The Copy Number of Chloroplast Gene Minicircles Changes Dramatically with Growth Phase in the Dinoflagellate Amphidinium operculatum

Protist

Volumn 158, Issue 1, 2007, Pages 89-103

  Koumandou, V L ^a   Howe, Christopher J ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

biogenesis; Dinophyceae; organelle; photosystem; plasmid; plastid

Indexed keywords

ALGAE; AMPHIDINIUM OPERCULATUM; DINOPHYCEAE;

EID: 33845710553     PISSN: 14344610     EISSN: 16180941     Source Type: Journal    
DOI: 10.1016/j.protis.2006.08.003     Document Type: Article

References (42)

1. Allen J.F., and Raven J.A. Free-radical-induced mutation vs redox regulation: costs and benefits of genes in organelles. J Mol Evol 42 (1996) 482-492
2. Allen J.R., Roberts T.M., Loeblich A.R.I., and Klotz L.C. Characterization of the DNA from the dinoflagellate Crypthecodinium cohnii and implications for nuclear organization. Cell 6 (1975) 161-169
3. Bachvaroff T.R., Concepcion G.T., Rogers C.R., Herman E.M., and Delwiche C.F. Dinoflagellate expressed sequence tag data indicate massive transfer of chloroplast genes to the nuclear genome. Protist 155 (2004) 65-78
4. Barbrook A.C., and Howe C.J. Minicircular plastid DNA in the dinoflagellate Amphidinium operculatum. Mol Gen Genet 263 (2000) 152-158
5. Barbrook A.C., Symington H., Nisbet R.E.R., Larkum A., and Howe C.J. Organisation and expression of the plastid genome of the dinoflagellate Amphidinium operculatum. Mol Genet Genomics 266 (2001) 632-638
6. Bendich A.J. Why do chloroplasts and mitochondria contain so many copies of their genome?. BioEssays 6 (1987) 279-282
7. Birky Jr. C.W. Relaxed cellular controls and organelle heredity. Science 222 (1983) 468-475
8. Coleman A.W., and Nerozzi A.M. Temporal and spatial coordination of cells with their plastid component. Int Rev Cytol 193 (1999) 125-164
9. Galleron C., and Durrand A.M. Cell cycle and DNA synthesis in a marine dinoflagellate Amphidinium carterae. Protoplasma 100 (1979) 155-165
10. Green B.R. The chloroplast genome of dinoflagellates - a reduced instruction set?. Protist 155 (2004) 23-31
11. Guillard R.R.L. Division Rates. In: Stein J.R. (Ed). Handbook of Phycological Methods: Culture Methods and Growth Measurements (1973), Cambridge University Press, Cambridge pp 289-320
12. Hackett J.D., Yoon H.S., Soares M.B., Bonaldo M.F., Casavant T.L., Scheetz T.E., Nosenko T., and Bhattacharya D. Migration of the plastid genome to the nucleus in a peridinin dinoflagellate. Curr Biol 14 (2004) 213-218
13. Holm-Hansen O. Algae: amounts of DNA and organic carbon in single cells. Science 163 (1969) 87-88
14. Howe C.J., Barbrook A.C., Koumandou V.L., Nisbet R.E.R., Symington H.A., and Wightman T.F. Evolution of the chloroplast genome. Philos Trans R Soc Lond B 358 (2003) 99-107
15. Koumandou V.L., Nisbet R.E.R., Barbrook A.C., and Howe C.J. The dinoflagellate chloroplast genome: where have all the genes gone?. Trends Genet 20 (2004) 261-267
16. Laatsch T., Zauner S., Stoebe-Maier B., Kowallik K.V., and Maier U.-G. Plastid-derived single gene minicircles of the dinoflagellate Ceratium horridum are localized in the nucleus. Mol Biol Evol 21 (2004) 1318-1322
17. LaJeunesse T.C., Lambert G., Andersen R.A., Coffroth M.A., and Galbraith D.W. Symbiodinium (Pyrrhophyta) genome sizes (DNA content) are smallest among dinoflagellates. J Phycol 41 (2005) 880-886
18. Landry M.R., Brown S.L., Neveux J., Dupouy C., Blanchot J., Christensen S., and Bidigare R.R. Phytoplankton growth and microzooplankton grazing in high-nutrient, low-chlorophyll waters of the equatorial Pacific: community and taxon-specific rate assessments from pigment and flow cytometric analyses. J Geophys Res 108 (2003) 8142
19. Lawrence M.E., and Possingham J.V. Microspectrofluorometric measurement of chloroplast DNA in dividing and expanding leaf cells of Spinacea oleracea. Plant Physiol 81 (1986) 708-710
20. Le Q.H., Markovic P., Hastings J.W., Jovine R.V.M., and Morse D. Structure and organisation of the peridinin-chlorophyll a-binding protein gene in Gonyaulax polyedra. Mol Gen Genet 255 (1997) 595-604
21. Lee D.Y., and Clayton D.A. Initiation of mitochondrial DNA replication by transcription and R-loop processing. J Biol Chem 273 (1998) 30614-30621
22. Leighfield T.A., and Van Dolah F.M. Cell cycle regulation in a dinoflagellate, Amphidinium operculatum: identification of the diel entraining cue and a possible role for cyclic AMP. J Exp Mar Biol Ecol 262 (2001) 177-197
23. Maguire M.J., Goff L.J., and Coleman A.W. In situ plastid and mitochondrial DNA determination: implication of the observed minimal plastid number. Am J Bot 82 (1995) 1496-1506
24. Martin W., Stoebe B., Goremykin V., Hansmann S., Hasegawa M., and Kowallik K.V. Gene transfer to the nucleus and the evolution of chloroplasts. Nature 393 (1998) 162-165
25. Nakamura S., Itoh S., and Kuroiwa T. Behavior of chloroplast nucleus during chloroplast development and degeneration in Chlamydomonas reinhardtii. Plant Cell Physiol 27 (1986) 775-784
26. Nisbet RER (2004). The Chloroplast Genome of the Dinoflagellate Amphidinium operculatum. PhD thesis, University of Cambridge
27. Nisbet R.E.R., Koumandou V.L., Barbrook A.C., and Howe C.J. Novel plastid gene minicircles in the dinoflagellate Amphidinium operculatum. Gene 331 (2004) 141-147
28. Oldenburg D.J., and Bendich A.J. Changes in the structure of DNA molecules and the amount of DNA per plastid during chloroplast development in maize. J Mol Biol 344 (2004) 1311-1330
29. Rizzo P.J. Biochemistry of the Dinoflagellate Nucleus. In: Taylor F.J.R. (Ed). The Biology of Dinoflagellates (1987), Blackwell Scientific Publications, Oxford pp 143-173
30. Rowan B., Oldenburg D.J., and Bendich A.J. The demise of chloroplast DNA in Arabidopsis. Curr Genet 46 (2004) 176-181
31. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning: A Laboratory Manual. 2nd ed (1989), Cold Spring Harbor Press, Cold Spring Harbor
32. Schinkel A.H., and Tabak H.F. Mitochondrial RNA polymerase: dual role in transcription and replication. Trends Genet 5 (1989) 149-154
33. Shaver J.M., Oldenburg D.J., and Bendich A.J. Changes in chloroplast DNA during development in tobacco, Medicago truncatula, pea, and maize. Planta 224 (2006) 72-82
34. Sorhannus U., and Fox M. Synonymous and nonsynonymous substitution rates in diatoms: a comparison between chloroplast and nuclear genes. J Mol Evol 48 (1999) 209-212
35. Steele R.E., and Rae P.M.M. Ordered distribution of modified bases in the DNA of a dinoflagellate. Nucleic Acids Res 8 (1980) 4709-4725
36. Stoebe B., and Kowallik K.V. Gene-cluster analysis in chloroplast genomics. Trends Genet 15 (1999) 344-347
37. Sugiura M. The chloroplast genome. Plant Mol Biol 19 (1992) 149-168
38. Takishita K., Ishikura M., Koike K., and Maruyama T. Comparison of phylogenies based on nuclear-encoded SSU rDNA and plastid-encoded psbA in the symbiotic dinoflagellate genus Symbiodinium. Phycologia 42 (2003) 285-291
39. Wang Y., Jensen L., Horjup P., and Morse D. Synthesis and degradation of dinoflagellate plastid-encoded psbA proteins are light-regulated not circadian-regulated. Proc Natl Acad Sci USA 102 (2005) 2844-2849
40. Wolfe K.H., Li W.-H., and Sharp P.M. Rates of nucleotide subsitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA 84 (1987) 9054-9058
41. Zhang Z., Green B.R., and Cavalier-Smith T. Single gene circles in dinoflagellate chloroplast genomes. Nature 400 (1999) 155-159
42. Zhang Z., Green B.R., and Cavalier-Smith T. Phylogeny of ultra-rapidly evolving dinoflagellate chloroplast genes: a possible common origin for sporozoan and dinoflagellate plastids. J Mol Evol 51 (2000) 26-40