subtilis [11–13], for a review see 14. The T box elements are widely distributed, being present in Firmicutes, δ-proteobacteria, Chloroflexi, Deinococcales/Thermales and Actinobacteria,

selleck and control expression of genes involved in cellular activities other than tRNA charging such as amino acid biosynthesis, amino acid Apoptosis Compound Library manufacturer transport and regulation of amino acid metabolism [15–17]. The T-box regulatory element is usually a 200-300 nucleotide untranslated RNA leader sequence containing a conserved T box sequence, stem-loop structures and a conditional Rho-independent terminator located upstream of the start codon [11–13]. Two specific interactions between tRNAs and T box leader sequences enable recognition of cognate tRNA species and distinction between charged and uncharged pools of tRNA. The NCCA sequence in the acceptor stem of a nonacylated-tRNA interacts with the UGGN sequence within the T box

sequence (N varies CA3 according to the identity of the discriminator base of each tRNA) [13, 14, 18, 19]. This interaction cannot occur when a tRNA is aminoacylated, thereby distinguishing between charged and uncharged tRNAs. Specificity for cognate tRNAs is achieved by the presence of a specifier codon within a bulge in stem I of the leader sequence that interacts with the anticodon sequence of each tRNA. (eg. See Additional file 1, Figure S5). Thus for T box control of AARS expression, a high level of an uncharged tRNA (necessitating increased AARS production) causes interaction between that tRNA and its cognate T box element that stabilizes the anti-termination structure ADAMTS5 of the leader sequence allowing transcription of the AARS gene to proceed. A high level of aminoacylated-tRNAs in contrast cannot interact with the leader sequence allowing formation of the Rho-independent terminator

and preventing continued transcription of the gene. While most eubacteria encode either a class I or a class II LysRS, all sequenced strains of B. cereus (except strain AH820) and B. thuringiensis encode a copy of both enzyme types [8, 16, 17]. In Bacillus cereus strain 14579, the LysRS2-encoding lysS gene is positioned at the end of an operon encoding genes involved in folate metabolism, its normal position in most Bacilli while the lysK gene encoding the class I-type LysRS1 is located elsewhere on the chromosome. Shaul et al. (2006) show that this LysRS1 is closely related to the class I LysRS1 of Pyrococcus, suggesting that it has been acquired by B. cereus by horizontal transfer [20]. The function of LysRS1 in B. cereus is not clear but it is expressed predominantly in stationary phase and can aminoacylate a novel tRNA species (tRNAOther) in concert with the class II LysRS enzyme [8]. Thus it may play a role in surviving nutritional downshift in B. cereus.