Phylogenetic position of an obligately chemoautotrophic, marine hydrogen-oxidizing bacterium, Hydrogenovibrio marinus, on the basis of 16S rRNA gene sequences and two form I RuBisCO gene sequences

Archives of Microbiology

Volumn 169, Issue 4, 1998, Pages 364-368

  Nishihara, Hirofumi ^a,c   Yaguchi, Toshiaki ^a   Chung, Seon Yong ^a   Suzuki, Ken Ichiro ^b   Yanagi, Miyoko ^a,e   Yamasato, Kazuhide ^a,e   Kodama, Tohru ^a,d   Igarashi, Yasuo ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b RIKEN BIORESOURCE CENTER   (Japan)

^c IBARAKI UNIVERSITY   (Japan)

^d SHINSHU UNIVERSITY   (Japan)

^e TOKYO UNIVERSITY OF AGRICULTURE   (Japan)

Author keywords

16S rRNA gene sequence; Form I RuBisCO sequences; Hydrogen oxidizing bacterium; Hydrogenovibrio marinus; Marine bacteria; Obligate chemolithoautotroph; Phylogeny

Indexed keywords

HYDROGEN; RIBOSOME RNA; RIBULOSEBISPHOSPHATE CARBOXYLASE; RNA 16S;

AMINO ACID SEQUENCE; ARTICLE; CHROMATIUM VINOSUM; GENE SEQUENCE; HYDROGENOVIBRIO MARINUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RNA GENE; SEQUENCE HOMOLOGY; THIOBACILLUS; VIBRIONACEAE;

BACTERIAL PROTEINS; CHROMOSOME MAPPING; DNA, RIBOSOMAL; ESCHERICHIA COLI; GENES, BACTERIAL; HYDROGEN; ISOENZYMES; MARINE BIOLOGY; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; OXIDATION-REDUCTION; PHYLOGENY; RECOMBINANT PROTEINS; RIBULOSE-BISPHOSPHATE CARBOXYLASE; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; TRANSFORMATION, BACTERIAL; VIBRIONACEAE; WATER MICROBIOLOGY;

ALLOCHROMATIUM VINOSUM; BACTERIA (MICROORGANISMS); CHROMATIACEAE; CHROMATIUM; GAMMAPROTEOBACTERIA; HYDROGENOVIBRIO MARINUS; PROKARYOTA; THIOBACILLUS; THIOMICROSPIRA; VIBRIONACEAE;

EID: 0031958767     PISSN: 03028933     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002030050584     Document Type: Article

References (33)

1. Ausubel FM et al. (1987) Current protocols in molecular biology. Wiley, New York
2. Bergh ERE et al. (1996) Primary structure and phylogeny of the Calvin cycle enzymes transketolase and fructosebisphosphate aldolase of Xanthobacter flavus. J Bacteriol 178:888-893
3. 2 RuBisCO from a marine obligately autotrophic hydrogen-oxidizing bacterium, Hydrogenovibrio marinus strain MH-110. FEMS Microbiol Lett 109:49-54
4. 2. Adv Microbiol Ecol 10:231-283
5. Delwiche CF, Palmer JD (1996) Rampant horizontal transfer and duplication of RuBisCO genes in eubacteria and plastids. Mol Biol Evol 13:873-882
6. Drobner E, Huber H, Stetter KO (1990) Thiobacillus ferrooxidans, a facultative hydrogen oxidizer. Appl Environ Microbiol 56: 2922-2923
7. English RS, Williams CA, Lorbach SC, Shively JM (1992) Two forms of ribulose-1,5-bisphosphate carboxylase/oxygenase from Thiobacillus denitrificans. FEMS Microbiol Lett 94:111-120
8. Felsenstein J (1993) PHYLIP (phylogeny inference package), version 3.5c. Department of Genetics, University of Washington, Seattle, WA
9. Hanahan D (1983) Studies on transformation of Escherichia coli with plasmids. J Mol Biol 166:557-580
10. Huber R et al. (1992) Aquifex pyrophilus, gen. nov. sp. nov., represents a novel group of marine hyperthermophilic hydrogen-oxidizing bacteria. Syst Appl Microbiol 15:340-351
11. Kawasumi T (1989) Genus Hydrogenobacter Kawasumi, Igarashi, Kodama and Minoda 1984. In: Staley JT, Bryant MP, Pfennig N, Holt JG (eds) Bergey's manual of systematic bacteriology, vol 3. Williams & Wilkins, Baltimore, pp 1872-1873
12. Kimura M, Ohta T (1972) On the stochastic model for estimation of mutation distance between homologous proteins. J Mol Evol 2:87-90
13. Kobayashi H et al. (1991) Sequence and expression of genes encoding the large and small subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase from Chromatium vinosum. Gene 97:55-62
14. Kuenen JG, Robertson LA, Tuovinen OH (1991) The genera Thiobacillus, Thiomicrospira and Thiosphaera. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes, 2nd edn, vol 3. Springer, Berlin Heidelberg New York, pp 2639-2657
15. Lipman DJ, Pearson WR (1985) Rapid and sensitive protein similarity searches. Science 227:1435-1441
16. Morse D, Salois P, Markovic P, Hastings JW (1995) A nuclear-encoded form II RuBisCO in dinoflagellates. Science 268:1622-1624
17. Muyzer G, Teske A, Wirsen CO, Jannasch HW (1995) Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol 164:165-172
18. Nishihara H, Igarashi Y, Kodama T (1990) A new isolate of Hydrogenobacter, an obligately chemolithoautotrophic, thermophilic, halophilic and aerobic hydrogen-oxidizing bacterium from seaside saline hot spring. Arch Microbiol 153:294-298
19. Nishihara H, Igarashi Y, Kodama T (1991) Hydrogenovibrio marinus gen. nov. sp. nov., a marine obligately chemolithoautotrophic hydrogen-oxidizing bacterium. Int J Syst Bacteriol 41: 130-133
20. Pfennig N, Trüper HG (1991) The family Chromatiaceae. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds), The prokaryotes, 2nd edn, vol 3. Springer, Berlin Heidelberg New York, pp 3200-3221
21. Pitulle C et al. (1994) Phylogenetic position of the genus Hydrogenobacter. Int J Syst Bacteriol 44:620-626
22. Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
23. Sambrook J, Fritsch T, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
24. Shima S, Suzuki K (1993) Hydrogenobacter acidophilus sp. nov., a thermoacidophilic, aerobic, hydrogen-oxidizing bacterium requiring elemental sulfur for growth. Int J Syst Bacteriol 43:703-708
25. Shinozaki K, Yamada C, Takahata N, Sugiura M (1983) Molecular cloning and sequence analysis of the cyanobacterial gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase. Proc Natl Acad Sci USA 80:4050-4054
26. Southern EM (1975) Detection of specific sequences among DNA fragments separated by electrophoresis. J Mol Biol 98:503-517
27. Stoner MT, Shively JM (1993) Cloning and expression of the D-ribulose-1,5-bisphosphate carboxyluse/oxygenase form II gene from Thiobacillus intermedius in Escherichia coli. FEMS Microbiol Lett 107:287-292
28. Tabita FR (1988) Molecular and cellular regulation of autotrophic carbon dioxide fixation in microorganisms. Microbiol Rev 52:155-189
29. Vieira J, Messing J (1987) Production of single-stranded plasmid DNA. Methods Enzymol 153:3-11
30. Whitney SM, Shaw DC, Yellowlees D (1995) Evidence that some dinoflagellates contain a ribulose-1,5-bisphosphate carboxylase/oxygenase related to that of the α-proteobacteria. Proc R Soc Lond [Biol] 259:271-275
31. 2 form of RuBisCO from a marine obligately autotrophic hydrogen-oxidizing bacterium, Hydrogenovibrio marinus strain MH-110. Biosci Biotech Biochem 58:1733-1737
32. Yanagi M, Yamasato K (1993) Phylogenetic analysis of the family Rhizobiaceae and related bacteria by sequencing of 16S rRNA gene using PCR and DNA sequencer. FEMS Microbiol Lett 107:115-120
33. Yanisch-Perron C, Vieira J, Messing J (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103-119