Analysis of transcript changes in a heme-deficient mutant of Escherichia coli in response to CORM-3 [Ru(CO)3Cl(glycinate)].

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(2015) in a study of the effects of carbon monoxide-releasing molecule-3 (CORM-3 [Ru(CO)3Cl(glycinate)]) on heme-deficient bacteria. The objective was to identify non-heme targets of CORM action. Carbon monoxide (CO) interacts with heme-containing proteins, in particular respiratory cytochromes; however, CORMs have been shown to elicit multifaceted effects in bacteria, suggesting that the compounds may have additional targets. We therefore sought to elucidate the activity of CORM-3, the first water-soluble CORM and one of the most characterised CORMs to date, in bacteria devoid of heme synthesis. Importantly, we also tested inactive CORM-3 (iCORM-3), a ruthenium co-ligand fragment that does not release CO, in order to differentiate between CO- and compound-related effects. A well-established hemA mutant of Escherichia coli was used for the study and, for comparison, parallel experiments were performed on the corresponding wild-type strain. Global transcriptomic changes induced by CORM-3 and iCORM-3 were evaluated using a Two-Color Microarray-Based Prokaryote Analysis (FairPlay III Labeling) by Agilent Technologies (Inc. 2009). Data acquisition was carried out using Agilent Feature Extraction software (v6.5) and data normalisation, as well as information about gene products and their function was obtained from GeneSpring GX v7.3 (Agilent Technologies). Functional category lists were created using KEGG (Kyoto Encyclopedia of Genes and Genomes). Relevant regulatory proteins for each gene were identified, where available, using regulonDB and EcoCyc (World Wide Web). Statistical data modelling was performed on the gene expression data to infer transcription factor activities. The transcriptomic data can be accessed through NCBI's Gene Expression Omnibus (GEO): series accession number GSE55097 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55097).", "claims": [{"id": "claim-method", "statement": "Identification of statistically significant gene expression changes was achieved by applying a t-test with a 2-fold cut-off and p < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26322270", "locator": "sections[11] \"Analysis of microarray data\" paragraph 2", "quote": "Identification of statistically significant gene expression changes was achieved by applying a t-test with a 2-fold cut-off and p < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO series accession number GSE55097 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55097).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26322270", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "The raw data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO series accession number GSE55097 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55097)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used statistical modelling of gene-expression data to infer transcription-factor activities, and deposited the raw transcriptomic data in NCBI’s Gene Expression Omnibus under accession number GSE55097.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26322270", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Statistical data modelling was performed on the gene expression data to infer transcription factor activities."}, {"asset": "source:pmid:26322270", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The transcriptomic data can be accessed through NCBI's Gene Expression Omnibus (GEO): series accession number GSE55097 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55097)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used statistical modelling of gene-expression data to infer transcription-factor activities, and deposited the raw transcriptomic data in NCBI’s Gene Expression Omnibus under accession number GSE55097.", "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:26322270"], "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. 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