Identification of transcribed and persistent variants of the psbA gene carried by plastid minicircles in a dinoflagellate

Current Genetics

Volumn 55, Issue 5, 2009, Pages 583-591

  Iida, Satoko ^a   Kobiyama, Atsushi ^b   Ogata, Takehiko ^b   Murakami, Akio ^a  

^a KOBE UNIVERSITY   (Japan)

^b KITASATO UNIVERSITY   (Japan)

Author keywords

Dinoflagellate; Genome rearrangement; Heteroplasmy; Organelle; Photosystem II; Plastid genome

Indexed keywords

MESSENGER RNA; MINICIRCLE DNA; PROTEIN PSBA; PROTOZOAL PROTEIN; UNCLASSIFIED DRUG;

ALEXANDRIUM TAMARENSE; CONTROLLED STUDY; DINOFLAGELLATE; DNA RECOMBINATION; DNA REPLICATION; GENE IDENTIFICATION; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC CODE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHOTOSYSTEM II; PLASTID GENOME; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN VARIANT; PROTOZOAL GENETICS; REVIEW; RNA EDITING; RNA SPLICING; SEQUENCE ANALYSIS; START CODON; STOP CODON;

BASE SEQUENCE; DINOFLAGELLIDA; DNA PRIMERS; MOLECULAR SEQUENCE DATA; PHOTOSYSTEM II PROTEIN COMPLEX; PLASTIDS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

ALEXANDRIUM TAMARENSE; DINOPHYCEAE;

EID: 70349988281     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00294-009-0271-9     Document Type: Review

References (55)

1. Bachvaroff TR, Concepcion GT, Rogers CR, Herman EM, Delwiche CF (2003) Dinoflagellate expressed sequence tag data indicate massive transfer of chloroplast genes to the nuclear genome. Protist 155:65-78
2. Barbrook AC, Howe CJ (2000) Minicircular plastid DNA in the dinoflagellate Amphidinium operculatum. Mol Gen Genet 263:152-158
3. Barbrook AC, Symington H, Nisbet RER, Larkum A, Howe CJ (2001) Organisation and expression of the plastid genome of the dinoflagellate Amphidinium operculatum. Mol Genet Genomics 266:632-638
4. Barbrook AC, Visram S, Douglas AE, Howe CJ (2006a) Molecular diversity of dinoflagellate symbionts of Cnidaria: The psb A minicircle of Symbiodinium. Protist 157:159-171
5. Barbrook AC, Santucci N, Plenderleith LJ, Hiller RG, Howe CJ (2006b) Comparative analysis of dinoflagellate chloroplast genomes reveals rRNA and tRNA genes. BMC Genomics 7:297
6. Bedbrook JR, Kolodner R (1979) The structure of chloroplast DNA. Ann Rev Plant Physiol 30:593-620
7. Birky CW Jr (1983) Relaxed cellular controls and organelle heredity. Science 222:468-475
8. Birky CW Jr (2001) The inheritance of genes in mitochondria and chloroplasts: Laws, mechanisms and models. Annu Rev Genet 35:125-148
9. Bock R (2001) Transgenic plastids in basic research and plant biotechnology. J Mol Biol 312:425-438
10. Bock R (2007) Structure, function, and inheritance of plastid genomes. In: Bock R (ed) Cell and molecular biology of plastids. Topics in current genetics, vol 19. Springer, Berlin, pp 29-63
11. Day A, Madesis P (2007) DNA replication, recombination, and repair in plastids. In: Bock R (ed) Cell and molecular biology of plastids. Topics in current genetics, vol 19. Springer, Berlin, pp 65-119
12. Douglas S (1994) Chloroplast origins and evolution. In: Bryant DA (ed) The molecular biology of cyanobacteria. Kluwer, Dordrecht, pp 91-118
13. Golden S (1994) Light-responsive gene expression and the biochemistry of the photosystem II reaction center. In: Bryant DA (ed) The molecular biology of cyanobacteria. Kluwer, Dordrecht, pp 693-714
14. Green BR (2004) The chloroplast genome of dinoflagellates - a reduced instruction set? Protist 155:23-31
15. Hackett JD, Bhattacharya D (2006) The genomes of dinoflagellates. In: Katz LA, Bhattacharya D (eds) Genomics and evolution of microbial eukaryotes. Oxford University Press, New York, pp 48-63
16. Hackett JD, Yoon HS, Soares MB, Bonaldo MF, Casavant TL, Scheetz TE, Nosenko T, Bhattacharya D (2004) Migration of the plastid genome to the nucleus in a peridinin dinoflagellate. Curr Biol 14:213-218
17. Hackett JD, Scheetz TE, Yoon HS, Soares MB, Bonaldo MF, Casavant TL, Bhattacharya D (2005) Insights into a dinoflagellate genome through expressed sequence tag analysis. BMC Genomics 6:80
18. 559 α) genes in tandem in Amphidinium carterae plastid DNA. FEBS Lett 505:449-452
19. Howe CJ, Nisbet RER, Barbrook AC (2008) The remarkable chloroplast genome of dinoflagellates. J Exp Bot 59:1035-1045
20. Iida S, Kobiyama A, Ogata T, Murakami A (2008) The D1 and D2 proteins of dinoflagellates: Unusually accumulated mutations which influence on PSII photoreaction. Photosynth Res 98:415-425
21. Iwasaki H (1961) The life-cycle of Porphyra tenera in vitro. Biol Bull 121:173-187
22. Khakhlova O, Bock R (2006) Elimination of deleterious mutations in plastid genomes by gene conversion. Plant J 46:85-94
23. Kobiyama A, Ikeda Y, Koike K, Ogata T (2006) Isolation of a differentially expressed gene in separate mating types of the dinoflagellate A. tamarense. Eur J Phycol 42:183-190
24. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings Bioinformat 5:150-163
25. Laatsch T, Zauner S, Stoebe-Maier B, Kowallik KV, Maier U-G (2004) Plastid-derived single gene minicircles of the dinoflagellate Ceratium horridum are localized in the nucleus. Mol Biol Evol 21:1318-1322
26. Lajeunesse TC, Lambert G, Anderson RA, Coffroth MA, Galbraith DW (2005) Symbiodinium (Pyrrhophyta) genome sizes (DNA content) are smallest among dinoflagellates. J Phycol 41:880-886
27. Liu Y-G, Mitsukawa N, Oosumi T, Whittier RF (1995) Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junctions by thermal asymmetric interlaced PCR. Plant J 8:457-463
28. Maier RM, Schmitz-Linneweber C (2004) Plastid genomes. In: Daniel H, Chase CD (eds) Molecular biology and biotechnology of plant organelles. Springer, Dordrecht, pp 115-150
29. Moore RB, Ferguson KM, Loh WKW, Hoegh-Guldberg O, Carter DA (2003) Highly organized structure in the non-coding region of the psbA minicircle from clade C Symbiodinium. Int J Syst Evol Microbiol 53:1725-1734
30. Nelson MJ, Green BR (2005) Double hairpin elements and tandem repeats in the non-coding region of Adenoides eludens chloroplast gene minicircles. Gene 358:102-110
31. Nelson MJ, Dang Y, Filek E, Zhang Z, Yu VWC, Ishida K-I, Green BR (2007) Identification and transcription of transfer RNA genes in dinoflagellate plastid minicircles. Gene 392:291-298
32. Nisbet RER, Koumandou VL, Barbrook AC, Howe CJ (2004) Novel plastid gene minicircles in the dinoflagellate Amphidinium operculatum. Gene 331:141-147
33. Nisbet RER, Hiller RG, Barry ER, Skene P, Barbrook AC, Howe CJ (2008) Transcript analysis of dinoflagellate plastid gene minicircles. Protist 159:31-39
34. Palmer JD (1985) Comparative organization of chloroplast genomes. Ann Rev Genet 19:325-354
35. Palmer JD (2003) The symbiotic birth and spread of plastids: How many times and whodunit? J Phycol 39:4-11
36. Palmer JD, Delwiche CF (1998) The origin and evolution of plastids and their genomes. In: Soltis DE, Soltis PS, Doyle JJ (eds) Molecular systematics of plants II: DNA sequencing. Kluwer, Boston, pp 375-409
37. Rochaix JD (1995) Chlamydomonas reinhardtii as the photosynthetic yeast. Annu Rev Genet 29:209-230
38. Sambrook J, Russell DW (2001) Molecular cloning: A laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
39. Santos SR, Taylor DJ, Kinzie RA III, Sakai K, Coffroth MA (2002) Evolution of length variation and heteroplasmy in the chloroplast rDNA of symbiotic dinoflagellates (Symbiodinium, Dinophyta) and a novel insertion in the universal core region of the large subunit rDNA. Phycologia 41:311-318
40. Satoh K, Wydrzynski TJ, Govindjee (2005) Introduction to photosystem II. In: Wydrzynski TJ, Satoh K (eds) Advances in photosynthesis and respiration (vol 22). Photosystem II: The light-driven water: plastoquinone oxidoreductase. Springer, Dordrecht, pp 11-22
41. Shikanai T, Obokata J (2008) Machinery of RNA editing in plant organelles. In: Smith HC (ed)MRNA and DNA editing: molecular mechanisms and their integration into biological systems. Wiley, Hoboken, pp 99-119
42. Sicora CI, Appleton SE, Brown CM, Chung J, Chandler J, Cockshutt AM, Vass I, Campbell DA (2006) Cyanobacterial psbA families in Anabaena and Synechocystis encode trace, constitutive and UVB-induced D1 isoforms. Biochim Biophys Acta 1757:47-56
43. Sicora CI, Brown CM, Cheregi O, Vass I, Campbell DA (2008) The psbA gene family responds differentially to light and UVB stress in Gloeobacter violaceus PCC 7421, a deeply divergent cyanobacterium. Biochim Biophys Acta 1777:130-139
44. Simpson CL, Stern DB (2002) The treasure trove of algal chloroplast genomes. Surprises in architecture and gene content, and their functional implications. Plant Physiol 129:957-966
45. Stern DB, Gruissem W (1987) Control of plastid gene expression: 3′ inverted repeats act as mRNA processing and stabilizing elements, but do not terminate transcription. Cell 51:1145-1157
46. Sugiura M (1992) The chloroplast genome. Plant Mol Biol 19:149-168
47. Takishita K, Uchida A (1999) Molecular cloning and nucleotide sequence analysis of psb A from the dinoflagellates: Origin of the dinoflagellate plastid. Phycol Res 47:207-216
48. Waller RF, Patron NJ, Keeling PJ (2006) Phylogenetic history of plastid-targeted proteins in the peridinin-containing dinoflagellate Heterocapsa triquetra. Int J Syst Evol Microbiol 56:1439-1447
49. Wang Y, Morse D (2006a) The plastid-encoded psbA gene in the dinoflagellate Gonyaulax is not encoded on a minicircle. Gene 371:206-210
50. Wang Y, Morse D (2006b) Rampant polyuridylylation of plastid gene transcripts in the dinoflagellate Lingulodinium. Nucleic Acid Res 34:613-619
51. Zauner S, Greilinger D, Laatsch T, Kowallik KV, Maier U-G (2004) Substitutional editing of transcripts from genes of cyanobacterial origin in the dinoflagellate Ceratium horridum. FEBS Lett 577:535-538
52. Zhang Z, Green BR, Cavalier-Smith T (1999) Single gene circles in dinoflagellate chloroplast genomes. Nature 400:155-159
53. Zhang Z, Cavalier-Smith T, Green BR (2001) A family of selfish minicircular chromosomes with jumbled chloroplast gene fragments from a dinoflagellate. Mol Biol Evol 18:1558-1565
54. Zhang Z, Cavalier-Smith T, Green BR (2002) Evolution of dinoflagellate unigenic minicircles and the partially concerted divergence of their putative replicon origins. Mol Biol Evol 19:489-500
55. Zoschke R, Liere K, Börner T (2007) From seedling to mature plant: Arabidopsis plastidial genome copy number, RNA accumulation and transcription are differentially regulated during leaf development. Plant J 50:710-722