{"doi":"10.1128/jb.00730-13","title":"Diversity of Cobalamin Riboswitches in the Corrinoid-Producing Organohalide Respirer Desulfitobacterium hafniense","abstract":"<jats:title>ABSTRACT</jats:title><jats:p>The strategic adaptation of prokaryotes in polluted niches involves the efficient regulation of their metabolism. The obligate anaerobe and metabolically versatile<jats:named-content xmlns:xlink=\"http://www.w3.org/1999/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Desulfitobacterium hafniense</jats:named-content>reductively dechlorinates halogenated organic compounds (so-called organohalides). Some<jats:named-content xmlns:xlink=\"http://www.w3.org/1999/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">D. hafniense</jats:named-content>strains carry out organohalide respiration (OHR), a process which requires the use of corrinoid as a cofactor in reductive dehalogenases, the key enzymes in OHR. We report here the diversity of the cobalamin riboswitches that possibly regulate the corrinoid metabolism for<jats:named-content xmlns:xlink=\"http://www.w3.org/1999/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">D. hafniense</jats:named-content>. The analysis of available<jats:named-content xmlns:xlink=\"http://www.w3.org/1999/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">D. hafniense</jats:named-content>genomes indicates the presence of 18 cobalamin riboswitches located upstream of genes whose products are mainly involved in corrinoid biosynthesis and transport. To obtain insight into their function, the secondary structures of three of these RNA elements were predicted by Mfold, as well as analyzed by in-line probing. These RNA elements both display diversity in their structural elements and exhibit various affinities toward adenosylcobalamin that possibly relates to their role in the regulation of corrinoid metabolism. Furthermore, adenosylcobalamin-induced<jats:italic>in vivo</jats:italic>repression of RNA synthesis of the downstream located genes indicates that the corrinoid transporters and biosynthetic enzymes in<jats:named-content xmlns:xlink=\"http://www.w3.org/1999/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">D. hafniense</jats:named-content>strain TCE1 are regulated at the transcriptional level. Taken together, the riboswitch-mediated regulation of the complex corrinoid metabolism in<jats:named-content xmlns:xlink=\"http://www.w3.org/1999/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">D. hafniense</jats:named-content>could be of crucial significance in environments polluted with organohalides both to monitor their intracellular corrinoid level and to coexist with corrinoid-auxotroph OHR bacteria.</jats:p>","journal":"Journal of Bacteriology","year":2013,"id":626484,"datarank":0.4943755299006494,"base_score":3.295836866004329,"endowment":3.295836866004329,"self_citation_contribution":0.4943755299006494,"citation_network_contribution":0.0,"self_endowment_contribution":0.4943755299006494,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":26,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1620574,"name":"Aurélie Duret","orcid":null,"position":1,"is_corresponding":false},{"id":1620576,"name":"Emmanuelle Rohrbach-Brandt","orcid":null,"position":2,"is_corresponding":false},{"id":1620577,"name":"Christof Holliger","orcid":null,"position":3,"is_corresponding":false},{"id":813406,"name":"Roland K. O. Sigel","orcid":"0000-0002-1307-7993","position":4,"is_corresponding":false},{"id":1620578,"name":"Julien Maillard","orcid":null,"position":5,"is_corresponding":false},{"id":1620573,"name":"Pallavi K. Choudhary","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Diversity of Cobalamin Riboswitches in the Corrinoid-Producing Organohalide Respirer Desulfitobacterium hafniense","abstract":"<jats:title>ABSTRACT</jats:title><jats:p>The strategic adaptation of prokaryotes in polluted niches involves the efficient regulation of their metabolism. The obligate anaerobe and metabolically versatile<jats:named-content xmlns:xlink=\"http://www.w3.org/1999/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Desulfitobacterium hafniense</jats:named-content>reductively dechlorinates halogenated organic compounds (so-called organohalides). Some<jats:named-content xmlns:xlink=\"http://www.w3.org/1999/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">D. hafniense</jats:named-content>strains carry out organohalide respiration (OHR), a process which requires the use of corrinoid as a cofactor in reductive dehalogenases, the key enzymes in OHR. We report here the diversity of the cobalamin riboswitches that possibly regulate the corrinoid metabolism for<jats:named-content xmlns:xlink=\"http://www.w3.org/1999/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">D. hafniense</jats:named-content>. The analysis of available<jats:named-content xmlns:xlink=\"http://www.w3.org/1999/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">D. hafniense</jats:named-content>genomes indicates the presence of 18 cobalamin riboswitches located upstream of genes whose products are mainly involved in corrinoid biosynthesis and transport. To obtain insight into their function, the secondary structures of three of these RNA elements were predicted by Mfold, as well as analyzed by in-line probing. These RNA elements both display diversity in their structural elements and exhibit various affinities toward adenosylcobalamin that possibly relates to their role in the regulation of corrinoid metabolism. Furthermore, adenosylcobalamin-induced<jats:italic>in vivo</jats:italic>repression of RNA synthesis of the downstream located genes indicates that the corrinoid transporters and biosynthetic enzymes in<jats:named-content xmlns:xlink=\"http://www.w3.org/1999/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">D. hafniense</jats:named-content>strain TCE1 are regulated at the transcriptional level. Taken together, the riboswitch-mediated regulation of the complex corrinoid metabolism in<jats:named-content xmlns:xlink=\"http://www.w3.org/1999/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">D. hafniense</jats:named-content>could be of crucial significance in environments polluted with organohalides both to monitor their intracellular corrinoid level and to coexist with corrinoid-auxotroph OHR bacteria.</jats:p>","is_dataset_classified":null,"base_score":3.295836866004329,"endowment":3.295836866004329,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"24039263","pmcid":"PMC3811592","openalex_id":"https://openalex.org/W2058505146","authors":[],"funders":[{"funder_name":"European Research Council","grant_id":"259092","title":null},{"funder_name":"Swiss National Science Foundation","grant_id":"108197","title":null},{"funder_name":"Swiss National Science Foundation","grant_id":"120627","title":"Molecular and ecological aspects of chloroethene-dehalorespiring bacteria"},{"funder_name":"Swiss National Science Foundation","grant_id":"138114","title":"Molecular and biochemical characterization of the organohalide respiration process in chloroethene dechlorinating bacteria"}],"total_grants":4,"fwci":1.3757,"citation_percentile":0.80327273,"influential_citations":0,"citation_trend":[{"year":2014,"count":1},{"year":2015,"count":3},{"year":2016,"count":6},{"year":2017,"count":5},{"year":2018,"count":2},{"year":2020,"count":1},{"year":2022,"count":3},{"year":2023,"count":2},{"year":2024,"count":1},{"year":2026,"count":2}],"oa_status":"bronze","license":"ASM Journals Non-Commercial TDM","oa_locations":[{"url":"https://jb.asm.org/content/jb/195/22/5186.full.pdf","host_type":"journal"},{"url":"https://jb.asm.org/content/jb/195/22/5186.full.pdf","host_type":"publisher"},{"url":"https://journals.asm.org/doi/pdf/10.1128/JB.00730-13","host_type":"publisher"},{"url":"https://doi.org/10.1128/jb.00730-13","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/24039263","host_type":"repository"},{"url":"https://www.zora.uzh.ch/89395","host_type":"repository"},{"url":"http://europepmc.org/articles/PMC3811592","host_type":"repository"},{"url":"http://infoscience.epfl.ch/record/189813","host_type":"repository"},{"url":"https://infoscience.epfl.ch/handle/20.500.14299/96138","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3811592","host_type":"repository"},{"url":"https://dx.doi.org/10.1128/jb.00730-13","host_type":""},{"url":"https://sonar.ch/global/documents/255168","host_type":""},{"url":"https://hdl.handle.net/20.500.14299/96138","host_type":""},{"url":"https://doi.org/10.5167/uzh-89395","host_type":""},{"url":"https://www.zora.uzh.ch/id/eprint/89395/","host_type":""},{"url":"http://dx.doi.org/10.1128/JB.00730-13","host_type":""}],"fields_of_study":["Porphyrin Metabolism and Disorders","Chemical Analysis and Environmental Impact","Folate and B Vitamins Research","0301 basic medicine","0303 health sciences","03 medical and health sciences","Corrinoids","Desulfitobacterium","Gene Expression Regulation, Bacterial","Models, Molecular","Nucleic Acid Conformation","Riboswitch","Transcription, Genetic","Vitamin B 12"],"mesh_terms":["Models, Molecular","Nucleic Acid Conformation","Transcription, Genetic","Vitamin B 12","Gene Expression Regulation, Bacterial","Corrinoids","Desulfitobacterium","Riboswitch"],"keywords":["Corrinoid","Adenosylcobalamin","Biology","Riboswitch","Biochemistry","RNA","Enzyme","Cofactor","Gene","Methyltransferase","Non-coding RNA","Methylation","10120 Department of Chemistry","Models, Molecular","Transcription, Genetic","2404 Microbiology","Gene Expression Regulation, Bacterial","Desulfitobacterium","Vitamin B 12","540 Chemistry","1312 Molecular Biology","Corrinoids","Nucleic Acid Conformation"],"sdg_mappings":[{"sdg_number":2,"sdg_label":"2. 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