Quantitative proteomics of a B12 -dependent alga grown in coculture with bacteria reveals metabolic tradeoffs required for mutualism.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29034959", "kind": "science-record", "revision": 6, "content_hash": "sha256:d03d4baf9651d8587b23e66365ed93c3a5df2899387501a098ea89a190267c31", "created_at": "2026-11-01T15:40:29Z", "updated_at": "2026-11-01T21:21:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Quantitative proteomics of a B12 -dependent alga grown in coculture with bacteria reveals metabolic tradeoffs required for mutualism.", "doi": "10.1111/nph.14832", "pmid": "29034959", "authors": ["Katherine E Helliwell", "Jagroop Pandhal", "Matthew B Cooper", "Joseph Longworth", "Ulrich Johan Kudahl", "David A Russo", "Eleanor V Tomsett", "Freddy Bunbury", "Deborah L Salmon", "Nicholas Smirnoff", "Phillip C Wright", "Alison G Smith"], "journal": "The New phytologist", "year": 2018, "abstract": "The unicellular green alga Lobomonas rostrata requires an external supply of vitamin B12 (cobalamin) for growth, which it can obtain in stable laboratory cultures from the soil bacterium Mesorhizobium loti in exchange for photosynthate. We investigated changes in protein expression in the alga that allow it to engage in this mutualism. We used quantitative isobaric tagging (iTRAQ) proteomics to determine the L. rostrata proteome grown axenically with B12 supplementation or in coculture with M. loti. Data are available via ProteomeXchange (PXD005046). Using the related Chlamydomonas reinhardtii as a reference genome, 588 algal proteins could be identified. Enzymes of amino acid biosynthesis were higher in coculture than in axenic culture, and this was reflected in increased amounts of total cellular protein and several free amino acids. A number of heat shock proteins were also elevated. Conversely, photosynthetic proteins and those of chloroplast protein synthesis were significantly lower in L. rostrata cells in coculture. These observations were confirmed by measurement of electron transfer rates in cells grown under the two conditions. The results indicate that, despite the stability of the mutualism, L. rostrata experiences stress in coculture with M. loti, and must adjust its metabolism accordingly.", "claims": [{"id": "claim-method", "statement": "To avoid using arbitrary thresholds for highlighting differentially expressed proteins, a t‐test was performed between replicate conditions to determine significance with fold change.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29034959", "locator": "sections[6] \"Protein identification and quantification\" paragraph 2", "quote": "To avoid using arbitrary thresholds for highlighting differentially expressed proteins, a t‐test was performed between replicate conditions to determine significance with fold change."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange (PXD005046).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29034959", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Data are available via ProteomeXchange (PXD005046)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:29034959"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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"access_statement_verbatim": "Data are available via ProteomeXchange (PXD005046).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Reduction in photosynthetic capacity in a mutualistic algal-bacterial co-culture revealed by quantitative proteomics", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:29034959:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f81a8eb0489ff2044d94a74869507525b08fe622e33d56e14678da922c4cc8d9", "bytes": 11065, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#nph14832-tbl-0001", "version": null, "note": "List of identified proteins altered in abundance in cocultures of Lobomonas rostrata vs axenic cultures", "structure": {"pmcid": "PMC5765456", "section_index": 12, "section_title": "Comparative proteomics reveals fundamental changes in metabolism of L. rostrata when grown in coculture with M. loti", "row_count": 155, "column_count": 5}, "table": {"label": "Table 1", "caption": "List of identified proteins altered in abundance in cocultures of Lobomonas rostrata vs axenic cultures", "rows": [["General function", "Uniprot entry", "Protein ID", "Protein function", "Fold‐change"], ["Protein metabolism", "A8ISZ1", "EF‐3", "Elongation factor EF‐3", "2.69"], ["A8HX38", "eEF1a1", "Eukaryotic translation elongation factor 1 alpha 1 (EC 3.6.5.3)", "2.55"], ["A8J597", "RPL12", "Ribosomal protein L12", "2.42"], ["I2FKQ9", "CPN60C", "Mitochondrial chaperonin 60", "2.41"], ["A8J8M9", "RPS20", "Ribosomal protein S20", "2.18"], ["A8J7C8", "KtRS", "Lysine–tRNA ligase (EC 6.1.1.6) (Lysyl‐tRNA synthetase)", "2.00"], ["Q66YD0", "VIPP1", "Chloroplast vesicle‐inducing protein in plastids 1", "1.98"], ["A8J5Z0", "RPP0", "Acidic ribosomal protein P0", "1.93"], ["A8I403", "RPS19", "Ribosomal protein S19", "1.89"], ["A8HTK7", "TBA1", "PsbA translation factor", "1.72"], ["A8JIB7", "CPN60A", "Chaperonin 60A", "1.72"], ["P25840", "HSP70", "Heat shock 70 kDa protein", "1.70"], ["A8ITH8", "CPN60B2", "Chaperonin 60B2", "1.52"], ["A8JHX9", "EFG2", "Elongation factor 2 (EC 3.6.5.3)", "1.51"], ["A8JCX9", "RPL40", "Ribosomal protein L40", "1.44"], ["A8J9Q1", "IPA1", "Importin subunit alpha", "1.33"], ["A8I232", "EIF2G", "Eukaryotic initiation factor", "1.28"], ["A8JIE0", "CPN20", "Chaperonin 20", "1.17"], ["A8IV59", "TIIC22", "22 kDa translocon at the inner membrane of chloroplasts (Fragment)", "−1.14"], ["A8J7T7", "CEP1", "Cysteine endopeptidase", "−1.16"], ["Q70DX8", "S1PRPS1", "Plastid ribosomal protein S1 (Ribosomal protein S1 homologue)", "−1.27"], ["P17746", "TUFA", "Elongation factor Tu, chloroplastic (EF‐Tu)", "−1.30"], ["E3SC57", "RPL3", "60S ribosomal protein L3 (Fragment)", "−1.34"], ["Q5QEB2", "EFTs", "Elongation factor Ts", "−1.34"], ["A8HME4", "RPS2", "Ribosomal protein S2", "−1.37"], ["A8IA39", "EFG1", "Chloroplast elongation factor G (EC 3.6.5.3)", "−1.41"], ["A8J282", "CYN20", "Peptidyl‐prolyl cis‐trans isomerase (EC 5.2.1.8) plastid", "−1.41"], ["E3SC50", "RPS9", "40S ribosomal protein S9 (Fragment)", "−1.42"], ["Q6Y683", "RAP41", "41 kDa ribosome‐associated protein (chloroplast)", "−1.49"], ["Q6Y682", "RAP38", "38 kDa ribosome‐associated protein (Chloroplast stem‐loop‐binding protein)", "−1.52"], ["Q8HTL1", "RPL5", "50S ribosomal protein L5, chloroplastic", "−1.52"], ["A8IVK1", "RPL8", "Ribosomal protein L8", "−1.53"], ["Q84U21", "ERY2", "50S ribosomal protein L22, chloroplastic", "−1.60"], ["Q7Y258", "PRPS5", "Ribosomal protein S5 (plastid)", "−1.61"], ["Q8GV23", "NAB1", "Nucleic acid binding protein (Putative nucleic acid binding protein)", "−1.90"], ["A8I8Z4", "PRPL1", "Plastid ribosomal protein L1", "−1.91"], ["A8IRU6", "CYN38", "Peptidyl‐prolyl cis‐trans isomerase, cyclophilin‐type (plastid)", "−1.97"], ["O20032", "RPS18", "30S ribosomal protein S18, chloroplastic", "−1.98"], ["A8HWS8", "PRPL28", "Plastid ribosomal protein L28", "−2.75"], ["Photosynthetic electron transfer", "A8IV40", "Fd", "Apoferredoxin", "−1.18"], ["A8I9I9", "Re", "Rieske ferredoxin", "−1.19"], ["A8J0E4", "PSBO", "Oxygen‐evolving enhancer protein 1 of photosystem II", "−1.21"], ["A8HXL8", "ATPC", "Chloroplast ATP synthase gamma chain", "−1.25"], ["B7U1J0", "ATPA", "ATP synthase subunit alpha, chloroplastic (EC 3.6.3.14)", "−1.32"], ["Q6PSL4", "HYDG", "Fe‐hydrogenase assembly protein (Hydrogenase assembly factor)", "−1.36"], ["A8J6Y8", "FNR2", "Ferredoxin–NADP reductase (EC 1.18.1.2)", "−1.63"], ["P53991", "PETH", "Ferredoxin–NADP reductase, chloroplastic (FNR) (EC 1.18.1.2)", "−1.66"], ["Carbon assimilation", "A8IVM9", "GCSP", "Glycine cleavage system, P protein (EC 1.4.4.2)", "−1.15"], ["Q6SA05", "RCA1", "Rubisco activase", "−1.23"], ["P23489", "RA", "Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic", "−1.36"], ["Q0ZAZ1", "GDH", "Glycolate dehydrogenase", "−1.37"], ["A8HP84", "GAP3", "Glyceraldehyde‐3‐phosphate dehydrogenase (EC 1.2.1.12) (EC 4.3.2.1)", "−1.47"], ["A8IPI7", "HPR1", "Hydroxypyruvate reductase", "−1.51"], ["A8IRK4", "SEBP1", "Sedoheptulose‐1,7‐bisphosphatase (EC 3.1.3.37)", "−1.53"], ["A8IKW6", "RPE1", "Ribulose‐phosphate 3‐epimerase (EC 5.1.3.1)", "−1.57"], ["A8I5A0", "CPLD45", "Predicted protein", "−1.58"], ["A8IKQ0", "FBP1", "Fructose‐1,6‐bisphosphatase (EC 3.1.3.11)", "−1.65"], ["Q42690", "FBA1", "Fructose‐bisphosphate aldolase 1, chloroplastic (EC 4.1.2.13)", "−1.71"], ["A8IRQ1", "RPI1", "Ribose‐5‐phosphate isomerase (EC 5.3.1.6)", "−1.72"], ["Q75NZ2", "LCIB", "Low‐CO2 inducible protein LCIB", "−1.77"], ["A8JC04", "PGK1", "Phosphoglycerate kinase (EC 2.7.2.3)", "−1.81"], ["P93109", "CA2", "Beta‐carbonic anhydrase", "−1.95"], ["Q39589", "BETA‐CA1", "Carbonic anhydrase", "−2.91"], ["Starch metabolism", "Q2VA40", "PHOA", "Phosphorylase (EC 2.4.1.1)", "1.48"], ["Q2VA41", "PHOB", "Phosphorylase (EC 2.4.1.1)", "1.42"], ["A8HS14", "STA1", "ADP‐glucose pyrophosphorylase (EC 2.7.7.27)", "−1.23"], ["Q9LLL6", "STA6", "ADP‐glucose pyrophosphorylase (EC 2.7.7.27)", "−1.34"], ["O64926", "SS", "Soluble starch synthase (EC 2.4.1.21)", "−1.81"], ["Glycolysis", "A8JHR9", "GAP1A", "Glyceraldehyde 3‐phosphate dehydrogenase, dominant splicing variant (EC 1.2.1.12)", "3.01"], ["A8 IE23", "PGI1", "Glucose‐6‐phosphate isomerase (EC 5.3.1.9)", "−1.22"], ["A8IVR6", "PYK2", "Pyruvate kinase (EC 2.7.1.40)", "−1.70"], ["A8JC04", "PGK1", "Phosphoglycerate kinase (EC 2.7.2.3)", "−1.81"], ["TCA cycle", "A8J2S0", "CIS2", "Citrate synthase (EC 2.3.3.1)", "1.82"], ["A8JHC9", "CIS1", "Citrate synthase", "1.49"], ["A8HMQ1", "ACH1", "Aconitate hydratase (EC 4.2.1.3)", "1.41"], ["Q9FNS5", "MDH5", "NADP‐Malate dehydrogenase (EC 1.1.1.82)", "−1.27"], ["A8HPL8", "DLD2", "Dihydrolipoamide dehydrogenase (EC 1.8.1.4)", "−1.58"], ["A8J7F6", "DLA2", "Dihydrolipoamide acetyltransferase (EC 2.3.1.12)", "−1.59"], ["Mitochondrial electron transfer chain", "A8JDV9", "ATP3", "F1F0 ATP synthase gamma subunit", "−1.17"], ["Q96550", "ATPA", "ATP synthase subunit alpha", "−1.32"], ["Q6V9B1", "NUOS8", "NADH:ubiquinone oxidoreductase subunit 8 (EC 1.6.5.3)", "−1.32"], ["A8IVJ7", "NUOS1", "NADH:ubiquinone oxidoreductase 76 kDa subunit", "−1.49"], ["Q6V9A8", "NUO7", "NADH:ubiquinone oxidoreductase 49 kD subunit (EC 1.6.5.3)", "−1.77"], ["Fatty acid biosynthesis", "A8HPL8", "DLD2*", "Dihydrolipoamide dehydrogenase (EC 1.8.1.4)", "−1.58"], ["A8J7F6", "DLA2*", "Dihydrolipoamide acetyltransferase (EC 2.3.1.12)", "−1.59"], ["A8JFI7", "EAR", "enoyl ACP reductase", "−1.92"], ["A8JGF4", "BC", "Biotin carboxylase, acetyl‐CoA carboxylase component", "−1.98"], ["Tetrapyrrole metabolism", "A8I980", "ALAD", "Delta‐aminolevulinic acid dehydratase (EC 4.2.1.24)", "1.41"], ["A8J7H3", "GSA", "Glutamate‐1‐semialdehyde aminotransferase (EC 5.4.3.8)", "−1.23"], ["A8HNE8", "CHLP", "Geranylgeranyl reductase (EC 1.3.1.‐)", "−1.33"], ["A8HPJ2", "POR", "Light‐dependent protochlorophyllide reductase (EC 1.3.1.33)", "−1.59"], ["Amino acid metabolism", "A8IH03", "PSAT", "Phosphoserine aminotransferase (EC 2.6.1.52)", "3.11"], ["A8J786", "HIS7", "Imidazole glycerol phosphate synthase (Fragment)", "2.95"], ["A8J2X6", "AGGPR", "N‐acetyl‐gamma‐glutamyl‐phosphate reductase", "2.29"], ["A8HXS9", "LEU2", "Isopropylmalate synthase (EC 2.3.3.13) (Fragment)", "2.18"], ["A8IXE0", "SAHH", "S‐Adenosylhomocysteine hydrolase (EC 3.3.1.1)", "1.99"], ["A8JFR4", "OTA1", "Ornithine transaminase (EC 2.6.1.13)", "1.95"], ["A8JG03", "LEU1", "Isopropylmalate dehydratase, large subunit", "1.94"], ["A8J979", "MCCA", "Methylcrotonoyl‐CoA carboxylase alpha subunit", "1.85"], ["A8I826", "HSK1", "Homoserine kinase (EC 2.7.1.39)", "1.81"], ["A8IMY5", "ANS1", "Anthranilate synthase, alpha subunit (Fragment)", "1.70"], ["A8J173", "ASD1", "Aspartate semialdehyde dehydrogenase", "1.62"], ["A8J2Z6", "ChS1", "Chorismate synthase (EC 4.2.3.5)", "1.47"], ["A8IX80", "AAD1", "Acetohydroxyacid dehydratase", "1.46"], ["A8ISB0", "OASTL4", "O‐acetylserine sulphydrolase; cysteine synthase (EC 2.5.1.47)", "1.42"], ["A8J355", "CGS1", "Cystathionine gamma‐synthase", "1.42"], ["A8J3D3", "HIS5", "Histidinol phosphate aminotransferase", "1.41"], ["A8ITU7", "PGD1", "D‐3‐phosphoglycerate dehydrogenase (EC 1.1.1.95)", "1.37"], ["O22547", "ALAS", "Acetolactate synthase", "1.20"], ["A8JIR0", "CPS1", "Carbamoyl phosphate synthase, large subunit (EC 6.3.5.5)", "−1.17"], ["P22675", "ARG7", "Argininosuccinate lyase (ASAL) (EC 4.3.2.1) (Arginosuccinase)", "−1.26"], ["A8I305", "GLN1", "Glutamine synthetase (EC 6.3.1.2)", "−1.43"], ["A8JBL3", "NAGS", "N‐acetylglutamate synthase (Fragment)", "−1.49"], ["Other", "A8IJL3", "MEP‐S", "2‐C‐methyl‐d‐erythritol 2,4‐cyclodiphosphate synthase (EC 4.6.1.12)", "2.02"], ["A8J841", "THICb", "Hydroxymethylpyrimidine phosphate synthase", "2.00"], ["A8HMC0", "CRT2", "Calreticulin 2, calcium‐binding protein", "1.53"], ["Q8LRU1", "FER1", "Pre‐apoferritin", "1.41"], ["Kinases", "A8JDN2", "ADK3", "Adenylate kinase 3 (EC 2.7.4.3)", "−1.97"], ["A8JH12", "–", "Nucleoside diphosphate kinase", "−1.97"], ["Redox proteins", "O22472", "CAT", "Catalase (EC 1.11.1.6)", "2.16"], ["A8HQT1", "PDI2", "Protein disulfide isomerase", "1.54"], ["A8IA77", "GSH1", "Gamma‐glutamylcysteine synthetase (EC 6.3.2.2)", "1.54"], ["A8IVV9", "", "Flavodoxin‐like protein (Fragment)", "−1.16"], ["A8IWK2", "–", "Ferredoxin thioredoxin reductase, catalytic chain", "−2.14"], ["N & S metabolism", "A8JHB4", "GSF1", "Ferredoxin‐dependent glutamate synthase", "1.29"], ["A8IXF1", "ATS1", "ATP‐sulfurylase", "1.15"], ["A8J6A7", "MET16", "Adenylylphosphosulfate reductase", "−1.27"], ["A8JGD1", "GDH2", "Glutamate dehydrogenase", "−1.36"], ["Cell structure/organization", "A8JB85", "APG8", "Autophagy protein", "3.84"], ["A8HW56", "CDC48", "Flagellar associated protein (EC 3.6.1.3)", "2.08"], ["A8J614", "FAP42", "Flagellar associated protein, adenylate/guanylate kinase‐like protein", "1.80"], ["A8IFL6", "FAP262", "Flagellar associated protein", "1.70"], ["A8JEQ8", "FAP79", "Flagellar associated protein", "1.31"], ["A8JAV1", "IDA5", "Actin", "−1.31"], ["P09205", "TUBA2", "Tubulin alpha‐2 chain", "−1.90"], ["A8IXZ0", "TUB1", "Beta tubulin 1 (Beta tubulin 2)", "−2.11"], ["Stress response", "Q39603", "HSP70B", "Heat shock protein 70B", "2.06"], ["A8IZU0", "HSP70C", "Heat shock protein 70C", "1.77"], ["P25840", "HSP70", "Heat shock 70 kDa protein", "1.70"], ["A8I7T1", "HSP90B", "Heat shock protein 90B (Fragment)", "1.62"], ["A8I972", "CLPB3", "ClpB chaperone, Hsp100 family", "1.61"], ["A8HYV3", "HSP70B", "Heat shock protein 70B", "1.32"], ["DNA and RNA metabolism", "A8JFP3", "–", "Histone 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