{"database":"PAXDB","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["http://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["224308"],"full_dataset_link":["https://pax-db.org/dataset/224308/1125588408"],"submitter_email":["mering@imls.uzh.ch"],"submitter_affiliation":["University of Zurich"],"sample_protocol":[""],"repository":["PAXDB"],"data_protocol":["For the rescaling, the\ndatasets are first parsed or processed such that the data reflect\nproportional abundances of whole protein molecules\n(i.e. proportionality to counts of complete, individual protein\nmolecules, not to molecular weights, protein volumes, or digested\npeptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up\nto one million; this means the abundance of each protein of\ninterest is finally expressed in (parts per million,) relative to\nall other proteins in a sample. \nFor a given protein abundance dataset, we then compute\nthe absolute log abundance ratios of all pairs of proteins\nannotated to be functionally linked. The median of these absolute\nlog abundance ratios represents an indirect quality\nmetric: the closer it is to zero, the better (i.e. the more there\nis consistency between abundance values and functional annotations\nsuch as protein complexes or pathways). We then\ncompute a background expectation for this metric, by permuting\nthe abundance values in a given dataset randomly,\nand recomputing the median log abundance ratios. The permutation\nis repeated several times, yielding a distribution of\nmedians. The actually observed median is then expressed as a\nZ-score distance to the random distribution ofmedians—this\ndistance is termed the interaction consistency score."],"pubmed_abstract":["Protein S-thiolation is a post-translational thiol-modification that controls redox-sensing transcription factors and protects active site cysteine residues against irreversible oxidation. In Bacillus subtilis the MarR-type repressor OhrR was shown to sense organic hydroperoxides via formation of mixed disulfides with the redox buffer bacillithiol (Cys-GlcN-Malate, BSH), termed as S-bacillithiolation. Here we have studied changes in the transcriptome and redox proteome caused by the strong oxidant hypochloric acid in B. subtilis. The expression profile of NaOCl stress is indicative of disulfide stress as shown by the induction of the thiol- and oxidative stress-specific Spx, CtsR, and PerR regulons. Thiol redox proteomics identified only few cytoplasmic proteins with reversible thiol-oxidations in response to NaOCl stress that include GapA and MetE. Shotgun-liquid chromatography-tandem MS analyses revealed that GapA, Spx, and PerR are oxidized to intramolecular disulfides by NaOCl stress. Furthermore, we identified six S-bacillithiolated proteins in NaOCl-treated cells, including the OhrR repressor, two methionine synthases MetE and YxjG, the inorganic pyrophosphatase PpaC, the 3-D-phosphoglycerate dehydrogenase SerA, and the putative bacilliredoxin YphP. S-bacillithiolation of the OhrR repressor leads to up-regulation of the OhrA peroxiredoxin that confers together with BSH specific protection against NaOCl. S-bacillithiolation of MetE, YxjG, PpaC and SerA causes hypochlorite-induced methionine starvation as supported by the induction of the S-box regulon. The mechanism of S-glutathionylation of MetE has been described in Escherichia coli also leading to enzyme inactivation and methionine auxotrophy. In summary, our studies discover an important role of the bacillithiol redox buffer in protection against hypochloric acid by S-bacillithiolation of the redox-sensing regulator OhrR and of four enzymes of the methionine biosynthesis pathway."],"pubmed_title":["S-bacillithiolation protects against hypochlorite stress in Bacillus subtilis as revealed by transcriptomics and redox proteomics."],"pubmed_authors":["Chi Bui Khanh BK, Gronau Katrin K, Mäder Ulrike U, Hessling Bernd B, Becher Dörte D, Antelmann Haike H"],"data_synonyms":["Add, DmelCG43443, ADD, ADD-87, Hts-RC, data, AU023367, Data Set, protein complex, supply, Proteins, Ovhts, Gene, HtsRC, CG9325, protein, neutral molecular compounds, protein-containing complex, Dmel_CG9325, Xt, Peptide, 1B1, add, Polypeptides, anon-EST:Posey9, protein polypeptide chains, native protein, peptido, htsRC, GLI3-190, natural protein, polypeptide chain, Add-hts, Protein, CG43443, Gene Products, l(2)k14523, Dmel_CG34197, l(2)00634, median, Ovhts-RC, background, supply and distribution, protein aggregate, all_pairs, molecule, Bph, molecula, Random selection by shearing, oligonucleotide random primer, proportion, HTS-R1, HTS, Hts, molecules, peptides, l(2)k06121, adducin, GLI3FL, distribution, AI854843, proportionality, add-like, HTS-RC, rate, proteins, Molekuel, Pdn, sample population, introduction, Protein Gene Products, Gene Proteins, Adducin, RANDOM, 10^[-6], ppm, sample, supply., quotient, Peptid, peptidos, Polypeptide, Attention Deficit Hyperactivity Disorder, l(2)01103, EST D, CG34197, HtsF, ratio"],"pubmed_title_synonyms":["Peptidomics., Bacillus subtilis var. natto, Gene Expression Monitoring, Profiling, Hypochlorous acid, Bacillus natto, Transcriptome, Transcriptome Profiling, Analyses, mRNA, Bacillus mesentericus, Transcriptome Profilings, Bacillus subtilis8, Monitorings, Gene, Transcriptomics, Hypochlorite, Differential Displays, Transcript Expression, Transcriptome Analysis, Bacillus subtilis/Bacillus globigii, Bacillus subtilis (natto), Transcriptome Analyses, Bacillus uniflagellatus, Monitoring, Gene Expression Profilings, Gene Expression, Differential Display, Transcript Expression Analysis, Gene Expression Analysis, mRNA Differential Displays, Transcript Expression Analyses, Gene Expression Analyses, Gene Expression Pattern Analysis, Redox, Vibrio subtilis, Bacillus subtilis subsp. natto, Gene Expression Monitorings, Natto Bacteria, Expression Analysis, Bacillus globigii, Analysis, Profilings, Expression Analyses, mRNA Differential Display, Oxidation Reduction, Hypochlorous Acids"],"name_synonyms":["Chi, l(3)Ca, multi-cellular organism, l(2)k04405, congenital hyperinsulinism, body, hypoglycemia hyperinsulinemic of infancy, mCRY, titin, whole body, hyperinsulinism congenital, 26S protease, l(3)62Ca, d-titin, 0020/01, threonine endopeptidase activity, l(2)04405, Mbh1, SLS, Sls, hyperinsulinemic hypoglycemia familial, ingensin, profilin, kettin, organism, large multicatalytic protease, chi, CFU-MC, HEL-S-66, sand, DmelCG1915, Titin, prosome, Crry, multicatalytic endopeptidase complex, animal, anon-CREST, Ket, CFU-Mast, tricorn proteinase, D-titin, l(3)j1D7, l(2)27/7, D88, whole organism, dLdb, CG9553, Ldb, LDB, AFCP, CHIP, colony forming unit mast cell, D-Titin, CG3924, CG18857, MIC10, DmelCG9553, ket, sam, sal, hyperinsulinism familial with pancreatic nesidioblastosis, TLX, chip, l(3)dre8, lens neutral proteinase, CG1915, dLDB/Chip, CT41299, multicatalytic proteinase (complex), Koerper, DmelCG3924, proteasome endopeptidase complex., KZ, polyhedral organelle, l(3)S002001, GH4, l(3)rL182, CG18242, tricorn protease, AHUS2, TRA2.10, Mcp, MCP, alkaline protease, multicatalytic proteinase, CG18245, Chic"],"pubmed_abstract_synonyms":["sodium salt, Ifm(2)RU1, Dm II, Peroxiredoxin V, PHGDHD, Compounds, A4, bacterium E3, Profiles, 3-Phosphoglycerate-NAD+ 2-Oxidoreductase, Peroxiredoxin I, Thiol, Myo, phosphoglyceric acid dehydrogenase activity, SerA, SERA, Oxidative DNA, Regions, Oxidative, Peroxiredoxin 4, Peroxiredoxin 5, ifm(2)2, oxidant, GlcN, Peroxiredoxin 2, 2-amino-3-mercaptopropanoic acid, Nitro-Oxidative Stresses, D 3 Phosphoglycerate Dehydrogenase, Peroxiredoxin 1, DNA Damage, Catalytic Core, 3-phosphoglyceric acid dehydrogenase activity, C, H(+)-PPase, hypochlorige Saeure, Escherichia/Shigella coli, Subunit, Thiol-Specific Antioxidant Protein, anabolism, M, Oxidative Cleavage, oxidizing agent, DROMHC, Subunits, proteins, 4930479N23, NLS1, D-3-Phosphoglycerate Dehydrogenase, Signatures, 3-phosphoglycerate:NAD+ 2-oxidoreductase activity, Eschericia coli, methionine anabolism., (1:1), 3 Phosphoglycerate NAD+ 2 Oxidoreductase, Thioredoxin Peroxidase 1, CG10604, Thioredoxin Peroxidase 2, ifm(2)RU2, Oxidative Stresses, Expression Signature, malate anion, hypochloric acid, Role Concepts, Gcsl, GCSl, Half Cystine, Catalytic Subunits, Inorganic, D-3-Phosphoglycerate, PGAD, sMHC, Thiols, Mercaptans, Proton-Translocating Pyrophosphatase, Oxidizing Agents, Zinc Cysteinate, Mercapto Compounds, Liquid Chromatography, Up-Regulation (Physiology), CG3780, ifm(2)RU1, Enteroaggregative E. coli, Sht, PGDH, methyltransferase, Role Concept, Diffusely Adherent E. coli, Expression Signatures, Domains, malate dianion, Role, Methionin, DNA Oxidative Damages, Hmet, BUSHY, (2R)-2-amino-3-sulfanylpropanoic acid, Expression Profile, Enteroinvasive E. coli, Upregulation, disodium salt, PDG, Reactive Site, Hydroperoxide Reductase, Nitro-Oxidative, Thioredoxin Dependent Peroxide Reductase 1, progressive pseudorheumatoid, Reactive Sites, DNA, Liquimeth, Thioredoxin Dependent Peroxide Reductase 2, 3-Phosphoglycerate-NAD+, Vitamin K-Dependent, Oxidation Reduction, lambdaE86, Oxidative Damage, Hypochlorous acid, 2-amino-4-(methylsulfanyl)butanoic acid, Peptidomics, Antioxidative, Dehydrogenase, Biocatalysts, Sulfhydryl, methyltetrahydropteroylpolyglutamate:homocysteine methyltransferase activity, Pyrophosphate Energized Inorganic Pyrophosphatase, L-Zystein, AI428350, methionine synthase (cobalamin-independent) activity, biosynthesis, Active Site, Transcription Factor, 3PHP reductase activity, Agent, PGD, Escherchia coli, Sites, Gene Products, Half-Cystine, 3-phosphate dehydrogenase activity, MAM, Oxidative Damages, D-3-phosphoglycerate:NAD+ oxidoreductase activity, 3 Phosphoglycerate Dehydrogenase, Vitamin K Dependent, Transcription, F15E12_6, Injury, 3-Phosphoglycerate Dehydrogenase, Receptor Up-Regulation, L Cysteine, E-920, Profile, Chlor(I)-saeure, Hcys, mal, oxidants, oxidising agents, synthesis, (S)-isomer, Enzyme, 2-amino-4-(methylthio)butanoic acid, Catalytic, CYSTEINE, Thioredoxin Peroxidase, Antioxidative Stresses, Phosphoglycerate Oxidoreductase, DmelCG10604, FREE CYSTEINE, SEDT-PA, oxidiser, (2R)-2-amino-3-mercaptopropanoic acid, metionina, Alkalescens-Dispar Group, HEL-S-113, Proteins, Active Sites, Pyrophosphate-Energized Inorganic Pyrophosphatase, Factor, EAggEC, Bacillus subtilis/Bacillus globigii, Anti-oxidative Stresses, Spx, SPX, L-Isomer, 3PGDH, buffer, Cell, of childhood, 5-methyltetrahydropteroyltri-L-glutamate:L-homocysteine S-methyltransferase activity, Concept, whole transcriptome, Mercaptan, Cofactor Protein S, native protein, methionine synthesis, 2-Oxidoreductase, Oxidative Nitrative Stresses, DmGCLM, Gene Expression Signatures, D- and L-HGA, malate, Catalytic Sites, spx, ATCMPG1, MET, Met, Proton-Translocating, ATCMPG2, Anti-oxidative Stress, DMDA1, Sulfhydryl Compound, DNA Oxidative Damage, box, Catalytic Domains, Peroxiredoxin II, alphaKG reductase activity, Peroxidoxin, (R)-2-amino-3-mercaptopropanoic acid, ion(2-), Peroxiredoxin IV, 2-Amino-3-mercaptopropionic acid, Oxidizing Agent, Thioredoxin-Dependent Peroxide Reductase 1, Thioredoxin-Dependent Peroxide Reductase 2, Gene Proteins, Bacterium coli commune, Compound, Mercapto, Gene Expression Profiles, Stress, H+ Pyrophosphatase, spondyloepiphyseal dysplasia tarda with progressive arthropathy, E920, Protein S, DNA Oxidative, E86, 3-Phosphoglycerate, E 920, PPAC, MHC, Stp, Gene Expression Profile, Nitrative Stress, Bsh, BSH, CCN6, Damage, oxidizers, hydroxybutanedioic acid, (R)-isomer, A10, DmelCG3780, L-Isomer Methionine, Methionine, mhc, Roles, malic acid, [ClOH], Bacillus subtilis subsp. natto, MetE, Nitro-Oxidative Stress, pathogenesis, Concepts, Cystein, Enterococcus coli, Vitamin K Dependent Protein S, Oxidative Injury, multicellular organismal biosynthetic process, FBgn0002741, Peroxiredoxin, CG17927, single-organism biosynthetic process, Oxidative Injuries, PPD, Oxidoreductase, Vitamin K-Dependent Protein S, mMHC, enzymes, Bacillus mesentericus, MUB3_18, cisteina, l(2)M66, Glucosamin, H+-Pyrophosphatase, Cts6, NLS, DmGCSl, E coli, MUB3.18, Oxidative DNA Damages, Anti-oxidative, LIBC, E. coli, phosphoglycerate oxidoreductase activity, Enteroaggregative Escherichia coli, Oxidative Stress Injuries, SerA 3PG dehydrogenase activity, Transcriptomes, l(2)k10423, Racemethionine, Mhc36B, l(2)36Ae, Proton-Pumping Inorganic, Pyrophosphate-Energized, Proton-Pumping Inorganic Pyrophosphatase, PRO, Expression Profiles, 2-Amino-4-(methylthio)butyric acid, Protector Protein (Mixed-Function Oxidase Systems), Hypochlorite, Cys, CYS, Phosphoglycerate, oxidizing agents, Gene Expression, Redox, Catalytic Regions, Oxidative and Nitrosative Stress, PGDH activity, 2-Amino-2-deoxy-glucose, progressive pseudorheumatoid chondrodysplasia, Region, regulator, and GLY protein 2, Domain, Transcriptome Profiles, Diffusely Adherent Escherichia coli, and GLY protein 1, C12orf39, Factors, Thiol Specific Antioxidant Protein, MS/MS, Npq, L-Cysteine, Proton Translocating Pyrophosphatase, Bacillus subtilis (natto), L-Cystein, methionine biosynthesis, DMDA, Agents, Alkyl Hydroperoxide Reductase C, Alkyl Hydroperoxide Reductase D, Biocatalyst, Oxidative Stress Injury, arthropathy, Alkyl Hydroperoxide Reductase, Bacillus globigii, Proton Pumping Inorganic Pyrophosphatase, Proteomes, Oxidative Stress, Cysteine Hydrochloride, Transcriptome Profile, glycerate 3-phosphate dehydrogenase activity, oxidizer, L Isomer, Oxidizing, Antioxidative Stress, DmelCG4919, Gene, TYPE, Glukosamin, Pyrophosphatase, Bacillus uniflagellatus, Buffer, Stresses, DAGA4, potassium salt, alpha-phosphoglycerate dehydrogenase activity, Oxidative Nitrative, Stress Injury, Oxidative Cleavages, L-Methionine, F15E12.6, Enteroinvasive Escherichia coli, Disulfide, SCG3, Reactive, Pedameth, Site, tetrahydropteroylglutamate-homocysteine transmethylase activity, MRP, Mrp, formation, Ifm(2)2, Oxidant, MS2, DmMHC, Up Regulation, Bacillus subtilis8, Alkyl, causes, GCLm, DmelCG17927, Catalytic Subunit, Nup, Anti oxidative Stress, Oxidative DNA Damage, Vibrio subtilis, causality, Cores, Natto Bacteria, 4919, Catalytic Cores, progressive pseudorheumatoid dysplasia, Hypochlorous Acids, Catalytic Region, Pyrophosphate-Energized Inorganic, calcium (hydroxy-1-malate) hexahydrate, spondyloepiphyseal dysplasia tarda - progressive arthropathy, methionine formation, CG4919, Bacterium coli, Transcriptome, DL-Methionine, Cofactor, Catalytic Site, DroMII, alpha-KG reductase activity, total expressed protein, enzyme activity, Peroxiredoxin-4, Inorganic Pyrophosphatase, Thioredoxin Peroxidase PMP20, Core, LGMD2C, Oxidative Nitrative Stress, Alkylhydroperoxide Reductase, D-3-phosphoglycerate dehydrogenase activity, Bacillus coli, CHE1, Protein, Active, 3-PGDH, (+-)-isomer, Gene Expression Signature, tetrahydropteroyltriglutamate methyltransferase activity, Zystein, tandem MS, HClO, Bacillus subtilis var. natto, Proton-Pumping, Bacillus natto, cobalamin-independent methionine synthase activity, 2-amino-3-sulfanylpropanoic acid, glycerate-1, homocysteine methylase activity, L-2-Amino-3-mercaptopropionic acid, Regulons, monopotassium salt, Cleavage, magnesium salt (2:1), Protein Gene Products, 3-phosphoglycerate dehydrogenase activity, MyHC, Hox11-310, 3-phospho-D-glycerate:NAD+ 2-oxidoreductase activity, SCARMD2, calcium salt, alpha-amino-gamma-methylmercaptobutyric acid, oxidisers, HOCl, Signature, Nitro Oxidative Stress, BUSHY GROWTH"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"B.subtilis - Whole organism, SC (Chi,mcp,2011)","description":"abundance based on Spectral counting, Interaction consistency score: 5.4, Coverage: 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