The H‐NS‐like protein StpA represses the RpoS (σ38) regulon during exponential growth of Salmonella Typhimurium

StpA is a paralogue of the nucleoid‐associated protein H‐NS that is conserved in a range of enteric bacteria and had no known function in Salmonella Typhimurium. We show that 5% of the Salmonella genome is regulated by StpA, which contrasts with the situation in Escherichia coli where deletion of stpA only had minor effects on gene expression. The StpA‐dependent genes of S. Typhimurium are a specific subset of the H‐NS regulon that are predominantly under the positive control of σ³⁸ (RpoS), CRP‐cAMP and PhoP. Regulation by StpA varied with growth phase; StpA controlled σ³⁸ levels at mid‐exponential phase by preventing inappropriate activation of σ³⁸ during rapid bacterial growth. In contrast, StpA only activated the CRP‐cAMP regulon during late exponential phase. ChIP‐chip analysis revealed that StpA binds to PhoP‐dependent genes but not to most genes of the CRP‐cAMP and σ³⁸ regulons. In fact, StpA indirectly regulates σ³⁸‐dependent genes by enhancing σ³⁸ turnover by repressing the anti‐adaptor protein rssC. We discovered that StpA is essential for the dynamic regulation of σ³⁸ in response to increased glucose levels. Our findings identify StpA as a novel growth phase‐specific regulator that plays an important physiological role by linking σ³⁸ levels to nutrient availability.     

DNA duplex stability as discriminative characteristic for Escherichia coli σ54- and σ28- dependent promoter sequences

The advent of modern high-throughput sequencing has made it possible to generate vast quantities of genomic sequence data. However, the processing of this volume of information, including prediction of gene-coding and regulatory sequences remains an important bottleneck in bioinformatics research. In this work, we integrated DNA duplex stability into the repertoire of a Neural Network (NN) capable of predicting promoter regions with augmented accuracy, specificity and sensitivity. We took our method beyond a simplistic analysis based on a single sigma subunit of RNA polymerase, incorporating the six main sigma-subunits of Escherichia coli. This methodology employed successfully re-discovered known promoter sequences recognized by E. coli RNA polymerase subunits σ²⁴, σ²⁸, σ³², σ³⁸, σ⁵⁴ and σ⁷⁰, with highlighted accuracies for σ²⁸- and σ⁵⁴- dependent promoter sequences (values obtained were 80% and 78.8%, respectively). Furthermore, the discrimination of promoters according to the σ factor made it possible to extract functional commonalities for the genes expressed by each type of promoter. The DNA duplex stability rises as a distinctive feature which improves the recognition and classification of σ²⁸- and σ⁵⁴- dependent promoter sequences. The findings presented in this report underscore the usefulness of including DNA biophysical parameters into NN learning algorithms to increase accuracy, specificity and sensitivity in promoter beyond what is accomplished based on sequence alone.     

Alternate promoters direct stress-induced transcription of the Bacillus subtilis clpC operon

clpC ofBacillus subtilis is part of an operon containing six genes. Northern blot analysis suggested that all genes are co-transcribed and encode stress-inducible proteins. Two promoters (P_A and P_B) were mapped upstream of the first gene. P_A resembles promoters recognized by the vegetative RNA polymerase Eσ^A. The other promoter (P_B) was shown to be dependent on σ^B, the general stress σ factor in B. subtilis, suggesting that clpC, a potential chaperone, is expressed in a σ^B-dependent manner. This is the first evidence that σ^B in B, subtilis is involved in controlling the expression of a gene whose counterpart, clpB, is subject to regulation by σ³² in Escherichia coli, indicating a new function of σ^B-dependent general stress proteins. P_B deviated from the consensus sequence of σ^B promoters and was only slightly induced by starvation conditions. Nevertheless, strong induction by heat, ethanol, and salt stress occurred at the σ^B-dependent promoter, whereas the vegetative promoter was only weakly induced under these conditions. However, in a sigB mutant, the σ^A-like promoter became inducible by heat and ethanol stress, completely compensating for sigB deficiency. Only the downstream σ^A-like promoter was induced by certain stress conditions such as hydrogen peroxide or puromycin. These results suggest that novel stress-induction mechanisms are acting at a vegetative promoter. Involvement of additional elements in this mode of induction are discussed.