Using the method for the identification of promoters recognized by the sporulation specific sigma factor (sigma F), we identified a positive 950 bp Sau3AI DNA fragment in Streptomyces coelicolor A3(2). High-resolution S1-nuclease mapping identified a potential promoter, PF35, in the E. coli two-plasmid system similar to the consensus sequence of Bacillus subtilis promoters recognized by the general stress-response sigma factor (sigma B). However, the putative sigF-dependent promoter, PF35, was inactive in S. coelicolor in the course of differentiation, and it was located divergently in the promoter region directing expression of the chiC gene encoding chitinase. Sequence analysis of the region potentially governed by PF35 revealed two translationally coupled genes encoding proteins similar to bacterial two-component regulatory systems, and with the highest similarity to the two-component system chiS, chiR, regulating chitinase activity in Streptomyces thermoviolaceus. However, the genes had a divergent orientation with respect to the PF35 promoter. Disruption of the S. coelicolor chiR gene appeared to have no obvious effect on growth, morphology, differentiation, and production of pigmented antibiotic actinorhodin and undecylprodigiosin. Moreover, the chiR disruption did not affect the overall chitinase activity.

• MeSH
• bakteriální proteiny chemie   genetika   metabolismus   MeSH
• chitinasy genetika   metabolismus   MeSH
• delece genu MeSH
• klonování DNA * MeSH
• molekulární sekvence - údaje MeSH
• operon MeSH
• promotorové oblasti (genetika) MeSH
• proteinkinasy * MeSH
• regulace genové exprese u bakterií genetika   MeSH
• sekvence aminokyselin MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA MeSH
• sigma faktor MeSH
• Streptomyces enzymologie   genetika   růst a vývoj   MeSH
• transkripční faktory * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny MeSH
• ChiR protein, Streptomyces MeSH Prohlížeč
• ChiS protein, Streptomyces thermoviolaceus MeSH Prohlížeč
• chitinase C-1 MeSH Prohlížeč
• chitinasy MeSH
• FliA protein, Bacteria MeSH Prohlížeč
• proteinkinasy * MeSH
• sigma faktor MeSH
• transkripční faktory * MeSH

A chromosomal DNA fragment of 8992 bp in size that has not been previously identified in Streptococcus agalactiae, was cloned and sequenced from strain 98-D60C. In particular, this 8992-bp fragment contained genes homologous to the sensor histidine kinase gene and the DNA-binding response-regulator gene of Streptococcus pneumoniae, and S. agalactiae bac gene. Structural and genetic features of the 8992-bp fragment were highly similar to those specific for bacterial pathogenicity islands. Analysis of epidemiologically unrelated S. agalactiae strains revealed that this fragment was present only in bac gene-positive strains. The possible origin of the 8992-bp fragment in S. agalactiae and its significance for molecular mechanisms of "bacteria-host" interactions are discussed.

• MeSH
• antigeny bakteriální genetika   MeSH
• bakteriální proteiny genetika   MeSH
• DNA bakterií analýza   MeSH
• faktory virulence genetika   MeSH
• genomové ostrovy genetika   MeSH
• lidé MeSH
• molekulární sekvence - údaje MeSH
• regulace genové exprese u bakterií genetika   MeSH
• sekvenční homologie nukleových kyselin MeSH
• Streptococcus agalactiae * genetika   patogenita   MeSH
• Streptococcus pneumoniae genetika   MeSH
• těhotenství MeSH
• Check Tag
• lidé MeSH
• těhotenství MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• antigeny bakteriální MeSH
• bakteriální proteiny MeSH
• DNA bakterií MeSH
• faktory virulence MeSH

BACKGROUND: Integration of multi-omics data can provide a more complex view of the biological system consisting of different interconnected molecular components, the crucial aspect for developing novel personalised therapeutic strategies for complex diseases. Various tools have been developed to integrate multi-omics data. However, an efficient multi-omics framework for regulatory network inference at the genome level that incorporates prior knowledge is still to emerge. RESULTS: We present IntOMICS, an efficient integrative framework based on Bayesian networks. IntOMICS systematically analyses gene expression, DNA methylation, copy number variation and biological prior knowledge to infer regulatory networks. IntOMICS complements the missing biological prior knowledge by so-called empirical biological knowledge, estimated from the available experimental data. Regulatory networks derived from IntOMICS provide deeper insights into the complex flow of genetic information on top of the increasing accuracy trend compared to a published algorithm designed exclusively for gene expression data. The ability to capture relevant crosstalks between multi-omics modalities is verified using known associations in microsatellite stable/instable colon cancer samples. Additionally, IntOMICS performance is compared with two algorithms for multi-omics regulatory network inference that can also incorporate prior knowledge in the inference framework. IntOMICS is also applied to detect potential predictive biomarkers in microsatellite stable stage III colon cancer samples. CONCLUSIONS: We provide IntOMICS, a framework for multi-omics data integration using a novel approach to biological knowledge discovery. IntOMICS is a powerful resource for exploratory systems biology and can provide valuable insights into the complex mechanisms of biological processes that have a vital role in personalised medicine.

• Klíčová slova
• Bayesian networks, Integrative analysis, Knowledge discovery, Multimodal omics, Regulatory networks,
• MeSH
• algoritmy MeSH
• Bayesova věta MeSH
• genové regulační sítě MeSH
• lidé MeSH
• nádory tračníku * MeSH
• systémová biologie metody   MeSH
• variabilita počtu kopií segmentů DNA * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

The BvgS/BvgA two-component system controls expression of ∼550 genes of Bordetella pertussis, of which, ∼245 virulence-related genes are positively regulated by the BvgS-phosphorylated transcriptional regulator protein BvgA (BvgA∼P). We found that a single G-to-T nucleotide transversion in the 5'-untranslated region (5'-UTR) of the rplN gene enhanced transcription of the ribosomal protein operon and of the rpoA gene and provoked global dysregulation of B. pertussis genome expression. This comprised overproduction of the alpha subunit (RpoA) of the DNA-dependent RNA polymerase, downregulated BvgA and BvgS protein production, and impaired production and secretion of virulence factors by the mutant. Nonetheless, the mutant survived like the parental bacteria for >2 weeks inside infected primary human macrophages and persisted within infected mouse lungs for a longer period than wild-type B. pertussis These observations suggest that downregulation of virulence factor production by bacteria internalized into host cells may enable persistence of the whooping cough agent in the airways.IMPORTANCE We show that a spontaneous mutation that upregulates transcription of an operon encoding ribosomal proteins and causes overproduction of the downstream-encoded α subunit (RpoA) of RNA polymerase causes global effects on gene expression levels and proteome composition of Bordetella pertussis Nevertheless, the resulting important downregulation of the BvgAS-controlled expression of virulence factors of the whooping cough agent did not compromise its capacity to persist for prolonged periods inside primary human macrophage cells, and it even enhanced its capacity to persist in infected mouse lungs. These observations suggest that the modulation of BvgAS-controlled expression of virulence factors may occur also during natural infections of human airways by Bordetella pertussis and may possibly account for long-term persistence of the pathogen within infected cells of the airways.

• Klíčová slova
• Bordetella pertussis, host-pathogen interactions, intracellular bacteria, macrophages, two-component regulatory systems, virulence regulation,
• Publikační typ
• časopisecké články MeSH

To elucidate the physiological meaning of OmpR-dependent expression of invasin gene (inv) inhibition in Yersinia enterocolitica, the function of the EnvZ/OmpR regulatory pathway in osmoregulation of inv expression was analyzed in detail. The osmoregulation of inv expression was found to be a multifaceted process involving both OmpR-dependent and -independent mechanisms. Analysis of inv transcription in strains lacking OmpR or EnvZ proteins indicated that kinase EnvZ is not the only regulator of OmpR phosphorylation. Using the transcriptional inv::lacZ fusion in a heterologous system (Escherichia coli) we tried to clarify the role of OmpR in the inv regulatory circuit composed of negative (H-NS) and positive (RovA) regulators of inv gene transcription. We were able to show a significant increase in inv expression in E. coli ompR background under H-NS( Ecoli )-repressed condition. Moreover, H-NS-mediated inv repression was relieved when RovA of Y. enterocolitica was expressed from a plasmid. Furthermore, we showed that RovA may activate inv expression irrespective on the presence of H-NS protein. Using this strategy we showed that OmpR of Y. enterocolitica decrease RovA-mediated inv activation.

• MeSH
• bakteriální adheziny genetika   MeSH
• bakteriální chromozomy genetika   MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• Escherichia coli genetika   metabolismus   MeSH
• fúze genů MeSH
• genetická transkripce MeSH
• lac operon genetika   MeSH
• osmolární koncentrace MeSH
• promotorové oblasti (genetika) MeSH
• regulace genové exprese u bakterií * MeSH
• trans-aktivátory genetika   metabolismus   MeSH
• Yersinia enterocolitica genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální adheziny MeSH
• bakteriální proteiny MeSH
• invasin, Yersinia MeSH Prohlížeč
• osmolarity response regulator proteins MeSH Prohlížeč
• trans-aktivátory MeSH

Bordetella pertussis is the causative agent of human whooping cough, a highly contagious respiratory disease which despite vaccination programs remains the major cause of infant morbidity and mortality. The requirement of the RNA chaperone Hfq for virulence of B. pertussis suggested that Hfq-dependent small regulatory RNAs are involved in the modulation of gene expression. High-throughput RNA sequencing revealed hundreds of putative noncoding RNAs including the RgtA sRNA. Abundance of RgtA is strongly decreased in the absence of the Hfq protein and its expression is modulated by the activities of the two-component regulatory system BvgAS and another response regulator RisA. Whereas RgtA levels were elevated under modulatory conditions or in the absence of bvg genes, deletion of the risA gene completely abolished RgtA expression. Profiling of the ΔrgtA mutant in the ΔbvgA genetic background identified the BP3831 gene encoding a periplasmic amino acid-binding protein of an ABC transporter as a possible target gene. The results of site-directed mutagenesis and in silico analysis indicate that RgtA base-pairs with the region upstream of the start codon of the BP3831 mRNA and thereby weakens the BP3831 protein production. Furthermore, our data suggest that the function of the BP3831 protein is related to transport of glutamate, an important metabolite in the B. pertussis physiology. We propose that the BvgAS/RisA interplay regulates the expression of RgtA which upon infection, when glutamate might be scarce, attenuates translation of the glutamate transporter and thereby assists in adaptation of the pathogen to other sources of energy.

• Klíčová slova
• Bordetella, riboregulation, sRNA, signal transduction, translational repression,
• MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• Bordetella pertussis genetika   metabolismus   MeSH
• glutamáty metabolismus   MeSH
• lidé MeSH
• malá nekódující RNA genetika   MeSH
• regulace genové exprese u bakterií MeSH
• signální transdukce * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny MeSH
• glutamáty MeSH
• malá nekódující RNA MeSH

The two-component system (TCS), which is one of the most evolutionarily conserved signaling pathway systems, has been known to regulate multiple biological activities and environmental responses in plants. Significant progress has been made in characterizing the biological functions of the TCS components, including signal receptor histidine kinase (HK) proteins, signal transducer histidine-containing phosphotransfer proteins, and effector response regulator proteins. In this review, our scope is focused on the diverse structure, subcellular localization, and interactions of the HK proteins, as well as their signaling functions during development and environmental responses across different plant species. Based on data collected from scientific studies, knowledge about acting mechanisms and regulatory roles of HK proteins is presented. This comprehensive summary ofthe HK-related network provides a panorama of sophisticated modulating activities of HK members and gaps in understanding these activities, as well as the basis for developing biotechnological strategies to enhance the quality of crop plants.

• Klíčová slova
• phosphorelay, plant development, plant growth, plant histidine kinases, stress responses, two-component system,
• MeSH
• histidin * MeSH
• histidinkinasa MeSH
• proteinkinasy MeSH
• rostliny MeSH
• vývoj rostlin * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• histidin * MeSH
• histidinkinasa MeSH
• proteinkinasy MeSH

The cytokinin response factors (CRFs) are a group of related AP2/ERF transcription factors that are transcriptionally induced by cytokinin. Here we explore the role of the CRFs in Arabidopsis thaliana growth and development by analyzing lines with decreased and increased CRF function. While single crf mutations have no appreciable phenotypes, disruption of multiple CRFs results in larger rosettes, delayed leaf senescence, a smaller root apical meristem (RAM), reduced primary and lateral root growth, and, in etiolated seedlings, shorter hypocotyls. In contrast, overexpression of CRFs generally results in the opposite phenotypes. The crf1,2,5,6 quadruple mutant is embryo lethal, indicating that CRF function is essential for embryo development. Disruption of the CRFs results in partially insensitivity to cytokinin in a root elongation assay and affects the basal expression of a significant number of cytokinin-regulated genes, including the type-A ARRs, although it does not impair the cytokinin induction of the type-A ARRs. Genes encoding homeobox transcription factors are mis-expressed in the crf1,3,5,6 mutant, including STIMPY/WOX9 that is required for root and shoot apical meristem maintenance roots and which has previously been linked to cytokinin. These results indicate that the CRF transcription factors play important roles in multiple aspects of plant growth and development, in part through a complex interaction with cytokinin signaling.

• Klíčová slova
• cell division, cytokinin, plant development, root meristem, senescence, transcription factors, two-component signaling,
• MeSH
• Arabidopsis genetika   růst a vývoj   fyziologie   MeSH
• cytokininy metabolismus   MeSH
• exprese genu MeSH
• fenotyp MeSH
• homeodoménové proteiny genetika   metabolismus   MeSH
• kořeny rostlin genetika   růst a vývoj   fyziologie   MeSH
• meristém genetika   růst a vývoj   fyziologie   MeSH
• mutace MeSH
• proteiny huseníčku genetika   metabolismus   MeSH
• regulace genové exprese u rostlin MeSH
• regulátory růstu rostlin metabolismus   MeSH
• semenáček genetika   růst a vývoj   fyziologie   MeSH
• signální transdukce * MeSH
• transkripční faktory genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• cytokininy MeSH
• homeodoménové proteiny MeSH
• proteiny huseníčku MeSH
• regulátory růstu rostlin MeSH
• transkripční faktory MeSH

In vitro fertilization (IVF) is fraught with problems and currently proteomics approaches are being tried out to examine the microenvironment of the follicle in order to assess biological and immunological parameters that may affect its development. Additionally, better understanding of reproductive process may help increase IVF birth rate per embryo transfer and at the same time avoid spontaneous miscarriages or life threatening conditions such as ovarian hyperstimulation syndrome. The primary aim of this study was to search for specific differences in protein composition of human follicular fluid (HFF) and plasma in order to identify proteins that accumulate or are absent in HFF. Depletion of abundant proteins combined with multidimensional protein fractionation allowed the study of middle- and lower-abundance proteins. Paired comparison study examining HFF with plasma/serum from women undergoing successful IVF revealed important differences in the protein composition which may improve our knowledge of the follicular microenvironment and its biological role. This study showed involvement of innate immune function of complement cascade in HFF. Complement inhibition and the presence of C-terminal fragment of perlecan suggested possible links to angiogenesis which is a vital process in folliculogenesis and placental development. Differences in proteins associated with blood coagulation were also found in the follicular milieu. Several specific proteins were observed, many of which have not yet been associated with follicle/oocyte maturation. These proteins together with their regulatory pathways may play a vital role in the reproductive process.

• MeSH
• 2D gelová elektroforéza MeSH
• fertilizace in vitro * MeSH
• folikulární tekutina chemie   metabolismus   MeSH
• hemolýza MeSH
• heparansulfát proteoglykany analýza   MeSH
• imunoblotting MeSH
• klusterin analýza   MeSH
• komplement 4 analýza   metabolismus   MeSH
• komplement C3 analýza   metabolismus   MeSH
• lidé MeSH
• proteom analýza   metabolismus   MeSH
• reprodukovatelnost výsledků MeSH
• shluková analýza MeSH
• signální transdukce MeSH
• vysokoúčinná kapalinová chromatografie MeSH
• Check Tag
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• heparansulfát proteoglykany MeSH
• klusterin MeSH
• komplement 4 MeSH
• komplement C3 MeSH
• perlecan MeSH Prohlížeč
• proteom MeSH

Multistep phosphorelay (MSP) signaling integrates hormonal and environmental signals to control both plant development and adaptive responses. Type-A RESPONSE REGULATOR (RRA) genes, the downstream members of the MSP cascade and cytokinin primary response genes, are thought to mediate primarily the negative feedback regulation of (cytokinin-induced) MSP signaling. However, transcriptional data also suggest the involvement of RRA genes in stress-related responses. By employing evolutionary conservation with the well-characterized Arabidopsis thaliana RRA genes, we identified five and 38 novel putative RRA genes in Brassica oleracea and Brassica napus, respectively. Our phylogenetic analysis suggests the existence of gene-specific selective pressure, maintaining the homologs of ARR3, ARR6, and ARR16 as singletons during the evolution of Brassicaceae. We categorized RRA genes based on the kinetics of their cytokinin-mediated up-regulation and observed both similarities and specificities in this type of response across Brassicaceae species. Using bioinformatic analysis and experimental data demonstrating the cytokinin and abiotic stress responsiveness of the A. thaliana-derived TCSv2 reporter, we unveil the mechanistic conservation of cytokinin- and stress-mediated up-regulation of RRA genes in B. rapa and B. napus. Notably, we identify partial cytokinin dependency of cold stress-induced RRA transcription, thus further demonstrating the role of cytokinin signaling in crop adaptive responses.

• Klíčová slova
• Arabidopsis thaliana, Brassica napus, Brassica oleracea, Brassica rapa, cytokinins, multistep phosphorelay, osmotic stress, salinity, two-component signaling, type-A response regulator,
• MeSH
• Arabidopsis genetika   fyziologie   metabolismus   MeSH
• Brassica napus genetika   fyziologie   metabolismus   MeSH
• Brassica * genetika   fyziologie   metabolismus   MeSH
• cytokininy * metabolismus   MeSH
• fylogeneze MeSH
• fyziologický stres * MeSH
• regulace genové exprese u rostlin MeSH
• regulátory růstu rostlin metabolismus   MeSH
• rostlinné proteiny * genetika   metabolismus   MeSH
• signální transdukce MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• cytokininy * MeSH
• regulátory růstu rostlin MeSH
• rostlinné proteiny * MeSH