Open Access Highly Accessed Research article

Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus

Kuo-Hsiang Tang1, Kerrie Barry2, Olga Chertkov3, Eileen Dalin2, Cliff S Han3, Loren J Hauser4, Barbara M Honchak1, Lauren E Karbach17, Miriam L Land4, Alla Lapidus5, Frank W Larimer4, Natalia Mikhailova5, Samuel Pitluck2, Beverly K Pierson6 and Robert E Blankenship1*

Author Affiliations

1 Department of Biology and Department of Chemistry, Campus Box 1137, Washington University in St. Louis, St. Louis, MO 63130, USA

2 Lawrence Berkeley National Laboratory & Production Genomics Facility, The DOE Joint Genome Institute, Walnut Creek, CA 94598, USA

3 The DOE Joint Genome Institute and Bioscience Division, M888, Los Alamos National Laboratory, Los Alamos, NM 87544, USA

4 Computational Biology and Bioinformatics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA

5 The DOE Joint Genome Institute, Walnut Creek, CA 94598, USA

6 Department of Biology, CMB 1088, University of Puget Sound, Tacoma, WA 98416, USA

7 Current: Baylor College of Medicine, Houston, TX 77030

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BMC Genomics 2011, 12:334  doi:10.1186/1471-2164-12-334

Published: 29 June 2011



Chloroflexus aurantiacus 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, Chloroflexi species are the earliest branching bacteria capable of photosynthesis, and Cfl. aurantiacus has been long regarded as a key organism to resolve the obscurity of the origin and early evolution of photosynthesis. Cfl. aurantiacus 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.


The complete genomic sequence of Cfl. aurantiacus has been determined, analyzed and compared to the genomes of other photosynthetic bacteria.


Abundant genomic evidence suggests that there have been numerous gene adaptations/replacements in Cfl. aurantiacus 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 Cfl. aurantiacus. Genes for the chimeric photosystem, photosynthetic electron transport chain, the 3-hydroxypropionate autotrophic carbon fixation cycle, CO2-anaplerotic pathways, glyoxylate cycle, and sulfur reduction pathway are present. The central carbon metabolism and sulfur assimilation pathways in Cfl. aurantiacus are discussed. Some features of the Cfl. aurantiacus genome are compared with those of the Roseiflexus castenholzii genome. Roseiflexus castenholzii is a recently characterized FAP bacterium and phylogenetically closely related to Cfl. aurantiacus. According to previous reports and the genomic information, perspectives of Cfl. aurantiacus in the evolution of photosynthesis are also discussed.


The genomic analyses presented in this report, along with previous physiological, ecological and biochemical studies, indicate that the anoxygenic phototroph Cfl. aurantiacus has many interesting and certain unique features in its metabolic pathways. The complete genome may also shed light on possible evolutionary connections of photosynthesis.