The genetic interaction network of CCW12, a Saccharomyces cerevisiae gene required for cell wall integrity during budding and formation of mating projections.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:21320323", "kind": "science-record", "revision": 7, "content_hash": "sha256:40766f5a9afb7df01d1122090c7ecd44a20f62adb8fea89e6ac83300da8569e7", "created_at": "2026-11-01T15:14:34Z", "updated_at": "2026-11-01T21:19:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The genetic interaction network of CCW12, a Saccharomyces cerevisiae gene required for cell wall integrity during budding and formation of mating projections.", "doi": "10.1186/1471-2164-12-107", "pmid": "21320323", "authors": ["Enrico Ragni", "Heidi Piberger", "Christine Neupert", "Jesús García-Cantalejo", "Laura Popolo", "Javier Arroyo", "Markus Aebi", "Sabine Strahl"], "journal": "BMC genomics", "year": 2011, "abstract": "BACKGROUND: Mannoproteins construct the outer cover of the fungal cell wall. The covalently linked cell wall protein Ccw12p is an abundant mannoprotein. It is considered as crucial structural cell wall component since in baker's yeast the lack of CCW12 results in severe cell wall damage and reduced mating efficiency.\nRESULTS: In order to explore the function of CCW12, we performed a Synthetic Genetic Analysis (SGA) and identified genes that are essential in the absence of CCW12. The resulting interaction network identified 21 genes involved in cell wall integrity, chitin synthesis, cell polarity, vesicular transport and endocytosis. Among those are PFD1, WHI3, SRN2, PAC10, FEN1 and YDR417C, which have not been related to cell wall integrity before. We correlated our results with genetic interaction networks of genes involved in glucan and chitin synthesis. A core of genes essential to maintain cell integrity in response to cell wall stress was identified. In addition, we performed a large-scale transcriptional analysis and compared the transcriptional changes observed in mutant ccw12Δ with transcriptomes from studies investigating responses to constitutive or acute cell wall damage. We identified a set of genes that are highly induced in the majority of the mutants/conditions and are directly related to the cell wall integrity pathway and cell wall compensatory responses. Among those are BCK1, CHS3, EDE1, PFD1, SLT2 and SLA1 that were also identified in the SGA. In contrast, a specific feature of mutant ccw12Δ is the transcriptional repression of genes involved in mating. Physiological experiments substantiate this finding. Further, we demonstrate that Ccw12p is present at the cell periphery and highly concentrated at the presumptive budding site, around the bud, at the septum and at the tip of the mating projection.\nCONCLUSIONS: The combination of high throughput screenings, phenotypic analyses and localization studies provides new insight into the function of Ccw12p. A compensatory response, culminating in cell wall remodelling and transport/recycling pathways is required to buffer the loss of CCW12. Moreover, the enrichment of Ccw12p in bud, septum and mating projection is consistent with a role of Ccw12p in preserving cell wall integrity at sites of active growth.The microarray data produced in this analysis have been submitted to NCBI GEO database and GSE22649 record was assigned.", "claims": [{"id": "claim-method", "statement": "p-values were obtained using hypergeometric distribution statistics; default setting in FunCatDB tools, MIPS", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:21320323", "locator": "sections[8] \"Global transcriptional responses of the ccw12Δ mutant\" paragraph 6", "quote": "p-values were obtained using hypergeometric distribution statistics; default setting in FunCatDB tools, MIPS"}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray data produced in this analysis have been submitted to NCBI GEO database and GSE22649 record was assigned.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:21320323", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "The microarray data produced in this analysis have been submitted to NCBI GEO database and GSE22649 record was assigned."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used hierarchical clustering to compare the ccw12Δ transcriptome with transcriptomes from other cell wall mutants and stress conditions; the underlying microarray data were deposited in NCBI GEO under accession GSE22649. Its headline finding is that a compensatory cell-wall response is required to buffer the loss of CCW12.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:21320323", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The combination of high throughput screenings, phenotypic analyses and localization studies provides new insight into the function of Ccw12p."}, {"asset": "source:pmid:21320323", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A compensatory response, culminating in cell wall remodelling and transport/recycling pathways is required to buffer the loss of CCW12."}, {"asset": "source:pmid:21320323", "locator": "sections[9] \"Comparison of the ccw12Δ transcriptome with transcriptional profiles from other cell wall-related mutants\" paragraph 2", "quote": "In order to compare transcriptional changes in the ccw12Δ mutant with transcriptomes from previous studies investigating responses to constitutive cell wall damage caused by deletions of cell wall-related genes, such as GAS1, FKS1, KRE6 and MNN9, and transient cell wall damage induced by CR or Zymolyase treatment [15,16], data were organized by hierarchical clustering (see Methods)."}, {"asset": "source:pmid:21320323", "locator": "sections[9] \"Comparison of the ccw12Δ transcriptome with transcriptional profiles from other cell wall-related mutants\" paragraph 4", "quote": "Cluster I includes 20 genes that were highly induced in the majority of the mutants/conditions analysed."}, {"asset": "source:pmid:21320323", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "The microarray data produced in this analysis have been submitted to NCBI GEO database and GSE22649 record was assigned."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used hierarchical clustering to compare the ccw12Δ transcriptome with transcriptomes from other cell wall mutants and stress conditions; the underlying microarray data were deposited in NCBI GEO under accession GSE22649. 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"2.3", ""], ["YOR382w", "FIT2", "GPI-anchored cell wall protein", "3.3", ""], ["YPL163c", "SVS1", "Cell wall and vacuolar protein", "2.3", ""]], "row_count": 34, "column_count": 5, "numeric_cells": 80, "header_rows": 1, "locator": "section[8]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:21320323:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8316a64a413942c221981d127c8e21e1ccfd356e8b19b32ee300e8022d705da4", "bytes": 1233, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[2]#T3", "version": null, "note": "Mating related genes modulated in the ccw12Δ transcriptional response", "structure": {"pmcid": "PMC3049148", "section_index": 8, "section_title": "Global transcriptional responses of the ccw12Δ mutant", "row_count": 14, "column_count": 5}, "table": {"label": "Table 3", "caption": "Mating related genes modulated in the ccw12Δ 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Methods Microarray analysis of differential gene expression SEY", "pplementary Material Additional file 1ccw12Δ microarray datasetClick here for file Additional file 2", "plementary Materials Additional file 1ccw12Δ microarray datasetClick here for file Additional file 2"], "order_basis": "paper_text_order:2426", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["CWI pathway. Cell extracts were analysed by Western blot using phospho-p44/p42 MAPK antibodies to det", "e protein. Protein extracts were analysed by immunoblotting using α-phospho-p44/p42 MAP kinase antibodie"], "order_basis": "paper_text_order:3961", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ion SEY6210 and ccw12Δ (MEY12A) strains were cultured in YPD supplemented with adenine (39 mg/l) to a"], "order_basis": "paper_text_order:6585", "id": "assay:3"}]}