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Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll-based photoheterotroph belonging to the phylum Acidobacteria

Authors

  • Amaya M. Garcia Costas,

    1. Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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    • Present address: Department of Biological and Physical Sciences, Montana State University-Billings, Billings, MT 59101, USA.

  • Zhenfeng Liu,

    1. Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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  • Lynn P. Tomsho,

    1. Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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  • Stephan C. Schuster,

    1. Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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  • David M. Ward,

    1. Departments of Land Resources and Environmental Sciences
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  • Donald A. Bryant

    Corresponding author
    1. Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    2. Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
      E-mail dab14@psu.edu; Tel. (+1) 814 865 1992; Fax (+1) 814 863 7024.
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E-mail dab14@psu.edu; Tel. (+1) 814 865 1992; Fax (+1) 814 863 7024.

Summary

Candidatus Chloracidobacterium thermophilum, which naturally inhabits microbial mats of alkaline siliceous hot springs in Yellowstone National Park, is the only known chlorophototroph in the phylum Acidobacteria. The Ca. C. thermophilum genome was composed of two chromosomes (2 683 362 bp and 1 012 010 bp), and both encoded essential genes. The genome included genes to produce chlorosomes, the Fenna-Matthews-Olson protein, bacteriochlorophylls a and c as principal pigments, and type-1, homodimeric reaction centres. Ca. C. thermophilum is an aerobic photoheterotroph that lacks the ability to synthesize several essential nutrients. Key genes of all known carbon fixation pathways were absent, as were genes for assimilatory nitrate and sulfate reduction and vitamin B12 synthesis. Genes for the synthesis of branched-chain amino acids (valine, isoleucine and leucine) were also absent, but genes for catabolism of these compounds were present. This observation suggested that Ca. C. thermophilum may synthesize branched-chain amino acids from an intermediate(s) of the catabolic pathway by reversing these reactions. The genome encoded an aerobic respiratory electron transport chain that included NADH dehydrogenase, alternative complex III and cytochrome oxidase. The chromosomes of the laboratory isolate were compared with assembled, metagenomic scaffolds from the major Ca. C. thermophilum population in hot-spring mats. The larger chromosomes of the two populations were highly syntenous but significantly divergent (∼13%) in sequence. In contrast, the smaller chromosomes have undergone numerous rearrangements, contained many transposases, and might be less constrained by purifying selection than the large chromosomes. Some transposases were homologous to those of mat community members from other phyla.

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