Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 21, 2014, Pages 7795-7800

  Zeng, Yonghui ^a   Feng, Fuying ^b   Medová, Hana ^a   Dean, Jason ^a   Koblížek, Michal ^a,c  

^a INSTITUTE OF MICROBIOLOGY   (China)

^b INNER MONGOLIA AGRICULTURAL UNIVERSITY   (China)

^c UNIVERSITY OF SOUTH BOHEMIA   (Czech Republic)

Author keywords

Aerobic photoheterotroph; Anoxygenic photosynthesis; Bacterial pigments; Fluorescence imaging system; Horizontal gene transfer

Indexed keywords

BACTERIOCHLOROPHYLL A; BACTERIOPHEOPHYTIN; FRESH WATER; QUINONE DERIVATIVE;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM COLONY; BACTERIUM ISOLATION; CARBON FIXATION; CARBON UTILIZATION; CITRIC ACID CYCLE; DNA BASE COMPOSITION; GEMMATIMONADETE; GENE CLUSTER; GLYCOLYSIS; HORIZONTAL GENE TRANSFER; NONHUMAN; OXIDATION REDUCTION POTENTIAL; OXIDATIVE PHOSPHORYLATION; PHOTOSYNTHESIS; PHOTOTROPHIC BACTERIUM; PHOTOTROPHY; PHYLOGENY; PHYLUM; PRIORITY JOURNAL; RHODOBACTER CAPSULATUS;

AEROBIC PHOTOHETEROTROPH; ANOXYGENIC PHOTOSYNTHESIS; BACTERIAL PIGMENTS; FLUORESCENCE IMAGING SYSTEM; HORIZONTAL GENE TRANSFER;

BACTERIA; BASE SEQUENCE; CHINA; CLUSTER ANALYSIS; FLUOROMETRY; LAKES; LIKELIHOOD FUNCTIONS; MICROSCOPY, FLUORESCENCE; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHOTOSYSTEM II PROTEIN COMPLEX; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; SPECTRUM ANALYSIS;

EID: 84901659542     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1400295111     Document Type: Article

References (59)

1. Canfield DE, Rosing MT, Bjerrum C (2006) Early anaerobic metabolisms. Philos Trans R Soc Lond B Biol Sci 361(1474):1819-1834, discussion 1835-1836. (Pubitemid 44580385)
2. Hohmann-Marriott MF, Blankenship RE (2011) Evolution of photosynthesis. Annu Rev Plant Biol 62:515-548.
3. Falkowski PG, Raven JA (2007) Aquatic Photosynthesis (Princeton Univ Press, Princeton, NJ), 2nd Ed, p 484.
4. Nisbet EG, Sleep NH (2001) The habitat and nature of early life. Nature 409(6823): 1083-1091. (Pubitemid 32206166)
5. Kasting JF, Siefert JL (2002) Life and the evolution of Earth's atmosphere. Science 296(5570):1066-1068. (Pubitemid 34517114)
6. Raymond J (2008) Coloring in the tree of life. Trends Microbiol 16(2):41-43.
7. Overmann J, Garcia-Pichel F (2013) The phototrohic way of life. The Prokaryotes: Prokaryotic Communities and Ecophysiology, eds Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (Springer, Berlin), 4th Ed, pp 203-257.
8. Gest H, Blankenship RE (2004) Time line of discoveries: Anoxygenic bacterial photosynthesis. Photosynth Res 80(1-3):59-70. (Pubitemid 38889616)
9. Pierson BK, Castenholz RW (1974) A phototrophic gliding filamentous bacterium of hot springs, Chloroflexus aurantiacus, gen. and sp. nov. Arch Microbiol 100(1):5-24.
10. Gest H, Favinger JL (1983) Heliobacterium chlorum, an anoxygenic brownish-green photosynthetic bacterium containing a "new" form of bacteriochlorophyll. Arch Microbiol 136:11-16.
11. Bryant DA, et al. (2007) Candidatus Chloracidobacterium thermophilum: An aerobic phototrophic Acidobacterium. Science 317(5837):523-526. (Pubitemid 47196118)
12. Söhngen C, Bunk B, Podstawka A, Gleim D, Overmann J (2014) BacDive-the Bacterial Diversity Metadatabase. Nucleic Acids Res42(Database issue, D1):D592-D599.
13. Yarza P, et al. (2008) The All-Species Living Tree project: A 16S rRNA-based phylo-genetic tree of all sequenced type strains. Syst Appl Microbiol 31(4):241-250.
14. Zhang H, et al. (2003) Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. Int J Syst Evol Microbiol 53(Pt 4):1155-1163. (Pubitemid 36896531)
15. Davis KER, Joseph SJ, Janssen PH (2005) Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Appl Environ Microbiol 71(2):826-834. (Pubitemid 40223569)
16. Joseph SJ, Hugenholtz P, Sangwan P, Osborne CA, Janssen PH (2003) Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 69(12):7210-7215. (Pubitemid 38585371)
17. Yen HC, Marrs B (1976) Map of genes for carotenoid and bacteriochlorophyll biosynthesis in Rhodopseudomonas capsulata. J Bacteriol 126(2):619-629.
18. Youvan DC, Bylina EJ, Alberti M, Begusch H, Hearst JE (1984) Nucleotide and deduced polypeptide sequences of the photosynthetic reaction-center, B870 antenna, and flanking polypeptides from R. capsulata. Cell 37(3):949-957.
19. Zsebo KM, Hearst JE (1984) Genetic-physical mapping of a photosynthetic gene cluster from R. capsulata. Cell 37(3):937-947.
20. Haselkorn R, et al. (2001) The Rhodobacter capsulatus genome. Photosynth Res 70(1): 43-52. (Pubitemid 34128537)
21. Swingley WD, Blankenship RE, Raymond J (2009) Evolutionary relationships among purple photosynthetic bacteria and the origin of proteobacterial photosynthetic systems. Advances in Photosynthesis and Respiration, The Purple Phototrophic Bacteria, eds Hunter CN, Daldal F, Thurnauer MC, Beatty JT (Springer, Dordrecht, The Netherlands), Vol 28, pp 17-29.
22. Zheng Q, et al. (2011) Diverse arrangement of photosynthetic gene clusters in aerobic anoxygenic phototrophic bacteria. PLoS ONE 6(9):e25050.
23. Xiong J, Inoue K, Bauer CE (1998) Tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from Heliobacillus mobilis. Proc Natl Acad Sci USA 95(25):14851-14856. (Pubitemid 29003720)
24. Nagashima S, et al. (2012) Complete genome sequence of phototrophic betapro-teobacterium Rubrivivax gelatinosus IL144. J Bacteriol 194(13):3541-3542.
25. Strnad H, et al. (2010) Complete genome sequence of the photosynthetic purple nonsulfur bacterium Rhodobacter capsulatus SB 1003. J Bacteriol 192(13):3545-3546.
26. Berg IA (2011) Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. Appl Environ Microbiol 77(6):1925-1936.
27. Yurkov VV, Beatty JT (1998) Aerobic anoxygenic phototrophic bacteria. Microbiol Mol Biol Rev 62(3):695-724. (Pubitemid 28415551)
28. Koblízek M, Mlcousková J, Kolber Z, Kopecký J (2010) On the photosynthetic properties of marine bacterium COL2P belonging to Roseobacter clade. Arch Microbiol 192(1):41-49.
29. Takaichi S, Maoka T, Takasaki K, Hanada S (2010) Carotenoids of Gemmatimonas aurantiaca (Gemmatimonadetes): Identification of a novel carotenoid, deoxyoscillol 2-rhamnoside, and proposed biosynthetic pathway of oscillol 2, 2'-dirhamnoside. Mi-crobiol-Sgm 156:757-763.
30. Takaichi S (2009) Distribution and biosynthesis of carotenoids. Advances in Photosynthesis and Respiration, The Purple Phototrophic Bacteria, eds Hunter CN, Daldal F, Thurnauer MC, Beatty JT (Springer, Dordrecht, The Netherlands), Vol 28, pp 97-117.
31. Hauruseu D, Koblízek M (2012) Influence of light on carbon utilization in aerobic anoxygenic phototrophs. Appl Environ Microbiol 78(20):7414-7419.
32. DeBruyn JM, Nixon LT, Fawaz MN, Johnson AM, Radosevich M (2011) Global bio-geography and quantitative seasonal dynamics of Gemmatimonadetes in soil. Appl Environ Microbiol 77(17):6295-6300.
33. Boldareva-Nuianzina EN, Bláhová Z, Sobotka R, Koblízek M (2013) Distribution and origin of oxygen-dependent and oxygen-independent forms of Mg-protoporphyrin monomethylester cyclase among phototrophic proteobacteria. Appl Environ Microbiol 79(8):2596-2604.
34. Sun SL, et al. (2011) Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: The CAMERA resource. Nucleic Acids Res 39(Database issue): D546-D551.
35. Raymond J, Zhaxybayeva O, Gogarten JP, Gerdes SY, Blankenship RE (2002) Whole-genome analysis of photosynthetic prokaryotes. Science 298(5598):1616-1620. (Pubitemid 35387199)
36. Gibson LCD, Willows RD, Kannangara CG, von Wettstein D, Hunter CN (1995) Magnesium-protoporphyrin chelatase of Rhodobacter sphaeroides: Reconstitution of activity by combining the products of the bchH,-I, and-D genes expressed in Escherichia coli. Proc Natl Acad Sci USA 92(6):1941-1944.
37. Fujita Y, Matsumoto H, Takahashi Y, Matsubara H (1993) Identification of a nifDK-like gene (ORF467) involved in the biosynthesis of chlorophyll in the cyanobacterium Plectonema boryanum. Plant Cell Physiol 34(2):305-314.
38. Bryant DA, et al. (2012) Comparative and functional genomics of anoxygenic green bacteria from the taxa Chlorobi, Chloroflexi, and Acidobacteria. Advances in Photosynthesis and Respiration, Functional Genomics and Evolution of Photosynthetic Systems, eds Burnap RL, Vermaas W (Springer, Dordrecht, The Netherlands), Vol 35, pp 47-102.
39. Marrs B (1981) Mobilization of the genes for photosynthesis from Rhodopseudomonas capsulata by a promiscuous plasmid. J Bacteriol 146(3):1003-1012. (Pubitemid 11048861)
40. Petersen J, et al. (2012) Think pink: Photosynthesis, plasmids and the Roseobacter clade. Environ Microbiol 14(10):2661-2672.
41. Marrs B (1974) Genetic recombination in Rhodopseudomonas capsulata. Proc Natl Acad Sci USA 71(3):971-973.
42. Lang AS, Beatty JT (2000) Genetic analysis of a bacterial genetic exchange element: The gene transfer agent of Rhodobacter capsulatus. Proc Natl Acad Sci USA 97(2): 859-864. (Pubitemid 30070400)
43. Mann NH, Cook A, Millard A, Bailey S, Clokie M (2003) Marine ecosystems: Bacterial photosynthesis genes in a virus. Nature 424(6950):741. (Pubitemid 37021693)
44. Lindell D, et al. (2004) Transfer of photosynthesis genes to and from Prochlorococcus viruses. Proc Natl Acad Sci USA 101(30):11013-11018. (Pubitemid 38989576)
45. Sharon I, et al. (2009) Photosystem I gene cassettes are present in marine virus genomes. Nature 461(7261):258-262.
46. Li ZW, Wang ZY, Liu L (2012) Characteristics of meanders and oxbow lakes in Qinghai-Tibet plateau. River Flow2012, ed Murillo Munoz RE (CRC Press, Boca Raton, FL), Vol 1, pp 727-734.
47. Mischke S, Demske D, Schudack ME (2003) Hydrologic and climatic implications of a multidisciplinary study of the mid to late Holocene Lake Eastern Juyanze. Chin Sci Bull 48(14):1411-1417. (Pubitemid 44561395)
48. Qi SZ, Luo F (2007) Environmental degradation problems in the Heihe River Basin, northwest China. Water Environ J 21(2):142-148. (Pubitemid 46831373)
49. Hartmann K, Wunnemann B (2009) Hydrological changes and Holocene climate variations in NW China, inferred from lake sediments of Juyanze palaeolake by factor analyses. Quat Int 194:28-44.
50. Atamna-Ismaeel N, et al. (2012) Bacterial anoxygenic photosynthesis on plant leaf surfaces. Environ Microbiol Rep 4(2):209-216.
51. Permentier HP, et al. (2000) Composition and optical properties of reaction centre core complexes from the green sulfur bacteria Prosthecochloris aestuarii and Chlorobium tepidum. Photosynth Res 64(1):27-39. (Pubitemid 32100082)
52. Goecks J, Nekrutenko A, Taylor J, Team G; Galaxy Team (2010) Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11(8):R86.
53. Zerbino DR, Birney E (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5):821-829. (Pubitemid 351645072)
54. Aziz RK, et al. (2008) The RAST Server: Rapid annotations using subsystems technology. BMC Genomics 9:75.
55. Van Domselaar GH, et al. (2005) BASys: A Web server for automated bacterial genome annotation. Nucleic Acids Res 33(Web Server issue):W455-9. (Pubitemid 44529961)
56. Darling ACE, Mau B, Blattner FR, Perna NT (2004) Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14(7):1394-1403. (Pubitemid 39029237)
57. Quast C, et al. (2013) The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res 41(Database issue, D1):D590-D596.
58. Ludwig W, et al. (2004) ARB: A software environment for sequence data. Nucleic Acids Res 32(4):1363-1371. (Pubitemid 38854737)
59. Tamura K, et al. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731-2739.