title: The genome of Syntrophorhabdus aromaticivorans strain UI provides new insights for syntrophic aromatic compound metabolism and electron flow.
abstract: How aromatic compounds are degraded in various anaerobic ecosystems (e.g. groundwater, sediments, soils and wastewater) is currently poorly understood. Under methanogenic conditions (i.e. groundwater and wastewater treatment), syntrophic metabolizers are known to play an important role. This study explored the draft genome of Syntrophorhabdus aromaticivorans strain UI and identified the first syntrophic phenol-degrading phenylphosphate synthase (PpsAB) and phenylphosphate carboxylase (PpcABCD) and syntrophic terephthalate-degrading decarboxylase complexes. The strain UI genome also encodes benzoate degradation through hydration of the dienoyl-coenzyme A intermediate as observed in Geobacter metallireducens and Syntrophus aciditrophicus. Strain UI possesses electron transfer flavoproteins, hydrogenases and formate dehydrogenases essential for syntrophic metabolism. However, the biochemical mechanisms for electron transport between these H2 /formate-generating proteins and syntrophic substrate degradation remain unknown for many syntrophic metabolizers, including strain UI. Analysis of the strain UI genome revealed that heterodisulfide reductases (HdrABC), which are poorly understood electron transfer genes, may contribute to syntrophic H2 and formate generation. The genome analysis further identified a putative ion-translocating ferredoxin : NADH oxidoreductase (IfoAB) that may interact with HdrABC and dissimilatory sulfite reductase gamma subunit (DsrC) to perform novel electron transfer mechanisms associated with syntrophic metabolism.
authors.affiliation: Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
authors.forename: Masaru K
authors.initials: MK
authors.lastname: Nobu
authors.affiliation: Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.|Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Narihiro
authors.affiliation: Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.|Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
authors.forename: Tamaki
authors.initials: T
authors.lastname: Hideyuki
authors.affiliation: Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province, China.
authors.forename: Yan-Ling
authors.initials: YL
authors.lastname: Qiu
authors.affiliation: Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Sekiguchi
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: Los Alamos National Laboratory, Los Alamos, NM, USA.
authors.forename: Lynne
authors.initials: L
authors.lastname: Goodwin
authors.affiliation: Los Alamos National Laboratory, Los Alamos, NM, USA.
authors.forename: Karen W
authors.initials: KW
authors.lastname: Davenport
authors.affiliation: Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.|Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, Hokkaido, Japan.
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Kamagata
authors.affiliation: Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
authors.forename: Wen-Tso
authors.initials: WT
authors.lastname: Liu
mesh_terms: D000693:Anaerobiosis / Q000502:physiology; D019755:Carbon-Carbon Lyases / Q000378:metabolism; D002262:Carboxy-Lyases / Q000378:metabolism; D020564:Deltaproteobacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D004579:Electron Transport / Q000502:physiology*; D004583:Electrons; D005288:Ferredoxins / Q000378:metabolism; D005560:Formate Dehydrogenases / Q000378:metabolism; D005561:Formates / Q000378:metabolism; D016680:Genome, Bacterial / Q000235:genetics; D006864:Hydrogenase / Q000378:metabolism; D010088:Oxidoreductases / Q000378:metabolism; D019800:Phenol / Q000378:metabolism
chemical_list: D005288:Ferredoxins; D005561:Formates; C030544:formic acid; D019800:Phenol; D010088:Oxidoreductases; D006864:Hydrogenase; C087171:heterodisulfide reductase; D005560:Formate Dehydrogenases; D019755:Carbon-Carbon Lyases; D002262:Carboxy-Lyases