"Green-like" and "red-like" rubisCO cbbL genes in Rhodobacter azotoformans

Molecular Biology and Evolution

Volumn 20, Issue 5, 2003, Pages 821-830

  Uchino, Yoshihito ^a   Yokota, Akira ^b  

^a Institute for Fermentation Osaka   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

Form I RubisCO large subunit; Green like and red like cbbL; Horizontal gene transfer; Rhodobacter azotoformans

Indexed keywords

PROTEIN; PROTEIN CBBL; RIBULOSEBISPHOSPHATE CARBOXYLASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; DOT HYBRIDIZATION; GENE CLUSTER; GENE LOCATION; GENETIC CODE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; RHODOBACTER; RHODOBACTER AZOTOFORMANS; RHODOBACTER BLASTICUS; RHODOBACTER CAPSULATUS; RHODOBACTER SPHAEROIDES; RHODOBACTER VELDKAMPII;

BASE SEQUENCE; BLOTTING, SOUTHERN; CLUSTER ANALYSIS; CODON; DNA PRIMERS; ELECTROPHORESIS; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RHODOBACTER; RIBULOSE-BISPHOSPHATE CARBOXYLASE; SEQUENCE ANALYSIS, DNA;

PROKARYOTA; RHODOBACTER; RHODOBACTER AZOTOFORMANS; RHODOBACTER BLASTICUS; RHODOBACTER CAPSULATUS; RHODOBACTER SPHAEROIDES; RHODOBACTER VELDKAMPII; RHODOPSEUDOMONAS;

EID: 0037694034     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg100     Document Type: Article

References (27)

1. Adachi, J., and M. Hasegawa. 1996. Computer science monographs, No. 28. MOLPHY version 2.3. - Programs for molecular phylogenetics based on maximum likelihood. Institute of Statistical Mathematics, Tokyo.
2. Delwiche, C. F., and J. D. Palmer. 1996. Rampant horizontal transfer and duplication of RubisCO genes in eubacteria and plastids. Mol. Biol. Evol. 13:873-882.
3. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
4. Fitch, W. M. 1971. Towards defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20:406-416.
5. 2 fixation operon of Rhodobacter sphaeroides. J. Biol. Chem. 266:14646-14653.
6. Hansen, T. A., and J. F. Imhoff. 1985. Rhodobacter veldkampii, a new species of phototrophic purple nonsulfur bacteria. Int. J. Syst. Bacteriol. 35:115-116.
7. Hasegawa, M., and H. Kishino. 1994. Accuracies of the simple methods for estimating the bootstrap probability of a maximum-likelihood tree. Mol. Biol. Evol. 11:142-145.
8. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
9. Hiraishi, A., K. Muramatsu, and Y. Ueda. 1996. Molecular genetic analysis of Rhodobacter azotoformans sp. nov. and related species of phototrophic bacteria. System. Appl. Microbiol. 19:168-177.
10. Hiraishi, A., K. Muramatsu, and K. Urata. 1995. Characterization of new denitrifying Rhodobacter strains isolated from photosynthetic sludge for wastewater treatment. J. Ferment. Bioeng. 79:39-44.
11. Hiraishi, A., and Y. Ueda. 1994. Intrageneric structure of the genus Rhodobacter: transfer of Rhodobacter sulfidophilus and related marine species to the genus Rhodovulum gen. nov. Int. J. Syst. Bacteriol. 44:15-23.
12. Horken, K. M., and F. R. Tabita. 1999. The "green" form I ribulose 1,5-bisphosphate carboxylase/oxygenase from the nonsulfur purple bacterium Rhodobacter capsulatus. J Bacteriol. 181:3935-3941.
13. Jones, D. T., W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Applic. Biosci. 8:275-282.
14. Kawasaki, H., Y. Hoshino, H. Kuraishi, and K. Yamasato. 1992. Rhodocista centenaria gen. nov., sp. nov., a cyst-forming anoxygenic phototrophic bacterium and its phylogenetic position in the Proteobacteria alpha group. J. Gen. Appl. Microbiol. 38:541-551.
15. Kimura, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
16. Kobayashi, H., A. M. Viale, T. Takabe, T. Akazawa, K. Wada, K. Shinozaki, K. Kobayashi, and M. Sugiura. 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.
17. Kusano, T., T. Takeshima, C. Inoue, and K. Sugawara. 1991. Evidence for two sets of structural genes coding for ribulose bisphosphate carboxylase in Thiobacillus ferrooxidans. J. Bacteriol. 173:7313-7323.
18. Kusian, B., R. Bednarski, M. Husemann, and B. Bowien. 1995. Characterization of the duplicate ribulose-1,5-bisphosphate carboxylase genes and cbb promoters of Alcaligenes eutrophus. J. Bacteriol. 177:4442-4450.
19. Nishihara, H., T. Yaguchi, S. Y. Chung, K. Suzuki, M. Yanagi, K. Yamasato, T. Kodama, and Y. Igarashi. 1998. 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. Arch. Microbiol. 169:364-368.
20. Paoli, G. C., F. Soyer, J. M. Shively, and F. R. Tabita. 1998. Rhodobacter capsulatus genes encoding form I ribulose-1,5-bisphosphate carboxylase/oxy-genase (cbbLS) and neighbouring genes were acquired by a horizontal gene transfer. Microbiology 144:219-227.
21. Saitou, N., and M. Nei. 1987. The Neighbor-Joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
22. Swofford, D. L. 2000. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Mass.
23. Tamura, K., and M. Nei. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10: 512-526.
24. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
25. Viale, A. M., H. Kobayashi, and T. Akazawa. 1989. Expressed genes for plant-type ribulose 1,5-bisphosphate carboxylase/oxygenase in the photosynthetic bacterium Chromatium vinosum, which possesses two complete sets of the genes. J. Bacteriol. 171:2391-2400.
26. Yang, Z. 2000. Phylogenetic analysis by maximum likelihood (PAML), Version 3.0. University College London, London.
27. Yang, Z., and R. Nielsen. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17:32-43.