Induction by Bradyrhizobium diazoefficiens of Different Pathways for Growth in D-mannitol or L-arabinose Leading to Pronounced Differences in CO2 Fixation, O2 Consumption, and Lateral-Flagellum Production.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29922265", "kind": "science-record", "revision": 6, "content_hash": "sha256:397c32fdf10265dfc6952943c11ee79ff6a18e1851699d0b287504a569694274", "created_at": "2026-11-01T15:40:35Z", "updated_at": "2026-11-01T21:21:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Induction by Bradyrhizobium diazoefficiens of Different Pathways for Growth in D-mannitol or L-arabinose Leading to Pronounced Differences in CO2 Fixation, O2 Consumption, and Lateral-Flagellum Production.", "doi": "10.3389/fmicb.2018.01189", "pmid": "29922265", "authors": ["Carolina Cogo", "Julieta Pérez-Giménez", "Chandrasekar B Rajeswari", "María F Luna", "Aníbal R Lodeiro"], "journal": "Frontiers in microbiology", "year": 2018, "abstract": "Bradyrhizobium diazoefficiens, a soybean N2-fixing symbiont, constitutes the basic input in one of the most prominent inoculant industries worldwide. This bacterium may be cultured with D-mannitol or L-arabinose as carbon-plus-energy source (C-source) with similar specific growth rates, but with higher biomass production with D-mannitol. To better understand the bacterium's carbon metabolism, we analyzed, by liquid chromatography and tandem mass spectrometry (MS), the whole set of proteins obtained from cells grown on each C-source. Among 3,334 proteins identified, 266 were overproduced in D-mannitol and 237 in L-arabinose, but among these, only 22% from D-mannitol cultures and 35% from L-arabinose cultures were annotated with well defined functions. In the D-mannitol-differential pool we found 19 enzymes of the pentose-phosphate and Calvin-Benson-Bassham pathways and accordingly observed increased extracellular-polysaccharide production by D-mannitol grown bacteria in a CO2-enriched atmosphere. Moreover, poly-3-hydroxybutyrate biosynthesis was increased, suggesting a surplus of reducing power. In contrast, the L-arabinose-differential pool contained 11 enzymes of the L-2-keto-3-deoxyarabonate pathway, 4 enzymes for the synthesis of nicotinamide-adenine dinucleotide from aspartate, with those cultures having a threefold higher O2-consumption rate than the D-mannitol cultures. The stoichiometric balances deduced from the modeled pathways, however, resulted in similar O2 consumptions and ATP productions per C-mole of substrate. These results suggested higher maintenance-energy demands in L-arabinose, which energy may be used partly for flagella-driven motility. Since B. diazoefficiens produces the lateral-flagella system in only L-arabinose, we calculated the O2-consumption rates of a lafR::Km mutant devoid of lateral flagella cultured in L-arabinose or D-mannitol. Contrary to that of the wild-type, the O2-consumption rate of this mutant was similar on both C-sources, and accordingly outcompeted the wild-type in coculture, suggesting that the lateral flagella behaved as parasitic structures under these conditions. Proteomic data are available via ProteomeXchange with identifier PXD008263.", "claims": [{"id": "claim-method", "statement": "For proteomic comparisons, we employed duplicate or triplicate independent cultures (biologic replicates) from each culture medium and each subcellular fraction. With these replicates we constructed volcano plots to compare the samples using the logarithmic values of the ratio of the areas under the peaks along with the statistical significance of those values assessed by the Student-t-test (not shown).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29922265", "locator": "sections[10] \"Statistical Procedures\" paragraph 2", "quote": "For proteomic comparisons, we employed duplicate or triplicate independent cultures (biologic replicates) from each culture medium and each subcellular fraction. With these replicates we constructed volcano plots to compare the samples using the logarithmic values of the ratio of the areas under the peaks along with the statistical significance of those values assessed by the Student-t-test (not shown)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Vizcaíno et al., 2016) partner repository with the dataset identifier PXD008263 and 10.6019/PXD008263.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29922265", "locator": "sections[11] \"Data Submission\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Vizcaíno et al., 2016) partner repository with the dataset identifier PXD008263 and 10.6019/PXD008263."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study identified 3,334 proteins by liquid chromatography–tandem mass spectrometry; differential expression was defined by a Student’s t-test with fold changes greater than 2 and p-values below 0.05, and the underlying proteomics dataset was deposited in ProteomeXchange/PRIDE as PXD008263.", "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:29922265"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29922265", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmicb.2018.01189", "sha256": "sha256:407b673d7ab9cfe4d83860f4cc454d6e47edc314cd6f50c93fc8b4fbd0fd0330", "bytes": 74652, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fmicb.2018.01189", "version": null, "note": "Full article fetched from PMC; 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Pyruvate dehydrogenase E1 component.", "In only Mtl", "In only Mtl"], ["blr3224", "Q89QA6", "", "ABC transporter ATP-binding protein. Putative sorbitol/mannitol transport system.", "In only Mtl", "NS"], ["blr3225", "Q89QA5", "", "Oxidoreductase. Similar to putative Glucose/ribitol oxidoreductase.", "5.0927", "In only Mtl"], ["blr3226", "Q89QA4", "", "Ribitol kinase", "3.9234", "-"], ["blr3227", "Q89QA3", "", "Putative fructokinase.", "In only Mtl", "-"], ["bll3754", "Q89NT0", "gph", "Phosphoglycolate phosphatase.", "In only Mtl", "NS"], ["bll6549", "Q89FZ9", "", "D-3-phosphoglycerate:NAD+ oxidoreductase", "In only Mtl", "-"], ["blr7063", "Q89EL0", "", "Probable 2-ketogluconate reductase.", "2.5998", "-"], ["", "", "", "Ara catabolic pathway", "", ""], ["bll1188", "Q89V68", "atpB", "ATP synthase subunit a.", "-", "In only Ara"], ["blr2316", "Q89ST4", "", "Probable NADH-ubiquinone oxidoreductase chain F.", "In only Ara", "-"], ["blr2929", "Q89R43", "", "Hydroxypyruvate isomerase.", "NS", "In only Ara"], ["blr2974", "Q89QZ8", "", "Dehydratase. Similar to a putative D-galactarate dehydratase.", "-1.2323", "-"], ["bll3156", "Q89QH2", "frc", "Formyl-CoA:oxalate CoA-transferase.", "-2.1294", "In only Ara"], ["bll3157", "Q89QH1", "oxc", "Oxalyl-CoA carboxy-lyase.", "-2.3829", "NS"], ["blr3166", "Q89QG2", "gcl", "Glyoxylate carboligase.", "In only Ara", "In only Ara"], ["blr3167", "Q89QG1", "hyi", "Hydroxypyruvate isomerase.", "In only Ara", "In only Ara"], ["blr3168", "Q89QG0", "", "Tartronate semialdehyde reductase.", "In only Ara", "In only Ara"], ["blr3205", "Q89QC3", "", "Dehydrogenase. Similar to Galactose 1-dehydrogenase.", "-", "-3.3450"], ["blr3207", "Q89QC1", "", "L-arabinonolactonase.", "-4.7706", "In only Ara"], ["bll7287", "Q89E00", "dgoA", "2-dehydro-3-deoxyphosphogalactonate aldolase.", "-1.4610", "-"], ["", "", "", "NAD and FAD production", "", ""], ["blr0430", "Q89X84", "nadD", "Probable nicotinate-nucleotide adenylyltransferase.", "-1.3324", "-"], ["bll2541", "Q89S64", "nadB", "L-aspartate oxidase.", "In only Ara", "-1.7782"], ["bll4547", "Q89LJ7", "nadE", "Glutamine-dependent NAD(+) synthetase.", "-1.2616", "-"], ["bll7452", "Q89DI7", "ribH2", "6,7-dimethyl-8-ribityllumazine synthase 2.", "In only Ara", "-"], ["blr8123", "Q89BM5", "", "MutT/nudix family protein.", "-1.3450", "NS"], ["", "", "", "PHB synthesis and degradation", "", ""], ["bll0225", "Q89XT2", "phaB", "Acetoacetyl CoA reductase.", "2.7381", "NS"], ["blr0227", "Q89XT0", "phaR", "Transcriptional regulator of polyhydroxybutirate synthesis.", "1.6828", "NS"], ["blr0908", "Q89VY7", "", "Hypothetical protein. Similar to PHB depolymerase.", "In only Ara", "-2.0085"], ["bll4360", "Q89M33", "phaC1", "Poly-3-hydroxybutyrate synthase.", "2.7271", "NS"], ["bll6073", "Q89HC1", "phaC2", "Polyhydroxybutirate synthase PhaC2.", "In only Ara", "NS"], ["", "", "", "Biotin synthesis", "", ""], ["blr2097", "H7C6S8", "bioF", "8-amino-7-oxononanoate synthase.", "-", "In only Mtl"], ["blr2098", "Q9AMS4", "bioD", "ATP-dependent dethiobiotin synthetase.", "In only Mtl", "-"], ["blr2099", "H7C6S2", "bioA", "Adenosylmethionine-8-amino-7-oxononanoate aminotransferase.", "In only Mtl", "-"], ["blr2221", "Q89T29", "bioA", "Adenosylmethionine-8-amino-7-oxononanoate aminotransferase", "1.1619", "-"], ["bll6273", "Q89GS2", "", "Probable biotin sulfoxide reductase.", "In only Ara", "-"], ["", "", "", "Cell motility and chemotaxis", "", ""], ["blr2343", "Q89SQ7", "cheA", "Chemotaxis two-component sensor histidine kinase.", "NS", "-1.8082"], ["blr2344", "Q89SQ6", "cheWII", "CheWII protein.", "In only Ara", "NS"], ["blr2345", "Q89SQ5", "mcpK", "Methyl-accepting chemotaxis protein.", "NS", "-1.8623"], ["blr2346", "Q89SQ4", "cheW", "CheW protein.", "In only Ara", "-"], ["blr2347", "Q89SQ3", "", "Methyl-accepting chemotaxis protein.", "NS", "-1.5919"], ["blr2349", "Q89SQ1", "cheB", "Chemotaxis response regulator protein-glutamate methylesterase of group 3 operon.", "-", "In only Ara"], ["blr2931", "Q89R41", "", "Putative methyl-accepting chemotaxis protein.", "-", "In only Ara"], ["bll6858", "Q89F43", "flgEL", "Lateral flagellar hook protein", "In only Ara", "-"], ["bll6865", "Q89F36", "lafA2", "Lateral flagellin 2", "In only Ara", "In only Ara"], ["bll6866", "Q89F35", "lafA1", "Lateral flagellin 1", "In only Ara", "In only Ara"]], "row_count": 64, "column_count": 6, "numeric_cells": 143, "header_rows": 2, "locator": "section[13]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:29922265:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": 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"row_count": 7, "column_count": 7}, "table": {"label": "Table 4", "caption": "Specific rates (±SD) of substrate consumption, product formation, and growth yields of B. diazoefficiens growing in batch cultures in the exponential growth phase.", "rows": [["Propertya", "Wild-type", "lafR::Km mutant"], ["", "HMY-Mtl", "HMY-Ara", "Ratio Ara/Mtl", "HMY-Mtl", "HMY-Ara", "Ratio Ara/Mtl"], ["μmax (h-1)", "0.04 ± 0.01", "0.04 ± 0.02", "1.0", "0.03 ± 0.01", "0.03 ± 0.01", "1.0"], ["qO2max (mmol.g-1.h-1)", "0.86 ± 0.02", "2.53 ± 0.11", "2.9", "1.26 ± 0.12", "1.63 ± 0.07", "1.3"], ["yx/s (C-mole.C-mole-1)", "0.50 ± 0.10", "0.27 ± 0.08", "0.5", "0.52 ± 0.13", "0. 41 ± 0.07", "0.8"], ["qS max (mC-mole.g-1 .h-1)", "2.81 ± 0.46", "7.66 ± 0.47", "2.7", "2.17 ± 0.34", "2.90 ± 0.64", "1.3"], ["qCO2max (mmole.g-1 .h-1)", "0.67 ± 0.03", "2.39 ± 0.05", "3.6", "0.60 ± 0.01", "1.05 ± 0.08", "1.7"]], "row_count": 7, "column_count": 7, "numeric_cells": 35, "header_rows": 2, "locator": 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With these replicates we constructed volcano plots to compare the samples using the logarithmic values of the ratio of the areas under the peaks along with the statistical significance of those values assessed by the Student-t-test (not shown)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["ols_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ols."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": ["PXD008263 and 10.6019/PXD008263"], "resolved_accessions": [], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Vizcaíno et al., 2016) partner repository with the dataset identifier PXD008263 and 10.6019/PXD008263."], "basis": "The paper names PXD008263 and 10.6019/PXD008263, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. 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This bacterium may be cultured with D-mannitol or L-arabinose as carbon-plus-ene", "a lafR::Km mutant devoid of lateral flagella cultured in L-arabinose or D-mannitol. Contrary to that"], "order_basis": "paper_text_order:334", "id": "assay:1"}, {"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["nalyzed, by liquid chromatography and tandem mass spectrometry (MS), the whole set of proteins obtained fro", "parasitic structures under these conditions. 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