Proteomic Analysis of Proteins Related to Defense Responses in Arabidopsis Plants Transformed with the rolB Oncogene.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36768198", "kind": "science-record", "revision": 4, "content_hash": "sha256:173d4cfeb433e4d34039cda3c5d9ddf38f48bc18453999377c9808873ad6c1b0", "created_at": "2026-11-01T19:01:21Z", "updated_at": "2026-11-01T22:51:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic Analysis of Proteins Related to Defense Responses in Arabidopsis Plants Transformed with the rolB Oncogene.", "doi": "10.3390/ijms24031880", "pmid": "36768198", "authors": ["Yulia V Vereshchagina", "Anastasiya A Mironova", "Dmitry V Bulgakov", "Victor P Bulgakov"], "journal": "International journal of molecular sciences", "year": 2023, "abstract": "During Agrobacterium rhizogenes-plant interaction, the rolB gene is transferred into the plant genome and is stably inherited in the plant's offspring. Among the numerous effects of rolB on plant metabolism, including the activation of secondary metabolism, its effect on plant defense systems has not been sufficiently studied. In this work, we performed a proteomic analysis of rolB-expressing Arabidopsis thaliana plants with particular focus on defense proteins. We found a total of 77 overexpressed proteins and 64 underexpressed proteins in rolB-transformed plants using two-dimensional gel electrophoresis and MALDI mass spectrometry. In the rolB-transformed plants, we found a reduced amount of scaffold proteins RACK1A, RACK1B, and RACK1C, which are known as receptors for activated C-kinase 1. The proteomic analysis showed that rolB could suppress the plant immune system by suppressing the RNA-binding proteins GRP7, CP29B, and CP31B, which action are similar to the action of type-III bacterial effectors. At the same time, rolB plants induce the massive biosynthesis of protective proteins VSP1 and VSP2, as well as pathogenesis-related protein PR-4, which are markers of the activated jasmonate pathway. The increased contents of glutathione-S-transferases F6, F2, F10, U19, and DHAR1 and the osmotin-like defense protein OSM34 were found. The defense-associated protein PCaP1, which is required for oligogalacturonide-induced priming and immunity, was upregulated. Moreover, rolB-transformed plants showed the activation of all components of the PYK10 defense complex that is involved in the metabolism of glucosinolates. We hypothesized that various defense systems activated by rolB protect the host plant from competing phytopathogens and created an effective ecological niche for A. rhizogenes. A RolB → RACK1A signaling module was proposed that might exert most of the rolB-mediated effects on plant physiology. Our proteomics data are available via ProteomeXchange with identifier PXD037959.", "claims": [{"id": "claim-method", "statement": "Two independent categories were compared using the Student’s t test while comparisons among multiple groups were performed using analysis of variance (ANOVA), followed by a multiple comparison protocol. The inter-group comparison was made using Fisher’s protected least significant difference (PLSD) post-hoc test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36768198", "locator": "sections[25] \"4.6.4. Statistical Analyses\" paragraph 2", "quote": "Two independent categories were compared using the Student’s t test while comparisons among multiple groups were performed using analysis of variance (ANOVA), followed by a multiple comparison protocol. The inter-group comparison was made using Fisher’s protected least significant difference (PLSD) post-hoc test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry data have been deposited to ProteomeXchange via the PRIDE partner repository with the dataset identifier PXD037959 (Project DOI: 10.6019/PXD037959).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36768198", "locator": "sections[32] \"Data Availability Statement\" paragraph 2", "quote": "The mass spectrometry data have been deposited to ProteomeXchange via the PRIDE partner repository with the dataset identifier PXD037959 (Project DOI: 10.6019/PXD037959)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The proteomic analysis identified 77 overexpressed and 64 underexpressed proteins in rolB-transformed plants.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36768198", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We found a total of 77 overexpressed proteins and 64 underexpressed proteins in rolB-transformed plants using two-dimensional gel electrophoresis and MALDI mass spectrometry."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The proteomic analysis identified 77 overexpressed and 64 underexpressed proteins in rolB-transformed plants.", "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:36768198"], "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:PXD037959"], "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:PXD037959"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36768198", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms24031880", "sha256": "sha256:585325460bfaf6e027ee95e27bc3d5641df35984b9c0a803ebf4bcf41b06b8fd", "bytes": 87795, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms24031880", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9915171", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD037959", "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=PXD037959", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD037959", "version": null, "note": "The mass spectrometry data have been deposited to ProteomeXchange via the PRIDE partner repository with the dataset identifier PXD037959 (Project DOI: 10.6019/PXD037959).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry data have been deposited to ProteomeXchange via the PRIDE partner repository with the dataset identifier PXD037959 (Project DOI: 10.6019/PXD037959).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomic analysis of proteins related to defense responses in Arabidopsis plants transformed with the rolB oncogene", "resolution_checked_at": "2026-11-01T18:46:41Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD037959 not downloaded", "asset:data:geo:PXD037959 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Two independent categories were compared using the Student’s t test while comparisons among multiple groups were performed using analysis of variance (ANOVA), followed by a multiple comparison protocol. The inter-group comparison was made using Fisher’s protected least significant difference (PLSD) post-hoc test."}}], "targets": [], "gaps": []}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["PXD037959"], "resolved_accessions": ["PXD037959"], "statements": ["The mass spectrometry data have been deposited to ProteomeXchange via the PRIDE partner repository with the dataset identifier PXD037959 (Project DOI: 10.6019/PXD037959)."], "basis": "The paper names PXD037959 in ProteomeXchange and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:36768198", "data:geo:PXD037959"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD037959"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:26:57Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 25208, "completion_tokens": 2458, "cached_tokens": 265}}, "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:36768198", "type": "paper", "label": "pmid:36768198"}, {"id": "source:pmid:36768198", "type": "manuscript", "label": "PMID 36768198 full text"}, {"id": "data:geo:PXD037959", "type": "dataset", "label": "GEO PXD037959"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36768198", "type": "paper", "label": "pmid:36768198"}, {"id": "source:pmid:36768198", "type": "manuscript", "label": "PMID 36768198 full text"}, {"id": "data:geo:PXD037959", "type": "dataset", "label": "GEO PXD037959"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36768198", "type": "extraction", "used": ["source:pmid:36768198"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD037959", "type": "accession_resolution", "used": ["data:geo:PXD037959"], "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:36768198", "parent_hash": "sha256:5d39e01131c0cf28e1e0e3719ae890fc9db154926c8ee28052897c43a23f6459", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PXD037959 licence not read", "asset:data:geo:PXD037959 not downloaded", "execution.not_run", "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": ["Proteomic Analysis of Proteins Related to Defense Resp", "n as receptors for activated C-kinase 1. The proteomic analysis showed that rolB could suppress the", "lB-mediated effects on plant physiology. Our proteomics data are available via ProteomeXchange with", "of B5 line was selected to obtain plants for proteomic analysis. The F3 generation of B5 line exhib"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": [", but it did not show signs of dwarfism [9]. Real-time PCR analysis showed that the haploid B5 genome c"], "order_basis": "paper_text_order:3962", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Two independent categories were compared using the Student’s t test while comparisons among multiple groups were performed using analysis of variance (ANOVA), followed by a multiple comparison protocol. The inter-group comparison was made using Fisher’s protected least significant difference (PLSD) post-hoc test."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}