The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic as opposed to photosynthetic metabolism

School of Life Sciences, Arizona State University, Tempe, AZ 85287; Department Computational Biosciences, Arizona State University, Tempe, AZ 85287; Translational Genomics Research Institute, Phoenix, AZ, 85004; Departments of Biology and Chemistry, Washington University, St. Louis, MO 63130; Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, V6T 163, Canada; Inst. of Low Temp. Sci., Hokkaido University,Sapporo, 060-0819, Japan; Inst. for Genome Sciences and Policy, Duke University, Durham, NC 27708

^* To whom correspondence should be addressed. Email: jtouchman{at}tgen.org.

	Abstract

Purple aerobic anoxygenic phototrophs (AAPs) are the only known organisms that capture light energy to enhance growth only in the presence of oxygen, but do not produce oxygen. The highly adaptive AAPs compose greater 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 that 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 RuBisCO and phosphoribulokinase. Phylogenetic evidence implies that this absence could be due to a gene loss from a RuBisCO-containing -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 allow for 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.