Histidine kinase inhibitors impair shoot regeneration in Arabidopsis thaliana via cytokinin signaling and SAM patterning determinants.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36684719", "kind": "science-record", "revision": 4, "content_hash": "sha256:61f1c7b939f93e512a1e11bd935df71291ba1b0118fef0363766970b8d5c8b56", "created_at": "2026-11-01T19:01:13Z", "updated_at": "2026-11-01T22:51:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Histidine kinase inhibitors impair shoot regeneration in Arabidopsis thaliana via cytokinin signaling and SAM patterning determinants.", "doi": "10.3389/fpls.2022.894208", "pmid": "36684719", "authors": ["Robin Lardon", "Hoang Khai Trinh", "Xiangyu Xu", "Lam Dai Vu", "Brigitte Van De Cotte", "Markéta Pernisová", "Steffen Vanneste", "Ive De Smet", "Danny Geelen"], "journal": "Frontiers in plant science", "year": 2022, "abstract": "Reversible protein phosphorylation is a post-translational modification involved in virtually all plant processes, as it mediates protein activity and signal transduction. Here, we probe dynamic protein phosphorylation during de novo shoot organogenesis in Arabidopsis thaliana. We find that application of three kinase inhibitors in various time intervals has different effects on root explants. Short exposures to the putative histidine (His) kinase inhibitor TCSA during the initial days on shoot induction medium (SIM) are detrimental for regeneration in seven natural accessions. Investigation of cytokinin signaling mutants, as well as reporter lines for hormone responses and shoot markers, suggests that TCSA impedes cytokinin signal transduction via AHK3, AHK4, AHP3, and AHP5. A mass spectrometry-based phosphoproteome analysis further reveals profound deregulation of Ser/Thr/Tyr phosphoproteins regulating protein modification, transcription, vesicle trafficking, organ morphogenesis, and cation transport. Among TCSA-responsive factors are prior candidates with a role in shoot apical meristem patterning, such as AGO1, BAM1, PLL5, FIP37, TOP1ALPHA, and RBR1, as well as proteins involved in polar auxin transport (e.g., PIN1) and brassinosteroid signaling (e.g., BIN2). Putative novel regeneration determinants regulated by TCSA include RD2, AT1G52780, PVA11, and AVT1C, while NAIP2, OPS, ARR1, QKY, and aquaporins exhibit differential phospholevels on control SIM. LC-MS/MS data are available via ProteomeXchange with identifier PXD030754.", "claims": [{"id": "claim-method", "statement": "Peptide identification and quantification were done in MaxQuant and the DEqMS package (based on limma) was used for statistical testing (Cox and Mann, 2008; Ritchie et al., 2015; Tyanova et al., 2016a; Zhu et al., 2020b).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36684719", "locator": "sections[13] \"Phosphoproteome analysis uncovers TCSA-responsive phosphosites\" paragraph 2", "quote": "Peptide identification and quantification were done in MaxQuant and the DEqMS package (based on limma) was used for statistical testing (Cox and Mann, 2008; Ritchie et al., 2015; Tyanova et al., 2016a; Zhu et al., 2020b)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data generated in this study can be found in the PRIDE repository with identifier PXD030754. Processed results of the phosphoproteome analysis are available in Supplementary Data 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36684719", "locator": "sections[16] \"Data availability statement\" paragraph 2", "quote": "The raw data generated in this study can be found in the PRIDE repository with identifier PXD030754. Processed results of the phosphoproteome analysis are available in Supplementary Data 1."}], "state": "complete"}, {"id": "claim-target-result", "statement": "TCSA impedes cytokinin signal transduction during shoot regeneration and causes profound deregulation of Ser/Thr/Tyr phosphorylation.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36684719", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Investigation of cytokinin signaling mutants, as well as reporter lines for hormone responses and shoot markers, suggests that TCSA impedes cytokinin signal transduction via AHK3, AHK4, AHP3, and AHP5."}, {"asset": "source:pmid:36684719", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A mass spectrometry-based phosphoproteome analysis further reveals profound deregulation of Ser/Thr/Tyr phosphoproteins regulating protein modification, transcription, vesicle trafficking, organ morphogenesis, and cation transport."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "TCSA impedes cytokinin signal transduction during shoot regeneration and causes profound deregulation of Ser/Thr/Tyr phosphorylation.", "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:36684719"], "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:PXD030754"], "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:PXD030754"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36684719", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fpls.2022.894208", "sha256": "sha256:cdd9c513928e5790b554bcdd66db26833a2fe74654007051aee2618212ba042b", "bytes": 73044, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fpls.2022.894208", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9847488", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD030754", "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=PXD030754", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD030754", "version": null, "note": "The raw data generated in this study can be found in the PRIDE repository with identifier PXD030754. Processed results of the phosphoproteome analysis are available in Supplementary Data 1.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data generated in this study can be found in the PRIDE repository with identifier PXD030754. Processed results of the phosphoproteome analysis are available in Supplementary Data 1.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Histidine Kinase Inhibitors Impair Shoot Regeneration in Arabidopsis thaliana via Cytokinin Signalling and SAM Patterning Determinants", "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:PXD030754 not downloaded", "asset:data:geo:PXD030754 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Peptide identification and quantification were done in MaxQuant and the DEqMS package (based on limma) was used for statistical testing (Cox and Mann, 2008; Ritchie et al., 2015; Tyanova et al., 2016a; Zhu et al., 2020b)."}}], "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["PXD030754"], "resolved_accessions": ["PXD030754"], "statements": ["The raw data generated in this study can be found in the PRIDE repository with identifier PXD030754. Processed results of the phosphoproteome analysis are available in Supplementary Data 1."], "basis": "The paper names PXD030754 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:36684719", "data:geo:PXD030754"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD030754"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:24:04Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 20042, "completion_tokens": 2005, "cached_tokens": 188}}, "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:36684719", "type": "paper", "label": "pmid:36684719"}, {"id": "source:pmid:36684719", "type": "manuscript", "label": "PMID 36684719 full text"}, {"id": "data:geo:PXD030754", "type": "dataset", "label": "GEO PXD030754"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36684719", "type": "paper", "label": "pmid:36684719"}, {"id": "source:pmid:36684719", "type": "manuscript", "label": "PMID 36684719 full text"}, {"id": "data:geo:PXD030754", "type": "dataset", "label": "GEO PXD030754"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36684719", "type": "extraction", "used": ["source:pmid:36684719"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD030754", "type": "accession_resolution", "used": ["data:geo:PXD030754"], "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:36684719", "parent_hash": "sha256:b3c14a5a0b744dbcb18e88bdc6ddcaef635b086b7c78deca71f3ee780af50a3d", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PXD030754 licence not read", "asset:data:geo:PXD030754 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": ["ansduction via AHK3, AHK4, AHP3, and AHP5. A mass spectrometry-based phosphoproteome analysis further revea", "t differential phospholevels on control SIM. LC-MS/MS data are available via ProteomeXchange with"], "order_basis": "paper_text_order:879", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Peptide identification and quantification were done in MaxQuant and the DEqMS package (based on limma) was used for statistical testing (Cox and Mann, 2008; Ritchie et al., 2015; Tyanova et al., 2016a; Zhu et al., 2020b)."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}