Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus

<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p> <jats:italic>Chloroflexus aurantiacus</jats:italic> is a thermophilic filamentous anoxygenic phototrophic (FAP) bacterium, and can grow phototrophically under anaerobic conditions or chemotrophically under aerobic and dark conditions. According to 16S rRNA analysis, <jats:italic>Chloroflexi</jats:italic> species are the earliest branching bacteria capable of photosynthesis, and <jats:italic>Cfl. aurantiacus</jats:italic> has been long regarded as a key organism to resolve the obscurity of the origin and early evolution of photosynthesis. <jats:italic>Cfl. aurantiacus</jats:italic> contains a chimeric photosystem that comprises some characters of green sulfur bacteria and purple photosynthetic bacteria, and also has some unique electron transport proteins compared to other photosynthetic bacteria.</jats:p> </jats:sec> <jats:sec> <jats:title>Methods</jats:title> <jats:p>The complete genomic sequence of <jats:italic>Cfl. aurantiacus</jats:italic> has been determined, analyzed and compared to the genomes of other photosynthetic bacteria.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>Abundant genomic evidence suggests that there have been numerous gene adaptations/replacements in <jats:italic>Cfl. aurantiacus</jats:italic> to facilitate life under both anaerobic and aerobic conditions, including duplicate genes and gene clusters for the alternative complex III (ACIII), auracyanin and NADH:quinone oxidoreductase; and several aerobic/anaerobic enzyme pairs in central carbon metabolism and tetrapyrroles and nucleic acids biosynthesis. Overall, genomic information is consistent with a high tolerance for oxygen that has been reported in the growth of <jats:italic>Cfl. aurantiacus</jats:italic>. Genes for the chimeric photosystem, photosynthetic electron transport chain, the 3-hydroxypropionate autotrophic carbon fixation cycle, CO<jats:sub>2</jats:sub>-anaplerotic pathways, glyoxylate cycle, and sulfur reduction pathway are present. The central carbon metabolism and sulfur assimilation pathways in <jats:italic>Cfl. aurantiacus</jats:italic> are discussed. Some features of the <jats:italic>Cfl. aurantiacus</jats:italic> genome are compared with those of the <jats:italic>Roseiflexus castenholzii</jats:italic> genome. <jats:italic>Roseiflexus castenholzii</jats:italic> is a recently characterized FAP bacterium and phylogenetically closely related to <jats:italic>Cfl. aurantiacus</jats:italic>. According to previous reports and the genomic information, perspectives of <jats:italic>Cfl. aurantiacus</jats:italic> in the evolution of photosynthesis are also discussed.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusions</jats:title> <jats:p>The genomic analyses presented in this report, along with previous physiological, ecological and biochemical studies, indicate that the anoxygenic phototroph <jats:italic>Cfl. aurantiacus</jats:italic> has many interesting and certain unique features in its metabolic pathways. The complete genome may also shed light on possible evolutionary connections of photosynthesis.</jats:p> </jats:sec>