Alejandro Zavala

Aerobiosis Increases the Genomic Guanine Plus Cytosine Content (GC%) in Prokaryotes

The huge variation in the genomic guanine plus cytosine content (GC%) among prokar-yotes has been explained by two mutually exclusive hypotheses, namely, selectionist and neutralist. The former proposals have in common the assumption that this feature is a form of adaptation to some ecological or physiological condition. On the other hand, the neutralist interpretation states that the variations are due only to different mutational biases. Since all of the traits that have been proposed by the selectionists either appeared to be limited to certain genera or were invalidated by the availability of more data, they cannot be considered as a selective force influencing the genomic GC% across all prokaryotes. In this report we show that aerobic prokaryotes display a significant increment in genomic GC% in relation to anaerobic ones. This is the first time that a link between a metabolic character and GC% has been found, independently of phylogenetic relationships and with a statistically significant amount of data.

Correlations between genomic GC levels and optimal growth temperatures in prokaryotes

In prokaryotes, GC levels range from 25% to 75%, and T opt from ≈0 °C to >100 °C. When all species are considered together, no correlation is found between the two variables. Correlations are found, however, when Families of prokaryotes are analysed. Indeed, when Families comprising at least 10 species were studied (a set of 20 Families), positive correlations are found for 15 of them. Furthermore, a comparative analysis by independent contrasts made within the Families in order to control for phylogenetic non‐independence showed qualitatively equivalent results. We conclude that T opt is one of the factors that influences genomic GC in prokaryotes.

Translational selection shapes codon usage in the GC-rich genome of Chlamydomonas reinhardtii.

In unicellular species codon usage is determined by mutational biases and natural selection. Among prokaryotes, the influence of these factors is different if the genome is skewed towards AT or GC, since in AT‐rich organisms translational selection is absent. On the other hand, in AT‐rich unicellular eukaryotes the two factors are present. In order to understand if GC‐rich genomes display a similar behavior, the case of Chlamydomonas reinhardtii was studied. Since we found that translational selection strongly influences codon usage in this species, we conclude that there is not a common pattern among unicellular organisms.

The influence of translational selection on codon usage in fishes from the family Cyprinidae.

In this paper, the main factors shaping codon usage in three species of fishes that belong to the family Cyprinidae (namely Brachidanio rerio, Cyprinus carpio, and Carassius auratus) are reported. Correspondence analysis (COA), a commonly used multivariate statistical approach, was used to analyze codon usage bias. Our results show that the main trend is strongly correlated with the GC(3) content at silent sites of each sequence. On the other hand, the second axis discriminates between presumed highly and lowly expressed genes, a result that is confirmed by the distribution of matching expressed sequence tags (ESTs) along that axis. Translational selection appears, therefore, to influence synonymous codon usage in these fishes. The comparison of codon usages of the sequences displaying the extreme values on the second axis indicates that several codons are significantly incremented among the heavily expressed sequences. Interestingly, several of these triplets are not only shared by the three fishes but also by Xenopus laevis, another cold-blooded vertebrate in which translational selection influences codon choices. We postulate that natural selection was operative for codon usage in the last common ancestor of these fishes and Xenopus, and will probably be detected in cold-blooded vertebrates in general. Finally, we raise the possibility that the same phenomena will be found among warm-blooded vertebrates.

Synonymous Codon Choices in the Extremely GC-Poor Genome of Plasmodium falciparum: Compositional Constraints and Translational Selection

Abstract. We have analyzed the patterns of synonymous codon preferences of the nuclear genes of Plasmodium falciparum, a unicellular parasite characterized by an extremely GC-poor genome. When all genes are considered, codon usage is strongly biased toward A and T in third codon positions, as expected, but multivariate statistical analysis detects a major trend among genes. At one end genes display codon choices determined mainly by the extreme genome composition of this parasite, and very probably their expression level is low. At the other end a few genes exhibit an increased relative usage of a particular subset of codons, many of which are C-ending. Since the majority of these few genes is putatively highly expressed, we postulate that the increased C-ending codons are translationally optimal. In conclusion, while codon usage of the majority of P. falciparum genes is determined mainly by compositional constraints, a small number of genes exhibit translational selection.

Trends in Codon and Amino Acid Usage in Thermotoga maritima

Abstract. The usage of synonymous codons and the frequencies of amino acids were investigated in the complete genome of the bacterium Thermotoga maritima using a multivariate statistical approach. The GC3 content of each gene was the most prominent source of variation of codon usage. Surprisingly the usage of UGU and UGC (synonymous triplets coding for Cys, the least frequent amino acid in this species) was detected as the second most prominent source of variation. However, this result is probably an artifact due to the very low frequency of Cys together with the nonbiased composition of this genome. The third trend was related to the preferential usage of a subset of codons among highly expressed genes, and these triplets are presumed to be translationally optimal. Concerning the amino acid usage, the hydropathy level of each protein (and therefore the frequency of charged residues) was the main trend, while the second factor was related to the frequency of usage of the smaller residues, suggesting that the cell economy strongly influences the architecture of the proteins. The third axis of the analysis discriminated the usage of Phe, Tyr, Trp (aromatic residues) plus Cys, Met, and His. These six residues have in common the property of being the preferential targets of reactive oxygen species, and therefore the anaerobic condition of T. maritima is an important factor for the amino acid frequencies. Finally, the Cys content of each protein was the fourth trend.

The strength of translational selection for codon usage varies in the three replicons of Sinorhizobium meliloti

The genome of the nitrogen-fixing bacterium Sinorhizobium meliloti is composed of three replicons of 3.65 (chromosome), 1.35 (pSymA) and 1.68 Mb (pSymB), respectively. While the chromosome encodes for most of the housekeeping functions, the three elements may contribute to symbiosis, though pSymA is absolutely necessary for nodulation and nitrogen fixation, since it harbours all the characterized nodulation and symbiotic fixation genes. On the other hand, the majority of the sequences located in this megaplasmid are probably not expressed during the free-living stage of the organism. Since most of the sequences located in pSymA are transcribed only at the stage of bacteroids when most probably the fate of the bacterium is to die, the mutations occurring at this stage will not be fixed in the population. Therefore, if natural selection contributes to the codon usage pattern in this species, its effect will be much weaker for the genes placed in pSymA. A codon usage analysis of the genes comprising the three replicons is consistent with the conclusion that selection for translational speed shapes the codon usage of the two replicons which are important for competitive cell growth while the codon usage of the third replicon reflects primarily the mutational bias.

Compositional Correlations in the Chicken Genome

Abstract. This paper analyses the compositional correlations that hold in the chicken genome. Significant linear correlations were found among the regions studied—coding sequences (and their first, second, and third codon positions), flanking regions (5′ and 3′), and introns—as is the case in the human genome. We found that these compositional correlations are not limited to global GC levels but even extend to individual bases. Furthermore, an analysis of 1037 coding sequences has confirmed a correlation among GC3, GC2, and GC1. The implications of these results are discussed.