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Gene expression of wild type and lsr2 mutants of Streptomyces venezuelae during late development in liquid culture

ABSTRACT: Gene expression of wild type and lsr2 mutants of Streptomyces venezuelae during late development in liquid culture

PROVIDER: PRJNA475289 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7282580.fastq.gz	Fastqsanger.gz
	SRR7282571.fastq.gz	Fastqsanger.gz
	SRR7282581.fastq.gz	Fastqsanger.gz
	SRR7282572.fastq.gz	Fastqsanger.gz
	SRR7282582.fastq.gz	Fastqsanger.gz

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Gene expression of wild type and lsr2 mutants of Streptomyces venezuelae during late development in liquid culture

Project description:Comparing gene expression of wild type and lsr2 mutants, to determine the effect of Lsr2 on Streptomyces development and metabolism

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Lsr2 binding sites and gene expression of wild type and lsr2 mutants of Streptomyces venezuelae during late development in liquid culture

Project description:Lsr2 binding sites and gene expression of wild type and lsr2 mutants of Streptomyces venezuelae during late development in liquid culture

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Identifying Lsr2 binding sites in Streptomyces venezuelae

Project description:The goal of this work was to determine where Lsr2 binds within the S. venezuelae chromosome, and to differentiate between direct versus indirect effects by comparing our ChIP-seq results with RNA-seq results

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Identifying Lsr2 binding sites in Streptomyces venezuelae

Project description:Identifying Lsr2 binding sites in Streptomyces venezuelae

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Lsr2 binding sites and gene expression of wild type and lsr2 mutants of Streptomyces venezuelae during late development in liquid culture

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-06-09 | GSE115439 | GEO

ChIP-chip of HA-tagged Lsr2 in Mycobacterium tuberculosis and Mycobacterium smegmatis

Project description:Bacterial nucleoid-associated proteins play important roles in chromosome organization and global gene regulation. We find that Lsr2 of Mycobacterium tuberculosis is a novel nucleoid-associated protein that specifically binds AT-rich regions of the genome, including regions encoding major virulence factors, such as the ESX secretion systems, the lipid virulence factors PDIM/PGL, and the PE/PPE families of antigenic proteins. Comparison of genome-wide binding data with expression data indicates that Lsr2 binding results in transcriptional repression. Domain swamping experiments demonstrate that Lsr2 has an N-terminal dimerization domain and a C-terminal DNA binding domain. NMR analysis of the DNA binding domain of Lsr2 and its interaction with DNA reveals a novel structure and a unique mechanism that enables Lsr2 to discriminately target AT-rich sequences through interactions with the minor groove of DNA. Taken together, we provide evidence that mycobacteria have employed a structurally distinct molecule with an apparently different DNA recognition mechanism to achieve an equivalent function as the Enterobacteriaceae H-NS, coordinating global gene regulation and virulence in this group of medically important bacteria. Comparison of Lsr2 chromatin-immunoprecipitated DNA sequences to total reference DNA

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Mycobacterium tuberculosis Lsr2 is a global transcriptional regulator required for adaptation to changing oxygen levels and virulence

Project description:To survive a dynamic host environment, Mycobacterium tuberculosis must endure a series of challenges from reactive oxygen and nitrogen stress, to drastic shifts in oxygen availability. The mycobacterial Lsr2 protein has been implicated in reactive oxygen defense via direct protection of DNA. To examine the role of Lsr2 in pathogenesis and physiology of M. tuberculosis, we generated a strain deleted for lsr2. Analysis of the M. tuberculosis ?lsr2 strain demonstrated that Lsr2 is not required for DNA protection, as this strain was as equally susceptible as the wild-type to DNA-damaging agents. The lsr2 mutant did display severe growth defects under normoxic and hyperoxic conditions, but was not required for growth under low oxygen conditions. However, it was also required for adaptation to anaerobiosis. The defect in anaerobic adaptation led to a marked decrease in viability during, as well as a lag in recovery from, anaerobiosis. Gene expression profiling of ?lsr2 under aerobic and anaerobic conditions in conjunction with published DNA binding-site data indicate that Lsr2 is a global transcriptional regulator controlling adaptation to changing oxygen levels. The ?lsr2 strain was capable of establishing an early infection in the Balb/c mouse model; however, it was severely defective in persisting in the lungs and caused no discernible lung pathology. These findings demonstrate M. tuberculosis Lsr2 is a global transcriptional regulator required for control of genes involved in adaptation to extremes in oxygen availability and is required for persistent infection. Wild type H37Rv or lsr2 mutant strains were grown aerobically or in a Rach dormancy model in dubos tween albumin media and analyzed. Alternately, either aerobically grown or Rach model hypoxic samples were challenged with H2O2 samples and harvested 1h later. Experiments were repeated in triplicate or quadruplicate.

2014-05-24 | E-GEOD-57948 | biostudies-arrayexpress

Identification of transcription start sites in Streptomyces venezuelae at 10, 14, 18 and, 24 hours of culture by 5' tag RACE.

Project description:Identification of transcription start sites in Streptomyces venezuelae genome after 10, 14, 18 and, 24 hours of culture 5' tag RACE. The 4 time points correspond to late vegetative growth, initiation of sporulation, maturation of spores and, completion of sporulation.

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ChIP-chip of HA-tagged Lsr2 in Mycobacterium tuberculosis and Mycobacterium smegmatis

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Protein kinase B-mediated phosphorylation controls binding of global transcriptional regulator Lsr2 to DNA in Mycobacterium tuberculosis

Project description:Two billion people are estimated to have latent tuberculosis infection associated with dormant Mycobacterium tuberculosis. Mycobacteria possess a great portfolio of regulatory proteins which that control transitions betweento dormancy and resuscitation, including the essential protein kinase B (PknB). Here, we established that depletion of PknB resulted in global alteration of the M. tuberculosis transcriptome, and identified and implicated the DNA-binding protein Lsr2 as a main transcriptional regulator likely responsible for these changes. Furthermore, we showed that Lsr2 was phosphorylated by PknB in vitro and phosphorylation of Lsr2 on threonine 112 was important for M. tuberculosis growth and survival in the Wayne non-replicating persistence model. Our fluorescence anisotropy and electromobility shift assays revealed demonstrated that phosphorylation prevented reduced affinity of Lsr2 binding to DNA, and ChHIP-sequencing experiments confirmed increased DNA binding by of a phosphoablative (T112A) Lsr2 mutant in M. tuberculosis. According to our structural modelling studies revealed that phosphomimetic T112D mutation (T112D) to Lsr2 resulted in increased dynamics of the C-terminal part and a shift of the DNA binding loop of in the Lsr2 DNA binding domain, which disrupted prevented the DNA-protein interactions. Our findings suggest that PknB- mediated phosphorylation of Lsr2 is necessary for fine- tuning of gene expression during M. tuberculosis growth and transition to dormancy enabling M. tuberculosis to adapt and survive to cause disease.

2019-10-02 | E-MTAB-7627 | biostudies-arrayexpress

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