The genome of Heliobacterium modesticaldum, a phototrophic representative of the Firmicutes containing the simplest photosynthetic apparatus

Journal of Bacteriology

Volumn 190, Issue 13, 2008, Pages 4687-4696

  Sattley, W Matthew ^a   Madigan, Michael T ^b   Swingley, Wesley D ^c   Cheung, Patricia C ^a   Clocksin, Kate M ^b   Conrad, Amber L ^d   Dejesa, Liza C ^d   Honchak, Barbara M ^a   Jung, Deborah O ^b   Karbach, Lauren E ^a   Kurdoglu, Ahmet ^d   Lahiri, Surobhi ^a   Mastrian, Stephen D ^d   Page, Lawrence E ^a   Taylor, Heather L ^d   Wang, Zi T ^a   Raymond, Jason ^e   Chen, Min ^f   Blankenship, Robert E ^a   Touchman, Jeffrey W ^d,g  

^a WASHINGTON UNIVERSITY   (United States)

^b SOUTHERN ILLINOIS UNIVERSITY   (United States)

^c HOKKAIDO UNIVERSITY   (Japan)

^d TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f UNIVERSITY OF SYDNEY   (Australia)

^g ARIZONA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; CITRATE LYASE; HYDRACRYLIC ACID; LYASE; MALYL COENZYME A LYASE; NITROGEN; RIBULOSEBISPHOSPHATE CARBOXYLASE;

ARTICLE; AUTOTROPHY; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BACTERIAL PHENOMENA AND FUNCTIONS; CARBON DIOXIDE FIXATION; CARBON METABOLISM; CELL ACTIVITY; CITRIC ACID CYCLE; FIRMICUTES; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC COMPLEMENTATION; GRAM POSITIVE BACTERIUM; HELIOBACTERIUM; HELIOBACTERIUM MODESTICALDUM; NITROGEN FIXATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHOTOSYNTHESIS; PHOTOTROPH; PRIORITY JOURNAL; PROTEOBACTERIA; SPECIES; THERMOPHILIC BACTERIUM;

ANAEROBIOSIS; DNA, BACTERIAL; GENOME, BACTERIAL; GRAM-POSITIVE BACTERIA; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHOTOSYNTHESIS; PHOTOSYNTHETIC REACTION CENTER COMPLEX PROTEINS; PHOTOTROPHIC PROCESSES; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); FIRMICUTES; HELIOBACTERIUM MODESTICALDUM; PROTEOBACTERIA;

EID: 46049109918     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.00299-08     Document Type: Article

References (58)

1. Akochy, P.-M., D. Bernard, P. H. Roy, and J. Lapointe. 2004. Direct glutaminyl-tRNA biosynthesis and indirect asparaginyl-tRNA biosynthesis in Pseudomonas aeruginosa PAO1. J. Bacteriol. 186:767-776.
2. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
3. Amesz, J. 1995. The antenna-reaction center complex of heliobacteria, p. 687-697. In R. E. Blankenship, M. T. Madigan, and C. E. Bauer (ed.), Anoxygenic photosynthetic bacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
4. Asao, M., D. O. Jung, L. A. Achenbach, and M. T. Madigan. 2006. Heliorestis convoluta sp. nov., a coiled, alkaliphilic heliobacterium from the Wadi El Natroun, Egypt. Extremophiles 10:403-410.
5. Batzoglou, S., D. B. Jaffe, K. Stanley, J. Butler, S. Gnerre, E. Mauceli, B. Berger, J. P. Mesirov, and E. S. Lander. 2002. ARACHNE: a whole-genome shotgun assembler. Genome Res. 12:177-189.
6. Beer-Romero, P., and H. Gest. 1987. Heliobacillus mobilis, a peritrichously flagellated anoxyphototroph containing bacteriochlorophyll g. FEMS Microbiol. Lett. 41:109-114.
7. Berg, I. A., D. Kockelkorn, W. Buckel, and G. Fuchs. 2007. A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318:1782-1786.
8. Bryantseva, I. A., V. M. Gorlenko, E. I. Kompantseva, L. A. Achenbach, and M. T. Madigan. 1999. Heliorestis daurensis, gen. nov. sp. nov., an alkaliphilic rod-to-coiled-shaped phototrophic heliobacterium from a Siberian soda lake. Arch. Microbiol. 172:167-174.
9. Bryantseva, I. A., V. M. Gorlenko, E. I. Kompantseva, T. P. Tourova, B. B. Kuznetsov, and G. A. Osipov. 2000. Alkaliphilic heliobacterium Heliorestis baculata sp. nov. and emended description of the genus Heliorestis. Arch. Microbiol. 174:283-291.
10. Chen, J. S. 2004. Nitrogen fixation in the clostridia, p. 53-64. In W. Klipp, B. Masepohl, J. R. Gallon, and W. E. Newton (ed.), Genetics and regulation of nitrogen fixation in free-living bacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
11. Chew, A. G. M., and D. A. Bryant. 2007. Characterization of a plant-like protochlorophyllide a divinyl reductase in green sulfur bacteria. J. Biol. Chem. 282:2967-2975.
12. Gln amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis. Proc. Natl. Acad. Sci. USA 95:12838-12843.
13. Dubey, V. S., R. Bhalla, and R. Luthra. 2003. An overview of the non-mevalonate pathway for terpenoid biosynthesis in plants. J. Biosci. 28:637-646.
14. Enkh-Amgalan, J., H. Kawasaki, H. Oh-oka, and T. Seki. 2006. Cloning and characterization of a novel gene involved in nitrogen fixation in Heliobacterium chlorum: a possible regulatory gene. Arch. Microbiol. 186:327-337.
15. 2 genes in the Gram-positive phototrophic bacterium Heliobacterium chlorum. Int. J. Syst. Evol. Microbiol. 56:65-74.
16. Fuller, R. C., S. G. Sprague, H. Gest, and R. E. Blankenship. 1985. A unique photosynthetic reaction center from Heliobacterium chlorum. FEBS Lett. 182:345-349.
17. H-regulated promoter. Gene 217:31-40.
18. Heinnickel, M., and J. H. Golbeck. 2007. Heliobacterial photosynthesis. Photosynth. Res. 92:35-53.
19. B in Heliobacterium modesticaldum. Biochemistry 46:2530-2536.
20. Ito, H., M. Yokono, R. Tanaka, and A. Tanaka. 2008. Identification of a novel vinyl reductase gene essential for the biosynthesis of monovinyl chlorophyll in Synechocystis sp. PCC6803. J. Biol. Chem. 283:9002-9011.
21. Kimble, L. K., and M. T. Madigan. 1992. Evidence for an alternative nitrogenase in Heliobacterium gestii. FEMS Microbiol. Lett. 100:255-260.
22. Kimble, L. K., A. K. Stevenson, and M. T. Madigan. 1994. Chemotrophic growth of heliobacteria in darkness. FEMS Microbiol. Lett. 115:51-55.
23. Kimble, L. K., L. Mandelco, C. R. Woese, and M. T. Madigan. 1995. Heliobacterium modesticaldum, sp. nov., a thermophilic heliobacterium of hot springs and volcanic soils. Arch. Microbiol. 163:259-267.
24. Kimble-Long, L. K., and M. T. Madigan. 2001. Molecular evidence that the capacity for endosporulation is universal among phototrophic heliobacteria. FEMS Microbiol. Lett. 199:191-195.
25. Klappenbach, J. A., J. M. Dunbar, and T. M. Schmidt. 2000. rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol. 66:1328-1333.
26. X of photosystem I in Heliobacillus mobilis. Photosynth. Res. 41:115-123.
27. Kramer, D. M., B. Schoepp, U. Liebl, and W. Nitschke. 1997. Cyclic electron transfer in Heliobacillus mobilis involving a menaquinol-oxidizing cytochrome bc complex and an RCI-type reaction center. Biochemistry 36:4203-4211.
28. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5:150-163.
29. Loveless, T. M., and P. E. Bishop. 1999. Identification of genes unique to Mo-independent nitrogenase systems in diverse diazotrophs. Can. J. Microbiol. 45:312-317.
30. Ludwig, M., R. Schulz-Friedrich, and J. Appel. 2006. Occurrence of hydrogenases in cyanobacteria and anoxygenic photosynthetic bacteria: implications for the phylogenetic origin of cyanobacterial and algal hydrogenases. J. Mol. Evol. 63:758-768.
31. Madigan, M. T. 1995. Microbiology of nitrogen fixation by anoxygenic photosynthetic bacteria, p. 915-928. In R. E. Blankenship, M. T. Madigan, and C. E. Bauer (ed.), Anoxygenic photosynthetic bacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
32. Madigan, M. T. 2001. Heliobacteriaceae, p. 625-630. In D. R. Boone, R. W. Castenholz, and G. M. Garrity (ed.), Bergey's manual of systematic bacteriology, 2nd ed., vol. 1. Springer-Verlag, New York, NY.
33. Madigan, M. T. 2006. The family Heliobacteriaceae, p. 951-964. In M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, and E. Stackebrandt (ed.), The prokaryotes, 4th ed. Springer, New York, NY.
34. Madigan, M. T., and J. G. Ormerod. 1995. Taxonomy, physiology, and ecology of heliobacteria, p. 17-30. In R. E. Blankenship, M. T. Madigan, and C. E. Bauer (ed.), Anoxygenic photosynthetic bacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
35. Margolis, P. S., A. Driks, and R. Losick. 1993. Sporulation gene spoIIB from Bacillus subtilis. J. Bacteriol. 175:528-540.
36. Merrick, M. J. 2004. Regulation of nitrogen fixation in free-living diazotrophs. p. 197-223. In W. Klipp, B. Masepohl, J. R. Gallon, and W. E. Newton (ed.), Genetics and regulation of nitrogen fixation in free-living bacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
37. Miller, K. R., J. S. Jacob, U. Smith, S. Kolaczkowski, and M. K. Bowman. 1986. Heliobacterium chlorum: cell organization and structure. Arch. Microbiol. 146:111-114.
38. X and its function in the homodimeric reaction center of Heliobacterium modesticaldum. Biochemistry 45:6306-6316.
39. Naclerio, G., L. Baccigalupi, R. Zilhao, M. De Felice, and E. Ricca. 1996. Bacillus subtilis spore coat assembly requires cotH gene expression. J. Bacteriol. 178:4375-4380.
40. Nonaka, H., G. Keresztes, Y. Shinoda, Y. Ikenaga, M. Abe, K. Naito, K. Inatomi, K. Furukawa, M. Inui, and H. Yukawa. 2006. Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195. J. Bacteriol. 188:2262-2274.
41. Oh-oka, H. 2007. Type 1 reaction center of photosynthetic heliobacteria. Photochem. Photobiol. 83:177-186.
42. Oh-oka, H., M. Iwaki, and S. Itoh. 2002. Electron donation from membrane-bound cytochrome c to the photosynthetic reaction center in whole cells and isolated membranes of Heliobacterium gestii. Photosynth. Res. 71:137-147.
43. Ormerod, J. G., L. K. Kimble, T. Nesbakken, Y. A. Torgersen, C. R. Woese, and M. T. Madigan. 1996. Heliophilum fasciatum gen. nov. sp. nov. and Heliobacterium gestii sp. nov.: endospore-forming heliobacteria from rice field soils. Arch. Microbiol. 165:226-234.
44. 13C-NMR study of carbon metabolism in heliobacteria. Photosynth. Res. 41:75-88.
45. Raymond, J., J. L. Siefert, C. R. Staples, and R. E. Blankenship. 2004. The natural history of nitrogen fixation. Mol. Biol. Evol. 21:541-554.
46. Rey, F. E., Y. Oda, and C. S. Harwood. 2006. Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris. J. Bacteriol. 188:6143-6152.
47. + reductase from the green sulfur bacterium Chlorobium tepidum. Biochim. Biophys. Acta 1597:123-132.
48. Stackebrandt, E., C. Sproer, F. A. Rainey, J. Burghardt, O. Pauker, and H. Hippe. 1997. Phylogenetic analysis of the genus Desulfotomaculum: evidence for the misclassification of Desulfotomaculum guttoideum and description of Desulfotomaculum orientis as Desulfosporosinus orientis gen. nov., comb. nov. Intl. J. Syst. Bacteriol. 47:1134-1139.
49. Stevenson, A. K., L. K. Kimble, C. R. Woese, and M. T. Madigan. 1997. Characterization of new phototrophic heliobacteria and their habitats. Photosynth. Res. 53:1-12.
50. Stothard, P., and D. S. Wishart. 2005. Circular genome visualization and exploration using CGView. Bioinformatics 21:537-539.
51. Swingley, W. D., S. Sadekar, S. D. Mastrian, H. J. Matthies, J. Hao, H. Ramos, C. R. Acharya, A. L. Conrad, H. L. Taylor, L. C. Dejesa, M. K. Shah, M. E. O'Huallachain, M. T. Lince, R. E. Blankenship, J. T. Beatty, and J. W. Touchman. 2007. The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism. J. Bacteriol. 189:683-690.
52. 30 carotenoid 4,4′-diaponeurosporene, not neurosporene. Arch. Microbiol. 168:277-281.
53. Takaichi, S. 1999. Carotenoids and carotenogenesis in anoxygenic photosynthetic bacteria, p. 39-69. In H. A. Frank, R. J. Cogdell, A. Young, and G. Britton (ed.), The photochemistry of carotenoids: applications in biology. Kluwer Academic Publishers, Dordrecht, The Netherlands.
54. Thauer, R. K. 2007. A fifth pathway of carbon fixation. Science 318:1732-1733.
55. Trost, J. T., and R. E. Blankenship. 1989. Isolation of a photoactive photosynthetic reaction center-core antenna complex from Heliobacillus mobilis. Biochemistry 28:9898-9904.
56. 1- hydroxychlorophyll a as a functional reaction center pigment in heliobacteria. Biochim. Biophys. Acta 1058:356-362.
57. Webster, L. T. 1967. Studies of the acetyl coenzyme A synthetase reaction. J. Biol. Chem. 242:1232-1240.
58. Xiong, J., K. Inoue, and C. E. Bauer. 1998. Tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from Heliobacillus mobilis. Proc. Natl. Acad. Sci. USA 95:14851-14856.