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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Klebsiella pneumoniae: WT vs. Hfq mutant

ABSTRACT: Transcriptional profiling of K. pneumoniae comparing the wild type strain (S5) with a hfq deletion mutant (H0201). Goal was to determine the effects of Hfq absence on global K. pneumoniae gene expression. WT vs. Hfq mutant. Eight replicates for each ORF presented in the 44K array.

ORGANISM(S): Klebsiella pneumoniae

SUBMITTER: Yichyi Lai

PROVIDER: E-GEOD-29448 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Impact of Hfq on global gene expression and virulence in Klebsiella pneumoniae.

Chiang Ming-Ko MK Lu Min-Chi MC Liu Li-Cheng LC Lin Ching-Ting CT Lai Yi-Chyi YC

PloS one 20110714 7

Klebsiella pneumoniae is responsible for a wide range of clinical symptoms. How this bacterium adapts itself to ever-changing host milieu is still a mystery. Recently, small non-coding RNAs (sRNAs) have received considerable attention for their functions in fine-tuning gene expression at a post-transcriptional level to promote bacterial adaptation. Here we demonstrate that Hfq, an RNA-binding protein, which facilitates interactions between sRNAs and their mRNA targets, is critical for K. pneumon ...[more]

PMID: 21779404

Similar Datasets

Klebsiella pneumoniae: WT vs. Hfq mutant

Project description:Transcriptional profiling of K. pneumoniae comparing the wild type strain (S5) with a hfq deletion mutant (H0201). Goal was to determine the effects of Hfq absence on global K. pneumoniae gene expression.

2013-01-11 | GSE29448 | GEO

B. subtilis: temporal expression response to amino acid treatment

Project description:Microorganisms can restructure their transcriptional output to adapt to environmental conditions by sensing endogenous metabolite pool. In this study, an Agilent customized microarray representing approximately 4,106 genes was used to study temporal transcript profiles of Bacillus subtilis in response to valine, glutamate and glutamine pulses. Amino-acid-regulated genes were identified having significantly changed expression at one or more time points in response to pulses of valine, glutamate, and glutamine, respectively, and Val-, Glu and Gln-specific genes were further distinguished from them. Different amino acid treatments were compared in terms of both the global temporal profiles and the 5-minute quick regulations, and between-experiment differential genes were identified. The highlighted genes were analyzed based on diverse sources of gene functions using a variety of computational tools, including T-profiler analysis, hierarchical clustering and enrichment of functional categories. The results revealed the common and distinct modes of action of these three amino acids, and should help to elucidate the specific signaling mechanism of each amino acid as an effector. Three amino acids (Glutamate, Glutamine, and Valine) were adopted to perturb the culture of subtilis. Four time-points were investigated for each perturbation. There are two replicates for the first time-point of Valine-treatment experiment.

2010-05-05 | E-GEOD-17243 | biostudies-arrayexpress

Hfq-coIP overgrowth

Project description:The small RNAs associated with protein Hfq constitute one of the largest classes of post-transcriptional regulators known to date. Most previously investigated members of this class are encoded by conserved free-standing genes. Here, deep sequencing of Hfq-bound transcripts from multiple stages of growth of Salmonella Typhimurium revealed a plethora of new small RNA species from within mRNA loci, including DapZ which overlaps with the 3’ region of the biosynthetic gene, dapB. Synthesis of the DapZ small RNA is independent of DapB protein synthesis, and controlled by HilD, the master regulator of Salmonella invasion genes. DapZ carries a short G/U-rich domain similar to that of the globally acting GcvB small RNA, and uses GcvB-like seed pairing to repress translation of the major ABC transporters, DppA and OppA. This exemplifies double functional output from an mRNA locus by the production of both a protein and an Hfq-dependent trans-acting RNA. Our atlas of Hfq targets suggests that the 3’ regions of mRNA genes constitute a rich reservoir to feed the Hfq network with new regulatory small RNAs. Hfq-associated RNAs were systemically analyzed in Salmonella at 7 different growth stages in standard labortory condition (LB)

2012-10-01 | E-GEOD-38884 | biostudies-arrayexpress

High hydrostatic pressure adaptive strategies in an obligate piezophile Pyrococcus yayanosii and piezosensible Pyrococcus furiosus

Project description:Pyrococcus yayanosii CH1 is the first and only obligate piezophilic hyperthermophilic microorganism discovered so far, that extends the physical and chemical limits of life on Earth and strengthens the idea of the existence of a hyperthermophilic biosphere in the depth of our planet. It was isolated from the Ashadze hydrothermal vent at 4,100 m depth. Multi-omics analyses where performed in order to study the mechanisms implemented by the cell to face high hydrostatic pressure variations. In silico analyses showed that P. yayanosii genome is highly adapted to its harsh environment with precisely a loss of aromatic amino acid biosynthesis and the high constitutive expression of the energy metabolism compared to others non obligate piezophilic Pyrococus. Differential proteomics and transcriptomics analyses identified key hydrostatic pressure responsive genes involved in translation, chemotaxis, energy metabolism (hydrogenases and formate metabolism) and CRISPR-cas. Cells were grown at different hydrostatic pressures (20, 52 and 80 Mpa for P. yayanosii and 0.1 and 45 Mpa for P. furiosus) until they reached the middle of the exponential phase. Each culture was done 3 times independantly.

2015-09-09 | E-GEOD-72783 | biostudies-arrayexpress

ENF1 (enlarged fil expression domain1) vs wild-type Col.

Project description:ENF1 gene (AT1G79440) encodes succinic semialdehyde dehydrogenase. Loss-of-function mutant of ENF1 shows pleiotropic phenotypes, including abnormal gene expression along the adaxial-abaxial axis in leaf development. enf1-1 allele has a point mutation in the splicing accepter site of 11th intron of ENF1. enf1-6 allele has T-DNA insertion in 5th exon of ENF1. Differential gene expression between in enf1 and in wild type was measured at shoot apex of six-day-after-sowing seedlings. Independent experiments for wild type, enf1-1, and enf1-6 were performed four, three, and three times, respectively.

2013-10-21 | E-GEOD-24895 | biostudies-arrayexpress

Hfq is involved in global protein expression and stress response in Bordetella pertussis

Project description:In this study, we used gel-free nanoLC-MS/MS-based proteomics to compare the protein profile of B. pertussis wild type and an isogenic hfq defective mutant strain under control an iron limited conditions. We found that Hfq affects the abundance of 302 proteins, which represents 8% of the total B. pertussis coding sequence. The absence of Hfq induced changes in the abundance of proteins involved in metabolic pathways, stress response and virulence. Hfq was also found involved in B. pertussis adaptation to iron starvation, one of the main stresses this pathogen faces inside the host. Altogether, these results indicate that B. pertussis Hfq is involved in bacterial physiological processes as well as bacterial pathogenesis.

2020-02-18 | PXD011753 | Pride

Comparison of the transcriptomes of a Pasteurella multocida VP161 wild-type strain with a Pasteurella multocida VP161 hfq mutant

Project description:Objectives: To determine the transcripts that are differentially expressed in a hfq mutant. Hfq is an RNA chaperone that mediates many interactions between regultory RNAs and their mRNA targets. Analysis of the transcriptomes of the Pasteurella multocida wild-type strain and the Pasteurella multocida hfq mutant will allow for identification of genes controlled by hfq and the sRNAs with which it interacts. Methods: RNA sequencing was employed to determine the transcriptomes of a wild-type Pasteurella multocida strain and a hfq mutant strain. Comparison of these two transcriptomes allows for determination of differentially expressed genes and therefore those genes controlled by Hfq and sRNAs with which it interacts.

2016-03-02 | E-GEOD-77721 | biostudies-arrayexpress

Comparison of the expression profiles of 630E strain and a hfQ mutant after 7.5h of growth in Tyt

Project description:Clostridium difficile is an emergent human pathogen and the most common cause of nosocomial diarrhea. Our recent deep-sequencing data strongly suggest the importance of RNA-based mechanisms for the control of gene expression in C. difficile. The RNA chaperon protein Hfq is a key component of post-transcriptional regulatory network in various bacterial systems. In an effort to understand the function of Hfq in C. difficile, we have constructed and characterized an Hfq-depleted strain in this bacterium. We present evidence that Hfq is necessary for the normal cell growth, for the establishment of bacillary form and might be involved in metabolic adaptations, stress response and sporulation, important during C. difficile infection cycle. In accordance to these phenotypic changes, our transcriptome analysis revealed pleiotropic effects of Hfq on gene expression in C. difficile. This microarray analysis showed altered expression of genes encoding cell wall and membrane transport components, sporulation proteins, as well as stress response, transcriptional regulator genes and genes of unknown function. Remarkably, a great number of genes belonging to the regulon dependent on sporulation-specific sigma K factor were generally up-regulated in the strain depleted for Hfq. Many important metabolic pathways were also affected by Hfq depletion. Finally, the altered accumulation of several previously identified sRNAs suggests potential involvement of Hfq in these regulatory RNA function. Altogether, these results provide evidence for the pleiotropic role of Hfq protein in C. difficile physiology expanding our knowledge of Hfq-dependent regulation in Gram-positive bacteria. Two-conditions experiments, 630E strain vs. hfQ mutant grown in TYt, 4 biological replicates for each condition.

2014-07-15 | E-GEOD-49168 | biostudies-arrayexpress

Comparison of the expression profiles of 630E strain and an Hfq antisense after 7.5h of growth in Tyt

Project description:Transcriptional profiling of C. difficile 630E strain vs. an Hfq antisense after 7.5h of growth inTYt. Two-conditions experiments, 630E strain vs. Hfq antisense grown in TYt, 4 biological replicates for each condition.

2014-07-15 | E-GEOD-55273 | biostudies-arrayexpress

RIL-seq of Klebsiella pneumoniae SGH10 grown in LB or DMEM medium

Project description:RIL-seq experiment allows identification of pairs of interacting RNA molecules while bound to the Hfq protein. SGH10 bacteria were grown under DMEM (Dulbecco's Modified Eagle Medium) and LB (Lysogeny broth) conditions. RIL-seq was performed as previously described in Melamed et al. 2018 with adaptation of the computational analysis to the SGH10. It was applied to three biological replicates, for each growth condition. Libraries were sequenced by paired-end sequencing using Nextseq 500 Sequencer (Illumina). sequence fragments were mapped to SGH10 which contains a chromosome NZ_CP025080.1 and a plasmid NZ_CP025081.1. RIL-seq derived sequence fragments that mapped to the same locus or to two different loci were defined as single and chimeric fragments respectively. Chimeric fragments that appeared statistically significantly more than expected at random (S-chimeras) were considered as representing putative interacting RNAs.

2023-12-01 | E-MTAB-13342 | biostudies-arrayexpress

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