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Quantitative Proteomics Reveals Dormancy Related Proteins Mediated Attenuation Program in Mycobacterium Strain

ABSTRACT: To better understand the virulence difference among different MTB strains and identify new targets for therapeutic intervention under hypoxia condition, we compared the global protein expression at the protein level by quantitative proteomics among H37Rv, H37Ra and BCG.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Mycobacterium Tuberculosis H37rv

SUBMITTER: Sun jinshuai

LAB HEAD: Ping Xu

PROVIDER: PXD023788 | Pride | 2022-04-04

REPOSITORIES: Pride

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			Action	DRS
	20210123_MTB_TMT10_1.raw	Raw
	20210123_MTB_TMT10_10.raw	Raw
	20210123_MTB_TMT10_2.raw	Raw
	20210123_MTB_TMT10_3.raw	Raw
	20210123_MTB_TMT10_4.raw	Raw

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Quantitative proteomics reveals that dormancy-related proteins mediate the attenuation in mycobacterium strains.

Wang Hong H Wan Li L Shi Jiahui J Zhang Tao T Zhu Huiming H Jiang Songhao S Meng Shuhong S Wu Shujia S Sun Jinshuai J Chang Lei L Zhang Liqun L Wan Kanglin K Yang Jiaqi J Zhao Xiuqin X Liu Haican H Zhang Yao Y Dai Erhei E Xu Ping P

Virulence 20211201 1

Although members of the <i>Mycobacterium tuberculosis</i> complex (MTBC) exhibit high similarity, they are characterized by differences with respect to virulence, immune response, and transmissibility. To understand the virulence of these bacteria and identify potential novel therapeutic targets, we systemically investigated the total cell protein contents of virulent H37Rv, attenuated H37Ra, and avirulent <i>M. bovis</i> BCG vaccine strains at the log and stationary phases, based on tandem mass ...[more]

PMID: 34634997

Similar Datasets

Quantitative Proteomics Reveals Dormancy Related Proteins Mediated Attenuation Program in Mycobacterium Strain

Project description:To better understand the virulence difference among different MTB strains and identify new targets for therapeutic intervention under hypoxia condition, we compared the global protein expression at the protein level by quantitative proteomics among H37Rv, H37Ra and BCG.

2022-04-01 | PXD017174 | Pride

Quantitative proteomic and phosphoproteomic analysis of H37Ra and H37Rv strains of Mycobacterium tuberculosis

Project description:Mycobacterium tuberculosis, the causative agent of tuberculosis accounts for 1.5 million annual deaths worldwide. The two well-characterized strains of the parental H37 strain namely, H37Ra and H37Rv show different pathogenic phenotypes. In order to identify factors that are responsible for virulence, we compared the proteome and the phosphoproteome profiles of virulent (H37Rv) and virulence attenuated (H37Ra) strains of M. tuberculosis. Quantitative proteomic analysis resulted in the identification and quantitation of 2,709 proteins and 505 phosphosites. Comparative analysis revealed over 5-fold overexpression of several proteins associated with virulence. Our data indicates that there are definable molecular differences between H37Rv and H37Ra strains at both the proteome and phosphoproteome levels which may explain the virulence and phenotypic differences.

2017-05-08 | PXD004161 | Pride

Mycobacterial strain-specific temporal modulations of newly synthesized macrophage secretome

Project description:THP-1 macrophages were infected with four strains of Mycobacterium tuberculosis to study the temporal dynamics of newly synthesized proteins in the secretome. Temporal snapshots of secretome reflect the macrophage response to pathogenicity which in combination with intracellular events, completes the disease picture. However, such studies are compromised by limitations of quantitative proteomics. Metabolic labeling by SILAC allows a 3-plex experiment while isobaric chemical labeling by iTRAQ/TMT allows up to 8 to 10-plex respectively. This makes studying temporal proteome dynamics an intangible and elusive proposition. We have developed a new variant of hyperplexing method, combining triplex SILAC with 6-plex iTRAQ to achieve 18-plex quantitation in a single MS run. THP-1 macrophages were infected with H37Ra, H37Rv, BND433 and JAL2287 and the newly synthesized secreted host proteins were studied over six temporal frame still 30 hours post infection, at a difference of 4 hours each. For quantitation, the strains were encoded with two sets of triple SILAC- H37Ra & H37Rv in one and BND433 & JAL2287 in another with a control in each. These sets were then iTRAQ labeled to encode for temporal profiles across six time points in 6-plex iTRAQ. Effectively a 36-plex design with 4 replicates of each set, these experiments were completed within few days on the mass spectrometer. Using MaxQuant and in house developed tools and pipelines, we have analysed the data to map the temporal and strain specific dynamics of newly synthesized proteins in host. Hyperplexing enables large scale spatio-temporal systems biology studies where large number of samples can be processed simultaneously and in quantitative manner.

2016-08-10 | PXD004281 | Pride

Integrated multi-omic analysis of Mycobacterium tuberculosis isolates identifies ethionamide resistance-associated gene pair Rv3094c-Rv3095

Project description:Global control of the tuberculosis (TB) epidemic is seriously threatened by increasing prevalence of drug resistant (DR) M. tuberculosis (MTB) isolates. Many genome-wide studies have identified DR-associated SNPs and investigated their role in DR mechanisms. However, DR in ~30% of isolates has no clear genetic basis. DR mechanisms related to variation in gene/protein expression are known, but not well-studied.

2023-03-10 | PXD017079 | Pride

proteomics analysis of virulent and avirulent strains of mycobacterium

Project description:label free quantification analysis was performed on four strains of mycobacterium tuberculosis. The four strains are H37Rv, H37Ra, BND and JAL. The purpose of this study is to identify strain specific proteome expression pattern among the four strains.

2016-05-10 | PXD001188 | Pride

Integrated multi-omic analysis of M. tuberculosis H37Ra redefines virulence attributes

Project description:M. tuberculosis H37Ra, an avirulent tubercle bacillus, is a commonly used model to investigate virulence attenuation in M. tuberculosis. Comparative high-throughput studies have earlier correlated its avirulence to the presence of specific mutations or absence of certain proteins. However, a recent sequencing study of H37Ra has disproved several genomic differences earlier reported to be associated with virulence. This warrants further investigations on the H37Ra proteome as well. In this study, we carried out an integrated analysis of the genome, transcriptome and proteome of H37Ra. In addition to confirming single nucleotide variations and insertion-deletions that were reported earlier, our study provides novel insights into the mutation spectrum in the promoter regions of 7 genes. In all, we provide protein coding evidence for 3,199 proteins representing ~79% of the total predicted gene count. Transcriptome analysis revealed the expression of 3,945 high-confidence transcripts including several transcripts mapping to the genome that were previously thought to be non-coding. We identified 9 genes whose coding potential was hitherto reported to be absent in H37Ra . These include 2 putative virulence factors belonging to ESAT-6 like family of proteins. Furthermore, proteogenomic analysis enabled us to identify 63 novel proteins coding genes and correct 25 existing gene models in H37Ra genome. A majority of these were found to be conserved in the virulent strain H37Rv as well as in other mycobacterial sp. suggesting that that the differences in the virulent and avirulent strains of M. tuberculosis are not entirely dependent on the expression of certain proteins or their absence but may possibly be ascertained to functional changes.

2018-10-22 | PXD008555 | Pride

Identification of quantitative proteomic differences between mycobacterial lineages with altered virulence

Project description:Mycobacterium tuberculosis is the causitive agent of TB, which is a global epidemic that has claimed millions of lives. Some clinical strains of M.tb have significantly more severe clinical outcomes, while some other mycobacteria ordinarily do not cause disease in humans. The biological processes underpinning this difference are poorly understood. Thus, this project aimed to identify proteomic differences between more virulent strains of the MTBC (Beijing, J37Rv, CAS and LAM) vs those strains that only cause disease in severely immune compromised humans (Bovis, Smegmatis and Avium). We hypothesise that these differences may offer insight into the molecular mechanisms by which M.tb has become more virulent by evading drug treatment or evading the host immune system more effectively.

2016-05-23 | PXD004165 | Pride

Genome-wide characterization of a novel necrotic granuloma model of latent tuberculosis infection and reactivation in mice

Project description:We sought to develop and characterize a novel paucibacillary model in mice, which develop necrotic lung granulomas following infection with Mycobacterium tuberculosis. Paucibacillary infection was established, recapitulating the sterilizing activities of human LTBI regimens. TNF neutralization led to increased lung bacillary load, disrupted granuloma architecture with expanded necrotic foci and reduced tissue hypoxia, and accelerated animal mortality. TNF-neutralized mouse lungs and sera showed significant upregulation of IFN?, IL-1?, IL-6, IL-10, CCL2, CCL3, and matrix metalloproteinase genes Six weeks after aerosol-immunization with recombinant M. bovis BCG overexpressing the 30-kilodalton antigen, C3HeB/FeJ mice were aerosol-infected with M. tuberculosis H37Rv. Six weeks later, mice were treated with one of three standard regimens for latent TB infection (LTBI) or TNF-neutralizing antibody. Mouse lungs were analyzed by histology, positron emission tomography/computed tomography, whole-genome microarrays, and RT-PCR. Lungs and sera were studied by multiplex enzyme-linked immunosorbent assays

2014-02-20 | E-GEOD-55183 | biostudies-arrayexpress

Three-dimensional low shear culture of Mycobacterium bovis BCG induces biofilm formation and antimicrobial drug tolerance

Project description:Mycobacteria naturally grow as corded biofilms in liquid media without detergent. Such detergent-free biofilm phenotypes may reflect the growth pattern of bacilli in tuberculous lung lesions. New strategies are required to treat tuberculosis that is responsible for more deaths each year than any other bacterial disease. The lengthy six-month regimen for drug-sensitive tuberculosis is necessary to remove antimicrobial drug tolerant populations of bacilli that persist through drug therapy. The role of biofilm-like growth in the generation of these sub-populations remains poorly understood despite the hypothesized clinical significance and mounting evidence of biofilms in pathogenesis. We adapted a three-dimensional Rotary Cell Culture System to model M. bovis BCG biofilm growth in low-shear detergent-free liquid suspension. Importantly, biofilms formed without attachment to artificial surfaces and without severe nutrient starvation or environmental stress. Biofilm-derived planktonic bacilli were tolerant to isoniazid and streptomycin, but not rifampicin. This phenotypic drug tolerance was lost after passage in drug-free media. Transcriptional profiling revealed induction of cell surface regulators, sigE and BCG_0559c alongside the ESX-5 secretion apparatus in these low-shear liquid-suspension biofilms. Supernatant from biofilms induced greater pro-inflammatory cytokine release from macrophages. This study engineers and characterizes mycobacteria grown as a suspended biofilm, illuminating new drug discovery pathways for this deadly disease.

2021-01-29 | E-MTAB-9904 | biostudies-arrayexpress

Expression Analysis of Trimethyltin Chlorides (TMT) Impact on Embryonic Development

Project description:Investigation of whole genome expression pattern of 60 and 72 hours post fertilization Danio Rerio embryos exposed to TMT and vehicle control Embryos were exposed to 10uM TMT or control from 48hpf to 60 or 72 hpf. Three replicates were collected for each time point. 40 embryos were pooled to comprise a replicate.

2011-03-23 | E-GEOD-28131 | biostudies-arrayexpress