Dual Element (C/Cl) Isotope Analysis Indicates Distinct Mechanisms of Reductive Dehalogenation of Chlorinated Ethenes and Dichloroethane in Dehalococcoides mccartyi Strain BTF08 With Defined Reductive Dehalogenase Inventories.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32903289", "kind": "science-record", "revision": 6, "content_hash": "sha256:6ed23a7d836b583dcf16ea052c8e072c7fbcafd3e89b16c80af335d524ea1b87", "created_at": "2026-11-01T15:41:09Z", "updated_at": "2026-11-01T21:23:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Dual Element (C/Cl) Isotope Analysis Indicates Distinct Mechanisms of Reductive Dehalogenation of Chlorinated Ethenes and Dichloroethane in Dehalococcoides mccartyi Strain BTF08 With Defined Reductive Dehalogenase Inventories.", "doi": "10.3389/fmicb.2020.01507", "pmid": "32903289", "authors": ["Steffi Franke", "Katja Seidel", "Lorenz Adrian", "Ivonne Nijenhuis"], "journal": "Frontiers in microbiology", "year": 2020, "abstract": "Dehalococcoides mccartyi strain BTF08 has the unique property to couple complete dechlorination of tetrachloroethene and 1,2-dichloroethane to ethene with growth by using the halogenated compounds as terminal electron acceptor. The genome of strain BTF08 encodes 20 genes for reductive dehalogenase homologous proteins (RdhA) including those described for dehalogenation of tetrachloroethene (PceA, PteA), trichloroethene (TceA) and vinyl chloride (VcrA). Thus far it is unknown under which conditions the different RdhAs are expressed, what their substrate specificity is and if different reaction mechanisms are employed. Here we found by proteomic analysis from differentially activated batches that PteA and VcrA were expressed during dechlorination of tetrachloroethene to ethene, while TceA was expressed during 1,2-dichloroethane dehalogenation. Carbon and chlorine compound-specific stable isotope analysis suggested distinct reaction mechanisms for the dechlorination of (i) cis-dichloroethene and vinyl chloride versus (ii) tetrachloroethene. This differentiation was observed independent of the expressed RdhA proteins. Differently, two stable isotope fractionation patterns were observed for 1,2-dichloroethane transformation, for cells with distinct RdhA inventories. Conclusively, we could link specific RdhA expression with functions and provide an insight into the apparently substrate-specific reaction mechanisms in the pathway of reductive dehalogenation in D. mccartyi strain BTF08. Data are available via ProteomeXchange with identifiers PXD018558 and PXD018595.", "claims": [{"id": "claim-method", "statement": "Based on the slope of the regression a two-tailed T-test was uses to calculate the 95% confidence interval (data evaluation in Microsoft Excel).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32903289", "locator": "sections[8] \"Evaluation of Isotopic Data\" paragraph 6", "quote": "Based on the slope of the regression a two-tailed T-test was uses to calculate the 95% confidence interval (data evaluation in Microsoft Excel)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found at: http://www.proteomexchange.org/, PXD018558 and PXD018595.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32903289", "locator": "sections[19] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found at: http://www.proteomexchange.org/, PXD018558 and PXD018595."}], "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:32903289"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD018558"], "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": ["data:geo:PXD018558"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32903289", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmicb.2020.01507", "sha256": "sha256:81624207e68553f907afeebad7e17e6740294cca6ef963f71a0c971c34db29d2", "bytes": 39576, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fmicb.2020.01507", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7396605", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD018558", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD018558", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD018558", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found at: http://www.proteomexchange.org/, PXD018558 and PXD018595.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found at: http://www.proteomexchange.org/, PXD018558 and PXD018595.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Dual element (C/Cl) isotope analysis indicates distinct mechanisms of reductive dehalogenation of chlorinated ethenes and dichloroethane in Dehalococcoides mccartyi strain BTF08 with defined reductive dehalogenase inventories", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD018595", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD018595", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD018595", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found at: http://www.proteomexchange.org/, PXD018558 and PXD018595.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found at: http://www.proteomexchange.org/, PXD018558 and PXD018595.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Part2: Dual element (C/Cl) isotope analysis indicates distinct mechanisms of reductive dehalogenation of chlorinated ethenes and dichloroethane in Dehalococcoides mccartyi strain BTF08 with defined reductive dehalogenase inventories", "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:32903289:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f743a08ede4bcba268630e2a1493e180d99da28cb248a9a485aa9ae5d02d6dfb", "bytes": 216, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T1", "version": null, "note": "Expression of reductive dehalogenase homologous proteins (RdhA).", "structure": {"pmcid": "PMC7396605", "section_index": 14, "section_title": "Dehalogenation Activity in Growing Cultures Correlates With Electron Acceptor Change", "row_count": 1, "column_count": 1}, "table": {"label": "TABLE 1", "caption": "Expression of reductive dehalogenase homologous proteins (RdhA).", "rows": [[""]], "row_count": 1, "column_count": 1, "numeric_cells": 0, "header_rows": 0, "locator": "section[14]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32903289:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:76199e12da9dc7b7b1e215e964446047eeeb42990b3bd7cbc7596b8c0f2fc499", "bytes": 680, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#T2", "version": null, "note": "Substrate specificity of expressed reductive dehalogenases.", "structure": {"pmcid": "PMC7396605", "section_index": 15, "section_title": "Analysis of the Expression of RdhA Proteins in vivo in Response to Electron Acceptor Change", "row_count": 9, "column_count": 6}, "table": {"label": "TABLE 2", "caption": "Substrate specificity of expressed reductive dehalogenases.", "rows": [["Cultivation electron acceptor", "Relative abundance of reductive dehalogenases in the culture [%]", "Electron acceptor in the resting-cells activity test", "Dehalogenation activity"], ["", "VcrAbtf08", "TceAbtf08", "PteAbtf08", "", ""], ["PCE", "83", "–", "17", "PCEcDCE1,2-DCAVC", "+++++n.s.d.+++"], [""], ["cDCE", "96", "–", "4", "PCEcDCE1,2-DCAVC", "++++++++"], [""], ["1,2-DCA", "2", "98", "–", "PCEcDCE1,2-DCAVC", "+++++ ++"], [""], ["VC", "97", "–", "3", "PCEcDCE1,2-DCAVC", "++++n.s.d. +++"]], "row_count": 9, "column_count": 6, "numeric_cells": 16, "header_rows": 2, "locator": "section[15]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:32903289:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d6588b4b76ef7b0e7a02b81e4547339d977afab26a55f262e89993e5e504c76a", "bytes": 2065, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#T3", "version": null, "note": "Summary of isotope fractionation analysis.", "structure": {"pmcid": "PMC7396605", "section_index": 17, "section_title": "Stable Isotope Fractionation Patterns Suggest Distinct Dehalogenation Mechanisms", "row_count": 18, "column_count": 10}, "table": {"label": "TABLE 3", "caption": "Summary of isotope fractionation analysis.", "rows": [["electron acceptor", "carbon", "chlorine", "2D"], ["L1", "RC", "εC [‰]", "R2", "AKIE", "εCl [‰]", "R2", "AKIE", "Λ", "R2"], ["PCE", "PCE", "−5.1 ± 2.1", "0.92", "1.015 ± 0.012", "−2.5 ± 2.6", "0.76", "1.030 ± 0.014", "3.5 ± 0.8", "0.88"], ["", "1,2-DCA", "n.d.", "n.d.", "n.d."], ["", "cDCE", "−23.3 ± 3.0", "0.97", "1.102 ± 0.019", "−1.9 ± 0.4", "0.93", "1.006 ± 0.003", "12.2 ± 2.5", "0.90"], ["", "VC", "−31.7 ± 3.2", "0.98", "1.069 ± 0.008", "−1.7 ± 0.3", "0.98", "1.034 ± 0.001", "15.1 ± 3.6", "0.88"], ["1,2-DCA", "PCE", "−9.8 ± 1.4", "0.97", "1.042 ± 0.006", "−3.2 ± 0.7", "0.89", "1.061 ± 0.009", "2.5 ± 0.5", "0.95"], ["", "1,2-DCA", "−27.5 ± 4.1", "0.92", "c: 1.058 ± 0.018 sw: 1.129 ± 0.021", "−5.3 ± 0.6", "0.96", "c: 1.009 ± 0.003 sw: 1.023 ± 0.003", "5.3 ± 0.6", "0.94"], ["", "cDCE", "−21.2 ± 2.5", "0.96", "1.093 ± 0.012", "−2.5 ± 1.0", "0.75", "1.011 ± 0.001", "7.9 ± 2.5", "0.81"], ["", "VC", "−18.7 ± 3.4", "0.91", "1.040 ± 0.008", "−1.0 ± 0.5", "0.63", "1.002 ± 0.001", "12.6 ± 4.8", "0.69"], ["cDCE", "PCE", "−8.6 ± 2.0", "0.88", "1.037 ± 0.009", "−1.9 ± 0.4", "0.89", "1.032 ± 0.008", "3.0 ± 0.5", "0.94"], ["", "1,2-DCA", "−18.5 ± 4.2", "0.80", "c: 1.038 ± 0.022 sw: 1.086 ± 0.024", "−4.5 ± 1.6", "0.70", "c: 1.009 ± 0.003 sw: 1.018 ± 0.005", "2.0 ± 0.5", "0.89"], ["", "cDCE", "−24.3 ± 3.1", "0.95", "1.096 ± 0.030", "−1.2 ± 0.4", "0.74", "1.005 ± 0.002", "9.6 ± 4.4", "0.63"], ["", "VC", "−20.0 ± 6.3", "0.80", "1.039 ± 0.015", "−0.4 ± 0.4", "0.31", "1.001 ± 0.001", "10.5 ± 6.8", "0.61"], ["VC", "PCE", "−7.7 ± 1.5", "0.90", "1.033 ± 0.007", "−5.6 ± 1.0", "0.94", "1.038 ± 0.009", "2.7 ± 0.5", "0.92"], ["", "1,2-DCA", "n.d.", "n.d.", "n.d."], ["", "cDCE", "−14.7 ± 5.1", "0.73", "1.064 ± 0.024", "−1.0 ± 0.5", "0.56", "1.004 ± 0.002", "12.0 ± 2.0", "0.97"], ["", "VC", "−23.7 ± 3.2", "0.95", "1.051 ± 0.007", "−1.6 ± 0.4", "0.92", "1.003 ± 0.001", "11.0 ± 2.9", "0.88"]], "row_count": 18, "column_count": 10, "numeric_cells": 118, "header_rows": 2, "locator": "section[17]/table-wrap[1]#T3"}}], "gaps": ["asset:data:geo:PXD018558 not downloaded", "asset:data:geo:PXD018558 licence not read", "asset:data:geo:PXD018595 not downloaded", "asset:data:geo:PXD018595 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "two-tailed T-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Based on the slope of the regression a two-tailed T-test was uses to calculate the 95% confidence interval (data evaluation in Microsoft Excel)."}}], "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": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (two-tailed T-test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": "R1", "reachable": true, "accessions": ["PXD018558", "PXD018595"], "resolved_accessions": ["PXD018558", "PXD018595"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found at: http://www.proteomexchange.org/, PXD018558 and PXD018595."], "basis": "The paper names PXD018558, PXD018595 in ProteomeXchange Consortium and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:32903289", "data:geo:PXD018558", "asset:table:pmid:32903289:1", "asset:table:pmid:32903289:2", "asset:table:pmid:32903289:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD018558"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:25Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 33061, "completion_tokens": 1268, "cached_tokens": 21504}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:32903289", "type": "paper", "label": "pmid:32903289"}, {"id": "source:pmid:32903289", "type": "manuscript", "label": "PMID 32903289 full text"}, {"id": "data:geo:PXD018558", "type": "dataset", "label": "GEO PXD018558"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32903289", "type": "paper", "label": "pmid:32903289"}, {"id": "source:pmid:32903289", "type": "manuscript", "label": "PMID 32903289 full text"}, {"id": "data:geo:PXD018558", "type": "dataset", "label": "GEO PXD018558"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32903289", "type": "extraction", "used": ["source:pmid:32903289"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD018558", "type": "accession_resolution", "used": ["data:geo:PXD018558"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:32903289", "parent_hash": "sha256:42bcf21eb0a41888736b184ebd3f3ca5f54103181a2e0309d64a191456e58cca", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD018558 licence not read", "asset:data:geo:PXD018558 not downloaded", "asset:data:geo:PXD018595 licence not read", "asset:data:geo:PXD018595 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["on mechanisms are employed. Here we found by proteomic analysis from differentially activated batch", ". Cell Harvesting and Sample Preparation for Proteomic Analysis Dehalococcoides mccartyi strain BTF", "Ratios by Gas Chromatography – Isotope Ratio Mass Spectrometry Carbon isotope ratios were determined via co", "able isotope analyses using GC-isotope ratio mass spectrometry (IRMS). The organic mixture was separated by"], "order_basis": "paper_text_order:823", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["Analysis of the Expression of RdhA Proteins in vivo in Response to Electron Acceptor Change The"], "order_basis": "paper_text_order:5983", "id": "assay:2"}]}