Dataset Information

?I from Bacillus subtilis: Impact on Gene Expression and Characterization of ?I-Dependent Transcription That Requires New Types of Promoters with Extended -35 and -10 Elements.

ABSTRACT: The ?I sigma factor from Bacillus subtilis is a ? factor associated with RNA polymerase (RNAP) that was previously implicated in adaptation of the cell to elevated temperature. Here, we provide a comprehensive characterization of this transcriptional regulator. By transcriptome sequencing (RNA-seq) of wild-type (wt) and ?I-null strains at 37°C and 52°C, we identified ?130 genes affected by the absence of ?I Further analysis revealed that the majority of these genes were affected indirectly by ?I The ?I regulon, i.e., the genes directly regulated by ?I, consists of 16 genes, of which eight (the dhb and yku operons) are involved in iron metabolism. The involvement of ?I in iron metabolism was confirmed phenotypically. Next, we set up an in vitro transcription system and defined and experimentally validated the promoter sequence logo that, in addition to -35 and -10 regions, also contains extended -35 and -10 motifs. Thus, ?I-dependent promoters are relatively information rich in comparison with most other promoters. In summary, this study supplies information about the least-explored ? factor from the industrially important model organism B. subtilisIMPORTANCE In bacteria, ? factors are essential for transcription initiation. Knowledge about their regulons (i.e., genes transcribed from promoters dependent on these ? factors) is the key for understanding how bacteria cope with the changing environment and could be instrumental for biotechnologically motivated rewiring of gene expression. Here, we characterize the ?I regulon from the industrially important model Gram-positive bacterium Bacillus subtilis We reveal that ?I affects expression of ?130 genes, of which 16 are directly regulated by ?I, including genes encoding proteins involved in iron homeostasis. Detailed analysis of promoter elements then identifies unique sequences important for ?I-dependent transcription. This study thus provides a comprehensive view on this underexplored component of the B. subtilis transcription machinery.

SUBMITTER: Ramaniuk O

PROVIDER: S-EPMC6088155 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

σI from Bacillus subtilis: Impact on Gene Expression and Characterization of σI-Dependent Transcription That Requires New Types of Promoters with Extended -35 and -10 Elements.

Ramaniuk Olga O Převorovský Martin M Pospíšil Jiří J Vítovská Dragana D Kofroňová Olga O Benada Oldřich O Schwarz Marek M Šanderová Hana H Hnilicová Jarmila J Krásný Libor L

Journal of bacteriology 20180810 17

The σI sigma factor from Bacillus subtilis is a σ factor associated with RNA polymerase (RNAP) that was previously implicated in adaptation of the cell to elevated temperature. Here, we provide a comprehensive characterization of this transcriptional regulator. By transcriptome sequencing (RNA-seq) of wild-type (wt) and σI-null strains at 37°C and 52°C, we identified ∼130 genes affected by the absence of σI Further analysis revealed that the majority of th ...[more]

PMID: 29914988

Similar Datasets

Project description:The Gram-positive model organism Bacillus subtilis responds to environmental stressors by activating the alternative sigma factor σB. The sensing apparatus upstream of σB activation is thought to consist of cytoplasmic stressosomes-megadalton-sized protein complexes that include five paralogous proteins known as RsbRs. The RsbRs are presumed to be involved in stress sensing and the subsequent response. Perturbations to the RsbR complement in stressosomes by engineering cells that produce only one of the RsbR paralogs ("single-RsbR strains") lead to altered σB response dynamics with respect to timing and magnitude. Here, we asked whether such changes to σB response dynamics impact the relative fitness of a strain. We competed strain pairs with different RsbR complements under ethanol and sodium chloride stress and found not only differences in relative fitness among wild-type and single-RsbR strains but also different relative fitness values in the two different stressors. We found that the presence of RsbRA, which dominates the wild-type σB response, enhances fitness in ethanol but is detrimental to fitness in NaCl. Meanwhile, RsbRD-only cells were among the most fit in NaCl. Strains producing hybrid RsbR fusion proteins displayed different fitness values that depended on the RsbR proteins from which they were derived. Our results here suggest that σB response dynamics can impact fitness, highlighting the physiological importance of the unusual stressosome-based general stress response system of B. subtilis.ImportanceThe model bacterium Bacillus subtilis uses cytoplasmic multiprotein complexes, termed stressosomes, to activate the alternative sigma factor σB when facing environmental stresses. We have previously shown that genetically manipulating the complement of putative sensor proteins in stressosomes can alter the dynamics of the σB response in terms of its magnitude and timing. However, it is unknown whether these response dynamics impact the fitness of cells challenged by environmental stressors. Here, we examine the fitness of strains with different σB responses by competing strain pairs in exponential-phase co-cultures under environmental stress. We find that strains with different response dynamics show different competitive indices that differ by stressor. These results suggest that the dynamics of the σB response can affect the fitness of cells facing environmental stress, highlighting the relevance of different σB dynamics.

Dataset Information

?I from Bacillus subtilis: Impact on Gene Expression and Characterization of ?I-Dependent Transcription That Requires New Types of Promoters with Extended -35 and -10 Elements.

Publications

σ<sup>I</sup> from Bacillus subtilis: Impact on Gene Expression and Characterization of σ<sup>I</sup>-Dependent Transcription That Requires New Types of Promoters with Extended -35 and -10 Elements.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets