Comparative analysis of the base composition and codon usages in fourteen mycobacteriophage genomes

To study the possible codon usage and base composition variation in the bacteriophages, fourteen mycobacteriophages were used as a model system here and both the parameters in all these phages and their plating bacteria, M. smegmatis had been determined and compared. As all the organisms are GC-rich, the GC contents at third codon positions were found in fact higher than the second codon positions as well as the first + second codon positions in all the organisms indicating that directional mutational pressure is strongly operative at the synonymous third codon positions. Nc plot indicates that codon usage variation in all these organisms are governed by the forces other than compositional constraints. Correspondence analysis suggests that: (i) there are codon usage variation among the genes and genomes of the fourteen mycobacteriophages and M. smegmatis, i.e., codon usage patterns in the mycobacteriophages is phage-specific but not the M. smegmatis-specific; (ii) synonymous codon usage patterns of Barnyard, Che8, Che9d, and Omega are more similar than the rest mycobacteriophages and M. smegmatis; (iii) codon usage bias in the mycobacteriophages are mainly determined by mutational pressure; and (iv) the genes of comparatively GC rich genomes are more biased than the GC poor genomes. Translational selection in determining the codon usage variation in highly expressed genes can be invoked from the predominant occurrences of C ending codons in the highly expressed genes. Cluster analysis based on codon usage data also shows that there are two distinct branches for the fourteen mycobacteriophages and there is codon usage variation even among the phages of each branch.     

Compositional correlation studies among the three different codon positions in 12 bacterial genomes

Compositional distributions in the three codon positions of the coding sequences of 12 fully sequenced prokaryotic genomes, which are publicly available, were investigated. A universal compositional correlation was observed in most of the genomes under investigation irrespective of their overall genomic GC contents. In all the genomes, the GC contents at the first codon positions are always greater than the overall GC contents of the genomes whereas the reverse is true in the case of second codon positions. GC contents at the third codon positions are higher than the overall genomic GC contents in high GC containing genomes, and the opposite situation was found in case of low GC genomes except for Helicobacter pylori. In high-GC rich genomes, the GC contents at the first + second codon positions are less than the GC contents at the third codon positions, and they are low in low-GC genomes except for Helicobacter pylori. The distributions of four bases at the three different positions were also investigated for all 12 organisms. It was observed that in high-GC genomes G is the most dominant base and in low-GC genomes A is the most dominant base in the first codon positions. But purine bases, i.e., (A + G), predominantly occur in the first codon position. In the second codon position, A is the most dominant base in most of the organisms and G is the least dominant base in all the organisms. There is no unique regular pattern of individual bases at the third codon positions; however, there are significant differences in the occurrences of (G + C) contents in the third codon positions among the different organisms. Calculations of dinucleotide frequencies in 12 different organisms indicate that in GC-rich genomes GG, GC, CC, and CG dinucleotides are the most dominant whereas the reverse is true in case of low-GC genomes. Biological implications of these results are discussed in this paper.     

A universal compositional correlation among codon positions.

We have investigated the compositional distributions of third codon positions of genes from the 16 prokaryotes and seven eukaryotes for which the largest numbers of coding sequences are available in data banks. In prokaryotes, both narrow and broad distributions were found. In eukaryotes, distributions were very broad (except for Saccharomyces cerevisiae) and remarkably different for different genomes. In low-GC genomes, third codon positions were lower in GC than first + second codon positions and trailed towards high GC; the opposite situation was found for high-GC genomes. In all genomes, first codon positions were higher in GC than second codon positions. We then investigated the compositional correlations between third and first + second codon positions in prokaryotic genomes (the 16 mentioned above plus 87 additional ones) and in genome compartments of eukaryotes. A general, common relationship was found, which also holds within the same (heterogeneous) genomes. This universal correlation is due to the fact that the relative effects of compositional constraints on different codon positions are the same, on the average, whatever the genome under consideration.     

Organisms can essentially be classified according to two codon patterns

We recently classified 23 bacteria into two types based on their complete genomes; “S-type” as represented by Staphylococcus aureus and “E-type” as represented by Escherichia coli. Classification was characterized by concentrations of Arg, Ala or Lys in the amino acid composition calculated from the complete genome. Based on these previous classifications, not only prokaryotic but also eukaryotic genome structures were investigated by amino acid compositions and nucleotide contents. Organisms consisting of 112 bacteria, 15 archaea and 18 eukaryotes were classified into two major groups by cluster analysis using GC contents at the three codon positions calculated from complete genomes. The 145 organisms were classified into “AT-type” and “GC-type” represented by high A or T (low G or C) and high G or C (low A or T) contents, respectively, at every third codon position. Reciprocal changes between G or C and A or T contents at the third codon position occurred almost synchronously in every codon among the organisms. Correlations between amino acid concentrations (Ala, Ile and Lys) and the nucleotide contents at the codon position were obtained in both “AT-type” and “GC-type” organisms, but with different regression coefficients. In certain correlations of amino acid concentrations with GC contents, eukaryotes, archaea and bacteria showed different behaviors; thus these kingdoms evolved differently. All organisms are basically classifiable into two groups having characteristic codon patterns; organisms with low GC and high AT contents at the third codon position and their derivatives, and organisms with an inverse relationship.     

Mutational pressure in genomes of alphaherpesviruses infecting human

Genomes of the herpes simplex viruses are extremely enriched with GC. Elevated G+C level in genomes of the simplex viruses is a result of their long-term evolution under the influence of the mutational pressure. We counted the rates of nucleotide substitutions from gene coding major capsid protein (MCP) (G+C = 0.68, 3GC = 0.89) of human simplex virus 1 (HSV-1) to the MCP gene (G+C = 0.70, 3GC = 0.91) of HSV-2 (the first pair of genes) and from the same MCP gene of HSV-1 to the homologous gene (G+C = 0.73, 3GC = 0.99) from cercopithecine herpes virus 16 (the second pair of genes). The rates of transitions from A-T to G-C base pairs increases 2.17-, 3.09-, and 1.27-fold in the first, second, and third codon positions, respectively, if compared those rates between the second and first pair of genes (the growth of GC-richness is only 3%). This effect is due to an approximately 90% GC-richness of the third codon positions in all those genes. Transitions caused by the strong mutational pressure (from A-T to G-C base pairs) have a low probability to occur in the third positions, but high probability to occur in the first and second positions. For MCP gene of human herpes 3, the probability of the occurrence of transition caused by mutational pressure in the third codon position is 2.36 times higher than in MCP gene of HSV1, and 3 times higher than in MCP gene of HSV2. These data could provide an explanation of rarely occurring relapses of herpes Zoster infection and frequently occurring relapses of herpes simplex infection.     

The Evolutionary Divergence of psbA Gene in Synechococcus and Their Myoviruses in the East China Sea

Marine Synechococcus is a principal component of the picophytoplankton and makes an important contribution to primary productivity in the ocean. Synechophages, infecting Synechococcus, are believed to have significant influences on the distribution and abundance of their hosts. Extensive previous ecological studies on cyanobacteria and viruses have been carried out in the East China Sea (ECS). Here we investigate the diversity and divergence of Synechococcus and their myoviruses (Synechomyoviruses) based on their shared photosynthesis psbA gene. Synechococcus is dominated by subclades 5.1A I, 5.1A II and 5.1A IV in the ECS, and clades I and II are the dominant groups in the Synechomyoviruses. As two phylogenetically independent clades, there is much higher diversity of the Synechomyoviruses than Synechococcus. Obvious partitioning characteristics of GC and GC3 (the GC content at the third codon position) contents are obtained among different picophytoplankton populations and their phages. The GC3 content causes the psbA gene in Synechococcus to have a higher GC content, while the opposite is true in the Synechomyoviruses. Analyzing more than one-time difference of the codon usage frequency of psbA sequences, the third position nucleotides of preferred codons for Synechococcus are all G and C, while most Synechomyoviral sequences (72.7%) have A and T at the third position of their preferred codons. This work shed light on the ecology and evolution of phage-host interactions in the environment.     

Compositional properties of nuclear genes from cold-blooded vertebrates

Summary We have investigated the compositional properties of coding sequences from cold-blooded vertebrates and we have compared them with those from warm-blooded vertebrates. Moreover, we have studied the compositional correlations of coding sequences with the genomes in which they are contained, as well as the compositional correlations among the codon positions of the genes analyzed.The distribution of GC levels of the third codon positions of genes from cold-blooded vertebrates are distinctly different from those of warm-blooded vertebrates in that they do not reach the high values attained by the latter. Moreover, coding sequences from cold-blooded vertebrates are either equal, or, in most cases, lower in GC (not only in third, but also in first and second codon positions) than homologous coding sequences from warm-blooded vertebrates; higher values are exceptional. These results at the gene level are in agreement with the compositional differences between cold-blooded and warm-blooded vertebrates previously found at the whole genome (DNA) level (Bernardi and Bernardi 1990a,b).Two linear correlations were found: one between the GC levels of coding sequences (or of their third codon positions) and the GC levels of the genomes of cold-blooded vertebrates containing them; and another between the GC levels of third and first+ second codon positions of genes from cold-blooded vertebrates. The first correlation applies to the genomes (or genome compartments) of all vertebrates and the second to the genes of all living organisms. These correlations are tantamount to a genomic code.     

Study of Completed Archaeal Genomes and Proteomes： Hypothesis of Strong Mutational AT Pressure Existed in Their Common Predecessor

The number of completely sequenced archaeal genomes has been sufficient for a large-scale bioinformatic study.We have conducted analyses for each coding region from 36 archaeal genomes using the original CGS algorithm by calculating the total GC content(G+C),GC content in first,second and third codon positions as well as in fourfold and twofold degenerated sites from third codon positions,levels of arginine codon usage(Arg2:AGA/G;Arg4:CGX),levels of amino acid usage and the entropy of amino acid content distribution.In archaeal genomes with strong GC pressure,arginine is coded preferably by GC-rich Arg4 codons,whereas in most of archaeal genomes with G+C0.6,arginine is coded preferably by AT-rich Arg2 codons.In the genome of Haloquadratum walsbyi,which is closely related to GC-rich archaea,GC content has decreased mostly in third codon positions,while Arg4Arg2 bias still persists.Proteomes of archaeal species carry characteristic amino acid biases:levels of isoleucine and lysine are elevated,while levels of alanine,histidine,glutamine and cytosine are relatively decreased.Numerous genomic and proteomic biases observed can be explained by the hypothesis of previously existed strong mutational AT pressure in the common predecessor of all archaea.     

Correlations between the compositional properties of human genes,codon usage,and amino acid composition of proteins

Summary We have analyzed the correlation that exists between the GC levels of third and first or second codon position for about 1400 human coding sequences. The linear relationship that was found indicates that the large differences in GC level of third codon positions of human genes are paralleled by smaller differences in GC levels of first and second codon positions. Whereas third codon position differences correspond to very large differences in codon usage within the human genome, the first and second codon position differences correspond to smaller, yet very remarkable, differences in the amino acid composition of encoded proteins. Because GC levels of codon positions are linearly correlated with the GC levels of the isochores harboring the corresponding genes, both codon usage and amino acid composition are different for proteins encoded by genes located in isochores of different GC levels. Furthermore, we have also shown that a linear relationship with a unity slope and a correlation coefficient of 0.77 exists between GC levels of introns and exons from the 238 human genes currently available for this analysis. Introns are, however, about 5% lower in GC, on average, than exons from the same genes.     

Genomic Conflict Settled in Favour of the Species Rather Than the Gene at Extreme GC Percentage Values

Wada and colleagues have shown that, whether prokaryotic or eukaryotic, each gene has a "homostabilising propensity" to adopt a relatively uniform GC percentage (GC%). Accordingly, each gene can be viewed as a "microisochore" occupying a discrete GC% niche of relatively uniform base composition amongst its fellow genes. Although first, second and third codon positions usually differ in GC%, each position tends to maintain a uniform, gene-specific GC% value. Thus, within a genome, genic GC% values can cover a wide range. This is most evident at third codon positions, which are least constrained by amino acid encoding needs. In 1991, Wada and colleagues further noted that, within a phylogenetic group, genomic GC% values can also cover a wide range. This is again most evident at third codon positions. Thus, the dispersion of GC% values among genes within a genome matches the dispersion of GC% values among genomes within a phylogenetic group. Wada described the context-independence of plots of different codon position GC% values against total GC% as a "universal" characteristic. Several studies relate this to recombination. We have confirmed that third codon positions usually relate more to the genes that contain them than to the species. However, in genomes with extreme GC% values (low or high), third codon positions tend to maintain a constant GC%, thus relating more to the species than to the genes that contain them. Genes in an extreme-GC% genome collectively span a smaller GC% range, and mainly rely on first and second codon positions for differentiation as "microisochores". Our results are consistent with the view that differences in GC% serve to recombinationally isolate both genome sectors (facilitating gene duplication) and genomes (facilitating genome duplication, e.g. speciation). In intermediate-GC% genomes, conflict between the needs of the species and the needs of individual genes within that species is minimal. However, in extreme-GC% genomes there is a conflict, which is settled in favour of the species (i.e. group selection) rather than in favour of the gene (genic selection).     

Gene expression,nucleotide composition and codon usage bias of genes associated with human Y chromosome

Analysis of codon usage pattern is important to understand the genetic and evolutionary characteristics of genomes. We have used bioinformatic approaches to analyze the codon usage bias (CUB) of the genes located in human Y chromosome. Codon bias index (CBI) indicated that the overall extent of codon usage bias was low. The relative synonymous codon usage (RSCU) analysis suggested that approximately half of the codons out of 59 synonymous codons were most frequently used, and possessed a T or G at the third codon position. The codon usage pattern was different in different genes as revealed from correspondence analysis (COA). A significant correlation between effective number of codons (ENC) and various GC contents suggests that both mutation pressure and natural selection affect the codon usage pattern of genes located in human Y chromosome. In addition, Y-linked genes have significant difference in GC contents at the second and third codon positions, expression level, and codon usage pattern of some codons like the SPANX genes in X chromosome.     

Patterns of codon usage bias in three dicot and four monocot plant species

Codon usage in nuclear genes of four monocot and three dicot species was analyzed to find general patterns in codon choice of plant species. Codon bias was correlated with GC content at the third codon position. GC contents were higher in monocot species than in dicot species at all codon positions. The high GC contents of monocot species might be the result of relatively strong mutational bias that occurred in the lineage of the Poaceae species. In both dicot and monocot species, the effective number of codons (ENCs) for most genes was similar to that for the expected ENCs based on the GC content at the third codon positions. G and C ending codons were detected as the "preferred" codons in monocot species, as in Drosophila. Also, many "preferred" codons are the same in dicot species. Pyrimidine (C and T) is used more frequently than purine (G and A) in four-fold degenerate codon groups.     

G and T Nucleotide Contents Show Specie-Invariant Negative Correlation for All Three Codon Positions

Abstract

The nucleotide contents of the three codon positions show a number of statistical pairwise correlations, some of which are universal for all analysed genomes. Among the most prominent of these correlations are negative correlations between G and T contents found in genes of all species analysed. The pair A/C, which is complementary to G/T shows similar negative correlation in genes of most species. In the genes of several species including all mammalian genes studied, positive correlations between A and T contents, and G and C contents are found. Since these regularities are observed in all three codon positions they are connected with amino-acid content of proteins. Such correlations may origin from features of the mutation process or/and translation reading frame check. The well-known bias of the preference for G in the first codon position and its deficiency in the second is accompanied by opposite bias in T content. In the third codon position there is no general nucleotide preference, but its content is often biased with regard to GC content of the gene. G and T contents in this case are always shifted in the opposite directions Several ideas are drawn to explain this preference.     

Compositional pressure and translational selection determine codon usage in the extremely GC-poor unicellular eukaryote Entamoeba histolytica

It is widely accepted that the compositional pressure is the only factor shaping codon usage in unicellular species displaying extremely biased genomic compositions. This seems to be the case in the prokaryotes Mycoplasma capricolum, Rickettsia prowasekii and Borrelia burgdorferi (GC-poor), and in Micrococcus luteus (GC-rich). However, in the GC-poor unicellular eukaryotes Dictyostelium discoideum and Plasmodium falciparum, there is evidence that selection, acting at the level of translation, influences codon choices. This is a twofold intriguing finding, since (1) the genomic GC levels of the above mentioned eukaryotes are lower than the GC% of any studied bacteria, and (2) bacteria usually have larger effective population sizes than eukaryotes, and hence natural selection is expected to overcome more efficiently the randomizing effects of genetic drift among prokaryotes than among eukaryotes. In order to gain a new insight about this problem, we analysed the patterns of codon preferences of the nuclear genes of Entamoeba histolytica, a unicellular eukaryote characterised by an extremely AT-rich genome (GC = 25%). The overall codon usage is strongly biased towards A and T in the third codon positions, and among the presumed highly expressed sequences, there is an increased relative usage of a subset of codons, many of which are C-ending. Since an increase in C in third codon positions is 'against' the compositional bias, we conclude that codon usage in E. histolytica, as happens in D. discoideum and P. falciparum, is the result of an equilibrium between compositional pressure and selection. These findings raise the question of why strongly compositionally biased eukaryotic cells may be more sensitive to the (presumed) slight differences among synonymous codons than compositionally biased bacteria.     

Clonorchis sinensis: codon usage in nuclear genes

Codon usage in Clonorchis sinensis was analyzed using 12,515 codons from 38 coding sequences. Total GC content was 49.83%, and GC1, GC2 and GC3 contents were 56.32%, 43.15% and 50.00%, respectively. The effective number of codons converged at 51-53 codons. When plotted against total GC content or GC3, codon usage was distributed in relation to GC3 biases. Relative synonymous codon usage for each codon revealed a single major trend, which was highly correlated with GC content at the third position when codons began with A or U at the first two positions. In codons beginning with G or C base at the first two positions, the G or C base rarely occurred at the third position. These results suggest that codon usage is shaped by a bias towards G or C at the third base, and that this is affected by the first and second bases.     

Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species

A detailed comparison was made of codon usage of chloroplast genes with their host (nuclear) genes in the four angiosperm speciesOryza sativa, Zea mays, Triticum aestivum andArabidopsis thaliana. The average GC content of the entire genes, and at the three codon positions individually, was higher in nuclear than in chloroplast genes, suggesting different genomic organization and mutation pressures in nuclear and chloroplast genes. The results of Nc-plots and neutrality plots suggested that nucleotide compositional constraint had a large contribution to codon usage bias of nuclear genes inO. sativa, Z. mays, andT. aestivum, whereas natural selection was likely to be playing a large role in codon usage bias in chloroplast genomes. Correspondence analysis and chi-test showed that regardless of the genomic environment (species) of the host, the codon usage pattern of chloroplast genes differed from nuclear genes of their host species by their AU-richness. All the chloroplast genomes have predominantly A- and/or U-ending codons, whereas nuclear genomes have G-, C- or U-ending codons as their optimal codons. These findings suggest that the chloroplast genome might display particular characteristics of codon usage that are different from its host nuclear genome. However, one feature common to both chloroplast and nuclear genomes in this study was that pyrimidines were found more frequently than purines at the synonymous codon position of optimal codons.     

Codon usage and genome composition

Summary The GC levels of codon third positions from 49 genomes coveering a wide phylogenetic range are linearly correlated with the GC levels of the corresponding genomes. Three different relationships have been found: one for prokaryotes and viruses, one for lower eukaryotes, and one for vertebrates. All points not fitting the first relationship can be brought into quasi coincidence with it when plotted against GC levels of coding sequences.