Hexameric arginine repressor, ArgR, is the feedback regulator of bacterial L-arginine regulons, and sensor of L-arg that controls transcription of genes for its synthesis and catabolism. Although ArgR function, as well as its secondary, tertiary, and quaternary structures, is essentially the same in E. coli and B. subtilis, the two proteins differ significantly in sequence, including residues implicated in the response to L-arg. Molecular dynamics simulations are used here to evaluate the behavior of intact B. subtilis ArgR with and without L-arg, and are compared with prior MD results for a domain fragment of E. coli ArgR. Relative to its crystal structure, B. subtilis ArgR in absence of L-arg undergoes a large-scale rotational shift of its trimeric subassemblies that is very similar to that observed in the E. coli protein, but the residues driving rotation have distinct secondary and tertiary structural locations, and a key residue that drives rotation in E. coli is missing in B. subtilis. The similarity of trimer rotation despite different driving residues suggests that a rotational shift between trimers is integral to ArgR function. This conclusion is supported by phylogenetic analysis of distant ArgR homologs reported here that indicates at least three major groups characterized by distinct sequence motifs but predicted to undergo a common rotational transition. The dynamic consequences of L-arg binding for transcriptional activation of intact ArgR are evaluated here for the first time in two-microsecond simulations of B. subtilis ArgR. L-arg binding to intact B. subtilis ArgR causes a significant further shift in the angle of rotation between trimers that causes the N-terminal DNA-binding domains lose their interactions with the C-terminal domains, and is likely the first step toward adopting DNA-binding-competent conformations. The results aid interpretation of crystal structures of ArgR and ArgR-DNA complexes.

• MeSH
• alosterická regulace MeSH
• arginin chemie   metabolismus   MeSH
• Bacillus subtilis chemie   genetika   metabolismus   MeSH
• bakteriální proteiny chemie   genetika   metabolismus   MeSH
• entropie MeSH
• Escherichia coli chemie   genetika   metabolismus   MeSH
• fylogeneze MeSH
• konformace proteinů, alfa-helix MeSH
• konformace proteinů, beta-řetězec MeSH
• proteinové domény MeSH
• regulon genetika   MeSH
• represorové proteiny chemie   genetika   metabolismus   MeSH
• sekvence aminokyselin MeSH
• sekvenční seřazení MeSH
• simulace molekulární dynamiky MeSH
• vazba proteinů MeSH
• vodíková vazba MeSH
• Publikační typ
• časopisecké články MeSH

The membrane-embedded FtsH proteases found in bacteria, chloroplasts, and mitochondria are involved in diverse cellular processes including protein quality control and regulation. The genome of the model cyanobacterium Synechocystis sp PCC 6803 encodes four FtsH homologs designated FtsH1 to FtsH4. The FtsH3 homolog is present in two hetero-oligomeric complexes: FtsH2/3, which is responsible for photosystem II quality control, and the essential FtsH1/3 complex, which helps maintain Fe homeostasis by regulating the level of the transcription factor Fur. To gain a more comprehensive insight into the physiological roles of FtsH hetero-complexes, we performed genome-wide expression profiling and global proteomic analyses of Synechocystis mutants conditionally depleted of FtsH3 or FtsH1 grown under various nutrient conditions. We show that the lack of FtsH1/3 leads to a drastic reduction in the transcriptional response to nutrient stress of not only Fur but also the Pho, NdhR, and NtcA regulons. In addition, this effect is accompanied by the accumulation of the respective transcription factors. Thus, the FtsH1/3 complex is of critical importance for acclimation to iron, phosphate, carbon, and nitrogen starvation in Synechocystis.plantcell;31/12/2912/FX1F1fx1.

• MeSH
• aklimatizace genetika   MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• dusík nedostatek   metabolismus   MeSH
• exprese genu MeSH
• fosfáty nedostatek   metabolismus   MeSH
• fosforylace MeSH
• fotosystém II (proteinový komplex) chemie   genetika   metabolismus   MeSH
• metaloproteasy genetika   metabolismus   MeSH
• mutace MeSH
• proteiny vázající fosfáty genetika   metabolismus   MeSH
• proteolýza MeSH
• proteom genetika   metabolismus   MeSH
• proteomika MeSH
• regulace genové exprese u bakterií genetika   MeSH
• regulon genetika   MeSH
• represorové proteiny genetika   metabolismus   MeSH
• ribozomální proteiny genetika   metabolismus   MeSH
• Synechocystis enzymologie   metabolismus   MeSH
• transkripční faktory genetika   metabolismus   MeSH
• uhlík nedostatek   metabolismus   MeSH
• živiny nedostatek   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Bordetella pertussis is a Gram-negative strictly human pathogen of the respiratory tract and the etiological agent of whooping cough (pertussis). Previously, we have shown that RNA chaperone Hfq is required for virulence of B. pertussis. Furthermore, microarray analysis revealed that a large number of genes are affected by the lack of Hfq. This study represents the first attempt to characterize the Hfq regulon in bacterial pathogen using an integrative omics approach. Gene expression profiles were analyzed by RNA-seq and protein amounts in cell-associated and cell-free fractions were determined by LC-MS/MS technique. Comparative analysis of transcriptomic and proteomic data revealed solid correlation (r2 = 0.4) considering the role of Hfq in post-transcriptional control of gene expression. Importantly, our study confirms and further enlightens the role of Hfq in pathogenicity of B. pertussis as it shows that Δhfq strain displays strongly impaired secretion of substrates of Type III secretion system (T3SS) and substantially reduced resistance to serum killing. On the other hand, significantly increased production of proteins implicated in transport of important metabolites and essential nutrients observed in the mutant seems to compensate for the physiological defect introduced by the deletion of the hfq gene.

• MeSH
• Bordetella pertussis genetika   metabolismus   MeSH
• chromatografie kapalinová MeSH
• genová ontologie MeSH
• lidé MeSH
• protein hostitelského faktoru 1 genetika   metabolismus   MeSH
• proteom MeSH
• proteomika * metody   MeSH
• regulace genové exprese u bakterií * MeSH
• regulon * MeSH
• sekreční systém typu III genetika   metabolismus   MeSH
• stanovení celkové genové exprese * metody   MeSH
• tandemová hmotnostní spektrometrie MeSH
• transkriptom MeSH
• výpočetní biologie metody   MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články 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

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 these genes were affected indirectly by σI The σI regulon, i.e., the genes directly regulated by σI, consists of 16 genes, of which eight (the dhb and yku operons) are involved in iron metabolism. The involvement of σI 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, σI-dependent promoters are relatively information rich in comparison with most other promoters. In summary, this study supplies information about the least-explored σ factor from the industrially important model organism B. subtilisIMPORTANCE In bacteria, σ factors are essential for transcription initiation. Knowledge about their regulons (i.e., genes transcribed from promoters dependent on these σ 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 σI regulon from the industrially important model Gram-positive bacterium Bacillus subtilis We reveal that σI affects expression of ∼130 genes, of which 16 are directly regulated by σI, including genes encoding proteins involved in iron homeostasis. Detailed analysis of promoter elements then identifies unique sequences important for σI-dependent transcription. This study thus provides a comprehensive view on this underexplored component of the B. subtilis transcription machinery.

• MeSH
• Bacillus subtilis genetika   MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• DNA řízené RNA-polymerasy genetika   MeSH
• genetická transkripce * MeSH
• operon MeSH
• promotorové oblasti (genetika) * MeSH
• regulace genové exprese u bakterií * MeSH
• regulon MeSH
• sigma faktor genetika   MeSH
• transkriptom MeSH
• železo metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

BACKGROUND: Identifying regulons of sigma factors is a vital subtask of gene network inference. Integrating multiple sources of data is essential for correct identification of regulons and complete gene regulatory networks. Time series of expression data measured with microarrays or RNA-seq combined with static binding experiments (e.g., ChIP-seq) or literature mining may be used for inference of sigma factor regulatory networks. RESULTS: We introduce Genexpi: a tool to identify sigma factors by combining candidates obtained from ChIP experiments or literature mining with time-course gene expression data. While Genexpi can be used to infer other types of regulatory interactions, it was designed and validated on real biological data from bacterial regulons. In this paper, we put primary focus on CyGenexpi: a plugin integrating Genexpi with the Cytoscape software for ease of use. As a part of this effort, a plugin for handling time series data in Cytoscape called CyDataseries has been developed and made available. Genexpi is also available as a standalone command line tool and an R package. CONCLUSIONS: Genexpi is a useful part of gene network inference toolbox. It provides meaningful information about the composition of regulons and delivers biologically interpretable results.

• MeSH
• Bacteria genetika   MeSH
• časové faktory MeSH
• databáze genetické * MeSH
• Eukaryota genetika   MeSH
• genové regulační sítě * MeSH
• lidé MeSH
• regulace genové exprese * MeSH
• regulon genetika   MeSH
• reprodukovatelnost výsledků MeSH
• Saccharomyces cerevisiae genetika   MeSH
• software * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Bordetella pertussis, the causative agent of human whooping cough (pertussis) produces a complex array of virulence factors in order to establish efficient infection in the host. The RNA chaperone Hfq and small regulatory RNAs are key players in posttranscriptional regulation in bacteria and have been shown to play an essential role in virulence of a broad spectrum of bacterial pathogens. This study represents the first attempt to characterize the Hfq regulon of the human pathogen B. pertussis under laboratory conditions as well as upon passage in the host and indicates that loss of Hfq has a profound effect on gene expression in B. pertussis. Comparative transcriptional profiling revealed that Hfq is required for expression of several virulence factors in B. pertussis cells including the Type III secretion system (T3SS). In striking contrast to the wt strain, T3SS did not become operational in the hfq mutant passaged either through mice or macrophages thereby proving that Hfq is required for the functionality of the B. pertussis T3SS. Likewise, expression of virulence factors vag8 and tcfA encoding autotransporter and tracheal colonization factor, respectively, was strongly reduced in the hfq mutant. Importantly, for the first time we demonstrate that B. pertussis T3SS can be activated upon contact with macrophage cells in vitro.

• MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• bakteriální RNA genetika   metabolismus   MeSH
• Bordetella pertussis genetika   metabolismus   patogenita   MeSH
• buněčné linie MeSH
• faktory virulence rodu Bordetella genetika   metabolismus   MeSH
• infekce bakteriemi rodu Bordetella mikrobiologie   MeSH
• interakce hostitele a patogenu MeSH
• makrofágy metabolismus   mikrobiologie   MeSH
• myši MeSH
• protein hostitelského faktoru 1 nedostatek   genetika   MeSH
• regulace genové exprese u bakterií * MeSH
• regulon MeSH
• sekreční systém typu III genetika   metabolismus   MeSH
• sekreční systém typu V genetika   metabolismus   MeSH
• stanovení celkové genové exprese MeSH
• transkriptom MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The Corynebacterium glutamicum genome codes for 7 sigma subunits (factors) of RNA polymerase (RNAP): primary sigma factor SigA (σ(A)), primary-like SigB and 5 other alternative sigma factors (SigC, SigD, SigE, SigH and SigM). Each sigma factor is responsible for recognizing promoters of genes belonging to a regulon (sigmulon) involved in specific functions of the cell. Most promoters of C. glutamicum housekeeping genes are recognized by RNAP+σ(A), whereas σ(B) is involved in transcription of a large group of genes active during the transition phase between the exponential and stationary growth phases when various stress factors threaten to damage the cell. The σ(H) regulon consists of the genes involved in heat shock response including those coding for regulators and other sigma factors. It seems therefore that σ(H) occupies a central position in the cross-regulated network of sigma factors and controls their concerted response to various stress conditions in C. glutamicum. The σ(M) factor was found to regulate genes responding to oxidative stress. The main role of σ(E) is to activate genes involved in response to a cell surface stress. Promoters of individual classes recognized by different sigma factors are compiled and the respective consensus sequences of their key recognition motifs (-35 and -10 regions) are derived. In a number of genes, two or more promoters controlled by the same or different sigma factors were discovered. These multiple, overlapping or dual promoters contribute to a complex gene transcription control mechanisms that integrate internal and external signals and tune gene expression in cells as required by environmental and physiological conditions.

• MeSH
• Corynebacterium glutamicum genetika   metabolismus   MeSH
• DNA řízené RNA-polymerasy genetika   metabolismus   MeSH
• fyziologický stres genetika   MeSH
• genové regulační sítě MeSH
• molekulární sekvence - údaje MeSH
• promotorové oblasti (genetika) MeSH
• regulace genové exprese u bakterií MeSH
• regulon MeSH
• sekvence aminokyselin MeSH
• sekvence nukleotidů MeSH
• sigma faktor genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

Acne vulgaris doprovázená seboroe, v některých případech i dalšími projevy hyperandrogenémie, patří mezi nejčastější onemocnění pubertálního věku. I když u žen trpících akné, seboroe i lehčím hirsutizmem se nachází ve většině případů normální hladiny androgenů v séru, léčba hormonálními kombinovanými kontraceptivy přináší velmi dobrý léčebný efekt. Obzvláště kombinované preparáty s obsahem antiandrogenů jsou terapií kauzální, neboť blokují androgenní účinek na receptorové úrovni, oslabují aktivitu enzymu 5 alfa-reduktázy a potlačují hypotalamohypofyzární funkce. Nejvýraznější antiandrogenní aktivitu má cyproteronacetát, následován chlormadinon acetátem, dienogestem a drospirenonem. Avšak jen některé z hormonálních kombinovaných přípravků mají přímo schválenou indikaci k léčbě acne vulgaris a seboroe. Z nich zejména kombinované hormonální kontraceptivum s obsahem 35 µg etinylestradiolu a 2 mg cyproteronacetátu patří v dermatologii mezi dlouhodobě ověřený a nejčastěji aplikovaný přípravek (Diane® 35).

Acne vulgaris combined usually with seborrhoea and in some persons with signs of hyperandrogenaemia ranks among the most common conditions in adolescents. In spite of the fact that in females suffering from acne, hyperseborrhoea, and mild forms of hirsutism serum androgen levels are usually not elevated, treatment with combined contraceptive drugs is mostly effective. Drugs contaning anti-androgenic components are the most suitable ones due to the blocking effect on the receptor level for androgens. The activity of the enzyme 5 alpha-reductase is markedly diminished. The most considerable anti-androgenic activity was observed in cyproteronacetate, followed by chlormadinon, dienogest, and drospirenone. Indication of only several combined contraceptive drugs has been approved directly for treatment of acne vulgaris and seborrhoea. The best suitable contraceptive combination contains 35 µg of ethinylestradiol and 2 mg of cyproteronacetate. This combination is the most effective and commonly used one in dermatology (Diane® 35).

• Klíčová slova
• Belara, Jeanine, Loette, Pramino,
• MeSH
• acne vulgaris MeSH
• androgeny agonisté   farmakologie   terapeutické užití   MeSH
• antagonisté androgenů aplikace a dávkování   farmakologie   terapeutické užití   MeSH
• chlormadinon antagonisté a inhibitory   aplikace a dávkování   farmakologie   MeSH
• cyproteronacetát antagonisté a inhibitory   aplikace a dávkování   farmakologie   MeSH
• desogestrel aplikace a dávkování   farmakologie   MeSH
• hyperandrogenismus farmakoterapie   MeSH
• kontraceptiva orální kombinovaná farmakologie   chemie   terapeutické užití   MeSH
• regulon MeSH
• spironolakton aplikace a dávkování   farmakologie   MeSH

• MeSH
• acetylmuramyl-alanyl-isoglutamin aplikace a dávkování   terapeutické užití   MeSH
• bakteriální polysacharidy imunologie   terapeutické užití   MeSH
• dithiokarb aplikace a dávkování   terapeutické užití   MeSH
• fixní kombinace léků MeSH
• hodnocení léčiv metody   využití   MeSH
• imunologické faktory * terapeutické užití   MeSH
• interferony imunologie   účinky léků   MeSH
• interleukiny imunologie   MeSH
• lidé MeSH
• prodigiozan terapeutické užití   MeSH
• regulon * imunologie   účinky léků   MeSH
• selen terapeutické užití   MeSH
• teoretické modely * MeSH
• vitaminy terapeutické užití   MeSH
• Check Tag
• lidé MeSH