title: Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach.
abstract: The extremely halophilic archaeon Halobacterium NRC-1 can switch from aerobic energy production (energy from organic compounds) to anaerobic phototrophy (energy from light) by induction of purple membrane biogenesis. The purple membrane is made up of multiple copies of a 1:1 complex of bacterioopsin (Bop) and retinal called bacteriorhodopsin that functions as a light-driven proton pump. A light- and redox-sensing transcription regulator, Bat, regulates critical genes encoding the biogenesis of the purple membrane. To better understand the regulatory network underlying this physiological state, we report a systems approach using global mRNA and protein analyses of four strains of Halobacterium sp.: the wild-type, NRC-1; and three genetically perturbed strains: S9 (bat+), a purple membrane overproducer, and two purple membrane deficient strains, SD23 (a bop knockout) and SD20 (a bat knockout). The integrated DNA microarray and proteomic data reveal the coordinated coregulation of several interconnected biochemical pathways for phototrophy: isoprenoid synthesis, carotenoid synthesis, and bacteriorhodopsin assembly. In phototrophy, the second major biomodule for ATP production, arginine fermentation, is repressed. The primary systems level insight provided by this study is that two major energy production pathways in Halobacterium sp., phototrophy and arginine fermentation, are inversely regulated, presumably to achieve a balance in ATP production under anaerobic conditions.
authors.affiliation: Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103-8904, USA. nbaliga@systemsbiology.org
authors.forename: Nitin S
authors.initials: NS
authors.lastname: Baliga
authors.forename: Min
authors.initials: M
authors.lastname: Pan
authors.forename: Young Ah
authors.initials: YA
authors.lastname: Goo
authors.forename: Eugene C
authors.initials: EC
authors.lastname: Yi
authors.forename: David R
authors.initials: DR
authors.lastname: Goodlett
authors.forename: Krassen
authors.initials: K
authors.lastname: Dimitrov
authors.forename: Paul
authors.initials: P
authors.lastname: Shannon
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.forename: Wailap Victor
authors.initials: WV
authors.lastname: Ng
authors.forename: Leroy
authors.initials: L
authors.lastname: Hood
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D019843:Archaeal Proteins / Q000235:genetics; D001436:Bacteriorhodopsins / Q000235:genetics; D001665:Binding Sites; D004734:Energy Metabolism; D015964:Gene Expression Regulation, Bacterial; D006217:Halobacterium / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D011401:Promoter Regions, Genetic; D020543:Proteome; D012333:RNA, Messenger / Q000235:genetics; D013045:Species Specificity; D014157:Transcription Factors / Q000378:metabolism; D014161:Transduction, Genetic
chemical_list: D019843:Archaeal Proteins; D020543:Proteome; D012333:RNA, Messenger; D014157:Transcription Factors; D001436:Bacteriorhodopsins; D000255:Adenosine Triphosphate