title: Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough.
abstract: Crp/Fnr-type global transcriptional regulators regulate various metabolic pathways in bacteria and typically function in response to environmental changes. However, little is known about the function of four annotated Crp/Fnr homologs (DVU0379, DVU2097, DVU2547, and DVU3111) in Desulfovibrio vulgaris Hildenborough. A systematic study using bioinformatic, transcriptomic, genetic, and physiological approaches was conducted to characterize their roles in stress responses. Similar growth phenotypes were observed for the crp/fnr deletion mutants under multiple stress conditions. Nevertheless, the idea of distinct functions of Crp/Fnr-type regulators in stress responses was supported by phylogeny, gene transcription changes, fitness changes, and physiological differences. The four D. vulgaris Crp/Fnr homologs are localized in three subfamilies (HcpR, CooA, and cc). The crp/fnr knockout mutants were well separated by transcriptional profiling using detrended correspondence analysis (DCA), and more genes significantly changed in expression in a ΔDVU3111 mutant (JW9013) than in the other three paralogs. In fitness studies, strain JW9013 showed the lowest fitness under standard growth conditions (i.e., sulfate reduction) and the highest fitness under NaCl or chromate stress conditions; better fitness was observed for a ΔDVU2547 mutant (JW9011) under nitrite stress conditions and a ΔDVU2097 mutant (JW9009) under air stress conditions. A higher Cr(VI) reduction rate was observed for strain JW9013 in experiments with washed cells. These results suggested that the four Crp/Fnr-type global regulators play distinct roles in stress responses of D. vulgaris. DVU3111 is implicated in responses to NaCl and chromate stresses, DVU2547 in nitrite stress responses, and DVU2097 in air stress responses.
authors.affiliation: Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, USA. zhou@ou.edu
authors.forename: Aifen
authors.initials: A
authors.lastname: Zhou
authors.forename: Yunyu I
authors.initials: YI
authors.lastname: Chen
authors.forename: Grant M
authors.initials: GM
authors.lastname: Zane
authors.forename: Zhili
authors.initials: Z
authors.lastname: He
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Hemme
authors.forename: Marcin P
authors.initials: MP
authors.lastname: Joachimiak
authors.forename: Jason K
authors.initials: JK
authors.lastname: Baumohl
authors.forename: Qiang
authors.initials: Q
authors.lastname: He
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Fields
authors.forename: Adam P
authors.initials: AP
authors.lastname: Arkin
authors.forename: Judy D
authors.initials: JD
authors.lastname: Wall
authors.forename: Terry C
authors.initials: TC
authors.lastname: Hazen
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
mesh_terms: D000388:Air; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D002840:Chromates / Q000378:metabolism / Q000633:toxicity; D019295:Computational Biology; D002373:Cyclic AMP Receptor Protein / Q000235:genetics / Q000378:metabolism*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D016969:Desulfovibrio vulgaris / Q000235:genetics / Q000254:growth & development / Q000378:metabolism / Q000502:physiology*; D017353:Gene Deletion; D015964:Gene Expression Regulation, Bacterial; D008969:Molecular Sequence Data; D009573:Nitrites / Q000378:metabolism / Q000633:toxicity; D017422:Sequence Analysis, DNA; D012965:Sodium Chloride / Q000378:metabolism / Q000633:toxicity; D013312:Stress, Physiological; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D002840:Chromates; D002373:Cyclic AMP Receptor Protein; D004269:DNA, Bacterial; D009573:Nitrites; D014157:Transcription Factors; D012965:Sodium Chloride