title: The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally.
abstract: Despite the importance of maintaining redox homeostasis for cellular viability, how cells control redox balance globally is poorly understood. Here we provide new mechanistic insight into how the balance between reduced and oxidized electron carriers is regulated at the level of gene expression by mapping the regulon of the response regulator ArcA from Escherichia coli, which responds to the quinone/quinol redox couple via its membrane-bound sensor kinase, ArcB. Our genome-wide analysis reveals that ArcA reprograms metabolism under anaerobic conditions such that carbon oxidation pathways that recycle redox carriers via respiration are transcriptionally repressed by ArcA. We propose that this strategy favors use of catabolic pathways that recycle redox carriers via fermentation akin to lactate production in mammalian cells. Unexpectedly, bioinformatic analysis of the sequences bound by ArcA in ChIP-seq revealed that most ArcA binding sites contain additional direct repeat elements beyond the two required for binding an ArcA dimer. DNase I footprinting assays suggest that non-canonical arrangements of cis-regulatory modules dictate both the length and concentration-sensitive occupancy of DNA sites. We propose that this plasticity in ArcA binding site architecture provides both an efficient means of encoding binding sites for ArcA, σ(70)-RNAP and perhaps other transcription factors within the same narrow sequence space and an effective mechanism for global control of carbon metabolism to maintain redox homeostasis.
authors.affiliation: Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
authors.forename: Dan M
authors.initials: DM
authors.lastname: Park
authors.forename: Md Sohail
authors.initials: MS
authors.lastname: Akhtar
authors.forename: Aseem Z
authors.initials: AZ
authors.lastname: Ansari
authors.forename: Robert
authors.initials: R
authors.lastname: Landick
authors.forename: Patricia J
authors.initials: PJ
authors.lastname: Kiley
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000235:genetics* / Q000378:metabolism; D016227:Benzoquinones / Q000378:metabolism; D001665:Binding Sites; D002244:Carbon / Q000378:metabolism; D018983:DNA Footprinting; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D003850:Deoxyribonuclease I / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D006873:Hydroquinones / Q000378:metabolism; D008565:Membrane Proteins / Q000235:genetics* / Q000378:metabolism; D010084:Oxidation-Reduction; D011494:Protein Kinases / Q000235:genetics* / Q000378:metabolism; D018085:Regulon; D012097:Repressor Proteins / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D001425:Bacterial Outer Membrane Proteins; D016227:Benzoquinones; D029968:Escherichia coli Proteins; D006873:Hydroquinones; D008565:Membrane Proteins; D012097:Repressor Proteins; C041610:arcA protein, E coli; C004532:quinone; D002244:Carbon; D011494:Protein Kinases; C065271:arcB protein, E coli; D012321:DNA-Directed RNA Polymerases; D003850:Deoxyribonuclease I