{"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":["1148"],"full_dataset_link":["https://pax-db.org/dataset/1148/1305834575"],"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":["Cyanobacteria, the only prokaryotes capable of oxygenic photosynthesis, are present in diverse ecological niches and play crucial roles in global carbon and nitrogen cycles. To proliferate in nature, cyanobacteria utilize a host of stress responses to accommodate periodic changes in environmental conditions. A detailed knowledge of the composition of, as well as the dynamic changes in, the proteome is necessary to gain fundamental insights into such stress responses. Toward this goal, we have performed a large-scale proteomic analysis of the widely studied model cyanobacterium Synechocystis sp. PCC 6803 under 33 different environmental conditions. The resulting high-quality dataset consists of 22,318 unique peptides corresponding to 1955 proteins, a coverage of 53% of the predicted proteome. Quantitative determination of protein abundances has led to the identification of 1198 differentially regulated proteins. Notably, our analysis revealed that a common stress response under various environmental perturbations, irrespective of amplitude and duration, is the activation of atypical pathways for the acquisition of carbon and nitrogen from urea and arginine. In particular, arginine is catabolized via putrescine to produce succinate and glutamate, sources of carbon and nitrogen, respectively. This study provides the most comprehensive functional and quantitative analysis of the Synechocystis proteome to date, and shows that a significant stress response of cyanobacteria involves an uncommon mode of acquisition of carbon and nitrogen."],"pubmed_title":["Global proteomics reveal an atypical strategy for carbon/nitrogen assimilation by a cyanobacterium under diverse environmental perturbations."],"pubmed_authors":["Wegener Kimberly M KM, Singh Abhay K AK, Jacobs Jon M JM, Elvitigala Thanura T, Welsh Eric A EA, Keren Nir N, Gritsenko Marina A MA, Ghosh Bijoy K BK, Camp David G DG, Smith Richard D RD, Pakrasi Himadri B HB"],"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":["carbono, Vitreous, atypia, C, Kohlenstoff, Vitreous Carbon, nitrogen, Stickstoff, aberrant, Carbon-12, nitrogeno., Peptidomics, Carbon, 6C, carbonium, N, atypical, carbon, defective, 7N, azote, carbone, Carbon 12"],"name_synonyms":["l(3)Ca, multi-cellular organism, body, mCRY, titin, whole body, 26S protease, l(3)62Ca, d-titin, 0020/01, threonine endopeptidase activity, Mbh1, SLS, Sls, ingensin, kettin, organism, large multicatalytic protease, CFU-MC, HEL-S-66, DmelCG1915, Titin, prosome, Crry, multicatalytic endopeptidase complex, animal, anon-CREST, Ket, CFU-Mast, tricorn proteinase, D-titin, l(3)j1D7, whole organism, AFCP, colony forming unit mast cell, D-Titin, CG18857, MIC10, ket, sam, sal, TLX, l(3)dre8, lens neutral proteinase, CG1915, CT41299, multicatalytic proteinase (complex), Koerper, proteasome endopeptidase complex., KZ, polyhedral organelle, l(3)S002001, l(3)rL182, CG18242, tricorn protease, AHUS2, TRA2.10, Mcp, MCP, alkaline protease, multicatalytic proteinase, CG18245"],"pubmed_abstract_synonyms":["host organism, scale tissue, Aluminum, glutamic acid dianion, determination, DL-Arginine Acetate, Glu, Mbp1, Monohydrate, Aphanocapsa sp. N-1, protein, Basodexan, 4-DIAMINOBUTANE, Photosynthetic Carbon Fixation, 4-butylenediamine, glutamate, Mendosicutes, Polypeptides, protein polypeptide chains, Succinate, 2-Aminoglutaric acid, peptido, Carbon-12, responsivity, Aluminum L-Glutamate, 1, Arg, protein aggregate, myd, Carbon Fixation, Putrescin, Ammonium Succinate, succinate anion, C, (S)-2-amino-5-guanidinopentanoic acid, E, peptides, Metabacteria, 2 Ethanedicarboxylic Acid, N, plant peltate hair, E927b, (S)-2-Amino-5-guanidinovaleric acid, 4-Butanedioic Acid, R, Tetramethylendiamin, Mbp-1, Arginine, proteins, Monohydrate DL-Arginine Acetate, Calvin-Benson-Bassham, Bacteria Woese et al. 2024, Prokaryotae, H2N(CH2)4NH2, Carbon, Calvin, Synechocystis sp. (ATCC 27184), Glutaminic acid, Procaryotae, 4-tetramethylenediamine, 4-Diaminobutane, L-Arginin, Archaebacteria, hydrogen glutamate, Data Set, aberrant, gyltl1b-b, Arginine Hydrochloride, L-Glutamic Acid, arginine, Calvin Benson Cycle, Potassium Succinate, Arginin, ur, predicted, Vitreous, Blue-Green, carbamide, Stickstoff, MDDGA6, mKIAA0609, Potassium Glutamate, Blue Green Bacteria, prokaryotes, KIAA0609, Synechocystis sp. PCC6803, D Glutamate, blue-green bacteria, activation, L-Arginine, fg, Epistemology, 4 Butanedioic Acid, gyltl1b, Blue Green Algae, butylenediamine, 6C, succinate, mdc1d, expanded, common, Calvin Benson Bassham Cycle, Aphanocapsa sp. (strain N-1), (D)-Isomer, 4-Butanediamine, L-Glutamic acid, MDC1D, Vitreous Carbon, H2NC(O)NH2, nitrogen, enr, enlarged, Blue-Green Algae, carbonium, D-Glutamate, 2-ammoniopentanedioate, Polypeptide, 7N, Blue Green, Proteomes, 1728, Prokaryota, DL-Glutamic acid, glutamic acid, big, Ammonium, atypia, Synechocystis 6803, 2-aminopentanedioate, Tetramethylenediamine, peltate hair, number, Goal, 2-Amino-5-guanidinovaleric acid, L Isomer, Gene, cyanophytes, Reductive Pentose Phosphate Cycle, carbon, Carbamide, Cyanobacteria, eubacteria, 4-diamine, protein-containing complex, presence, froggy, Gyltl1a, Aluminum L Glutamate, L-(+)-arginine, blue-green algae, Karbamid, large, Oxyphotobacteria, polypeptide chain, (2S)-2-amino-5-(carbamimidamido)pentanoic acid, Harg, Photosynthesis Dark Reactions, Cycle, Harnstoff, Gene Products, atypical, Bacteriobiota, Cyanophyta, Carmol, Glutamic acid, reactivity, succinates, study, Butanedioic Acid, MDDGB6, LARGE, cyanobacteria, Bacteria, Monera, glutamate(2-), Bacteria (ex Cavalier-Smith 1987), BPFD#36, Kohlenstoff, Algae, Synechocystis sp. (strain PCC 6803), great, L-Arg, Calvin-Benson-Bassham Cycle, peptidos, Archaebiota, Butane-1, Dark Reactions of Photosynthesis, 2-amino-5-(carbamimidamido)pentanoic acid, Potassium, bacteria, Cyanophyceae, Synechocystis PCC6803, succinic acid anion, protein complex, Photosynthetic, Proteins, Photosynthesis Dark Reaction, glutamate(1-), total expressed protein, defective, 2-amino-5-guanidinopentanoic acid, putrescina, L-Isomer, carbone, DL Arginine Acetate, Peptide, carbono, count in organism, native protein, natural protein, carbonyldiamide, L-Isomer Arginine, Blue-Green Bacteria, Glutamate, Protein, chemical analysis, 4 Diaminobutane, proteomic analysis, Cyanophycota, Hydrochloride, 4 Butanediamine, Glutamic Acid, Calvin-Benson Cycle, L Arginine, butanedioic acid, scales, Glutaminsaeure, L-Glutamate, L Glutamic Acid, Putreszin, DL-Glutaminic acid, 2-aminopentanedioic acid, scale, uree, not Bacteria Haeckel 1894, archaea, Oxygenic photosynthetic bacteria, Synechocystis sp. (PCC 6803), (2S)-2-amino-5-guanidinopentanoic acid, azote, ion(2-), Carbon 12, nitrogeno, Protein Gene Products, Gene Proteins, glutamic acid monoanion, Calvin Cycle, nitrogeno., prokaryote, L Glutamate, Synechocystis sp.PCC6803, Peptid, assay, (-)OOC-CH2-CH2-COO(-), response, Calvin-Benson, 2-Ethanedicarboxylic Acid, Synechocystis sp. ATCC 27184"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Synechocystis.sp. 6803 - Whole organism, SC (Wegener,mcp,2010)","description":"abundance based on Spectral counting, Interaction consistency score: 6.1, Coverage: 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