← All .science files
pmid:31578219
Critical Role of a Sheath Phosphorylation Site On the Assembly and Function of an Atypical Type VI Secretion System.
Jason Ziveri · Cerina Chhuon · Anne Jamet · Héloïse Rytter · Guénolé Prigent · Fabiola Tros · Monique Barel · Mathieu Coureuil · Claire Lays · Thomas Henry · Nicholas H Keep · Ida Chiara Guerrera · Alain Charbit
Molecular & cellular proteomics : MCP · 2019 doi:10.1074/mcp.RA119.001532
Paper
complete
Experiment
complete
Data
partial
Analysis
absent
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 13 items
claims array · 2 items
[0] object · 6 fields
[1] object · 6 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 2 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
gaps array · 2 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 0 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 2 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 1 item
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 8 items
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31578219", "kind": "science-record", "revision": 2, "content_hash": "sha256:e0fe3f30979dadd4dadc0441516dafa1e2aa1fa8c6c8acec0d41f6afe366fdf3", "created_at": "2026-11-01T17:33:05Z", "updated_at": "2026-11-01T18:51:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Critical Role of a Sheath Phosphorylation Site On the Assembly and Function of an Atypical Type VI Secretion System.", "doi": "10.1074/mcp.RA119.001532", "pmid": "31578219", "authors": ["Jason Ziveri", "Cerina Chhuon", "Anne Jamet", "Héloïse Rytter", "Guénolé Prigent", "Fabiola Tros", "Monique Barel", "Mathieu Coureuil", "Claire Lays", "Thomas Henry", "Nicholas H Keep", "Ida Chiara Guerrera", "Alain Charbit"], "journal": "Molecular & cellular proteomics : MCP", "year": 2019, "abstract": "The bacterial pathogen Francisella tularensis possesses a noncanonical type VI secretion system (T6SS) that is required for phagosomal escape in infected macrophages. KCl stimulation has been previously used to trigger assembly and secretion of the T6SS in culture. By differential proteomics, we found here that the amounts of the T6SS proteins remained unchanged upon KCl stimulation, suggesting involvement of post-translational modifications in T6SS assembly. A phosphoproteomic analysis indeed identified a unique phosphorylation site on IglB, a key component of the T6SS sheath. Substitutions of Y139 with alanine or phosphomimetics prevented T6SS formation and abolished phagosomal escape whereas substitution with phenylalanine delayed but did not abolish phagosomal escape in J774-1 macrophages. Altogether our data demonstrated that the Y139 site of IglB plays a critical role in T6SS biogenesis, suggesting that sheath phosphorylation could participate to T6SS dynamics.Data are available via ProteomeXchange with identifier PXD013619; and on MS-Viewer, key lkaqkllxwx.", "claims": [{"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD013619; and on MS-Viewer, key lkaqkllxwx", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31578219", "locator": "sections[0] \"Abstract\" paragraph 9", "quote": "Data are available via ProteomeXchange with identifier PXD013619; and on MS-Viewer, key lkaqkllxwx"}], "state": "complete"}, {"id": "claim-target-result", "statement": "Our data demonstrate that site Y139 of IglB plays a critical role in T6SS biogenesis, providing novel mechanistic insight into the role of sheath phosphorylation in T6SS biogenesis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:31578219", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our data demonstrate that site Y139 of IglB plays a critical role in T6SS biogenesis, providing novel mechanistic insight into the role of sheath phosphorylation in T6SS biogenesis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Our data demonstrate that site Y139 of IglB plays a critical role in T6SS biogenesis, providing novel mechanistic insight into the role of sheath phosphorylation in T6SS biogenesis.", "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:31578219"], "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:PXD013619"], "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:PXD013619"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31578219", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1074/mcp.RA119.001532", "sha256": "sha256:8ade7076396f5b649c986f1a1874f50e2c7b5804b863469df1fe64b54d8a8e5b", "bytes": 2134, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1074/mcp.RA119.001532", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6885697", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD013619", "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=PXD013619", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD013619", "version": null, "note": "Data are available via ProteomeXchange with identifier PXD013619; and on MS-Viewer, key lkaqkllxwx", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with identifier PXD013619; and on MS-Viewer, key lkaqkllxwx", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Phosphoproteomic analysis of Francisella", "resolution_checked_at": "2026-11-01T17:30:50Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD013619 not downloaded", "asset:data:geo:PXD013619 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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 (not named), 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": ["PXD013619"], "resolved_accessions": ["PXD013619"], "statements": ["Data are available via ProteomeXchange with identifier PXD013619; and on MS-Viewer, key lkaqkllxwx"], "basis": "The paper names PXD013619 in ProteomeXchange and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:31578219", "data:geo:PXD013619"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD013619"]}, "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": "2026-11-01T16:58:47Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 2104, "completion_tokens": 922, "cached_tokens": 128}}, "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:31578219", "type": "paper", "label": "pmid:31578219"}, {"id": "source:pmid:31578219", "type": "manuscript", "label": "PMID 31578219 full text"}, {"id": "data:geo:PXD013619", "type": "dataset", "label": "GEO PXD013619"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31578219", "type": "paper", "label": "pmid:31578219"}, {"id": "source:pmid:31578219", "type": "manuscript", "label": "PMID 31578219 full text"}, {"id": "data:geo:PXD013619", "type": "dataset", "label": "GEO PXD013619"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31578219", "type": "extraction", "used": ["source:pmid:31578219"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD013619", "type": "accession_resolution", "used": ["data:geo:PXD013619"], "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:31578219", "parent_hash": "sha256:4a2f50cdae3c4b4331015bfbd4d20e4aaeaefbb4f1cbeef76b835732e6fcd819", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:PXD013619 licence not read", "asset:data:geo:PXD013619 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"]}