A genetic code Boolean structure. I. The meaning of Boolean deductions

This paper proposes a genetic code Boolean structure derived from hydrogen bond numbers and chemical types of bases, purines and pyrimidines. It shows that in such Boolean structure, deductions comprise physico-chemical meaning. In particular, codons with adenine as a second base coding to hydrophilic amino acids are not deductible from codons with uracil in the same position, which code to hydrophobic amino acids. Boolean deductions could help us describe the gene evolution process. For instance, most of the reported mutations that confer drug resistance to the HIV protease gene correspond to deductions. What is more, in the human beta-globin gene a similar situation appears where most of the single codon mutations correspond to Boolean deductions from the respective wild-type codon.     

The evolution of proteins from random amino acid sequences. I. Evidence from the lengthwise distribution of amino acids in modern protein sequences

Summary We examine in this paper one of the expected consequences of the hypothesis that modern proteins evolved from random heteropeptide sequences. Specifically, we investigate the lengthwise distributions of amino acids in a set of 1,789 protein sequences with little sequence identity using the run test statistic (r _o) of Mood (1940,Ann. Math. Stat. 11, 367–392). The probability density ofr _o for a collection of random sequences has mean=0 and variance=1 [the N(0,1) distribution] and can be used to measure the tendency of amino acids of a given type to cluster together in a sequence relative to that of a random sequence. We implement the run test using binary representations of protein sequences in which the amino acids of interest are assigned a value of 1 and all others a value of 0. We consider individual amino acids and sets of various combinations of them based upon hydrophobicity (4 sets), charge (3 sets), volume (4 sets), and secondary structure propensity (3 sets). We find that any sequence chosen randomly has a 90% or greater chance of having a lengthwise distribution of amino acids that is indistinguishable from the random expectation regardless of amino acid type. We regard this as strong support for the random-origin hypothesis. However, we do observe significant deviations from the random expectation as might be expected after billions years of evolution. Two important global trends are found: (1) Amino acids with a strong α-helix propensity show a strong tendency to cluster whereas those with β-sheet or reverse-turn propensity do not. (2) Clustered rather than evenly distributed patterns tend to be preferred by the individual amino acids and this is particularly so for methionine. Finally, we consider the problem of reconciling the random nature of protein sequences with structurally meaningful periodic “patterns” that can be detected by sliding-window, autocorrelation, and Fourier analyses. Two examples, rhodopsin and bacteriorhodopsin, show that such patterns are a natural feature of random sequences.     

Role of mutational bias and natural selection on genome-wide nucleotide bias in prokaryotic organisms

Correlations between genomic GC contents and amino acid frequencies were studied in the homologous sequences of 12 eubacterial genomes. Results show that amino acids encoded by GC-rich codons increases significantly with genomic GC contents, whereas opposite trend was observed in case of amino acids encoded by GC-poor codons. Further studies show all the amino acids do not change in the predicted direction according to their genomic GC pressure, suggesting that protein evolution is not entirely dictated by their nucleotide frequencies. Amino acid substitution matrix calculated among hydrophobic, amphipathic and hydrophilic amino acid groups' shows that amphipathic and hydrophilic amino acids are more frequently substituted by hydrophobic amino acids than from hydrophobic to hydrophilic or amphipathic amino acids. This indicates that nucleotide bias induces a directional changes in proteome composition in such a way that underwent strong changes in hydropathy values. In fact, significant increases in hydrophobicity values have also been observed with the increase of genomic GC contents. Correlations between GC contents and amino acid compositions in three different predicted protein secondary structures show that hydropathy values increases significantly with GC contents in aperiodic and helix structures whereas strand structure remains insensitive with the genomic GC levels. The relative importance of mutation and selection on the evolution of proteins have been discussed on the basis of these results.     

A quantitative measure of error minimization in the genetic code

Summary We have calculated the average effect of changing a codon by a single base for all possible single-base changes in the genetic code and for changes in the first, second, and third codon positions separately. Such values were calculated for an amino acid's polar requirement, hydropathy, molecular volume, and isoelectric point. For each attribute the average effect of single-base changes was also calculated for a large number of randomly generated codes that retained the same level of redundancy as the natural code. Amino acids whose codons differed by a single base in the first and third codon positions were very similar with respect to polar requirement and hydropathy. The major differences between amino acids were specified by the second codon position. Codons with U in the second position are hydrophobic, whereas most codons with A in the second position are hydrophilic. This accounts for the observation of complementary hydropathy. Single-base changes in the natural code had a smaller average effect on polar requirement than all but 0.02% of random codes. This result is most easily explained by selection to minimize deleterious effects of translation errors during the early evolution of the code.     

Simulation of protein evolution by random fixation of allowed codons

Summary Computer simulation of protein evolution is based on a simple model consisting of random fixation of allowed codons (RFAC). Random replacement of single nucleotides occurs in a DNA sequence. If this results in any of the synonomous codons for allowed amino acids the mutation is fixed, if not, there is no change in the DNA and the cycle is repeated. Multiple fixations at the same nucleotide site, back mutations, degenerate fixations and coincidental identity of amino acids all occur. RFAC simulation begins with a single DNA sequence and follows a phylogeny based on the fossil record. The rate of fixation at the level of DNA is constant. The model upon which RFAC simulation is based is the same as the neutral theory of molecular evolution. The simulation is therefore a test of this theory. The results of simulated and real evolution are compared for fibrinopeptides A in mammals and cytochromes C and hemoglobin and chains in vertebrates. In each case the allowed variation at each site has been set equal to that observed, twice that observed and all protein amino acids. Rates of fixation vary from 2.4 × 10^–10 to 10^–5 accepted nucleotide fixations per codon per year. There is some, although never excellent, agreement between real and simulated evolution, the better fits are obtained in the cases of fibrinopeptides A and cytochromes C. The major source of discrepancy between real evolution and simulation is irregularities in the rates of real evolution. RFAC simulation is compared with the random evolutionary hit (REH) model, augmented maximum parsimony and the accepted point mutations (PAM) approach.     

Phenylalanine-Binding RNAs and Genetic Code Evolution

We isolated RNAs by selection–amplification, selecting for affinity to Phe–Sepharose and elution with free l-phenylalanine. Constant sequences did not contain Phe condons or anticodons, to avoid any possible confounding influence on initially randomized sequences. We examined the eight most frequent Phe-binding RNAs for inclusion of coding triplets. Binding sites were defined by nucleotide conservation, protection, and interference data. Together these RNAs comprise 70% of the 105 sequenced RNAs. The K _D for the strongest sites is ≈50 μM free amino acid, with strong stereoselectivity. One site strongly distinguishes free Phe from Trp and Tyr, a specificity not observed previously. In these eight Phe-binding RNAs, Phe codons are not significantly associated with Phe binding sites. However, among 21 characterized RNAs binding Phe, Tyr, Arg, and Ile, containing 1342 total nucleotides, codons are 2.7-fold more frequent within binding sites than in surrounding sequences in the same molecules. If triplets were not specifically related to binding sites, the probability of this distribution would be 4.8 × 10⁻¹¹. Therefore, triplet concentration within amino acid binding sites taken together is highly likely. In binding sites for Arg, Tyr, and Ile cognate codons are overrepresented. Thus Arg, Tyr, and Ile may be amino acids whose codons were assigned during an era of direct RNA–amino acid affinity. In contrast, Phe codons arguably were assigned by another criterion, perhaps during later code evolution.     

A New Approach to the Synthesis of Trinucleotide Phosphoramidites - Synthons for the Generation of Oligonucleotide/Peptide Libraries

Abstract

Trinucleotide phosphoramidites that correspond to the codons of all 20 amino acids were synthesized in high yield in 5g scale. Precursors of those amidites - trinucleotide phosphotriesters - have been prepared using the phosphotriester approach without protection of the 3′-hydroxyl function. More than 10 oligonucleotides up to 90 bases long have been synthesized by a phosphite-triester approach using new synthons. The 67-mer (12 random codons) has been used to generate a display library of 2 × 10⁸ complexity.     

Genetic evolution and codon usage analysis of NKX-2.5 gene governing heart development in some mammals

NKX-2.5 gene is responsible for cardiac development and its targeted disruption apprehends cardiac development at the linear heart tube stage. Bioinformatic analysis was employed to investigate the codon usage pattern and dN/dS of mammalian NKX-2.5 gene. The relative synonymous codon usage analysis revealed variation in codon usage and two synonymous codons namely ATA (Ile) and GTA (Val) were absent in NKX-2.5 gene across selected mammalian species suggesting that these two codons were possibly selected against during evolution. Parity rule 2 analysis of two and four fold amino acids showed CT bias whereas six-fold amino acids revealed GA bias. Neutrality analysis suggests that selection played a prominent role while mutation had a minor role. The dN/dS analysis suggests synonymous substitution played a significant role and it negatively correlated with p-distance of the gene. Purifying natural selection played a dominant role in the genetic evolution of NKX-2.5 gene in mammals.     

缺氮和复氮对菘蓝幼苗生长及氮代谢的影响

对基质育苗后水培的菘蓝进行缺氮与复氮处理,分析其生长情况及氮代谢产物含量的变化,探讨缺氮和复氮对菘蓝幼苗生长及氮代谢的影响,以提高菘蓝产量和品质以及栽培过程中的氮素利用效率。结果显示:(1)正常供氮条件下,菘蓝幼苗的叶绿素含量、谷氨酰胺合成酶(GS)活性、硝态氮含量、靛玉红含量为最高,而其株高、主根直径、根的鲜重与干重、叶的鲜重与干重、根系活力均最小。(2)缺氮处理增加了菘蓝幼苗的主根直径和根干重,提高其根系活力和硝酸还原酶(NR)活性,促进游离氨基酸在叶中的积累;但降低了GS的活性,也降低了叶中硝态氮、可溶性蛋白、靛玉红及根中游离氨基酸的含量;缺氮对叶中靛蓝的含量无明显影响。(3)复氮处理增加了菘蓝幼苗的株高、主根长、根鲜重、叶鲜重、叶干重,提高了其根系活力,降低了NR和GS的活性;与对照相比,复氮降低了叶中硝态氮含量,提高了叶中可溶性蛋白、靛蓝及根中游离氨基酸的含量,但对叶中游离氨基酸和靛玉红含量影响较小。研究表明,缺氮后再复氮有利于菘蓝幼苗叶的生长,同时有利于增加其叶内靛蓝含量,从而提高其产量和品质。     

Evolution of the mitochondrial genetic code I. Origin of AGR serine and stop codons in metazoan mitochondria

Summary AGA and AGG (AGR) are arginine codons in the universal genetic code. These codons are read as serine or are used as stop codons in metazoan mitochondria. The arginine residues coded by AGR in yeast orTrypanosoma are coded by arginine CGN throughout metazoan mitochondria. AGR serine sites in metazoan mitochondria are occupied mainly in corresponding sites in yeast orTrypanosoma mitochondria by UCN serine, AGY serine, or codons for amino acids other than serine or arginine. Based on these observations, we propose the following evolutionary events. AGR codons became unassigned because of deletion of tRNA Arg (UCU) and elimination of AGR codons by conversion to CGN arginine codons. Upon acquisition by serine tRNA of pairing ability with AGR codons, some codons for amino acids other than arginine mutated to AGR, and were caputed by anticodon GCU in serine tRNA. During vertebrate mitochondrial evolution, AGR stop codons presumably were created from UAG stop by deletion of the first nucleotide U and by use of R as the third nucleotide that had existed next to the ancestral UAG stop.     

Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape

Background  

The standard genetic code table has a distinctly non-random structure, with similar amino acids often encoded by codons series that differ by a single nucleotide substitution, typically, in the third or the first position of the codon. It has been repeatedly argued that this structure of the code results from selective optimization for robustness to translation errors such that translational misreading has the minimal adverse effect. Indeed, it has been shown in several studies that the standard code is more robust than a substantial majority of random codes. However, it remains unclear how much evolution the standard code underwent, what is the level of optimization, and what is the likely starting point.     

METHYLATED AMINO ACID RESIDUES OF PROTEINS OF BRAIN AND OTHER ORGANS

—Methods for the determination of methyl-lysine, methyllarginine and methylhistidine residues of tissue proteins are described. They consist of preliminary purification of basic amino acids, enzymic removal of lysine, arginine and histidine followed by amino acid analysis. Recovery rates and specificities of the method were satisfactory. The contents of methylamino acids in proteins of mammalian organs were determined. The distribution of proteins containing the methylamino acids in human brain showed that the concentrations of methyl-lysine and N^G,N′^G-dimethylarginine were highest in the gray matter of the cerebellar cortex and relatively high in regions rich in gray matter, while those of N^G-mono- and N^G,N′^G-dimethylarginine were highest in the white matter. The following findings suggest that most of the N^G-mono- and N^G,N′^G-dimethylarginine was associated with the myelin basic protein. The distribution of the methylarginine residues of acid-soluble proteins in bovine brains coincided with the cerebroside pattern. The concentrations of the amino acids in acid-soluble proteins of rat brain increased concomitantly with the increase of cerebroside. The methylamino acid content in proteins increased during the purification of the myelin basic protein from the white matter of human and bovine brains. Proteins containing N^G,N^G-dimethyiarginine and di- and trimethyl-lysine are concentrated in cell nuclei. The first amino acid was found mainly in nucleoplasmic proteins and the other two were found in histones. The concentration of 3-methylhistidine residue, highest in muscular proteins, is low in cerebral proteins and is probably derived from proteins of walls of blood vessels in the brain.     

Is the fixation of observable mutations distributed randomly among the three nucleotide positions of the codon?

Summary The distribution among the three nucleotide positions of the codons of 642 mutations fixed during the descent of 49 sequences of cytochromec was examined. This was compared to the distribution expected if the number of ways of getting a selectively acceptable amino acid alternative from a single nucleotide replacement at each coding position were random,i.e. proportional to the total number of ways of changing the encoded amino acid by a single nucleotide replacement at each coding position. It was found that the observed distribution was significantly different from random, there being 40% more mutations in the first coding position than in the second whereas one would have expected 10% more in the second than in the first. The probability of the result occurring by chance is < 10^–6.The same test was made on the distribution of 347 mutations fixed in the descent of 19 sequences of alpha hemoglobin and 286 mutations fixed in the descent of 16 beta and 4 delta hemoglobins. The result for the alpha hemoglobins was a similar non-randomness but the probability of its occurring by chance rose to 0.005. The result for the beta-delta hemoglobins was in the same direction but was not significant (p = 0.3). The degree of non-randomness among the three genes in the distribution of fixations over the three nucleotide positions of their codons appears to be correlated (negatively) with their rates of evolution, the plasticity required of the molecule to adapt to new environments, and the recency of exploitation of opportunities for change in functional specificity provided by such processes as gene duplication.     

Seasonal Changes of Nitrogen Storage Compounds in a Rhizomatous Grass Calamagrostis epigeios

The seasonal dynamics in content and distribution of N-rich compounds between overwintering organs of Calamagrostis epigeios were examined. Samples were taken both from plants grown in natural conditions and in containers with controlled nutrient supply. There were significant changes in content of nitrate, free amino acids and soluble protein in all investigated plant parts during the course of a year. Amino acids showed both the highest maximum and seasonal fluctuation among the all N compounds observed and, therefore, appear to have a central role in N storage. Their content rises in the autumn, remains stable during winter and declines quickly at the beginning of spring. The most abundant amino acids in the end of winter storage period - asparagine, arginine and glutamine - constituted about 90 % of N in fraction of free amino acids. The portion of N stored in soluble proteins, however, was considerably smaller compare to both amino acids and nitrate. The amount of N stored in rhizomes of C. epigeios was smaller than in roots and stubble base before the onset of spring re-growth. This indicates that roots and stubble base are particularly important for winter N storage in this species.     

Nitrogen remobilization in shoots of Paris polyphylla is altered by gibberellic acid application during senescence

Nitrogen remobilization during senescence has been studied in perennial herb Paris polyphylla. We analyzed changes in N content, amino acids, N-remobilization enzymes and effects of gibberellic acid (GA) during natural senescence. There was a gradual decrease in the contents of N, chlorophyll and soluble proteins and activities of glutamine synthetase (GS; EC 6.3.1.2) and glutamate dehydrogenase (GLDH; EC 1.4.1.2). Activity staining and Western blots showed that GS2 activity decreased, whereas GS1 activity was relatively stable over time. In contrast, the C/N ratio and total amino acid content increased. Among individual amino acids, the proportions of glutamine (Gln) and asparagine (Asn) increased, and proportions of arginine, aspartate and glycine decreased. Treatment with GA slowed the senescence and retarded decreases in the activities of GS and GLDH and the contents of N, chlorophyll and soluble proteins. Conversely, this treatment slowed increases in the C/N ratio, total free amino acid content, and proportions of Gln and Asn. We conclude that low N resorption efficiency during senescence of P. polyphylla results from a sharp decrease in N remobilization enzyme activity.     

Selection on Codon Usage for Error Minimization at the Protein Level

Given the structure of the genetic code, synonymous codons differ in their capacity to minimize the effects of errors due to mutation or mistranslation. I suggest that this may lead, in protein-coding genes, to a preference for codons that minimize the impact of errors at the protein level. I develop a theoretical measure of error minimization for each codon, based on amino acid similarity. This measure is used to calculate the degree of error minimization for 82 genes of Drosophila melanogaster and 432 rodent genes and to study its relationship with CG content, the degree of codon usage bias, and the rate of nucleotide substitution. I show that (i) Drosophila and rodent genes tend to prefer codons that minimize errors; (ii) this cannot be merely the effect of mutation bias; (iii) the degree of error minimization is correlated with the degree of codon usage bias; (iv) the amino acids that contribute more to codon usage bias are the ones for which synonymous codons differ more in the capacity to minimize errors; and (v) the degree of error minimization is correlated with the rate of nonsynonymous substitution. These results suggest that natural selection for error minimization at the protein level plays a role in the evolution of coding sequences in Drosophila and rodents.Reviewing Editor: Dr. Massimo Di Giulio     

The Evolution of Codon Preferences in Drosophila: A Maximum-Likelihood Approach to Parameter Estimation and Hypothesis Testing

Synonymous codon usage in related species may differ as a result of variation in mutation biases, differences in the overall strength and efficiency of selection, and shifts in codon preference—the selective hierarchy of codons within and between amino acids. We have developed a maximum-likelihood method to employ explicit population genetic models to analyze the evolution of parameters determining codon usage. The method is applied to twofold degenerate amino acids in 50 orthologous genes from D. melanogaster and D. virilis. We find that D. virilis has significantly reduced selection on codon usage for all amino acids, but the data are incompatible with a simple model in which there is a single difference in the long-term N _e, or overall strength of selection, between the two species, indicating shifts in codon preference. The strength of selection acting on codon usage in D. melanogaster is estimated to be |N _e s|≈ 0.4 for most CT-ending twofold degenerate amino acids, but 1.7 times greater for cysteine and 1.4 times greater for AG-ending codons. In D. virilis, the strength of selection acting on codon usage for most amino acids is only half that acting in D. melanogaster but is considerably greater than half for cysteine, perhaps indicating the dual selection pressures of translational efficiency and accuracy. Selection coefficients in orthologues are highly correlated (ρ= 0.46), but a number of genes deviate significantly from this relationship. Received: 20 December 1998 / Accepted: 17 February 1999     

Comparative study of translation termination sites and release factors (RF1 and RF2) in procaryotes

Translation termination is catalyzed by release factors that recognize stop codons. However, previous works have shown that in some bacteria, the termination process also involves bases around stop codons. Recently, Ito et al. analyzed release factors and identified the amino acids therein that recognize stop codons. However, the amino acids that recognize bases around stop codons remain unclear. To identify the candidate amino acids that recognize the bases around stop codons, we aligned the protein sequences of the release factors of various bacteria and searched for amino acids that were conserved specifically in the sequence of bacteria that seemed to regulate translation termination by bases around stop codons. As a result, species having several highly conserved residues in RF1 and RF2 showed positive correlations between their codon usage bias and conservation of the bases around the stop codons. In addition, some of the residues were located very close to the SPF motif, which deciphers stop codons. These results suggest that these conserved amino acids enable the release factors to recognize the bases around the stop codons. Present address (Y. Ozawa): Tokyo Research Laboratory, IBM Japan, Ltd., 1623-14 Shimotsuruma, Yamato-shi, Kanagawa 242-8502, Japan     

Identification of replication and stability functions in the complete nucleotide sequence of plasmid pUH24 from the cyanobacterium Synechococcus sp. PCC 7942

The complete nucleotide sequence is presented for pUH24, the small plasmid of Synechococcus sp. PCC 7942. pUH24 consists of 7835bp and has a G+C content of 59%. The distribution of translation start and stop codons in the sequence allows 36 open reading frames that potentially encode polypeptides of 50 or more amino acids. We postulate that eight of these open reading frames are actual coding sequences. A region has been identified, by experiment, that contains two functions, designated pmaA and pmaB, involved in the segregational stability of the plasmid. The minimal region of pUH24 fully capable of supporting autonomous replication consists of a 3.6kb DNA fragment, which is almost entirely occupied by two overlapping genes most likely coding for essential replication proteins (repA and repB).     

Improvement of a Chemically Defined Medium for the Sustained Growth of <Emphasis Type="Italic">Lactobacillus plantarum</Emphasis>: Nutritional Requirements

The aims of this work were to improve a basal synthetic medium (BM) for the growth of Lactobacillus plantarum strains and to establish their amino-acid requirements. Amino-acid use was analyzed in the most nutritionally demanding bacterium. First, the improved BM (L. plantarum synthetic medium [LPSM]) was created by increasing some vitamins in the BM, especially p-aminobenzoic acid, vitamin B₁₂, and biotin; 5-fold phenylalanine, histidine, isoleucine, leucine, lysine, methionine, proline, serine, threonine, and tryptophan; and 10-, 60-, and 75-fold valine, arginine, and tyrosine, respectively. With these additions, the N8 and N4 strains of L. plantarum grew rapidly to reach final cell densities similar to those obtained in Mann–Rogosa–Sharpe medium. When cysteine, leucine, valine, isoleucine, threonine, and glutamic acid were individually removed from this medium, bacterial growth significantly decreased or ceased, indicating that these amino acids are essential for growth. The N4 strain also required lysine and tryptophan in addition to the six amino acids necessary for growth. L. plantarum N4 mainly consumed essential amino acids, such as valine, lysine, cysteine, and threonine as well as the stimulatory amino acid, arginine. Thus, the BM was improved mainly on the basis of annulling limitations with respect to amino acids. With this, improved medium cell densities in the order of 10⁹ colony-forming units/mL have been achieved, indicating that LPSM medium could be used for conducting metabolic and genetic studies on L. plantarum. Their low levels in orange juice suggest that these amino acids may not satisfy the total nitrogen requirement for the development of L. plantarum in the natural environment.