Ontology highlight
ABSTRACT:
PROVIDER: PRJNA678618 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13065741.fastq.gz | Fastqsanger.gz | |||
| SRR13065742.fastq.gz | Fastqsanger.gz | |||
| SRR13065743.fastq.gz | Fastqsanger.gz | |||
| SRR13065744.fastq.gz | Fastqsanger.gz | |||
| SRR13065745.fastq.gz | Fastqsanger.gz |
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Project description:The pathogenic spirochete Borrelia burgdorferi senses and responds to diverse environmental challenges, including changes in nutrient availability, throughout its natural infectious cycle in Ixodes spp. ticks and mammalian hosts. This study examined the role of the putative DnaK suppressor protein (DksA) in the transcriptional response of B. burgdorferi to starvation. Wild-type and dksA-deficient B. burgdorferi strains were subjected to starvation by shifting mid-logarithmic cultures grown in BSK-II medium to serum-free RPMI medium for six hours under microaerobic conditions (5% CO2, 3% O2). Microarray analyses of wild-type B. burgdorferi revealed that genes encoding flagellar components, ribosomal proteins, and DNA replication machinery were downregulated in response to starvation. DksA mediated transcriptomic responses to starvation in B. burgdorferi as the dksA-deficient B. burgdorferi strain differentially expressed only 47 genes in response to starvation compared to the 500 genes differentially expressed by wild-type strains. Consistent with a role for DksA in the starvation response of B. burgdorferi, fewer CFUs were observed for dksA-deficient spirochetes after prolonged starvation in RPMI medium compared to wild-type B. burgdorferi. Transcriptomic analyses revealed a partial overlap between the DksA regulon and the regulon of the guanosine tetraphosphate and guanosine pentaphosphate [(p)ppGpp] synthase RelBbu, while the DksA regulon also included many plasmid-borne genes. Corresponding to a DksA-(p)ppGpp regulatory relationship, (p)ppGpp levels were constitutively elevated in the dksA-deficient strain compared to the wild-type strain. Together, these data indicate that DksA directs the stringent response with a regulatory interplay with (p)ppGpp that is fundamental to B. burgdorferi responses to the environment.
2018-12-18 | GSE119023 | GEO
Project description:To better understand the role of the (p)ppGpp-mediated stringent response in control of H. ducreyi virulence determinants, here we defined genes potentially regulated by either (p)ppGpp or DksA by using RNA-seq. We were able to show that loss of either (p)ppGpp or DksA resulted in dysregulation of multiple genes including several known virulence determinants. We also show that loss of (p)ppGpp or DksA resulted in differential expression of putative H. ducreyi small RNAs. RNA of Haemophilus ducreyi wildtype, relAspoT and dksA mutants were collected at mid-log, transition, and stationary phases of growth, in quadruplicate using stranded RNA -seq.
2015-06-04 | E-GEOD-67202 | biostudies-arrayexpress
Project description:Transcriptional profiles of wt and dksA minus Salmonella enterica sv Typhimurium 14028S in E salts minimal medium in response to 5 mM DETANONOate for 30 min Total RNA was harvested from three biological replicates of wt and dksA mutant cultures exposed or unexposed to 5mM DETANONOate for 30min in E salts minimal medium.
2014-03-31 | E-GEOD-33529 | biostudies-arrayexpress
Project description:To better understand the role of the (p)ppGpp-mediated stringent response in control of H. ducreyi virulence determinants, here we defined genes potentially regulated by either (p)ppGpp or DksA by using RNA-seq. We were able to show that loss of either (p)ppGpp or DksA resulted in dysregulation of multiple genes including several known virulence determinants. We also show that loss of (p)ppGpp or DksA resulted in differential expression of putative H. ducreyi small RNAs.
2015-06-04 | GSE67202 | GEO
Project description:Transcriptional profiles of wt and dksA minus Salmonella enterica sv Typhimurium 14028S in E salts minimal medium in response to 5 mM DETANONOate for 30 min
2014-03-31 | GSE33529 | GEO
Project description:In response to nutrient deprivation, bacteria activate a conserved stress response pathway called the stringent response (SR). In Caulobacter crescentus, SpoT synthesizes the secondary messengers (p)ppGpp, which affect transcriptional reprogramming by binding to RNA polymerase to downregulate anabolic gene transcription. (p)ppGpp can also impact the expression of anabolic genes by controlling the levels and activities of their transcriptional regulators. In Caulobacter, a major regulator of anabolic genes is the conserved transcription factor CdnL. If and how CdnL is controlled during the SR and why that might be functionally important is unclear. Here, we show that CdnL is regulated post-translationally in a manner dependent on SpoT and the ClpXP protease. We find that stabilization of CdnL causes misregulation of ribosomal and metabolic genes during starvation. Functionally, we demonstrate that the combined action of SR transcriptional regulators and CdnL clearance allows for rapid adaptation to nutrient repletion. We also find that cells that are unable to clear CdnL during starvation are outcompeted by wild-type cells when subjected to fluctuations in nutrients. We hypothesize that post-transcriptional clearance of CdnL during the SR, in conjunction with direct binding of (p)ppGpp and DksA to RNAP, are critical for altering the transcriptome in order to permit cell survival during nutrient stress.
2024-05-10 | GSE249185 | GEO
Project description:The regulatory role of the Fis protein in fis and in the transcription of several gene regions during mid-exponential and late-stationary phase, and during different growth aeration regimes, has been investigated. Studies were done during those two growth phases and in aerated and non-aerated (microaerobic) conditions, to measure Fis enrichment and binding peaks in strategic gene regions by genome-wide microarray analysis ChIP-chip. This research investigation points to central roles for SPI-1, SPI-2, DNA gyrase and topoisomerase I, the elements of the stringent response, and the regulatory function of Fis-binding patterns, in setting and re-setting the activity of the fis gene and other involved promoters as a function of the growth conditions and aeration regimes experienced by Salmonella.
2013-05-01 | GSE38661 | GEO
Project description:DksA is well-known for its regulatory role in the transcription of ribosomal RNA and genes involved in amino acid synthesis in many bacteria. DksA is also reported to control expression of virulence genes in pathogenic bacteria. Here, we elucidated the roles of the DksA-like protein (CJJ81176_0160, Cj0125c) in the pathogenesis of Campylobacter jejuni. Like in other bacteria, transcription of stable RNA was repressed by DksA under stressful conditions in C. jejuni. Transcriptomic and proteomic analyses of C. jejuni 81-176 and its isogenic dksA mutant showed differential expression of many genes involved in iron-related metabolism, flagellar synthesis and amino acid metabolism. Also the dksA mutant of C. jejuni demonstrated a decreased ability to invade into intestinal cells and to induce release of interleukin-8 from intestinal cells. These results suggest the DksA-like protein plays an important regulatory role in the physiology and virulence of C. jejuni. Keywords: dksA mutation of Campylobacter jejuni The design utilized a commercially available two color microarray slide for the enture transcriptome of Campylobacter jejuni. Six hybridizations were performed each with independently extracted samples of either C. jejuni wildtype of C. jejuni dksA mutant cDNA samples. A dye swap was utilized to help minimize dye dependent bias. Thus there were six biological replicates of each sample.
2008-05-05 | E-GEOD-9866 | biostudies-arrayexpress
Project description:Part of a study to determine the impact of genome evolution on host adaptation of a group of Salmonella Typhimurium. The experiment is designed to determine the impact of culture at elevated temperature on gene experssion.
2013-06-19 | GSE48061 | GEO