Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis

Kanaya, Shigehiko; Yamada, Yuko; Kudo, Yoshihisa; Ikemura, Toshimichi

doi:10.1016/s0378-1119(99)00225-5

Cited by 387 publications

(311 citation statements)

References 66 publications

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“…3, A and B, are comparable with the amounts of tRNA Asn (0.6 -1.2%) and tRNA Asp (0.8 -1.3%) that were determined in Bacillus subtilis, E. coli, and Mycoplasma capricolum using two-dimensional gel electrophoresis (Ref. 27 and references therein). These results suggest that the M. thermautotrophicus AspRS aminoacylated tRNA Asn and tRNA Asp , in contrast to the AspRSs from P. kodakaraensis or F. acidarmanus.…”

Section: Formation Of Archaeal Asn-trna By Two Different Routes-supporting

confidence: 75%

Evolutionary Divergence of the Archaeal Aspartyl-tRNA Synthetases into Discriminating and Nondiscriminating Forms

Hansen¹,

Feng²,

Toogood³

et al. 2002

Journal of Biological Chemistry

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Asparaginyl-tRNA (Asn-tRNA) is generated in nature via two alternate routes, either direct acylation of tRNA with asparagine by asparaginyl-tRNA synthetase (AsnRS) or in a two-step pathway that requires misacylated Asp-tRNA Asn as an intermediate. This misacylated aminoacyl-tRNA is formed by a nondiscriminating aspartyltRNA synthetase (AspRS), an enzyme that in addition to forming Asp-tRNA Asp also misacylates tRNA Asn . In contrast, a discriminating AspRS cannot acylate tRNA Asn . It has been suggested that the archaeal AspRS enzymes are nondiscriminating, whereas the bacterial ones discriminate. The archaeal and bacterial AspRS proteins are indeed distinct in sequence and structure. However, we show that both discriminating and nondiscriminating forms of AspRS exist among the archaea. Using unfractionated methanobacterial and pyrococcal tRNA, the Methanothermobacter thermautotrophicus AspRS acylated approximately twice as much tRNA as did AspRS from Pyrococcus kodakaraensis or Ferroplasma acidarmanus. Proof that Asp-tRNA Asn was generated by the methanogen synthetase was the conversion of AsptRNA formed by M. thermautotrophicus AspRS to AsntRNA by M. thermautotrophicus Asp-tRNA Asn amidotransferase. In contrast, Asp-tRNA formed by the Pyrococcus or Ferroplasma enzymes was not a substrate for the amidotransferase. Also, although all three AspRS enzymes charged tRNA Asp transcripts, only M. thermautotrophicus AspRS aspartylated the tRNA Asn transcript. Genomic analysis provides a rationale for the nature of these enzymes. The mischarging AspRS correlates with the absence in the genome of AsnRS and the presence of Asp-tRNA Asn amidotransferase, employed by the transamidation pathway. In contrast, the discriminating AspRS correlates with the absence of the amidotransferase and the presence of AsnRS, forming Asn-tRNA by direct aminoacylation. The high sequence identity, up to 60% between discriminating and nondiscriminating archaeal AspRSs, suggests that few mutational steps may be necessary to convert the tRNA-discriminating ability of a tRNA synthetase.

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Section: Formation Of Archaeal Asn-trna By Two Different Routes-supporting

confidence: 75%

Evolutionary Divergence of the Archaeal Aspartyl-tRNA Synthetases into Discriminating and Nondiscriminating Forms

Hansen¹,

Feng²,

Toogood³

et al. 2002

Journal of Biological Chemistry

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“…tRNA abundances have been quantified in E. coli (42) and B. subtilis (31), and in both species, codon usage is biased toward ''major'' codon(s) that are generally recognized by abundant tRNAs. Such patterns are consistent with major codon preference, or natural selection discriminating among synonymous codons to enhance translational elongation rates and͞or to reduce the frequency of amino acid misincorporations during protein synthesis (42)(43)(44).…”

Section: Discussionmentioning

confidence: 99%

Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis

Akashi

Gojobori²

2002

Proc. Natl. Acad. Sci. U.S.A.

603

605

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Biosynthesis of anEven if a substituted amino acid were truly neutral in a functional sense, it is highly unlikely that factors involved in the synthesis of the protein would render the substitution neutral in the broader sense of the organism's integrated functioning. The substituted amino acid must be present within the cell in equivalent quantity compared with the original amino acid and, indeed, its synthesis or derivation from other molecules and transport into the cell require an equivalent amount of energy output.R. C. Richmond (1)

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“…Proline is encoded by four codons (CCA, CCG, CCU and CCC), and the CCU codon employed as the specifier in proBA and proI (Fig. 3) is one of the two proline-specific codons (CCG and CCU) that are preferentially used in protein-encoding genes of B. subtilis (Kanaya et al, 1999). It should be noted in this context that B. subtilis possesses only one tRNA and that this single tRNA recognizes all four proline-encoding codons (Yamada et al, 2005).…”

Section: Discussionmentioning

confidence: 99%

T-box-mediated control of the anabolic proline biosynthetic genes of Bacillus subtilis

et al. 2011

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Bacillus subtilis possesses interlinked routes for the synthesis of proline. The ProJ-ProA-ProH route is responsible for the production of proline as an osmoprotectant, and the ProB-ProA-ProI route provides proline for protein synthesis. We show here that the transcription of the anabolic proBA and proI genes is controlled in response to proline limitation via a T-box-mediated termination/antitermination regulatory mechanism, a tRNA-responsive riboswitch. Primer extension analysis revealed mRNA leader transcripts of 270 and 269 nt for the proBA and proI genes, respectively, both of which are synthesized from SigA-type promoters. These leader transcripts are predicted to fold into two mutually exclusive secondary mRNA structures, forming either a terminator or an antiterminator configuration. Northern blot analysis allowed the detection of both the leader and the full-length proBA and proI transcripts. Assessment of the level of the proBA transcripts revealed that the amount of the full-length mRNA species strongly increased in proline-starved cultures. Genetic studies with a proB-treA operon fusion reporter strain demonstrated that proBA transcription is sensitively tied to proline availability and is derepressed as soon as cellular starvation for proline sets in. Both the proBA and the proI leader sequences contain a CCU proline-specific specifier codon prone to interact with the corresponding uncharged proline-specific tRNA. By replacing the CCU proline specifier codon in the proBA T-box leader with UUC, a codon recognized by a Phe-specific tRNA, we were able to synthetically re-engineer the proline-specific control of proBA transcription to a control that was responsive to starvation for phenylalanine.

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Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis

Cited by 387 publications

References 66 publications

Evolutionary Divergence of the Archaeal Aspartyl-tRNA Synthetases into Discriminating and Nondiscriminating Forms

Evolutionary Divergence of the Archaeal Aspartyl-tRNA Synthetases into Discriminating and Nondiscriminating Forms

Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis

T-box-mediated control of the anabolic proline biosynthetic genes of Bacillus subtilis

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