Bacteria have evolved structured RNAs that can associate with RNA polymerase (RNAP). Two of them have been known so far-6S RNA and Ms1 RNA but it is unclear if any other types of RNAs binding to RNAP exist in bacteria. To identify all RNAs interacting with RNAP and the primary σ factors, we have established and performed native RIP-seq in Bacillus subtilis, Corynebacterium glutamicum, Streptomyces coelicolor, Mycobacterium smegmatis and the pathogenic Mycobacterium tuberculosis. Besides known 6S RNAs in B. subtilis and Ms1 in M. smegmatis, we detected MTS2823, a homologue of Ms1, on RNAP in M. tuberculosis. In C. glutamicum, we discovered novel types of structured RNAs that associate with RNAP. Furthermore, we identified other species-specific RNAs including full-length mRNAs, revealing a previously unknown landscape of RNAs interacting with the bacterial transcription machinery.

• MeSH
• Bacillus subtilis genetika   metabolismus   MeSH
• bakteriální proteiny * metabolismus   genetika   MeSH
• bakteriální RNA * metabolismus   genetika   MeSH
• Corynebacterium glutamicum genetika   metabolismus   MeSH
• DNA řízené RNA-polymerasy * metabolismus   genetika   MeSH
• genetická transkripce MeSH
• konformace nukleové kyseliny MeSH
• Mycobacterium smegmatis genetika   metabolismus   enzymologie   MeSH
• Mycobacterium tuberculosis genetika   metabolismus   MeSH
• nekódující RNA MeSH
• regulace genové exprese u bakterií MeSH
• sigma faktor * metabolismus   genetika   MeSH
• Streptomyces coelicolor genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• 6S RNA MeSH Prohlížeč
• bakteriální proteiny * MeSH
• bakteriální RNA * MeSH
• DNA řízené RNA-polymerasy * MeSH
• nekódující RNA MeSH
• sigma faktor * MeSH

In this paper, correlation analysis of protein and mRNA levels in the soil dwelling bacteria Streptomyces coelicolor (S. coelicolor M145) is presented during development of the population as it grew in liquid medium using three biological and two technical replicates, measured during exponential growth, and its entry into the stationary phase. The proteome synthesis time series are compared with the gene expression time series measured previously under identical experimental conditions. Results reveal that about one third of protein/mRNA synthesis profiles are well correlated while another third are correlated negatively. Functional analysis of the highly correlated groups is presented. Based on numerical simulation, the negative correlation between protein and mRNA is shown to be caused by the difference between the rate of translation and protein degradation.

• Klíčová slova
• Streptomyces, computational modeling, mRNA/protein expression, mass spectrometry, proteins functional analysis,
• MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• messenger RNA genetika   metabolismus   MeSH
• proteom analýza   metabolismus   MeSH
• půda chemie   MeSH
• regulace genové exprese u bakterií MeSH
• stanovení celkové genové exprese MeSH
• Streptomyces coelicolor genetika   růst a vývoj   metabolismus   MeSH
• transkriptom * MeSH
• vývojová regulace genové exprese * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny MeSH
• messenger RNA MeSH
• proteom MeSH
• půda 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

Streptomyces coelicolor genome carries two apparently paralogous genes, SCO4164 and SCO5854, that encode putative thiosulfate sulfurtransferases (rhodaneses). These genes (and their presumed translation products) are highly conserved and widely distributed across actinobacterial genomes. The SCO4164 knockout strain was unable to grow on minimal media with either sulfate or sulfite as the sole sulfur source. The SCO5854 mutant had no growth defects in the presence of various sulfur sources; however, it produced significantly less amounts of actinorhodin. Furthermore, we discuss possible links between basic interconversions of inorganic sulfur species and secondary metabolism in S. coelicolor.

• MeSH
• anthrachinony metabolismus   MeSH
• antibakteriální látky metabolismus   MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• kultivační média metabolismus   MeSH
• sekundární metabolismus MeSH
• sírany metabolismus   MeSH
• Streptomyces coelicolor enzymologie   genetika   růst a vývoj   metabolismus   MeSH
• thiosulfátsulfurtransferasa genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• actinorhodin MeSH Prohlížeč
• anthrachinony MeSH
• antibakteriální látky MeSH
• bakteriální proteiny MeSH
• kultivační média MeSH
• sírany MeSH
• thiosulfátsulfurtransferasa MeSH

Transcriptional factors of the GntR family regulate numerous physiological and morphological processes in response to the nutrient state of bacterial cells. The number of GntR transcriptional factors in genomes of soil-dwelling actinomycetes is one of the highest among bacteria, reflecting both the large size of their chromosomes and the complex ecological niche that they occupy. However, very little is known about the roles of GntRs in actinomycete biology. Here, we analyzed the genome of model actinomycete, Streptomyces coelicolor A3(2), in an attempt to gain new insights into the function of GntR family. All 56 GntR proteins of M145 strain were classified into FadR, HutC, MocR, YtrA, and DevA subfamilies according to their secondary structure. We then checked for the presence of GntR orthologs in six other sequenced Streptomyces and one Kitasatospora genomes, revealing that 12 GntRs were conserved in all analyzed strains. Genomic analysis of the less studied YtrA type regulators revealed 160 sequences present in 88 members of Coriobacteridae, Rubrobacteridae, and Actinobacteridae subclasses. These proteins form seven dense clusters on the consensus phylogenetic tree and their genes are usually co-located with the genes for transport proteins. Probable operator sites were identified for orthologous groups of Sco0823 and Sco3812 proteins. All S. coelicolor YtrA-like regulatory genes (SCO0823, SCO1728, SCO3812) were analyzed at transcriptional level, knocked out, and introduced on moderate copy number plasmid in M145 strain. Also, gene SCO0824, a part of putative SCO0823 operon, was studied. Results of these experiments are discussed here.

• MeSH
• antibakteriální látky biosyntéza   MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• databáze genetické MeSH
• DNA vazebné proteiny genetika   metabolismus   MeSH
• fenotyp MeSH
• fylogeneze MeSH
• genetická transkripce * MeSH
• genom bakteriální MeSH
• genový knockout MeSH
• glukuronidasa metabolismus   MeSH
• multigenová rodina * MeSH
• otevřené čtecí rámce MeSH
• regulace genové exprese u bakterií * MeSH
• Streptomyces coelicolor klasifikace   genetika   metabolismus   MeSH
• transkripční faktory metabolismus   MeSH
• výpočetní biologie metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• antibakteriální látky MeSH
• bakteriální proteiny MeSH
• DNA vazebné proteiny MeSH
• glukuronidasa MeSH
• transkripční faktory MeSH

UNLABELLED: Protein turnover is essential in all living organisms for the maintenance of normal cell physiology. In eukaryotes, most cellular protein turnover involves the ubiquitin-proteasome pathway, in which proteins tagged with ubiquitin are targeted to the proteasome for degradation. In contrast, most bacteria lack a proteasome but harbor proteases for protein turnover. However, some actinobacteria, such as mycobacteria, possess a proteasome in addition to these proteases. A prokaryotic ubiquitination-like tagging process in mycobacteria was described and was named pupylation: proteins are tagged with Pup (prokaryotic ubiquitin-like protein) and directed to the proteasome for degradation. We report pupylation in another actinobacterium, Streptomyces coelicolor. Both the morphology and life cycle of Streptomyces species are complex (formation of a substrate and aerial mycelium followed by sporulation), and these bacteria are prolific producers of secondary metabolites with important medicinal and agricultural applications. The genes encoding the pupylation system in S. coelicolor are expressed at various stages of development. We demonstrated that pupylation targets numerous proteins and identified 20 of them. Furthermore, we established that abolition of pupylation has substantial effects on morphological and metabolic differentiation and on resistance to oxidative stress. In contrast, in most cases, a proteasome-deficient mutant showed only modest perturbations under the same conditions. Thus, the phenotype of the pup mutant does not appear to be due solely to defective proteasomal degradation. Presumably, pupylation has roles in addition to directing proteins to the proteasome. IMPORTANCE: Streptomyces spp. are filamentous and sporulating actinobacteria, remarkable for their morphological and metabolic differentiation. They produce numerous bioactive compounds, including antifungal, antibiotic, and antitumor compounds. There is therefore considerable interest in understanding the mechanisms by which Streptomyces species regulate their complex physiology and production of bioactive compounds. We studied the role in Streptomyces of pupylation, a posttranslational modification that tags proteins that are then directed to the proteasome for degradation. We demonstrated that the absence of pupylation had large effects on morphological differentiation, antibiotic production, and resistance to oxidative stress in S. coelicolor. The phenotypes of pupylation and proteasome-defective mutants differed and suggest that pupylation acts in a proteasome-independent manner in addition to its role in proteasomal degradation.

• MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• delece genu MeSH
• molekulární sekvence - údaje MeSH
• posttranslační úpravy proteinů MeSH
• sekvence aminokyselin MeSH
• sekvenční seřazení MeSH
• Streptomyces coelicolor genetika   růst a vývoj   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny MeSH

BACKGROUND: Bacterial spore germination is a developmental process during which all required metabolic pathways are restored to transfer cells from their dormant state into vegetative growth. Streptomyces are soil dwelling filamentous bacteria with complex life cycle, studied mostly for they ability to synthesize secondary metabolites including antibiotics. RESULTS: Here, we present a systematic approach that analyzes gene expression data obtained from 13 time points taken over 5.5 h of Streptomyces germination. Genes whose expression was significantly enhanced/diminished during the time-course were identified, and classified to metabolic and regulatory pathways. The classification into metabolic pathways revealed timing of the activation of specific pathways during the course of germination. The analysis also identified remarkable changes in the expression of specific sigma factors over the course of germination. Based on our knowledge of the targets of these factors, we speculate on their possible roles during germination. Among the factors whose expression was enhanced during the initial part of germination, SigE is though to manage cell wall reconstruction, SigR controls protein re-aggregation, and others (SigH, SigB, SigI, SigJ) control osmotic and oxidative stress responses. CONCLUSIONS: From the results, we conclude that most of the metabolic pathway mRNAs required for the initial phases of germination were synthesized during the sporulation process and stably conserved in the spore. After rehydration in growth medium, the stored mRNAs are being degraded and resynthesized during first hour. From the analysis of sigma factors we conclude that conditions favoring germination evoke stress-like cell responses.

• MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• časové faktory MeSH
• reakce na tepelný šok genetika   MeSH
• stanovení celkové genové exprese * MeSH
• Streptomyces coelicolor genetika   růst a vývoj   metabolismus   fyziologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny MeSH

The aim of this study was to contribute to clarifying the role of 6S RNA in the development and control of antibiotic biosynthesis in Streptomyces coelicolor. Due to the low energetic cost of gene silencing via 6S RNA, it is an easy and rapid means of down-regulating the expression of specific genes in response to signals from changes in the environment. The expression of 6S RNA in S. coelicolor is not constitutive, and its accumulation is adapted to changes in nutritional conditions. The 6S RNA of S. coelicolor is capable of interacting with RNA polymerase β β' subunits and is a template for the transcription of short pRNAs. Deletion of the ssrS gene from S. coelicolor affects the growth rate and causes changes in the expression of several pathway-specific genes involved in actinorhodin biosynthesis. The complementation of the ΔssrS strain with ssrS gene restored the wild-type levels of growth and actinorhodin production. We conclude that 6S RNA contributes to the optimization of cellular adaptation and is an important factor involved in the regulation of growth and expression of key genes for the biosynthesis of actinorhodin.

• MeSH
• antibakteriální látky biosyntéza   MeSH
• bakteriální RNA genetika   metabolismus   MeSH
• delece genu MeSH
• DNA řízené RNA-polymerasy metabolismus   MeSH
• nekódující RNA genetika   metabolismus   MeSH
• regulace genové exprese u bakterií * MeSH
• Streptomyces coelicolor genetika   růst a vývoj   metabolismus   MeSH
• testy genetické komplementace MeSH
• vazba proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• 6S RNA MeSH Prohlížeč
• antibakteriální látky MeSH
• bakteriální RNA MeSH
• DNA řízené RNA-polymerasy MeSH
• nekódující RNA MeSH
• RNA polymerase beta subunit MeSH Prohlížeč

The cell wall of the model actinomycete Streptomyces coelicolor M145 has recently been shown to contain the novel glycopolymer teichulosonic acid. The major building block of this polymer is 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid (Kdn), suggesting initial clues about the genetic control of biosynthesis of this cell wall component. Here, through genome mining and gene knockouts, we demonstrate that the sco4879-sco4882 genomic region of S. coelicolor M145 is necessary for biosynthesis of teichulosonic acid. Specifically, mutants carrying individual knockouts of sco4879, sco4880 and sco4881 genes do not produce Kdn-containing glycopolymer and instead accumulate the minor cell wall component poly(diglycosyl 1-phosphate). Our studies provide evidence that this region is at least partly responsible for biosynthesis of Kdn, whereas flanking genes might control the other steps of teichulosonic acid formation.

• MeSH
• bakteriální polysacharidy biosyntéza   MeSH
• buněčná stěna genetika   metabolismus   MeSH
• data mining MeSH
• DNA bakterií genetika   MeSH
• inzerční mutageneze MeSH
• klonování DNA MeSH
• kyseliny cukerné metabolismus   MeSH
• magnetická rezonanční spektroskopie MeSH
• Streptomyces coelicolor genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• 3-deoxyglycero-galacto-nonulosonic acid MeSH Prohlížeč
• bakteriální polysacharidy MeSH
• DNA bakterií MeSH
• kyseliny cukerné 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