substantial amount of cancellation occurs in most of the examples considered here, such CD contributions could be significant, especially in proteins of low helix content.     

Neutral adaptation of the genetic code to double-strand coding

Summary We lay new foundations to the hypothesis that the genetic code is adapted to evolutionary retention of information in the antisense strands of natural DNA/RNA sequences. In particular, we show that the genetic code exhibits, beyond the neutral replacement patterns of amino acid substitutions, optimal properties by favoring simultaneous evolution of proteins encoded in DNA/RNA sense-antisense strands. This is borne out in the sense-antisense transformations of the codons of every amino acid which target amino acids physicochemically similar to each other. Moreover, silent mutations in the sense strand generate conservative ones in its antisense counterpart and vice versa. Coevolution of proteins coded by complementary strands is shown to be a definite possibility, a result which does not depend on any physical interaction between the coevolving proteins. Likewise, the degree to which the present genetic code is dedicated to evolutionary sense-antisense tolerance is demonstrated by comparison with many randomized codes. Double-strand coding is quantified from an information-theoretical point of view.     

The quantitative genetics of the prevalence of infectious diseases: hidden genetic variation due to indirect genetic effects dominates heritable variation and response to selection

Infectious diseases have profound effects on life, both in nature and agriculture. However, a quantitative genetic theory of the host population for the endemic prevalence of infectious diseases is almost entirely lacking. While several studies have demonstrated the relevance of transmission of infections for heritable variation and response to selection, current quantitative genetics ignores transmission. Thus, we lack concepts of breeding value and heritable variation for endemic prevalence, and poorly understand response of endemic prevalence to selection. Here, we integrate quantitative genetics and epidemiology, and propose a quantitative genetic theory for the basic reproduction number R₀ and for the endemic prevalence of an infection. We first identify the genetic factors that determine the prevalence. Subsequently, we investigate the population-level consequences of individual genetic variation, for both R0 and the endemic prevalence. Next, we present expressions for the breeding value and heritable variation, for endemic prevalence and individual binary disease status, and show that these depend strongly on the prevalence. Results show that heritable variation for endemic prevalence is substantially greater than currently believed, and increases strongly when prevalence decreases, while heritability of disease status approaches zero. As a consequence, response of the endemic prevalence to selection for lower disease status accelerates considerably when prevalence decreases, in contrast to classical predictions. Finally, we show that most heritable variation for the endemic prevalence is hidden in indirect genetic effects, suggesting a key role for kin-group selection in the evolutionary history of current populations and for genetic improvement in animals and plants.     

The origin of the genetic code and protein synthesis

A model for a parallel evolution of the genetic code and protein synthesis is presented. The main tenet of this model is that the genetic code, that is, a correspondence between nucleotide and aminoacid coding units, originated from sequence-specific interaction between abiotically synthesized polynucleotides and polypeptides. A sequence-specific binding between oligonucleotides and oligopeptides is supported by experimental findings. Moreover, it is parsimonious enough to be consistent with the relatively simple chemistry of a primordial environment. Proximity between peptides and RNA increased the rate of formation of ester bonds between them. This lead to the accumulation of sequence-specific polypeptide-polynucleotide pairs, that is, of primordial-loaded tRNA. Condensation of short polypeptides into longer products could be catalyzed by a sequence-specific juxtaposition of loaded tRNA over complementary RNA, originating the core of protein synthesis. The accumulation of useful encoded products, for example, catalysts for tRNA loading (primordial aminoacyl-tRNA synthetases) or stabilizers of tRNA-mRNA interactions (primordial ribosomes), permitted the subsequent evolution of protein synthesis and of the genetic code to their mature form. This occurred via a parallel reduction in length of the interacting polynucleotides and polypeptides. Thus, it maintained the correct reading frame of mRNA from the preceding stages of evolution. Received: 27 September 1996 / Accepted: 17 May 1997