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Proteomic analysis of STnc470 deficient Salmonella Typhimurium cells

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

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: PXD003589 | Pride | 2017-05-03

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	110714_PPF_Zhou_ZP322_iTRAQ.group	Other
	110714_PPF_Zhou_ZP322_iTRAQ.wiff	Wiff
	110714_PPF_Zhou_ZP322_iTRAQ.wiff.scan	Wiff
	111014_PPF_Zhou1_ZP322_iTRAQ_05.group	Other
	111014_PPF_Zhou1_ZP322_iTRAQ_05.wiff	Wiff

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1 - 5 of 45

Publications

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

Project description:“Stress, survival and virulence: the multi-faceted host/microbial interactions.” Bacteria employ epinephrine and norepinephrine, which converge to distinct bacterial crucial processes, like survival and pathogenicity. A novel stress periplasmic membrane protein belonging to previously described BOF family, protein renamed here SrpP, and together with membrane sensor kinase QseC has an essential role in stress response and virulence of S. Typhimurium. SrpP employs its predicted binding pocket, specifically the SrpPE110 residue, and interacts with lipid A modification enzyme, LpxO dioxygenase. Upon this interaction SrpP in S. Typhimurium finely manages multiple membrane functions to culminate in survival upon stress and pathogenesis in vivo, connecting host-stress chemical signaling to cell stress in bacteria. Comparison of sensor histidine kinase qseC mutant expression levels versus wild type strain.

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

Transcriptional profile of Salmonella enterica serovar Typhimurium 4/74 wild-type and mutants using strand-specific RNA-seq

Project description:New tools for studying bacterial transcripts at the single nucleotide level offer an unparalleled opportunity to understand the bacterial transcriptome. For the model pathogen Salmonella enterica serovar Typhimurium, it is necessary to identify the regulatory inputs for all RNA transcripts, including small RNAs (sRNAs) and coding genes. Here, we use RNA-seq to define the transcriptomes of mutants lacking 18 global regulatory systems that, among other functions, modulate the expression of the SPI1 and SPI2 Type Three secretion systems in S. Typhimurium strain 4/74. We directly compared the roles of the major regulators of transcription, and reported the effects of the regulatory mutations on expression of sRNAs. We also use this method to describe the impact of the RNA chaperone Hfq upon the steady state levels of 280 sRNA transcripts. Transcriptome analysis of S. Typhimurium 4/74 using RNA isolated wild-type and mutants grown under infection-relevant conditions.

2016-08-09 | E-GEOD-79314 | biostudies-arrayexpress

RNA-seq analysis determined the effect of pat or cobB mutation on transcriptional levels in Salmonella Typhimurium 14028s.

Project description:Salmonella causes a range of diseases in different hosts, including enterocolitis and systemic infection. Lysine acetylation regulates many eukaryotic cellular processes, but its function in prokaryotes is largely unknown. Reversible acetylation in Salmonella Typhimurium depends on acetyltransferase Pat and nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase CobB. Here, we used cell and animal models to evaluate the virulence of pat and cobB deletion mutants in S. Typhimurium, and found that pat is essential for bacterial intestinal colonization, systemic infection and host inflammation response. Next, to understand the underlying mechanism, genome-wide transcriptome was analyzed. RNA-seq data showed the expression of Salmonella pathogenicity islands 1 (SPI-1) is partially dependent on pat. In addition, we found that HilD is a substrate of Pat, which is essential for maintaining HilD protein level. Taken together, these results suggested that protein acetylation system regulates SPI-1 expression by controlling HilD in a post-translational manner to mediate S. Typhimurium virulence. To use RNA-seq to analyze the transcriptome patterns of pat or cobB mutation in Salmonella Typhimurium 14028s.

2016-08-10 | E-GEOD-71907 | biostudies-arrayexpress

RNA-seq analysis of Salmonella enterica Typhimurium LT2

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

2013-03-26 | E-GEOD-45445 | biostudies-arrayexpress

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

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.

2017-06-29 | E-MTAB-5573 | biostudies-arrayexpress

Proteomic analysis of secreted proteins from Salmonella cells deficient in STnc470

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

2017-05-03 | PXD003590 | Pride

Gene transcriptional levels with or without acid treatment in Salmonella Typhimurium 14028s

Project description:Acetylation of lysine residues is conserved across organisms and plays important roles in various cellular functions. Maintaining intracellular pH homeostasis is crucial for the survival of enteric bacteria in acidic gastric tract. However, it remains unkown whether bacteria can utilize reversible protein acetylation system to adapt to acidic environment. Here we demonstrate that the protein acetylation/deacetylation is critical for Salmonella Typhimurium to survive in acidic environment. We first used RNA-seq to analyze the transcriptome patterns under acid stress, and found that the transcriptional levels of genes involved in NAD+/NADH metabolism were significantly changed, leading to the increase of intracellular NAD+/NADH ratio. Moreover, acid stress down-regulated the transcriptional level of pat (encoding an acetyltranseferase) and genes encoding adenylate cyclase and cAMP-regulatory protein (CRP) which regulates pat positively. Acid signal also affects TCA cycle to promote the consumption of Ac-CoA, which reduced the donor of acetylation. Lowered acetylation level is not only bacterial’s response to acid stress, but also positively regulates the survival rate of S. Typhimurium. The deletion mutant of pat had more stable intracellular pH, which paralleled with higher survival rate after acid treatment compared with the wild type strain and deletion mutant of cobB. Our data suggest that bacteria can down-regulate protein acetylation level to prevent intracellular pH further falling in acid stress, and this work may provide a new perspective to understand the bacterial acid resistance mechanism. To use RNA-seq to analyze the transcriptome patterns under acid stress

2015-04-16 | E-GEOD-67925 | biostudies-arrayexpress

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

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