σ factors are considered as positive regulators of gene expression. Here we reveal the opposite, inhibitory role of these proteins. We used a combination of molecular biology methods and computational modeling to analyze the regulatory activity of the extracytoplasmic σE factor from Streptomyces coelicolor. The direct activator/repressor function of σE was then explored by experimental analysis of selected promoter regions in vivo. Additionally, the σE interactome was defined. Taken together, the results characterize σE, its regulation, regulon, and suggest its direct inhibitory function (as a repressor) in gene expression, a phenomenon that may be common also to other σ factors and organisms.

• MeSH
• počítačová simulace MeSH
• sigma faktor genetika   MeSH
• Streptomyces coelicolor * genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• sigma faktor MeSH

Bacillus subtilis cells are well suited to study how bacteria sense and adapt to proteotoxic stress such as heat, since temperature fluctuations are a major challenge to soil-dwelling bacteria. Here, we show that the alarmones (p)ppGpp, well known second messengers of nutrient starvation, are also involved in the heat stress response as well as the development of thermo-resistance. Upon heat-shock, intracellular levels of (p)ppGpp rise in a rapid but transient manner. The heat-induced (p)ppGpp is primarily produced by the ribosome-associated alarmone synthetase Rel, while the small alarmone synthetases RelP and RelQ seem not to be involved. Furthermore, our study shows that the generated (p)ppGpp pulse primarily acts at the level of translation, and only specific genes are regulated at the transcriptional level. These include the down-regulation of some translation-related genes and the up-regulation of hpf, encoding the ribosome-protecting hibernation-promoting factor. In addition, the alarmones appear to interact with the activity of the stress transcription factor Spx during heat stress. Taken together, our study suggests that (p)ppGpp modulates the translational capacity at elevated temperatures and thereby allows B. subtilis cells to respond to proteotoxic stress, not only by raising the cellular repair capacity, but also by decreasing translation to concurrently reduce the protein load on the cellular protein quality control system.

• MeSH
• Bacillus subtilis genetika   MeSH
• bakteriální proteiny genetika   MeSH
• ligasy genetika   MeSH
• reakce na tepelný šok genetika   MeSH
• regulace genové exprese u bakterií genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny MeSH
• guanosine 3',5'-polyphosphate synthetases MeSH Prohlížeč
• ligasy MeSH

HrdB in streptomycetes is a principal sigma factor whose deletion is lethal. This is also the reason why its regulon has not been investigated so far. To overcome experimental obstacles, for investigating the HrdB regulon, we constructed a strain whose HrdB protein was tagged by an HA epitope. ChIP-seq experiment, done in 3 repeats, identified 2137 protein-coding genes organized in 337 operons, 75 small RNAs, 62 tRNAs, 6 rRNAs and 3 miscellaneous RNAs. Subsequent kinetic modeling of regulation of protein-coding genes with HrdB alone and with a complex of HrdB and a transcriptional cofactor RbpA, using gene expression time series, identified 1694 genes that were under their direct control. When using the HrdB-RbpA complex in the model, an increase of the model fidelity was found for 322 genes. Functional analysis revealed that HrdB controls the majority of gene groups essential for the primary metabolism and the vegetative growth. Particularly, almost all ribosomal protein-coding genes were found in the HrdB regulon. Analysis of promoter binding sites revealed binding motif at the -10 region and suggested the possible role of mono- or di-nucleotides upstream of the -10 element.

• MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• bakteriální RNA genetika   MeSH
• chromatinová imunoprecipitace MeSH
• DNA bakterií chemie   metabolismus   MeSH
• DNA vazebné proteiny metabolismus   MeSH
• exprese genu MeSH
• geny rRNA MeSH
• kinetika MeSH
• modely genetické MeSH
• promotorové oblasti (genetika) MeSH
• regulace genové exprese u bakterií MeSH
• regulon * MeSH
• RNA transferová genetika   MeSH
• sekvenční analýza DNA MeSH
• sigma faktor metabolismus   MeSH
• Streptomyces coelicolor genetika   metabolismus   MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny MeSH
• bakteriální RNA MeSH
• DNA bakterií MeSH
• DNA vazebné proteiny MeSH
• HrdB protein, Streptomyces MeSH Prohlížeč
• RNA transferová MeSH
• sigma faktor MeSH

Small RNAs (sRNAs) are molecules essential for a number of regulatory processes in the bacterial cell. Here we characterize Ms1, a sRNA that is highly expressed in Mycobacterium smegmatis during stationary phase of growth. By glycerol gradient ultracentrifugation, RNA binding assay, and RNA co-immunoprecipitation, we show that Ms1 interacts with the RNA polymerase (RNAP) core that is free of the primary sigma factor (σA) or any other σ factor. This contrasts with the situation in most other species where it is 6S RNA that interacts with RNAP and this interaction requires the presence of σA. The difference in the interaction of the two types of sRNAs (Ms1 or 6S RNA) with RNAP possibly reflects the difference in the composition of the transcriptional machinery between mycobacteria and other species. Unlike Escherichia coli, stationary phase M. smegmatis cells contain relatively few RNAP molecules in complex with σA. Thus, Ms1 represents a novel type of small RNAs interacting with RNAP.

• MeSH
• bakteriální chromozomy MeSH
• DNA řízené RNA-polymerasy metabolismus   MeSH
• konformace nukleové kyseliny MeSH
• malá nekódující RNA chemie   genetika   metabolismus   MeSH
• Mycobacterium smegmatis enzymologie   genetika   růst a vývoj   MeSH
• Mycobacterium genetika   MeSH
• sigma faktor metabolismus   MeSH
• syntenie MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA řízené RNA-polymerasy MeSH
• malá nekódující RNA MeSH
• sigma faktor MeSH

A computational model of gene expression was applied to a novel test set of microarray time series measurements to reveal regulatory interactions between transcriptional regulators represented by 45 sigma factors and the genes expressed during germination of a prokaryote Streptomyces coelicolor. Using microarrays, the first 5.5 h of the process was recorded in 13 time points, which provided a database of gene expression time series on genome-wide scale. The computational modeling of the kinetic relations between the sigma factors, individual genes and genes clustered according to the similarity of their expression kinetics identified kinetically plausible sigma factor-controlled networks. Using genome sequence annotations, functional groups of genes that were predominantly controlled by specific sigma factors were identified. Using external binding data complementing the modeling approach, specific genes involved in the control of the studied process were identified and their function suggested.

• MeSH
• genetická transkripce MeSH
• genové regulační sítě * MeSH
• kinetika MeSH
• modely genetické * MeSH
• počítačová simulace MeSH
• regulace genové exprese u bakterií * MeSH
• sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů MeSH
• sigma faktor metabolismus   MeSH
• spory bakteriální genetika   růst a vývoj   metabolismus   MeSH
• stanovení celkové genové exprese * MeSH
• Streptomyces coelicolor genetika   metabolismus   fyziologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• sigma faktor MeSH

tmRNA and protein SmpB are the main components required for rescue of stalled ribosomes incapable of properly elongating or terminating the polypeptide chain. We examined the tmRNA level and protein synthesis in Streptomyces aureofaciens, S. griseus and S. collinus synthesizing tetracycline, streptomycin and kirromycin, respectively, during various stress conditions. Downshift in temperature caused a decrease in protein synthesis but the level of tmRNA increased. Shift up in temperature induced decay of tmRNA in all strains and in S. collinus led to stimulation and in S. aureofaciens and S. griseus to inhibition of protein synthesis. At high NaCl concentrations protein synthesis was inhibited and tmRNA decayed. Shift in pH from 7.0 to 5.0 had no pronounced effect on the tmRNA level while upshift to pH 9.0 in S. collinus and S. aureofaciens caused inhibition of protein synthesis and decay of tmRNA in S. collinus. In contrast, protein synthesis and tmRNA level increased in S. griseus at the alkaline pH. Our data show that tmRNA abundance is important for survival of streptomycetes under certain unfavorable conditions.

• MeSH
• bakteriální RNA metabolismus   MeSH
• chlorid sodný škodlivé účinky   MeSH
• koncentrace vodíkových iontů MeSH
• messenger RNA metabolismus   MeSH
• northern blotting MeSH
• proteosyntéza MeSH
• RNA transferová metabolismus   MeSH
• Streptomyces aureofaciens fyziologie   MeSH
• Streptomyces fyziologie   MeSH
• teplota MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální RNA MeSH
• chlorid sodný MeSH
• messenger RNA MeSH
• RNA transferová MeSH
• tmRNA MeSH Prohlížeč