Identification of chlorophyllide a oxygenase in the Prochlorococcus genome by a comparative genomic approach

Plant and Cell Physiology

Volumn 47, Issue 12, 2006, Pages 1622-1629

  Satoh, Soichirou ^a   Tanaka, Ayumi ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

Author keywords

BLAST; Chlorophyll; Chlorophyllide a oxygenase; Comparative genomics; Prochlorococcus

Indexed keywords

CHLOROPHYLL A OXYGENASE; OXYGENASE; PLANT DNA;

AMINO ACID SEQUENCE; ARTICLE; COMPARATIVE STUDY; ENZYMOLOGY; GENE; GENETICS; GENOME; MOLECULAR GENETICS; PHYLOGENY; PROCHLOROCOCCUS; SYNECHOCOCCUS;

AMINO ACID SEQUENCE; DNA, PLANT; GENES, PLANT; GENOME, PLANT; MOLECULAR SEQUENCE DATA; OXYGENASES; PHYLOGENY; PROCHLOROCOCCUS; SYNECHOCOCCUS;

BRYOPHYTA; CHLOROPHYTA; EMBRYOPHYTA; PROCHLORALES; PROCHLOROCOCCUS; PROCHLOROCOCCUS MARINUS; PROCHLORON; PROCHLOROTHRIX; SYNECHOCOCCUS; SYNECHOCOCCUS SP.; SYNECHOCYSTIS; SYNECHOCYSTIS SP.;

EID: 33845686760     PISSN: 00320781     EISSN: 14719053     Source Type: Journal    
DOI: 10.1093/pcp/pcl026     Document Type: Article

References (31)

1. Chervitz, S.A., Aravind, L., Sherlock, G., Ball, C.A., Koonin, E.V., et al. (1998) Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science 282: 2022-2028.
2. Daubin, V., Moran, N.A. and Ochman, H. (2003) Phylogenetics and the cohesion of bacterial genomes. Science 301: 829-832.
3. Dufresne, A., Salanoubat, M., Partensky, F., Artiguenave, F., Axmann, I.M., et al. (2003) Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc. Natl Acad. Sci. USA 100: 10020-10025.
4. Felsenstein, J. (1989) PHYLIP - Phylogeny inference package (version 3.2). Cladistics 5: 164-166.
5. Hess, W.R., Rocap, G., Ting, C.S., Larimer, F., Stilwagen, S., Lamerdin, J. and Chisholm, S.W. (2001) The photosynthetic apparatus of Prochlorococcus: insights through comparative genomics. Photosynth. Res. 70: 53-71.
6. Jones, D.T., Taylor, W.R. and Thornton, J.M. (1992) The rapid generation of mutation data matrices from protein sequences. CABIOS 8: 275-282.
7. Koonin, E.V., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Krylov, D.M., et al. (2004) A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol. 5: R7.
8. Lindell, D., Sullivan, M.B., Johnson, Z.I., Tolonen, A.C., Rohwer, F. and Chisholm, S.W. (2004) Transfer of photosynthesis genes to and from Prochlorococcus viruses. Proc. Natl Acad. Sci. USA 101: 11013-11018.
9. Liu, H., Nolla, H.A. and Campbell, L. (1997) Prochlorococcus growth rate an contribution to primary production in the equatorial and subtropical North Pacific Ocean. Aquat. Microb. Ecol. 12: 39-47.
10. Nagata, N., Satoh, S., Tanaka, R. and Tanaka, A. (2004) Domain structures of chlorophyllide a oxygenase of green plants and Prochlorothrix hollandica in relation to catalytic functions. Planta 218: 1019-1025.
11. Nagata, N., Tanaka, R., Satoh, S. and Tanaka, A. (2005) Identification of a vinyl reductase gene for chlorophyll synthesis in Arabidopsis thaliana and implications for the evolution of Prochlorococcus species. Plant Cell 17: 233-240.
12. Ohtsuka, T., Ito, H. and Tanaka, A. (1997) Conversion of chlorophyll b to chlorophyll a and the assembly of chlorophyll with apoproteins by isolated chloroplasts. Plant Physiol. 113: 137-147.
13. Oster, U., Tanaka, R., Tanaka, A. and Rudiger, W. (2000) Cloning and functional expression of the gene encoding the key enzyme for chlorophyll b biosynthesis (CAO) from Arabidopsis thaliana. Plant J. 21: 305-310.
14. Palenik, B., Brahamsha, B., Larimer, F.W., Land, M., Hauser, L., et al. (2003) The genome of a motile marine Synechococcus. Nature 424: 1037-1042.
15. Partensky, F., Hess, W.R. and Vaulot, D. (1999) Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol. Mol. Biol. Rev. 63: 106-127.
16. Pinta, V., Picaud, M., Reiss-Husson, F. and Astier, C. (2002) Rubrivivax gelatinosus acsF (previously orf358) codes for a conserved, putative binuclear-iron-cluster-containing protein involved in aerobic oxidative cyclization of Mg-protoporphyrin IX monomethylester. J. Bacteriol. 184: 746-753.
17. Rasko, D.A., Myers, G.S. and Ravel, J. (2005) Visualization of comparative genomic analyses by BLAST score ratio. BMC Bioinformatics 6: 2.
18. Rippka, R., Coursin, T., Hess, W., Lichtle, C., Scanlan, D.J., Palinska, K.A., Iteman, I., Partensky, F., Houmard, J. and Herdman, M. (2000) Prochlorococcus marinus Chisholm et al 1992 subsp pastoris subsp nov strain PCC 9511, the first axenic chlorophyll a2/ b2-containing cyanobacterium (Oxyphotobacteria). Int. J. Syst. Evol. Microbiol. 50: 1833-1847.
19. Rocap, G., Larimer, F.W., Lamerdin, J., Malfatti, S., Chain, P., et al. (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424: 1042-1047.
20. Rubin, G.M., Yandell, M.D., Wortman, J.R., Gabor Miklos, G.L., Nelson, C.R., et al. (2000) Comparative genomics of the eukaryotes. Science 287: 2204-2215.
21. Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
22. Satoh, S., Ikeuchi, M., Mimuro, M. and Tanaka, A. (2001) Chlorophyll b expressed in cyanobacteria functions as a light-harvesting antenna in photosystem I through flexibility of the proteins. J. Biol. Chem. 276: 4293-4297.
23. Schon, A., Krupp, G., Gough, S., Berry-Lowe, S., Kannangara, C.G. and Soll, D. (1986) The RNA required in the first step of chlorophyll biosynthesis is a chloroplast glutamate tRNA. Nature 322: 281-284.
24. Tanaka, A., Ito, H., Tanaka, R., Tanaka, N.K., Yoshida, K. and Okada, K. (1998) Chlorophyll a oxygenase (CAO) is involved in chlorophyll b formation from chlorophyll a. Proc. Natl Acad. Sci. USA 95: 12719-12723.
25. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. and Higgins, D.G. (1997) The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 4876-4882.
26. Ting, C.S., Rocap, G., King, J. and Chisholm, S.W. (2002) Cyanobacterial photosynthesis in the oceans: the origins and significance of divergent light-harvesting strategies. Trends Microbiol. 10: 134-142.
27. Tomitani, A., Okada, K., Miyashita, H., Matthijs, H.C., Ohno, T. and Tanaka, A. (1999) Chlorophyll b and phycobilins in the common ancestor of cyanobacteria and chloroplasts. Nature 400: 159-162.
28. Urbach, E., Scanlan, D.J., Distel, D.J., Waterbury, J.B. and Chisholm, S.W. (1998) Rapid diversification of marine picophytoplankton with dissimilar light-harvesting structures inferred from sequence of Prochlorococcus and Synechococcus (Cyanobacteria). J. Mol. Evol. 46: 188-201.
29. West, N.J. and Scanlan, D.J. (1999) Niche-partitioning of Prochlorococcus populations in a stratified water column in the eastern North Atlantic Ocean. Appl. Environ. Microbiol. 65: 2585-2591.
30. Williams, J.G. (1988) Construction of specific mutations in photosystem II photosynthetic reaction center by genetic engineering methods in Synechosystis. Methods Enzymol. 167: 766-778.
31. Zapata, M. (2000) Separation of chlorophylls and carotenoids from marine phytoplankton: a new HPLC method using a reversed phase C8 column and pyridine-containing mobile phases. Mar. Ecol. Prog. Ser. 29-45.