A nucleomorph-encoded CbbX and the phylogeny of RuBisCo regulators

Molecular Biology and Evolution

Volumn 17, Issue 4, 2000, Pages 576-583

  Maier, Uwe G ^a   Fraunholz, Martin ^a   Zauner, Stefan ^a   Penny, Susanne ^b   Douglas, Susan ^b  

^a PHILIPPS UNIVERSITY MARBURG   (Germany)

^b NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

CbbR; CbbX; Cryptomonad; RbcR; RuBisCo

Indexed keywords

RIBULOSEBISPHOSPHATE CARBOXYLASE;

AMINO ACID SEQUENCE; ARTICLE; GENE CLUSTER; GENE EXPRESSION; GENE LOCATION; GENETIC ANALYSIS; GENETIC CODE; GENOME; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASTID; SEQUENCE ANALYSIS;

CRYPTOPHYTA; CYANOBACTERIA; EMBRYOPHYTA; GUILLARDIA THETA; PROTEOBACTERIA;

EID: 0034074145     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026337     Document Type: Article

References (50)

1. CAVALIER-SMITH, T. 1989. The kingdom Chromista. Pp. 379-405 in J. C. GREEN, B. S. C. LEADBEATER, and W. L. DIVER, eds. The Chromophyte algae: problems and perspectives. Oxford University Press, Oxford.
2. CORUZZI, G., R. BROGLIE, A. CASHMORE, and N. H. CHUA. 1983. Nucleotide sequences of two pea cDNA clones encoding the small subunit of ribulose 1,5-bisphosphate carboxylase and the major chlorophyll a/b-binding thylakoid polypeptide. Biol. Chem. 258:1399-402.
3. DELWICHE, C. F., and J. D. PALMER. 1996. Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids. Mol. Biol. Evol. 13:873-82.
4. _. 1997. Origins of plastids and their spread via secondary symbiosis. Plant Syst. Evol. 11(Suppl.):53-86.
5. DOUGLAS, S. E. 1994. Chloroplast origins and evolution. Pp. 91-118 in D. A. BRYANT, ed. The molecular biology of cyanobacteria. Kluwer Academic Press, the Netherlands.
6. DOUGLAS, S. E., and D. G. DURNFORD. 1989. The small subunit of ribulose-1,5-bisphosphate carboxylase is plastid-encoded in the chlorophyll c-containing alga Cryptomonas Φ. Plant Mol. Biol. 13:13-20.
7. DOUGLAS, S. E., D. G. DURNFORD, and C. W. MORDEN. 1990. Nucleotide sequence of the gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from the chlorophyll c-containing alga Cryptomonas Φ: evidence supporting the polyphyletic origin of plastids. J. Phycol. 26: 500-508.
8. DOUGLAS, S. E., C. A. MURPHY, D. F. SPENCE, and M. W. GRAY. 1991. Cryptomonad algae are evolutionary chimaeras of two phylogenetically distinct unicellular eukaryotes. Nature 350:148-151.
9. DOUGLAS, S. E., and S. L. PENNY. 1999. The plastid genome of the cryptophyte alga, Guillardia theta: complete sequence and conserved synteny groups confirm its common ancestry with red algae. J. Mol. Evol. 48:236-244.
10. FELSENSTEIN, J. 1989. PHYLIP (phylogeny inference package) version 3.5. Cladistics 5:164-166.
11. FRAUNHOLZ, M. J., J. WASTL, S. ZAUNER, S. A. RENSING, M. M. SCHERZINGER, and U.-G. MAIER. 1997. The evolution of cryptophytes. Plant Syst. Evol. 11(Suppl.): 163-174.
12. GIBBS, S. P. 1981. The chloroplast of some algal groups may have evolved from endosymbiotic eukaryotic algae. Ann. N.Y. Acad. Sci. 361:193-208.
13. GIBSON, J. L., D. L. FALCONE, and F. R. TABITA. 1991. Nucleotide sequence, transcriptional analysis, and expression of genes encoded within the form I CO2 fixation operon of Rhodobacter sphaeroides. J. Biol. Chem. 266:14646-14653.
14. GIBSON, J. L., and F. R. TABITA. 1996. The molecular regulation of the reductive pentose phosphate pathway in Proteobacteria and Cyanobacteria. Arch. Microbiol. 166:141-50.
15. _. 1997. Analysis of the cbbXYZ operon in Rhodobacter sphaeroides. J. Bacteriol. 179:663-669.
16. GILSON, P. R., U.-G. MAIER, and G. I. MCFADDEN. 1997. Size isn't everything: lessons in genetic miniaturisation from nucleomorphs. Curr. Opin. Genet. Dev. 7:800-806.
17. HALLICK, R., L. HONG, R. DRAGER, M. FAVREAU, A. MONFOR, B. ORSAT, A. SPIELMANN, and E. STUTZ. 1993. Complete sequence of Euglena gracilis chloroplast DNA. Nucleic Acids Res. 21:3537-3544.
18. HERRMANN, R. G. 1997. Eukaryotism, towards a new interpretation. Pp. 73-118 in H. E. A. SCHENK, R. G. HERRMANN, K. W. JEON, and W. SCHWEMMLER, eds. Eukaryotism and symbiosis. Springer, Heidelberg, Germany.
19. HIRATSUKA, J., H. SHIMADA, R. WHITTIER et al. (15 co-authors). 1989. The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol. Gen. Genet. 217:185-194.
20. KOSTRZEWA, M., K. VALENTIN, U. MAID, R. RADETZKY, and K. ZETSCHE. 1990. Structure of the rubisco operon from the multicellular red alga Antithamnion sp. Curr. Genet. 18: 465-469.
21. KOWALLIK, K. V., B. STÖBE, I. SCHAFFRAN, P. KROTH-PANIC, and U. FREIER. 1995. The chloroplast genome of a chlorophyll a+c-containing alga, Odontella sinensis. Plant Mol. Biol. Rep. 13:336-342.
22. KUSIAN, B., R. BEDNARSKI, M. HUSEMANN, and B. BOWIEN. 1995. Characterization of the duplicate ribulose-1,5-bisphosphate carboxylase genes and ebb promoters of Alcaligenes eutrophus. J. Bacteriol. 177:4442-4450.
23. KUSIAN, B., and B. BOWIEN. 1997. Organization and regulation of ebb CO2 assimilation genes in autotrophic bacteria. FEMS Microbiol. Rev. 21:135-155.
24. KUSIAN, B., J.-G. YOO, R. BEDNARSKI, and B. BOWIEN. 1992. The Calvin cycle enzyme pentose-5-phosphate 3-epimerase is encoded within the cfx operons of the chemoautotroph Alcaligenes eutrophus. J. Bacteriol. 174:7337-7344.
25. LOCKHART, P. J., M. A. STEEL, A. C. BARBROOK, D. HUSON, M. A. CHARLESTON, and C. J. HOWE. 1998. A covariotide model explaining apparent phylogenetic structure of oxygenic lineages. Mol. Biol. Evol. 15:1183-1118.
26. MCFADDEN, G. I., P. R. GILSON, S. E. DOUGLAS, T. CAVALIERSMITH, C. J. B. HOFMANN, and U.-G. MAIER. 1997. Bonsai genomics: sequencing the smallest eukaryotic genome. Trends Genet. 13:46-49.
27. MAIER, R. M., K. NECKERMANN, G. L. IGLOI, and H. J. KÖSSEL. 1995. Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. Mol. Biol. 251:614-628.
28. MAIER, U.-G., C. J. B. HOFFMANN, S. ESCHBACH, J. WOLTERS, and G. IGLOI. 1991 Demonstration of nucleomorph-encoded eukaryotic small subunit ribosomal RNA in cryptomonads. Mol. Gen. Genet. 230:155-160.
29. MARTIN, W., and R. G. HERRMANN. 1998. Gene transfer from organelles to the nucleus: how much, what happens, and why? Plant Physiol. 118:9-17.
30. MARTIN, W., and C. SCHNARRENBERGER. 1997. The evolution of the Calvin cycle from prokaryotic to eukaryotic chromosomes: a case study of functional redundancy in ancient pathways through endosymbiosis. Curr. Genet. 32:1-18.
31. MARTIN, W., B. STÖBE, V. GOREMYKIN, S. HANSMANN, and K. V. KOWALLIK. 1998. Evolutionary chloroplast genomics. Nature 393:162-165.
32. MEIJER, W. G., A. C. ARNBERG, H. G. ENEQUIST, P. TERPSTRA, M. E. LIDSTROM, and L. DIJKHUIZEN. 1991. Identification and organization of carbon dioxide fixation genes in Xanthobacter flavus H4-14. Mol. Gen. Genet. 225:320-330.
33. MORSE, D., P. SALVOLIS, P. MARKOVIC, and J. W. HASTINGS. 1995. A nuclear-encoded form II RuBisCo in dinoflagellates. Science 268:1622-1624.
34. OHTA, N. 1997. Analysis of a plastid gene cluster reveals a close relationship between Cyanidioschvzon and Cyanidium. J. Plant Res. 110:235-245.
35. OHYAMA, K., H. FUKUZAWA, T. KOHCHI et al. (13 co-authors). 1988. Structure and organization of Marchantia polymorpha chloroplast genome. I. Cloning and gene identification. J. Mol. Biol. 203:281-298.
36. PAOLI, G. C., P. VICHIVANIVES, and F. R. TABITA. 1998. Physiological control and regulation of the Rhodobacter capsulatus cbb operon. J. Bacteriol. 180:4258-4269.
37. PAOLI, G. C., F. SOYER, J. SHIVELY, and F. R. TABITA. 1998. Rhodobacter capsulatus genes encoding form I ribulose-1,5-bisphosphate carboxylase/oxygenase (cbbLS) and neighbouring genes were acquired by a horizontal gene transfer. Microbiology 144:219-227.
38. PIGGOT, P. J. 1996. Spore development in Bacillus subtilis. Curr. Opin. Genet. Dev. 6:531-537.
39. REITH, M., and J. MUNHOLLAND. 1995. Complete nucleotide sequence of the Porphyra purpurea chloroplast genome. Plant Mol. Biol. Rep. 13:332.
40. STIREWALT, V. L., C. B. MICHALOWSKI, W. LÖFFELHARDT, H. J. BOHNERT, and D. A. BRYANT. 1995. Nucleotide sequence of the cyanelle genome from Cyanophora paradoxa. Plant Mol. Biol. Rep. 13:327-332.
41. STÖBE, B., W. MARTIN, and K. V. KOWALLIK. 1998. Distribution and nomenclature of protein-encoding genes in 12 sequenced chloroplast genomes. Plant Mol. Biol. Rep. 16: 243-255.
42. SUGIURA, M. 1992. The chloroplast genome. Plant Mol. Biol. 19:149-168.
43. VAN DE PEER, Y., S. A. RENSING, U.-G. MAIER, and R. DE WÄCHTER. 1996. Substitution rate calibration of small subunit rRNA identifies chlorarachniophyte endosymbionts as remnants of green algae. Proc. Natl. Acad. Sci. USA 93: 7732-7736.
44. VAN DER AUWERA, G., C. J. B. HOFMANN, P. DE RIJK, and R. DE WACHTER. 1998. The origin of red algae and crytomonad nucleomorphs: a comparative phylogeny based on small and large subunit rRNA sequences of Palmaria palmata, Gracilaria verrucosa, and the Guillardia theta nucleomorph. Mol. Phylogenet. Evol. 10:333-342.
45. VAN KEULEN, G., L. GIRBAL, E. R. VAN DEN BERGH, L. DIJKHUIZEN, and W. G. MEIJER. 1998. The LysR-type transcriptional regulator CbbR controlling autotrophic CO2 fixation by Xanthobacter flavus is an NADPH sensor. J. Bacteriol. 180:1411-1417.
46. WAKASUGI, T., T. NAGAI, M. KAPOOR et al. (15 co-authors). 1997. Complete nucleotide sequence of the chloroplast genome from the green alga Chlorella vulgaris: the existence of genes possibly involved in chloroplast division. Proc. Natl. Acad. Sci. USA 94:5967-5972.
47. WAKASUGI, T., J. TSUDZUKI, S. ITO, K. NAKASHIMA, T. TSUDZUKI, and M. SUGIURA. 1994. Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc. Natl. Acad. Sci. USA 91:9794-9798.
48. WASTL, J., M. FRAUNHOLZ, S. ZAUNER, S. DOUGLAS, and U. G. MAIER. 1999. Ancient gene duplication and differential gene flow in plastid lineages: the GroEL/Cpn60 example. J. Mol. Evol. 48:112-117.
49. WATSON, G. M., J. P. YU, and F. R. TABITA. 1999. Unusual ribulose 1,5-bisphosphate carboxylase/oxygenase of anoxic Archaea. J. Bacteriol. 181:1569-1575.
50. WHITNEY, S. M., D. C. SHAW, and D. YELLOWLESS. 1995. Evidence that some dinoflagellates contain a ribulose-1,5-bisphosphate carboxylase/oxygenase related to that of the α-proteobacteria. Proc. R. Soc. Lond. B Biol. Sci. 259:271-275.