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Proteomic analysis of secreted proteins from Salmonella cells deficient in STnc470

ABSTRACT: This study has the main goal of studying the impact of the small non coding RNA STnc470 on protein expression and secretion.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. Sl1344

DISEASE(S): Salmonella Gastroenteritis

SUBMITTER: Ernesto Nakayasu

LAB HEAD: Daoguo Zhou

PROVIDER: PXD003590 | Pride | 2017-05-03

REPOSITORIES: Pride

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InvS Coordinates Expression of PrgH and FimZ and Is Required for Invasion of Epithelial Cells by Salmonella enterica serovar Typhimurium.

Wang Lu L Cai Xia X Wu Shuyan S Bomjan Rajdeep R Nakayasu Ernesto S ES Händler Kristian K Hinton Jay C D JCD Zhou Daoguo D

Journal of bacteriology 20170613 13

Deep sequencing has revolutionized our understanding of the bacterial RNA world and has facilitated the identification of 280 small RNAs (sRNAs) in Salmonella Despite the suspicions that sRNAs may play important roles in Salmonella pathogenesis, the functions of most sRNAs remain unknown. To advance our understanding of RNA biology in Salmonella virulence, we searched for sRNAs required for bacterial invasion into nonphagocytic cells. After screening 75 sRNAs, we discovered ...[more]

PMID: 28439039

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Proteomic analysis of STnc470 deficient Salmonella Typhimurium cells

Project description:This project has the main goal of determine the impact of the small non-coding RNA STnc470 on protein abundance in Salmonella Typhimurium.

2017-05-03 | PXD003589 | Pride

The conserved 3’ UTR-derived small RNA NarS mediates mRNA crossregulation during nitrate respiration

Project description:In pursuit of a biological role of Salmonella 3' UTR derived sRNA NarS ,we sought to determine potential target mRNAs of NarS under anaerobic conditions. To this end, we compared gene expression in NarS-deficient and NarS overexpression (from plasmid pPL-NarS) strains following a 30-minute anaerobic shock by RNA-seq.

2019-08-22 | E-MTAB-8244 | biostudies-arrayexpress

RNA-seq of wild-type Salmonella Typhimurium SL1344 and its AcrB D408A mutant

Project description:The aim of this experiment was to determine the changes in transcription caused by the loss of efflux function of AcrB. Three biological replicates per strain were grown in MOPS minimal medium to an OD600 of 0.6. Total RNA was extracted and DNase-treated. The samples were sent to BGI, Hong Kong for sequencing by Illumina Hiseq 4000.

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Project description:We performed whole-genome transcriptomic analyses of the Salmonella Typhimimurium genome during glucose-phosphate stress. In particular, we wanted to elucidate the role of the the small RNA SgrS and protein regulator SgrT in the stress response. Wild-type Salmonella cells, mutants of Salmonella either lacking sgrS or lacking SgrS RNA/ SgrT peptide function were subject to glucose-phoshate stress

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REPARATION: Ribosome Profiling Assisted (Re-) Annotation of Bacterial genomes

Project description:Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated techniques depend heavily on sequence context and often underestimate the complexity of the proteome. We developed REPARATION (RibosomeE Profiling Assisted (Re-)AnnotaTION), a de novo algorithm that takes advantage of experimental evidence from ribosome profiling (Ribo-seq) to delineate translated open reading frames (ORFs) in bacteria, independent of genome annotation. Ribo-seq next generation sequencing technique that provides a genome-wide snapshot of the position translating ribosome along an mRNA at the time of the experiment. REPARATION evaluates all possible ORFs in the genome and estimates minimum thresholds to screen for spurious ORFs based on a growth curve model. We applied REPARATION to three annotated bacterial species to obtain a more comprehensive mapping of their translation landscape in support of experimental data. In all cases, we identified hundreds of novel ORFs including variants of previously annotated and novel small ORFs (<71 codons). Our predictions were supported by matching mass spectrometry (MS) proteomics data and sequence conservation analysis. REPARATION is unique in that it makes use of experimental Ribo-seq data to perform de novo ORF delineation in bacterial genomes, and thus can identify putative coding ORFs irrespective of the sequence context of the reading frame.

2017-08-09 | PXD005844 | Pride

A Unique Ribosome Signature Reveals bacterium Translation Initiation Sites

Project description:Overnight stationary cultures of wild type S. Typhimurium (Salmonella enterica serovar Thyphimurium - strain SL1344) grown in LB media at 37°C with agitation (200 rpm) were diluted at 1:200 in LB and grown until they reached and OD600 of 0.5 (i.e., logarithmic (Log) phase grown cells). Bacterial cells were collected by centrifugation (6000 × g, 5 min) at 4°C, flash frozen in liquid nitrogen and cryogenically pulverized using liquid nitrogen cooled pestle and mortar. The frozen pellet of a 50 ml culture was re-suspended and thawed in 1 ml ice-cold lysis buffer (50 mm NH4HCO3 (pH 7.9) supplemented with a complete protease inhibitor cocktail tablet (Roche Diagnostics GmbH, Mannheim, Germany) and subjected to mechanical disruption by two repetitive freeze-thaw and sonication cycles (i.e. 2 minutes of sonication on ice for 20-s bursts at output level 4 with a 40% duty cycle (Branson Sonifier 250; Ultrasonic Convertor)). The lysate was cleared by centrifugation for 15 min at 16,000 × g and the protein concentration measured using the protein assay kit (Bio-Rad) according to the manufacturer's instructions. The lysate was added Gu.HCl (4M f.c.) and subjected to N-terminal COFRADIC analysis. Free amines were blocked at the protein level making use of an N-hydroxysuccinimide ester of (stable isotopic encoded) acetate (i.e. NHS esters of 13C2D3 acetate), which allows distinguishing in vivo and in vitro blocked N-terminal peptides. The modified protein sample was digested overnight with sequencing-grade modified trypsin (1/100 (w/w trypsin /substrate)) at 37°C and subsequent steps of the N-terminal COFRADIC procedure were performed.

2017-08-09 | PXD005579 | Pride

Expression profiling by array of Salmonella enterica serovar Typhimurium (SL1344) qseC mutant x wild type

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2012-05-31 | E-GEOD-38353 | biostudies-arrayexpress

PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline

Project description:Analysis of synthetic peptide reference datasets to demonstrate the performance of PTMProphet, a free and open-source software tool integrated into the Trans-Proteomic Pipeline, which reanalyzes identified spectra from any search engine for which pepXML output is available to provide localization confidence to enable appropriate further characterization of biologic events.

2019-07-18 | PXD013210 | Pride

AroA deficient Salmonella Typhimurium â More than an auxotrophic mutant

Project description:Recombinant attenuated Salmonella are believed to act as powerful live vaccine carrier able to elicit protection against many infectious agents. âaroA exhibits auxotrophy for aromatic amino acids and is commonly used for attenuation. Interestingly, deletion of aroA dramatically increased virulence of the Salmonella. Detailed analyses demonstrate that Salmonellaâs physiology is significantly altered, most likely due to osmotic imbalance and stress. The result is a serious influence of lipid and amino acid turn over, possible increasing sensitivity to penicillin, complement and phagocytic uptake. In addition, in concert with other immunomodulating mutations, the phase of flagella expression is changed. Furthermore, virulence associated genes like arnT or ansB were affected. These alterations could explain the increased virulence. Thus, intravenous application of âaroA Salmonella to mice significantly increased induction of pro-inflammatory cytokines. We also employed such bacteria in therapy against tumors and realized that âaroA strains display an improved anti-tumor activity. The samples of Salmonella Typhimurium Wild type strain and derivates (SF100 (ÎlpxR9 ÎpagL7 ÎpagP8), SF101 (ÎaroA), SF102 (ÎlpxR9 ÎpagL7 ÎpagP8 ÎaroA)) were analyzed by RNA-seq. The control samples were cultivated in the LB medium until the exponential phase. Four biological replicas were pooled in pairs to get two replicas for RNA extraction, library preparation and sequencing. Tumor samples were collected from mice infected with Wt Salmonella and SF102. Bacterial RNA was extracted from single tumors. The tumor samples were split into two technical replicas for sequencing library preparation.

2016-08-09 | E-GEOD-74433 | biostudies-arrayexpress

Intra-macrophage transcriptome of Salmonella enterica serovar Typhimurium 4/74 using strand-specific RNA-seq

Project description:Bacterial transcription is controlled by many transcription factors and promoters. Currently many promoters are mapped only in in vitro conditions. We use an intra-macrophage model to map the promoters and their expression in vivo. Transcriptome analysis of S.Typhimurium 4/74 within macrophages using RNA-seq in biological replicates. dRNA-seq also performed in biological replicates.

2015-07-30 | E-GEOD-59945 | biostudies-arrayexpress

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