title: The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism.
abstract: Purple aerobic anoxygenic phototrophs (AAPs) are the only organisms known to capture light energy to enhance growth only in the presence of oxygen but do not produce oxygen. The highly adaptive AAPs compose more than 10% of the microbial community in some euphotic upper ocean waters and are potentially major contributors to the fixation of the greenhouse gas CO2. We present the complete genomic sequence and feature analysis of the AAP Roseobacter denitrificans, which reveal clues to its physiology. The genome lacks genes that code for known photosynthetic carbon fixation pathways, and most notably missing are genes for the Calvin cycle enzymes ribulose bisphosphate carboxylase (RuBisCO) and phosphoribulokinase. Phylogenetic evidence implies that this absence could be due to a gene loss from a RuBisCO-containing alpha-proteobacterial ancestor. We describe the potential importance of mixotrophic rather than autotrophic CO2 fixation pathways in these organisms and suggest that these pathways function to fix CO2 for the formation of cellular components but do not permit autotrophic growth. While some genes that code for the redox-dependent regulation of photosynthetic machinery are present, many light sensors and transcriptional regulatory motifs found in purple photosynthetic bacteria are absent.
authors.affiliation: School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA.
authors.forename: Wesley D
authors.initials: WD
authors.lastname: Swingley
authors.forename: Sumedha
authors.initials: S
authors.lastname: Sadekar
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Mastrian
authors.forename: Heather J
authors.initials: HJ
authors.lastname: Matthies
authors.forename: Jicheng
authors.initials: J
authors.lastname: Hao
authors.forename: Hector
authors.initials: H
authors.lastname: Ramos
authors.forename: Chaitanya R
authors.initials: CR
authors.lastname: Acharya
authors.forename: Amber L
authors.initials: AL
authors.lastname: Conrad
authors.forename: Heather L
authors.initials: HL
authors.lastname: Taylor
authors.forename: Liza C
authors.initials: LC
authors.lastname: Dejesa
authors.forename: Maulik K
authors.initials: MK
authors.lastname: Shah
authors.forename: Maeve E
authors.initials: ME
authors.lastname: O'huallachain
authors.forename: Michael T
authors.initials: MT
authors.lastname: Lince
authors.forename: Robert E
authors.initials: RE
authors.lastname: Blankenship
authors.forename: J Thomas
authors.initials: JT
authors.lastname: Beatty
authors.forename: Jeffrey W
authors.initials: JW
authors.lastname: Touchman
mesh_terms: D000595:Amino Acid Sequence; D002876:Chromosomes, Bacterial / Q000235:genetics*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D053858:Metabolic Networks and Pathways; D008969:Molecular Sequence Data; D010788:Photosynthesis; D010802:Phylogeny; D041904:Roseobacter / Q000235:genetics* / Q000378:metabolism*; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial