Systematic study of gene expression and transcription organization in the gntZ–ywaA region of the Bacillus subtilis genome

Abstract

Within the framework of the international project ' The functional analysis of the Bacillus subtilis genome ' in Japan and Europe, the gene expression and transcription organization of the gntZ-ywaA region (160 kb) of the B. subtilis genome has been systematically analysed. First, all unanalysed genes comprising more than 80 amino acids (125 genes) in this region were inactivated through integration of plasmid pMUTIN. No essential gene was found which could not be inactivated. All the integrants grew normally in both nutrient sporulation medium and glucose minimal medium. But an integrant in the yxbG gene exhibited an oligosporogenic phenotype in the nutrient sporulation medium. The synthesis of β-galactosidase was examined, as a reporter for expression of the inactivated genes, during growth and sporulation in the two media. The results indicated that 36 % of the promoters were inactive when cells were grown in at least one of these two media. Furthermore, the transcription of the 119 genes in this region was analysed by Northern blotting, resulting in a transcription map. The results indicate that the gntZ-ywaA region contains at least 24 polycistronic operons, including several published ones. The operons newly found in this work are yxaAB, yxaGH, yxaJKL, yxbBA-yxnB-asnH-yxaM, yxbCD, yxcED, yxdJK, yxeFGH, yxeKLMNOPQ, yxeR-yxxB, hutPHUIGM, bglPH-yxiE, wapA-yxxG, yxiM-deaD, katB-yxiS, yxjCDEF, yxjJI and yxkF-mmsX.

Characterization of the Bacillus subtilis YxdJ response regulator as the inducer of expression for the cognate ABC transporter YxdLM

“…As reported previously (Yoshida et al, 2000) and in the present study, both operons are constitutively expressed at a very low level during the growth phase of B. subtilis. This complicates any studies of their promoter sequence and regulation.…”

“…The yxdJK and yxdLM genes, encoding the TCS and ABC transporter systems, respectively, and belonging to separate operons (Joseph et al, 2002;Yoshida et al, 2000) were shown to be functionally related (Joseph et al, 2002). As reported previously (Yoshida et al, 2000) and in the present study, both operons are constitutively expressed at a very low level during the growth phase of B. subtilis.…”

Carbon Catabolite Control of the Metabolic Network inBacillus subtilis

“…43) The yxkF-msmX operon probably involved in the transport of unknown sugars has been found to be under CcpA-mediated CCR. 25,49) Besides, the amyE gene encoding the extracellular -amylase hydrolyzing starch, 3,5) and the levDEFG-sacC operon encoding a fructose-specific phosphotransferase system and the extracellular levanase hydrolyzing fructose polymers and sucrose, 59,104) are also known to be subject to CcpA-mediated CCR. In addition, some members (lcfA-fadR-fadB-etfAB, fadNAE, and lcfB) of the FadR (formerly YsiA) regulon involved in fatty acid degradation 44,105) are under CcpA-dependent CCR (H. Matsuoka, and Y. Fujita, unpublished observation).…”

“…The operons involved in the catabolism of secondary carbon sources are as follows (the carbon sources in parentheses): gntRKPZ (gluconate), 16,35,36) xylAB (xylose), 9) iolABCDEFGHIJ (myo-inositol), 40,41,102) trePAR (trehalose), 25,47,103) galKT (galactose), 25) glpFK (glycerol), 33) glvARC (6-P--glucoside), 34) bglPH ( -glucoside), 26,27) yjlBCD-uxaC-yjmBCD-uxuA-yjmFexuTR-uxaBA (hexuronate), 25,48) xynPB ( -xyloside), 65) yxjC-scoAE-bdh ( -hydroxybutyrate), 25,49) ara-ABDLMNPQ-abfA (arabinose) 24,52,53) and abnA xsa (arabinose), 50) kdgRKAT (hexuronate), 25,42) and kduID (galacturonate). 43) The yxkF-msmX operon probably involved in the transport of unknown sugars has been found to be under CcpA-mediated CCR.…”

“…55) The yxkJ gene, probably encoding a citrate/malate transporter, is subject to CcpA-mediated CCR. 25,49) Transport systems for C4-dicarboxylates, such as malate, fumarate, and succinate, are encoded by dctP, whose expression is positively regulated by a two-component regulatory system encoded by dctS/dctR and is subject to CcpA-mediated CCR. 30) The B. subtilis respiration system is severely repressed by glucose.…”