title: Alternative Oxidase Transcription Factors AOD2 and AOD5 ofNeurospora crassaControl the Expression of Genes Involved in Energy Production and Metabolism.
abstract: InNeurospora crassa, blocking the function of the standard mitochondrial electron transport chain results in the induction of an alternative oxidase (AOX). AOX transfers electrons directly from ubiquinol to molecular oxygen. AOX serves as a model of retrograde regulation since it is encoded by a nuclear gene that is regulated in response to signals from mitochondria. TheN. crassatranscription factors AOD2 and AOD5 are necessary for the expression of the AOX gene. To gain insight into the mechanism by which these factors function, and to determine if they have roles in the expression of additional genes inN. crassa, we constructed strains expressing only tagged versions of the proteins. Cell fractionation experiments showed that both proteins are localized to the nucleus under both AOX inducing and noninducing conditions. Furthermore, chromatin immunoprecipitation and high throughput sequencing (ChIP-seq) analysis revealed that the proteins are bound to the promoter region of the AOX gene under both conditions. ChIP-seq also showed that the transcription factors bind to the upstream regions of a number of genes that are involved in energy production and metabolism. Dependence on AOD2 and AOD5 for the expression of several of these genes was verified by quantitative PCR. The majority of ChIP-seq peaks observed were enriched for both AOD2 and AOD5. However, we also observed occasional sites where one factor appeared to bind preferentially. The most striking of these was a conserved sequence that bound large amounts of AOD2 but little AOD5. This sequence was found within a 310 bp repeat unit that occurs at several locations in the genome.
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Qi
authors.affiliation: Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-4003.
authors.forename: Kristina M
authors.initials: KM
authors.lastname: Smith
authors.affiliation: Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-4003.
authors.forename: Erin L
authors.initials: EL
authors.lastname: Bredeweg
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.
authors.forename: Natasa
authors.initials: N
authors.lastname: Bosnjak
authors.affiliation: Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-4003.
authors.forename: Michael
authors.initials: M
authors.lastname: Freitag
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada frank.nargang@ualberta.ca.
authors.forename: Frank E
authors.identifier: 0000-0002-1383-4270
authors.initials: FE
authors.lastname: Nargang
mesh_terms: D002467:Cell Nucleus / Q000235:genetics; D004734:Energy Metabolism / Q000235:genetics*; D005656:Fungal Proteins / Q000235:genetics*; D015966:Gene Expression Regulation, Fungal / Q000235:genetics*; D016681:Genome, Fungal; D008928:Mitochondria / Q000378:metabolism; D024101:Mitochondrial Proteins / Q000235:genetics*; D009154:Mutation; D009492:Neurospora crassa / Q000235:genetics* / Q000378:metabolism; D010088:Oxidoreductases / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics; D000099188:Alternative Oxidase
chemical_list: D005656:Fungal Proteins; D024101:Mitochondrial Proteins; D010088:Oxidoreductases; D010940:Plant Proteins; D014157:Transcription Factors; D000099188:Alternative Oxidase
keywords: AOD2; AOD5; ChIP-seq; alternative oxidase; retrograde signaling