Polyuridylylation and processing of transcripts from multiple gene minicircles in chloroplasts of the dinoflagellate Amphidinium carterae

Plant Molecular Biology

Volumn 79, Issue 4-5, 2012, Pages 347-357

  Barbrook, Adrian C ^a   Dorrell, Richard G ^a   Burrows, Jennifer ^a   Plenderleith, Lindsey J ^a   Nisbet, R Ellen R ^a,b   Howe, Christopher J ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF SOUTH AUSTRALIA   (Australia)

Author keywords

Chloroplast; Minicircles; PolyU; Protist; Transcript processing

Indexed keywords

CIRCULAR DNA; POLYURIDYLIC ACID; PROTOZOAL DNA; PROTOZOAL RNA;

ARTICLE; BIOLOGICAL MODEL; CHLOROPLAST; CHLOROPLAST GENE; DINOFLAGELLATE; GENE; GENETICS; METABOLISM; RNA PROCESSING;

CHLOROPLASTS; DINOFLAGELLIDA; DNA, CIRCULAR; DNA, PROTOZOAN; GENES, CHLOROPLAST; GENES, PROTOZOAN; MODELS, BIOLOGICAL; POLY U; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, PROTOZOAN;

AMPHIDINIUM CARTERAE; DINOPHYCEAE; EUKARYOTA; HETEROCAPSA; PROTISTA;

EID: 84862007700     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-012-9916-z     Document Type: Article

References (49)

1. Aphasizheva I, Aphasizhev R (2010) RET1-catalyzed uridylylation shapes the mitochondrial transcriptome in Trypanosoma brucei. Mol Cell Biol 30: 1555-1567.
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 Genom 266: 632-638.
4. Barbrook AC, Santucci N, Plenderleith LJ, Hiller RG, Howe CJ (2006) Comparative analysis of dinoflagellate chloroplast genomes reveals rRNA and tRNA genes. BMC Genomics 7: 297.
5. Barkan A (2011) Expression of plastid genes: organelle-specific elaborations on a prokaryotic scaffold. Plant Physiol 155: 1520-1532.
6. Barkan A, Walker M, Nolasco M, Johnson D (1994) A nuclear mutation in maize blocks the processing and translation of several chloroplast mRNAs and provides evidence for the differential translation of alternative mRNA forms. EMBO J 13: 3170-3181.
7. Dang Y, Green BR (2009) Substitutional editing of Heterocapsa triquetra chloroplast transcripts and a folding model for its divergent chloroplast 16S rRNA. Gene 442: 73-80.
8. Dang YK, Green BR (2010) Long transcripts from dinoflagellate chloroplast minicircles suggest "rolling circle" transcription. J Biol Chem 285: 5196-5203.
9. Fujiwara S, Iwahashi H, Someya J, Nishikawa S, Minaka N (1993) Structure and cotranscription of the plastid-encoded rbcL and rbcS genes of Pleurochrysis carterae (Prymnesiophyta). J Phycol 29: 347-355.
10. Gabrielsen TM, Minge MA, Espelund M, Tooming-Klunderud A, Patil V, Nederbragt AJ, Otis C, Turmel M, Shalchian-Tabrizi K, Lemieux C, Jakobsen KS (2011) Genome evolution of a tertiary dinoflagellate plastid. PLos One 6: e19132.
11. Georg J, Honsel A, Voss B, Rennenberg H, Hess WR (2010) A long antisense RNA in plant chloroplasts. New Phytol 186: 615-622.
12. Green BR (2011) Chloroplast genomes of photosynthetic eukaryotes. Plant J 66: 34-44.
13. Gruissem W (1989) Chloroplast gene-expression-how plants turn their plastids on. Cell 56: 161-170.
14. 559 alpha) genes in tandem in Amphidinium carterae plastid DNA. FEBS Lett 505: 449-452.
15. Hoch B, Maier RM, Appel K, Igloi GL, Kössel H (1991) Editing of a chloroplast messenger-RNA by creation of an initiation codon. Nature 353: 178-180.
16. Hoppenrath M, Leander BS (2010) Dinoflagellate phylogeny as inferred from heat shock protein 90 and ribosomal gene sequences. PLoS One 5: e13220.
17. Hotto AM, Huston ZE, Stern DB (2010) Overexpression of a natural chloroplast-encoded antisense RNA in tobacco destabilizes 5S rRNA and retards plant growth. BMC Plant Biol 10: 213.
18. Howe CJ, Nisbet RER, Barbrook AC (2008) The remarkable chloroplast genome of dinoflagellates. J Exp Bot 59: 1035-1045.
19. Hwang SR, Tabita FR (1991) Cotranscription, deduced primary structure, and expression of the chloroplast-encoded rbcL and rbcS genes of the marine diatom Cylindrotheca sp strain-N1. J Biol Chem 266: 6271-6279.
20. Ibrahim F, Rymarquis LA, Kim EJ, Becker J, Balassa E, Green PJ, Cerutti H (2010) Uridylation of mature miRNAs and siRNAs by the MUT68 nucleotidyltransferase promotes their degradation in Chlamydomonas. Proc Nat Acad Sci USA 107: 3906-3911.
21. Iida S, Kobiyama A, Ogata T, Murakami A (2010) Differential DNA rearrangements of plastid genes, psbA and psbD, in two species of the dinoflagellate Alexandrium. Plant Cell Physiol 51: 1869-1877.
22. Imanian B, Pombert JF, Keeling PJ (2010) The complete plastid genomes of the two 'Dinotoms' Durinskia baltica and Kryptoperidinium foliaceum. PLoS One 5: e10711.
23. Jang YH, Park HY, Kim SK, Lee JH, Suh MC, Chung YS, Paek KH, Kim JK (2009) Survey of rice proteins interacting with OsFCA and OsFY Proteins which are homologous to the Arabidopsis flowering time proteins, FCA and FY. Plant Cell Physiol 50: 1479-1492.
24. Janouskovec J, Horak A, Obornik M, Lukes J, Keeling PJ (2010) A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids. Proc Nat Acad Sci USA 107: 10949-10954.
25. Kudla J, Hayes R, Gruissem W (1996) Polyadenylation accelerates degradation of chloroplast mRNA. EMBO J 15: 7137-7146.
26. Kyburz A, Friedlein A, Langen H, Keller W (2006) Direct interactions between subunits of CPSF and the U2 snRNP contribute to the coupling of pre-mRNA 3' end processing and splicing. Mol Cell 23: 195-205.
27. Lange H, Sement FM, Canaday J, Gagliardi D (2009) Polyadenylation-assisted RNA degradation processes in plants. Trends Plant Sci 14: 497-504.
28. McBride KE, Schaaf DJ, Daley M, Stalker DM (1994) Controlled expression of plastid transgenes in plants based on a nuclear DNA-encoded and plastid-targeted T7 RNA-polymerase. Proc Nat Acad Sci USA 91: 7301-7305.
29. Moore RB, Ferguson KM, Loh WKW, Hoegh-Guldberg C, 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. Nash EA, Barbrook AC, Edwards-Stuart RK, Bernhardt K, Howe CJ, Nisbet RER (2007) Organization of the mitochondrial genome in the dinoflagellate Amphidinium carterae. Mol Biol Evol 24: 1528-1536.
31. 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.
32. Nelson MJ, Dang YK, Filek E, Zhang ZD, Yu VWC, Ishida K, Green BR (2007) Identification and transcription of transfer RNA genes in dinoflagellate plastid minicircles. Gene 392: 291-298.
33. Nisbet RER, Koumandou VL, Barbrook AC, Howe CJ (2004) Novel plastid gene minicircles in the dinoflagellate Amphidinium operculatum. Gene 331: 141-147.
34. Nisbet RER, Hiller RG, Barry ER, Skene P, Barbrook AC, Howe CJ (2008) Transcript analysis of dinoflagellate plastid gene minicircles. Protist 159: 31-39.
35. Norbury CJ (2010) 3′ uridylation and the regulation of RNA function in the cytoplasm. Biochem Soc Trans 38: 1150-1153.
36. Pfalz J, Bayraktar OA, Prikryl J, Barkan A (2009) Site-specific binding of a PPR protein defines and stabilizes 5′ and 3′ mRNA termini in chloroplasts. EMBO J 28: 2042-2052.
37. Prikryl J, Rojas M, Schuster G, Barkan A (2011) Mechanism of RNA stabilization and translational activation by a pentatricopeptide repeat protein. Proc Nat Acad Sci USA 108: 415-420.
38. Rigo F, Martinson HG (2009) Polyadenylation releases mRNA from RNA polymerase II in a process that is licensed by splicing. RNA 15: 823-836.
39. Schmitz-Linneweber C, Small I (2008) Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci 13: 663-670.
40. Shalchian-Tabrizi K, Skanseng M, Ronquist F, Klaveness D, Bachvaroff TR, Delwiche CF, Botnen A, Tengs T, Jakobsen KS (2006) Heterotachy processes in rhodophyte-derived secondhand plastid genes: Implications for addressing the origin and evolution of dinoflagellate plastids. Mol Biol Evol 23: 1504-1515.
41. Shen B, Goodman HM (2004) Uridine addition after microRNA-directed cleavage. Science 306: 997.
42. Simon N, Cras AL, Foulon E, Lemee R (2009) Diversity and evolution of marine phytoplankton. Comptes Rendus Biologiques 332: 159-170.
43. Slomovic S, Portnoy V, Liveanu V, Schuster G (2006) RNA polyadenylation in prokaryotes and organelles; Different tails tell different tales. Crit Rev Plant Sci 25: 65-77.
44. Stern DB, Goldschmidt-Clermont M, Hanson MR (2010) Chloroplast RNA metabolism. Annu Rev Plant Biol 61: 125-155.
45. Walker G, Dorrell RG, Schlacht A, Dacks JB (2011) Eukaryotic systematics: a 2011 user's guide for cell biologists and parasitologists. Parasitology 138: 1638-1663.
46. Wang YL, Morse D (2006) Rampant polyuridylylation of plastid gene transcripts in the dinoflagellate Lingulodinium. Nucleic Acids Res 34: 613-619.
47. Zhang ZD, Green BR, Cavalier-Smith T (1999) Single gene circles in dinoflagellate chloroplast genomes. Nature 400: 155-159.
48. Zhang ZD, 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.
49. Zimmer SL, Schein A, Zipor G, Stern DB, Schuster G (2009) Polyadenylation in Arabidopsis and Chlamydomonas organelles: the input of nucleotidyltransferases, poly(A) polymerases and polynucleotide phosphorylase. Plant J 59: 88-99.