Relaxation of functional constraint on light-independent protochlorophyllide oxidoreductase in Thuja

Molecular Biology and Evolution

Volumn 23, Issue 5, 2006, Pages 941-948

  Kusumi, Junko ^a   Sato, Aya ^a   Tachida, Hidenori ^a  

^a KYUSHU UNIVERSITY   (Japan)

Author keywords

Conifer; Functional constraint; Light independent protochlorophyllide oxidoreductase; Nonsynonymous substitution rate

Indexed keywords

CHLOROPHYLL; GENE PRODUCT; OXIDOREDUCTASE; PLANT RNA; PROTOCHLOROPHYLLIDE; PROTOCHLOROPHYLLIDE OXIDOREDUCTASE; UNCLASSIFIED DRUG; PROTOCHLOROPHYLLIDE REDUCTASE;

CHLB GENE; CHLL GENE; CHLN GENE; CONFERENCE PAPER; ENZYME SUBUNIT; GENE MUTATION; LIGHT; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PLANT GROWTH; PLANT SEED; PLASTID; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA EDITING; SEQUENCE ANALYSIS; THUJA; ARTICLE; DNA SEQUENCE; ENZYMOLOGY; GENETICS; MOLECULAR EVOLUTION; MUTATION; PHENOTYPE; PHYLOGENY; SPECIES DIFFERENCE; TIME;

ALGAE; CONIFEROPHYTA; CUPRESSACEAE; THUJA; THUJA OCCIDENTALIS; THUJA PLICATA; THUJA STANDISHII;

EVOLUTION, MOLECULAR; LIGHT; MUTATION; OXIDOREDUCTASES ACTING ON CH-CH GROUP DONORS; PHENOTYPE; PHYLOGENY; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA EDITING; SEEDS; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; THUJA; TIME FACTORS;

EID: 33646568456     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msj097     Document Type: Conference Paper

References (35)

1. Armstrong, G. A. 1998. Greening in the dark:light-independent chlorophyll biosynthesis from anoxygenic photosynthetic bacteria to gymnosperms. J. Photochem. Photobiol. B Biol. 43:87-100.
2. Bock, R. 2000. Sense from nonsense: how the genetic information of chloroplasts is altered by RNA editing. Biochimie 82: 549-557.
3. Chinn, E., and J. Silverthorne. 1993. Light-dependent chloroplast development and expression of a light-harvesting chlorophyll a/b-binding protein gene in the gymnosperm Ginkgo biloba. Plant Physiol. 103:727-732.
4. Farjon, A. 1990. Pinaceae: drawings and descriptions of the genera: Abies, Cedrus, Pseudolarix, Keteleeria, Nothotsuga, Tsuga, Cathaya, Pseudotsuga, Larix and Picea. Regnum Vegetabile, vol. 121. Koeltz Scientific Books, Germany.
5. Freyer, R., M. C. Kiefer-Meyer, and H. Kossel. 1997. Occurrence of plastid RNA editing in all major lineages of land plants. Proc. Natl. Acad. Sci. USA 94:6285-6290.
6. Fujita, Y. 1996. Protochlorophyllide reduction: a key step in the greening of plants. Plant Cell Physiol. 37:411-421.
7. Fujita, Y., and C. E. Bauer. 2000. Reconstitution of light-independent protochlorophyllide reductase from purified BchL and BchN-BchB subunits. In vitro confirmation of nitrogenase-like features of a bacteriochlorophyll biosynthesis enzyme. J. Biol. Chem. 275:23583-23588.
8. Fujita, Y., Y. Takahashi, T. Kohchi, H. Ozeki, K. Ohyama, and H. Matsubara. 1989. Identification of a novel nifH-like (frxC) protein in chloroplasts of the liverwort Marchantia polymorpha. Plant Mol. Biol. 13:551-561.
9. Gadek, P. A., D. L. Alpers, M. M. Heslewood, and C. J. Quinn. 2000. Relationships within Cupressaceae sensu lato: a combined morphological and molecular approach. Am. J. Bot. 87:1044-1057.
10. Karpinska, B., S. Karpinski, and J. Hallgren. 1997. The chlB gene encoding a subunit of light-independent protochlorophyllide reductase is edited in chloroplasts of conifers. Curr. Genet. 31:343-347.
11. Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge.
12. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5:150-163.
13. Kusumi, J., Y. Tsumura, H. Yoshimaru, and H. Tachida. 2000. Phylogenetic relationships in Taxodiaceae and Cupressaceae sensu stricto based on matK gene, chlL gene, trnL-trnF IGS region, and trnL intron sequences. Am. J. Bot. 87:1480-1488.
14. Li, W. H., T. Gojobori, and M. Nei. 1981. Pseudogenes as a paradigm of neutral evolution. Nature 292:237-239.
15. Liu, X. Q., H. Xu, and C. Huang. 1993. Chloroplast chlB gene is required for light-independent chlorophyll accumulation in Chlamydomonas reinhardtii. Plant Mol. Biol. 23:297-308.
16. Mackinney, G. 1941. Absorption of light by chlorophyll solutions. J. Biol. Chem. 140:315-322.
17. Mariani, P., M. De Carli, N. Rascio, B. Baldan, G. Casadoro, G. Gennari, M. Bodner, and W. Larcher. 1990. Synthesis of chlorophyll and photosynthetic competence in etiolated and greening seedlings of Larix decidua as compared with Picea abies. J. Plant Physiol. 137:5-14.
18. Miller, C. N. 1977. Mesozoic conifers. Bot. Rev. 43:217-280.
19. _. 1988. The origin of modern conifer families. Pp. 448-486 in C. B. Beck, ed. Origin and evolution of gymnosperms. Columbia University Press, New York.
20. Miyata, T., and T. Yasunaga. 1981. Rapidly evolving mouse alpha-globin-related pseudo gene and its evolutionary history. Proc. Natl. Acad. Sci. USA 78:450-453.
21. Murray, M. G., and W. F. Thompson. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8:4321-4325.
22. Muse, S. V., and B. S. Gaut. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11:715-724.
23. Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
24. Page, C. N. 1990. Coniferophytina. Pp. 282-361 in K. U. Kramer and P. S. Green, eds. The families and genera of vascular plants, Vol. 1, Pteridophytes and gymnosperms. Springer-Verlag, Berlin, Germany.
25. Pond, S. L., S. D. Frost, and S. V. Muse. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21:676-679.
26. Richard, M., C. Tremblay, and G. Bellemare. 1994. Chloroplastic genomes of Ginkgo biloba and Chlamydomonas moewusii contain a chlB gene encoding one subunit of a light-independent protochlorophyllide reductase. Curr. Genet. 26:159-165.
27. Schoefs, B. 2001. The protochlorophyllide-chlorophyllide cycle. Photosynth. Res. 70:257-271.
28. Schoefs, B., and F. Franck. 2003. Protochlorophyllide reduction: mechanisms and evolutions. Photochem. Photobiol. 78: 543-557.
29. Skinner, J. S., and M. P. Timko. 1999. Differential expression of genes encoding the light-dependent and light-independent enzymes for protochlorophyllide reduction during development in loblolly pine. Plant Mol. Biol. 39:577-592.
30. Suzuki, J. Y., D. W. Bollivar, and C. E. Bauer. 1997. Genetic analysis of chlorophyll biosynthesis. Annu. Rev. Genet. 31:61-89.
31. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
32. Wakasugi, T., T. Hirose, M. Horihata, T. Tsudzuki, H. Kossel, and M. Sugiura. 1996. Creation of a novel protein-coding region at the RNA level in black pine chloroplasts: the pattern of RNA editing in the gymnosperm chloroplast is different from that in angiosperme. Proc. Natl. Acad. Sci. USA 93:8766-8770.
33. Wray, G. A., M. W. Hahn, E. Abouheif, J. P. Balhoff, M. Pizer, M. V. Rockman, and L. A. Romano. 2003. The evolution of transcriptional regulation in eukaryotes. Mol. Biol. Evol. 20:1377-1419.
34. Yamazaki, J., A. Ohashi, Y. Hashimoto, E. Negishi, S. Kumagai, T. Kubo, T. Oikawa, E. Maruta, and Y. Kamimura. 2003. Effects of high light and low temperature during harsh winter on needle photodamage of Abies mariesii growing at the forest limit on Mt. Norikura in Central Japan. Plant Sci. 165:257-264.
35. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.