Trends in Codon and Amino Acid Usage in Thermotoga maritima

Abstract

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.

Codon and Amino Acid Usage in Two Major Human Pathogens of Genus Bartonella -- Optimization Between Replicational-Transcriptional Selection, Translational Control and Cost Minimization

“…In both species of Bartonella the highly expressed genes seem to avoid aromatic amino acids and other large residues in their products as seen in other microbial organisms. 28,29,34 As already mentioned, this observation is compatible with the cost-minimization hypothesis of amino acid usage. 31 Finally, to explore the relationship between protein conservation and gene expression, we have compared the estimated pairwise non-synonymous divergences (d N ) between all orthologues of putative highly and lowly expressed genes pre-identified from the two extremes of axis 1 generated by COA on RSCU of the leading strand genes of two organisms.…”

“…Since the highly expressed genes are mostly located on the leading strand of replication, this observation indicates that proteins encoded by highly expressed genes are preferentially constructed with smaller residues because these residues are energetically less expensive, as were also reported for the proteins in Giardia lamblia 30 and Thermotoga maritime. 29 This indicates that B. henselae and B. quintana, both in spite of their intracellular lifestyle, follow the cost-minimization hypothesis.…”

“…This observation is surprising in view of the fact that the first axis of COA on amino acid frequencies in proteins of different organisms examined so far was found to be strongly correlated with a single parameter, hydrophobicity, in most cases. 28,29 But in the Bartonella species under examination, the mean hydropathy level and aromaticityboth seem to have nearly equal influence on the amino acid usage. The proteins present at the negative end of axis 1 in B. henselae or at the positive end in B. quintana are rich in hydrophobic residues, mostly represented by membrane proteins involved in signal transduction and several transports.…”

Translational selection is operative for synonymous codon usage in Clostridium perfringens and Clostridium acetobutylicum

“…This statistical approach has been widely used to investigate major trends in codon usage in several species of bacteria (Grantham et al, 1981;McInerney, 1998;Lafay et al, 1999;Zavala et al, 2002). The position of genes on the main axes generated by the analysis can subsequently be compared with biological properties of the sequences, such as expressivity, base composition, etc., which can help to understand the significance of each main trend.…”

Persistent biases in the amino acid composition of prokaryotic proteins

“…(1)(2)(3)(4)(5)(6)(7)(8) With the development of rapid sequencing methods, the genome sequence of prokaryotic organisms, Bacteria and Archaea, have become widely available. Several analyses of the codon-usage bias or the amino acid usage in reference proteomes have been published, such as those of Thermotoga maritima, (9) Pseudomonas aeruginosa, (10) Buchnera species, (11) or the three model prokaryotes Escherichia coli, Bacillus subtilis and Methanococcus jannaschii. (12) These studies revealed remarkable and possibly universal rules that we attempted to relate to the biological function and evolution of the proteins of the organisms of interest.…”