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References

  1. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. 2008. The RAST server: Rapid annotations using subsystems technology. BMC Genomics 9: 75.
    Pubmed CrossRef
  2. Bashiri G, Baker EN. 2012. Biology of cofactor F420 in mycobacteria. FEBS J. 279: 434-434.
  3. Berk H, Thauer RK. 1997. Function of coenzyme F-420dependent NADP reductase in methanogenic archaea containing an NADP-dependent alcohol dehydrogenase. Arch. Microbiol. 168: 396-402.
    Pubmed CrossRef
  4. Choi KP, Bair TB, Bae YM, Daniels L. 2001. Use of transposon Tn5367 mutagenesis and a nitroimidazopyranbased selection system to demonstrate a requirement for fbiA and fbiB in coenzyme F-420 biosynthesis by Mycobacterium bovis BCG. J. Bacteriol. 183: 7058-7066.
    Pubmed CrossRef
  5. Choi KP, Kendrick N, Daniels L. 2002. Demonstration that fbiC is required by Mycobacterium bovis BCG for coenzyme F-420 and FO biosynthesis. J. Bacteriol. 184: 2420-2428.
    Pubmed CrossRef
  6. Ebert S, Rieger PG, Knackmuss HJ. 1999. Function of coenzyme F-420 in aerobic catabolism of 2,4,6-trinitrophenol and 2,4-dinitrophenol by Nocardioides simplex FJ2-1A. J. Bacteriol. 181: 2669-2674.
    Pubmed
  7. Ermolaeva MD, White O, Salzberg SL. 2001. Prediction of operons in microbial genomes. Nucleic Acids Res. 29: 12161221.
    Pubmed CrossRef
  8. Fondi M, Emiliani G, Fani R. 2009. Origin and evolution of operons and metabolic pathways. Res. Microbiol. 160: 502512.
    Pubmed CrossRef
  9. Forouhar F, Abashidze M, Xu HM, Grochowski LL, Seetharaman J, Hussain M, et al. 2008. Molecular insights into the biosynthesis of the F-420 coenzyme. J. Biol. Chem. 283: 11832-11840.
    Pubmed CrossRef
  10. Garrity GM, Lilburn TG, Cole JR, Harrison SH, Euzeby J, Tindall BJ. 2007. Taxonomic Outline of the Bacteria and Archaea. Release 7.7. Michigan State University Board of Trustees. DOI: 10.1601/TOBA1607.1607.
  11. Goecks J, Nekrutenko A, Taylor J, Team G. 2010. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11: R86.
    Pubmed CrossRef
  12. Graham DE, Xu HM, White RH. 2003. Identification of the 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase required for coenzyme F-420 biosynthesis. Arch. Microbiol. 180: 455464.
  13. Graupner M, White RH. 2001. Biosynthesis of the phosphodiester bond in coenzyme F-420 in the methanoarchaea. Biochemistry 40: 10859-10872.
    Pubmed CrossRef
  14. Graupner M, White RH. 2003. Methanococcus jannaschii coenzyme F-420 analogs contain a terminal alpha-linked glutamate. J. Bacteriol. 185: 4662-4665.
  15. Graupner M, Xu HM, White RH. 2002. Characterization of the 2-phospho-L-lactate transferase enzyme involved in coenzyme F-420 biosynthesis in Methanococcus jannaschii. Biochemistry 41: 3754-3761.
  16. Grochowski LL, Xu HM, White RH. 2008. Identification and characterization of the 2-phospho-L-lactate guanylyltransferase involved in coenzyme F420 biosynthesis. Biochemistry 47:3033-3037.
  17. Kim SJ, Weon HY, Kim YS, Moon JY, Seok SJ, Hong SB, Kwon SW. 2012. Caenimonas terrae sp nov., isolated from a soil sample in Korea, and emended description of the genus Caenimonas Ryu et al. 2008. J. Microbiol. 50: 864-868.
  18. Lawrence J. 1999. Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr. Opin. Genet. Dev. 9: 642-648.
  19. Price MN, Arkin AP, Alm EJ. 2006. The life-cycle of operons. Plos Genetics 2: 859-873.
  20. Price MN, Huang KH, Alm EJ, Arkin AP. 2005. A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res. 33: 880-892.
  21. Ryu SH, Lee DS, Park M, Wang Q, Jang HH, Park W, Jeon CO. 2008. Caenimonas koreensis gen. nov., sp nov., isolated from activated sludge. Int. J. Syst. Evol. Microbiol. 58: 10641068.
  22. Selengut JD, Haft DH. 2010. Unexpected abundance of coenzyme F-420-dependent enzymes in Mycobacterium tuberculosis and other Actinobacteria. J. Bacteriol. 192: 5788-5798.
  23. Singh BK, Walker A. 2006. Microbial degradation of organophosphorus compounds. FEMS Microbiol. Rev. 30:428-471.
  24. Willems A, Gillis M. 2005. Family IV. Comamonadaceae, pp. 686-759. In Brenner DJ, Krieg NR, Staley JT (eds.). Bergey's Manual of Systematic Bacteriology. Springer, Germany.
  25. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-829.

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Note

J. Microbiol. Biotechnol. 2014; 24(11): 1490-1494

Published online November 28, 2014 https://doi.org/10.4014/jmb.1405.05039

Copyright © The Korean Society for Microbiology and Biotechnology.

Genome of Betaproteobacterium Caenimonas sp. Strain SL110 Contains a Coenzyme F420 Biosynthesis Gene Cluster

Xiuling Li 1, Fuying Feng 2 and Yonghui Zeng 3*

1Shandong Provincial Key Laboratory of Water and Soil Conservation & Environmental Protection, Linyi University, Linyi 276000, P.R. China, 2Institute for Applied and Environmental Microbiology, Inner Mongolia Agriculture University, Huhhot 010018, P.R. China, 3Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Ocean University, Zhanjiang 524025, P.R. China

Received: May 19, 2014; Accepted: July 16, 2014

Abstract

To probe the genomic properties of microbes thriving in desert lakes, we sequenced the full
genome of a betaproteobacterial strain (SL110) belonging to the understudied genus
Caenimonas of the family Comamonadaceae. This strain was isolated from a freshwater lake in
the western Gobi Desert, Northern China. Its genome contains genes encoding carbon
monoxide dehydrogenase, nitrate reductase, nitrite reductase, nitric oxide reductase, and
sulfur oxidation enzymes, highlighting the potentially important contribution of this group of
bacteria to the cycling of inorganic elements in nature. Unexpectedly, a coenzyme F420
biosynthesis gene cluster was identified. A further search for F420 biosynthesis gene homologs
in genomic databases suggests the possible widespread presence of F420 biosynthesis gene
clusters in proteobacterial genomes.

Keywords: genome sequencing, Caenimonas, F420 biosynthesis gene cluster, horizontal gene transfer, Proteobacteria, Actinobacteria

References

  1. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. 2008. The RAST server: Rapid annotations using subsystems technology. BMC Genomics 9: 75.
    Pubmed CrossRef
  2. Bashiri G, Baker EN. 2012. Biology of cofactor F420 in mycobacteria. FEBS J. 279: 434-434.
  3. Berk H, Thauer RK. 1997. Function of coenzyme F-420dependent NADP reductase in methanogenic archaea containing an NADP-dependent alcohol dehydrogenase. Arch. Microbiol. 168: 396-402.
    Pubmed CrossRef
  4. Choi KP, Bair TB, Bae YM, Daniels L. 2001. Use of transposon Tn5367 mutagenesis and a nitroimidazopyranbased selection system to demonstrate a requirement for fbiA and fbiB in coenzyme F-420 biosynthesis by Mycobacterium bovis BCG. J. Bacteriol. 183: 7058-7066.
    Pubmed CrossRef
  5. Choi KP, Kendrick N, Daniels L. 2002. Demonstration that fbiC is required by Mycobacterium bovis BCG for coenzyme F-420 and FO biosynthesis. J. Bacteriol. 184: 2420-2428.
    Pubmed CrossRef
  6. Ebert S, Rieger PG, Knackmuss HJ. 1999. Function of coenzyme F-420 in aerobic catabolism of 2,4,6-trinitrophenol and 2,4-dinitrophenol by Nocardioides simplex FJ2-1A. J. Bacteriol. 181: 2669-2674.
    Pubmed
  7. Ermolaeva MD, White O, Salzberg SL. 2001. Prediction of operons in microbial genomes. Nucleic Acids Res. 29: 12161221.
    Pubmed CrossRef
  8. Fondi M, Emiliani G, Fani R. 2009. Origin and evolution of operons and metabolic pathways. Res. Microbiol. 160: 502512.
    Pubmed CrossRef
  9. Forouhar F, Abashidze M, Xu HM, Grochowski LL, Seetharaman J, Hussain M, et al. 2008. Molecular insights into the biosynthesis of the F-420 coenzyme. J. Biol. Chem. 283: 11832-11840.
    Pubmed CrossRef
  10. Garrity GM, Lilburn TG, Cole JR, Harrison SH, Euzeby J, Tindall BJ. 2007. Taxonomic Outline of the Bacteria and Archaea. Release 7.7. Michigan State University Board of Trustees. DOI: 10.1601/TOBA1607.1607.
  11. Goecks J, Nekrutenko A, Taylor J, Team G. 2010. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11: R86.
    Pubmed CrossRef
  12. Graham DE, Xu HM, White RH. 2003. Identification of the 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase required for coenzyme F-420 biosynthesis. Arch. Microbiol. 180: 455464.
  13. Graupner M, White RH. 2001. Biosynthesis of the phosphodiester bond in coenzyme F-420 in the methanoarchaea. Biochemistry 40: 10859-10872.
    Pubmed CrossRef
  14. Graupner M, White RH. 2003. Methanococcus jannaschii coenzyme F-420 analogs contain a terminal alpha-linked glutamate. J. Bacteriol. 185: 4662-4665.
  15. Graupner M, Xu HM, White RH. 2002. Characterization of the 2-phospho-L-lactate transferase enzyme involved in coenzyme F-420 biosynthesis in Methanococcus jannaschii. Biochemistry 41: 3754-3761.
  16. Grochowski LL, Xu HM, White RH. 2008. Identification and characterization of the 2-phospho-L-lactate guanylyltransferase involved in coenzyme F420 biosynthesis. Biochemistry 47:3033-3037.
  17. Kim SJ, Weon HY, Kim YS, Moon JY, Seok SJ, Hong SB, Kwon SW. 2012. Caenimonas terrae sp nov., isolated from a soil sample in Korea, and emended description of the genus Caenimonas Ryu et al. 2008. J. Microbiol. 50: 864-868.
  18. Lawrence J. 1999. Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr. Opin. Genet. Dev. 9: 642-648.
  19. Price MN, Arkin AP, Alm EJ. 2006. The life-cycle of operons. Plos Genetics 2: 859-873.
  20. Price MN, Huang KH, Alm EJ, Arkin AP. 2005. A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res. 33: 880-892.
  21. Ryu SH, Lee DS, Park M, Wang Q, Jang HH, Park W, Jeon CO. 2008. Caenimonas koreensis gen. nov., sp nov., isolated from activated sludge. Int. J. Syst. Evol. Microbiol. 58: 10641068.
  22. Selengut JD, Haft DH. 2010. Unexpected abundance of coenzyme F-420-dependent enzymes in Mycobacterium tuberculosis and other Actinobacteria. J. Bacteriol. 192: 5788-5798.
  23. Singh BK, Walker A. 2006. Microbial degradation of organophosphorus compounds. FEMS Microbiol. Rev. 30:428-471.
  24. Willems A, Gillis M. 2005. Family IV. Comamonadaceae, pp. 686-759. In Brenner DJ, Krieg NR, Staley JT (eds.). Bergey's Manual of Systematic Bacteriology. Springer, Germany.
  25. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-829.