Systems-wide analysis of the GATC-binding nucleoid-associated protein Gbn and its impact on Streptomyces development
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ABSTRACT:
PROVIDER: PRJNA697922 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13577922.fastq.gz | Fastqsanger.gz | |||
| SRR13577923.fastq.gz | Fastqsanger.gz | |||
| SRR13577924.fastq.gz | Fastqsanger.gz | |||
| SRR13577925.fastq.gz | Fastqsanger.gz |
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Project description:We report the regulatory effect of a novel family of nucleoid-associated protein in Streptomyces coelicolor
2022-04-02 | GSE186136 | GEO
Project description:We report the DNA binding profile of a novel family of nucleoid-associated protein in Streptomyces coelicolor
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Project description:Systems-wide analysis of the GATC-binding nucleoid-associated protein Gbn and its impact on Streptomyces development
| PRJNA772719 | ENA
Project description:Nucleoid-associated proteins (NAPs) are small, highly abundant regulators with low sequence specificity and pleiotropic mutant phenotypes. They are involved in transcriptional and post-transcriptional control of gene expression, DNA protection/repair and nucleoid structuring. Discovery of the major NAPs has been largely haphazard and based with the Enterobacteriaceae, although some Actinomycete-specific NAPs (Mdp1, Lsr2, sIHF) are known. Here, we use LC-MS/MS to systematically search for novel NAPs in isolated nucleoids of the model actinomycete Streptomyces coelicolor. Based on the criteria of high abundance (emPAI) and predicted DNA-binding ability (DNAbinder) we identified a set of around twenty proteins with a good probability of being NAPs. The approach was apparently successful as the set included known major NAPs HupA, sIHF and Lsr2 as well as the global regulators BldD and CRP. It also included a number of proteins whose functions are not yet known (SCO0204, SCO3013, SCO4232, SCO4199 and SCO1839) which provide a useful set of candidates for further study.
2013-04-24 | PRD000736 | Pride
Project description:Two component sensor-response regulator systems (TCSs) are very common in the genomes of the Streptomyces species that have been fully sequenced to date. It has been suggested that this large number is an evolutionary response to the variable environment that Streptomyces encounter in soil. Notwithstanding this, TCSs are also more common in the sequenced genomes of other Actinomycetales when these are compared to the genomes of most other eubacteria. In this study, we have used DNA/DNA genome microarray analysis to compare fourteen Streptomyces species and one closely related genus to Streptomyces coelicolor in order to identify a core group of such systems. This core group is compared to the syntenous and non-syntenous TCSs present in the genome sequences of other Actinomycetales in order to separate the systems into those present in Actinomycetales in general, the Streptomyces specific systems and the species specific systems. Horizontal transfer does not seem to play a very important role in the evolution of the TCS complement analyzed in this study. However, cognate pairs do not necessarily seem to evolve at the same pace, which may indicate the evolutionary responses to environmental variation may be reflected differently in sequence changes within the two components of the TCSs. The overall analysis allowed subclassification of the orphan TCSs and the TCS cognate pairs and identification of possible targets for further study using gene knockouts, gene overexpression, reporter genes and yeast two hybrid analysis.
2009-01-31 | GSE13621 | GEO
Project description:Two component sensor-response regulator systems (TCSs) are very common in the genomes of the Streptomyces species that have been fully sequenced to date. It has been suggested that this large number is an evolutionary response to the variable environment that Streptomyces encounter in soil. Notwithstanding this, TCSs are also more common in the sequenced genomes of other Actinomycetales when these are compared to the genomes of most other eubacteria. In this study, we have used DNA/DNA genome microarray analysis to compare fourteen Streptomyces species and one closely related genus to Streptomyces coelicolor in order to identify a core group of such systems. This core group is compared to the syntenous and non-syntenous TCSs present in the genome sequences of other Actinomycetales in order to separate the systems into those present in Actinomycetales in general, the Streptomyces specific systems and the species specific systems. Horizontal transfer does not seem to play a very important role in the evolution of the TCS complement analyzed in this study. However, cognate pairs do not necessarily seem to evolve at the same pace, which may indicate the evolutionary responses to environmental variation may be reflected differently in sequence changes within the two components of the TCSs. The overall analysis allowed subclassification of the orphan TCSs and the TCS cognate pairs and identification of possible targets for further study using gene knockouts, gene overexpression, reporter genes and yeast two hybrid analysis. DNA/DNA comparative analysis using the University of Surrey PCR Microarray chip
2010-06-24 | E-GEOD-13621 | biostudies-arrayexpress
Project description:Bacterial chromosome structure is, to a great extent, organized by a diverse group of proteins collectively referred to as nucleoid-associated proteins (NAPs). Many NAPs have been well studied in Streptomyces, including Lsr2, HupA, HupS, and sIHF. Here, we show that SCO1839 represents a novel family of Actinobacteria NAPs and recognizes a consensus sequence consisting of GATC followed by (A/T)T. The protein, which is expressed in particular during sporulation, was designated Gbn for GATC-binding NAP. Deletion of gbn led to alterations in development and antibiotic production in Streptomyces coelicolor. Chromatin immunoprecipitation sequencing (ChIP-Seq) detected more than 2,800 binding regions, encompassing around 3,600 GATCWT motifs. This amounts to 55% of all such sequences in the S. coelicolor genome. DNA binding of Gbn in vitro minimally changes DNA conformation, suggesting a modest role in chromosome organization only, in addition to a gene regulatory role. Transcriptomics analysis showed that Gbn binding generally leads to reduced gene expression. The DNA binding profiles were nearly identical between vegetative and aerial growth. Exceptions are SCO1311 and SCOt32, for a tRNA editing enzyme and a tRNA that recognizes the rare leucine codon CUA, respectively, which nearly exclusively bound during vegetative growth. Taken together, our data show that Gbn is a highly pleiotropic NAP that impacts growth and development in streptomycetes. IMPORTANCE A large part of the chemical space of bioactive natural products is derived from Actinobacteria. Many of the biosynthetic gene clusters for these compounds are cryptic; in others words, they are expressed in nature but not in the laboratory. Understanding the global regulatory networks that control gene expression is key to the development of approaches to activate this biosynthetic potential. Chromosome structure has a major impact on the control of gene expression in eukaryotes. In bacteria, the organization of chromosome structure is mediated by multiple factors, including macromolecular biophysics processes, biological processes, and, more importantly, a diverse group of proteins referred to collectively as nucleoid-associated proteins (NAPs). We here present the discovery of a novel and extremely pleiotropic NAP, which we refer to as Gbn. Gbn is an Actinobacteria-specific protein that binds to GATC sequences, with a subtle but broad effect on global gene expression, especially during the late developmental stage. The discovery of Gbn is a new step toward better understanding of how gene expression and chromosome structure are governed in antibiotic-producing streptomycetes.
| S-EPMC9239103 | biostudies-literature
Project description:HU is a conserved prokaryotic nucleoid-associated protein known for its role in DNA binding and maintaining negative supercoils in DNA. HU also binds to a few RNAs but the natural targets are unknown. To understand the biology of HU interactions with RNA in Escherichia coli, potential HU-RNA in vivo complexes were immunoprecipitated and bound RNAs were examined by hybridization to whole-genome tiling arrays. We observed HU associations with rRNA, multiple tRNAs, a few sRNAs and a small, distinct set of mRNAs. More importantly, we also identified associations between HU and ten intragenic non-coding (nonc) RNAs, two of which are homologous to the annotated Bacterial Interspersed Mosaic Elements (BIME) and boxC elements; the other eight RNAs have not been annotated. We confirmed binding of HU to BIME RNA in vitro. Since HU and some unidentified RNAs have been implicated in the nucleoid structure, we explored an idea that HU, along with some or all of the nonc RNA species discovered here bind to BIME and/or boxC repeats to condense chromosomal DNA in a specific fashion. We propose that nonc RNAs may interact with both HU and DNA repeats to form ternary complexes, which are the anchoring points separating different chromosomal domains.
2012-12-07 | GSE28565 | GEO
Project description:In order to define the impact of phosphate (Pi) availability on cellular metabolism the project aimed to perform a comparative analysis of the proteomes of two Streptomyces strains with different abilities to produce antibiotics, S. coelicolor and S. lividans as well as of the pptA mutant of S. lividans, grown low (1mM) and high (5mM) phosphate (Pi) availability conditions. Interestingly, in contrast to most Streptomyces species, S. coelicolor produces more antibiotics in Pi proficiency than in Pi limitation, S. lividans does not produce antibiotics in any Pi conditions and the pptA mutant produces antibiotics only in Pi limitation. This in-depth proteomic comparison of three Streptomyces strains (S. coelicolor, S. lividans wt and pptA mutant), in different growth conditions (time and Pi concentration in the medium) was performed on four biological replicates. Protein abundance changes were determined using two label-free mass spectrometry based-quantification methods: spectral count (SC) and MS1 ion intensities named XIC (for eXtracted Ion Current). Our proteomic data reveal for the first time, the impact of Pi availability on the abundance of approximately 4000 proteins of these Streptomyces strains with different abilities to produce antibiotics. The most striking feature differentiating these strains was the much higher abundance of enzymes of the respiratory chain in both phosphate conditions in S. coelicolor compared to the S. lividans strains.
2022-02-04 | PXD029263 | Pride
Project description:The principal virulence determinant of Mycobacterium tuberculosis (Mtb), the ESX-1 protein secretion system, is positively controlled at the transcriptional level by EspR. Depletion of EspR reportedly affects a small number of genes, both positively or negatively, including a key ESX-1 component, the espACD operon. EspR is also thought to be an ESX-1 substrate. Using EspR-specific antibodies in ChIP-Seq experiments (chromatin immunoprecipitation followed by ultra-high throughput DNA sequencing) we show that EspR binds to at least 165 loci on the Mtb genome. Included in the EspR regulon are genes encoding not only EspA, but also EspR itself, the ESX-2 and ESX-5 systems, a host of diverse cell wall functions, such as production of the complex lipid PDIM (phenolthiocerol dimycocerosate) and the PE/PPE cell-surface proteins. EspR binding sites are not restricted to promoter regions and can be clustered. This suggests that rather than functioning as a classical regulatory protein EspR acts globally as a nucleoid-associated protein capable of long-range interactions consistent with a recently established structural model. EspR expression was shown to be growth phase-dependent, peaking in the stationary phase. Overexpression in Mtb strain H37Rv revealed that EspR influences target gene expression both positively or negatively leading to growth arrest. At no stage was EspR secreted into the culture filtrate. Thus, rather than serving as a specific activator of a virulence locus, EspR is a novel nucleoid-associated protein, with both architectural and regulatory roles, that impacts cell wall functions and pathogenesis through multiple genes. ChIP-Seq of EspR in Mtb H37Rv at mid-log phase of growth. Two independent experiments were performed. Input DNA (No IP) was used as a control.
2012-04-02 | E-GEOD-35149 | biostudies-arrayexpress