Summary: Bacillus subtilis responds to various stimuli (heat, ethanol and salt stress, energy starvation) with the induction of general stress proteins (GSPs). Most of them belong to the stress and stationary-phase regulon controlled by the alternative sigma factor σB. The majority of σB-dependent proteins are thought to provide a precautionary general stress resistance in stressed or starved cells. In this report, the identification and transcriptional analysis of nine new members of the σB regulon are described. The biochemical function was not determined for any of the proteins encoded by the nine new σB-dependent stress genes, however, similarities to proteins in the databases allowed a distinction between proteins with putative (i-iv) and unknown (v) function. The putative functions of BmrU, YcdF, YdaD, YdaP, YhdN and YocK underline the suggested protective role of σB-dependent GSPs and also elucidate new areas where σB might play an important role. (i) The finding that the bmrUR operon is under σB control indicates that the elimination of multidrug compounds might be a new function in multiple stress resistance. (ii) YcdF and YdaD resemble NAD(P)-dependent dehydrogenases. Both proteins could be involved in the generation of NAD(P)H and therefore in the maintenance of the intracellular redox balance under stress. (iii) The ydaP gene might belong to the increasing number of σB-dependent genes whose orthologues are under the control of σS in Escherichia coli, indicating that both regulons may fulfil similar functions. (iv) YhdN shows weak similarities to potassium ion channel proteins and YocK shows resemblance to the DnaK suppressor protein DksA. (v) Three new σB-dependent genes (ydaE, ydaG and yfkM) encoding proteins with still unknown functions were also described. Further analyses of corresponding mutants might allow a first prediction of their function within the framework of the general stress regulon.
ABSTRACT Gene arrays containing all currently known open reading frames of Bacillus subtilis were used to examine the general stress response of Bacillus . By proteomics, transcriptional analysis, transposon mutagenesis, and consensus promoter-based screening, 75 genes had previously been described as ς B -dependent general stress genes. The present gene array-based analysis confirmed 62 of these already known general stress genes and detected 63 additional genes subject to control by the stress sigma factor ς B . At least 24 of these 125 ς B -dependent genes seemed to be subject to a second, ς B -independent stress induction mechanism. Therefore, this transcriptional profiling revealed almost four times as many regulon members as the proteomic approach, but failure of confirmation of all known members of the ς B regulon indicates that even this approach has not yet elucidated the entire regulon. Most of the ς B -dependent general stress proteins are probably located in the cytoplasm, but 25 contain at least one membrane-spanning domain, and at least 6 proteins appear to be secreted. The functions of most of the newly described genes are still unknown. However, their classification as ς B -dependent stress genes argues that their products most likely perform functions in stress management and help to provide the nongrowing cell with multiple stress resistance. A comprehensive screening program analyzing the multiple stress resistance of mutants with mutations in single stress genes is in progress. The first results of this program, showing the diminished salt resistance of yjbC and yjbD mutants compared to that of the wild type, are presented. Only a few new ς B -dependent proteins with already known functions were found, among them SodA, encoding a superoxide dismutase. In addition to analysis of the ς B -dependent general stress regulon, a comprehensive list of genes induced by heat, salt, or ethanol stress in a ς B -independent manner is presented. Perhaps the most interesting of the ς B -independent stress phenomena was the induction of the extracytoplasmic function sigma factor ς W and its entire regulon by salt shock.
ABSTRACT A consensus-directed search for ς B promoters was used to locate potential candidates for new ς B -dependent genes in Bacillus subtilis . Screening of those candidates by oligonucleotide hybridizations with total RNA from exponentially growing or ethanol-stressed cells of the wild type as well as a sigB mutant revealed 22 genes that required ς B for induction by ethanol. Although almost 50% of the proteins encoded by the newly discovered ς B -dependent stress genes seem to be membrane localized, biochemical functions have so far not been defined for any of the gene products. Allocation of the genes to the ς B -dependent stress regulon may indicate a potential function in the establishment of a multiple stress resistance. AldY and YhdF show similarities to NAD(P)-dependent dehydrogenases and YdbP to thioredoxins, supporting our suggestion that ς B -dependent proteins may be involved in the maintenance of the intracellular redox balance after stress.
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