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Figure 4 | BMC Genomics

Figure 4

From: An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters

Figure 4

T-box regulation of tRNA ligase encoding genes in the Firmicutes . The color coding relates to the presence or absence of a T-box upstream of the genes encoding the amino acid-specific tRNA ligases in the various species and strains. Green indicates the tRNA ligase(s) is (are) regulated by a T-box and red that the tRNA ligase(s) is (are) not regulated by a T-box. Although most tRNA ligases are present in one copy on the genome, several organisms contain two, or in some cases three copies of specific ligases (indicated by a number in the box). Orange indicates that 1 of the 2 tRNA ligases is regulated by a T-box or 1 out of 3 in the case of the argS genes in B. cereus ATCC 10987 and the aspS genes in C. acetobutylicum. Light green indicates that the tRNA ligase is not the first in the operon, but is regulated by a T-box with the same specificity. Yellow color coding indicates that the regulated tRNA ligase is the second gene in an operon in combination with another tRNA ligase gene regulated by a T-box with different specificity. White indicates that no tRNA ligase of this type is present in the organism. In principle, a species needs at least one specific tRNA ligase for each amino acid. Nevertheless, there are exceptions. For instance, all but one (Clostridium perfringens) of the analyzed genomes lack the gene that encodes a Gln-tRNA ligase and the genomes of the Chloroflexi, Actinobacteria a nd Thermoanaerobacter tencongens also lack an Asn-tRNA ligase. In these cases, the biological role of the Gln-tRNA ligase is taken over by the Glu tRNA ligase, which couples a Glu residue to the tRNAGln. The residue is subsequently transformed into a Gln by a tRNA specific amidotransferase [66]. Similarly, an Asn-tRNAAsn is formed via transamidation of an Asp residue (Asp-tRNAAsn to Asn-tRNAAsn) in bacteria that lack an Asn tRNA ligase [67]. Consequently, we found that all species lacking either the Gln-tRNA ligase or the Asn-tRNA ligase have an orthologous gene coding for the corresponding amidotransferase. No T-boxes were identified upstream of those genes.

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