Distant sequences determine 5′ end formation of cox3 transcripts in Arabidopsis thaliana ecotype C24

Nucleic Acids Research

Volumn 33, Issue 15, 2005, Pages 4673-4682

  Forner, Joachim ^a   Weber, Bärbel ^a   Wiethölter, Caterina ^a   Meyer, Rhonda C ^b   Binder, Stefan ^a  

^a UNIVERSITY OF ULM   (Germany)

^b MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLOOXYGENASE 3; GENE PRODUCT; MESSENGER RNA; MITOCHONDRIAL DNA; PLANT RNA; ARABIDOPSIS PROTEIN; ATP9 PROTEIN, ARABIDOPSIS; MITOCHONDRIAL PROTEIN; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE;

ARABIDOPSIS; ARTICLE; COX3 GENE; ECOTYPE; GENE; GENE SEQUENCE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOME ANALYSIS; MITOCHONDRION; NONHUMAN; PLANT GENETICS; PRIORITY JOURNAL; BIOSYNTHESIS; CELL NUCLEUS; CHEMISTRY; DNA FLANKING REGION; GENE ORDER; GENETICS; METABOLISM; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; SOUTHERN BLOTTING;

ARABIDOPSIS THALIANA;

5' FLANKING REGION; ARABIDOPSIS; ARABIDOPSIS PROTEINS; BASE SEQUENCE; BLOTTING, SOUTHERN; CELL NUCLEUS; DNA, MITOCHONDRIAL; GENE ORDER; MITOCHONDRIAL PROTEINS; MITOCHONDRIAL PROTON-TRANSLOCATING ATPASES; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA, MESSENGER; VARIATION (GENETICS);

EID: 23844437407     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki774     Document Type: Article

References (44)

1. Unseld,M., Marienfeld,J.R., Brandt,P. and Brennicke,A. (1997) The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nature Genet., 15, 57-61.
2. Notsu,Y., Masood,S., Nishikawa,T., Kubo,N., Akiduki,G., Nakazono,M., Hirai,A. and Kadowaki,K. (2002) The complete sequence of the rice ( Oryza sativa L.) mitochondrial genome: Frequent DNA sequence acquisition and loss during the evolution of flowering plants. Mol. Genet. Genomics, 268, 434-445.
3. Kubo,T., Nishizawa,S., Sugawara,A., Itchoda,N., Estiati,A. and Mikami,T. (2000) The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNA(Cys)(GCA). Nucleic Acids Res., 28, 2571-2576.
4. Handa,H. (2003) The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana. Nucleic Acids Res., 31, 5907-5916.
5. Rapp,W.D. and Stern,D.B. (1992) A conserved 11 nucleotide sequence contains an essential promoter element of the maize mitochondrial atp1 gene. EMBO J., 11, 1065-1073.
6. Dombrowski,S., Hoffmann,M., Guha,C. and Binder,S. (1999) Continuous primary sequence requirements in the 18-nucleotide promoter of dicot plant mitochondria. J. Biol. Chem., 274, 10094-10099.
7. Hoffmann,M. and Binder,S. (2002) Functional importance of nucleotide identities within the pea atp9 mitochondrial promoter sequence. J. Mol. Biol., 320, 943-950.
8. Kühn,K., Weihe,A. and Borner,T. (2005) Multiple promoters are a common feature of mitochondrial genes in Arabidopsis. Nucleic Acids Res., 33, 337-346.
9. Hoffmann,M., Kuhn,J., Däschner,K. and Binder,S. (2001) The RNA world of plant mitochondria. Prog. Nucleic Acid Res. Mol. Biol., 70 119-154.
10. Kuhn,J., Tengler,U. and Binder,S. (2001) Transcript lifetime is balanced between stabilizing stem-loop structures and degradation-promoting polyadenylation in plant mitochondria. Mol. Cell. Biol., 21, 731-742.
11. Dombrowski,S., Brennicke,A. and Binder,S. (1997) 3′-Inverted repeats in plant mitochondrial mRNAs are processing signals rather than transcription terminators. EMBO J., 16, 5069-5076.
12. Gagliardi,D. and Leaver,C.J. (1999) Polyadenylation accelerates the degradation of the mitochondrial mRNA associated with cytoplasmic male sterility in sunflower. EMBO J., 18, 3757-3766.
13. Gagliardi,D., Perrin,R., Marechal-Drouard,L., Grienenberger,J.M. and Leaver,C.J. (2001) Plant mitochondrial polyadenylated mRNAs are degraded by a 3′- to 5′ exoribonuclease activity, which proceeds unimpeded by stable secondary structures. J. Biol. Chem., 276, 43541-43547.
14. Lupold,D.S., Caoile,A.G. and Stern,D.B. (1999) Polyadenylation occurs at multiple sites in maize mitochondrial cox2 mRNA and is independent of editing status. Plant Cell, 11, 1565-1578.
15. Bollenbach,T.J., Lange,H., Gutierrez,R., Erhardt,M., Stern,D.B. and Gagliardi, D. (2005) RNR1, a 3′-5′ exoribonuclease belonging to the RNR superfamily, catalyzes 3′ maturation of chloroplast ribosomal RNAs in Arabidopsis thaliana. Nucleic Acids Res., 33, 2751-2763.
16. Perrin,R., Meyer,E.H., Zaepfel,M., Kim,Y.J., Mache,R., Grienenberger,J.M., Gualberto,J.M. and Gagliardi,D. (2004) Two exoribonucleases act sequentially to process mature 3′-ends of atp9 mRNAs in Arabidopsis mitochondria. J. Biol. Chem., 279 25440-25446.
17. Marchfelder,A. (1995) Plant mitochondrial RNase P. Mol. Biol. Rep. 22, 151-156.
18. Perrin,R., Lange,H., Grienenberger,J.M. and Gagliardi,D. (2004) AtmtPNPase i s required for multiple aspects of the 18S rRNA metabolism in Arabidopsis thaliana mitochondria. Nucleic Acids Res., 32, 5174-5482.
19. Schuster,W. and Brennicke,A. (1989) Conserved sequence elements at putative processing sites in plant mitochondria. Curr. Genet., 15, 187-192.
20. Marchfelder,A. and Binder,S. (2004) Plastid and plant mitochondrial RNA processing and RNA stability. In Daniell,H. and Chase,C. (eds), Molecular Biology and Biotechnolgy of Plant Organelles. Springer, Dordrecht, Netherlands, pp. 261-294.
21. Meyer,R.C., Torjek,O., Becher,M. and Altmann,T. (2004) Heterosis of biomass production in Arabidopsis. Establishment during early development. Plant Physiol., 134, 1813-1823.
22. Klein,M., Binder,S. and Brennicke,A. (1998) Purification of mitochondria from Arabidopsis. Methods Mol. Biol., 82, 49-53.
23. Binder,S. (1995) Mitochondrial nucleic acid purification and analysis. Methods Mol. Biol., 49, 383-389.
24. Sambrook,J., Fritsch,E.F. and Maniatis,T. (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Habror Laboratory Press, Cold Spring Harbor, NY.
25. Kuhn,J. and Binder,S. (2002) RT-PCR analysis of 5′ to 3′-end-ligated mRNAs identifies the extremities of cox2 transcripts in pea mitochondria. Nucleic Acids Res., 30, 439-446.
26. Tatusova,T.A. and Madden,T.L. (1999) BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett., 174, 247-250.
27. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
28. Lin,X., Kaul,S., Rounsley,S., Shea,T.P., Benito,M.I., Town,C.D., Fujii,C.Y., Mason,T., Bowman,C.L., Barnstead,M. et al. (1999) Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature, 402, 761-768.
29. Stupar,R.M., Lilly,J.W., Town,C.D., Cheng,Z., Kaul,S., Buell,C.R. and Jiang,J. (2001) Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: Implication of potential sequencing errors caused by large-unit repeats. Proc. Natl Acad. Sci. USA, 98, 5099-5103.
30. Knoop, V. (2004) The mitochondrial DNA of land plants: Peculiarities in phylogenetic perspective. Curr. Genet., 46, 123-139.
31. Small,I., Isaac,P.C. and Leaver,C.J. (1987) Stoichiometric differences in DNA molecules containing the atpA gene suggest mechanisms for the generation of mitochondrial diversity in maize. EMBO J., 6, 865-869.
32. Small,I., Suffolk,R. and Leaver,C.J. (1989) Evolution of plant mitochondrial genomes via substoichiometric intermediates. Cell, 58, 69-76.
33. Jander,G., Norris,S.R., Rounsley,S.D., Bush,D.F., Levin,I.M. and Last,R.L. (2002) Arabidopsis map-based cloning in the post-genome era. Plant Physiol., 129, 440-450.
34. Schmid,K.J., Sorensen,T.R., Stracke,R., Torjek,O., Altmann,T., Mitchell-Olds,T. and Weisshaar,B. (2003) Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Res., 13, 1250-1257.
35. Andre,C., Levy,A. and Walbot,V. (1992) Small repeated sequences and the structure of plant mitochondrial genomes. Trends Genet., 8, 128-132.
36. Manna,E. and Brennicke,A. (1986) Site-specific circularization at an intragenic sequence in Oenothera mitochondria. Mol. Gen. Genet. 203, 377-381.
37. Sato,S., Nakamura,Y., Kaneko,T., Asamizu,E. and Tabata,S. (1999) Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res., 6, 283-290.
38. Sakamoto,W., Kondo,H., Murata,M. and Motoyoshi,F. (1996) Altered mitochondrial gene expression in a maternal distorted leaf mutant of Arabidopsis induced by chloroplast mutator. Plant Cell, 8 1377-1390.
39. Martinez-Zapater,J.M., Gil,P., Capel,J. and Somerville,C.R. (1992) Mutations at the Arabidopsis CHM locus promote rearrangements of the mitochondrial genome. Plant Cell, 4, 889-899.
40. Abdelnoor,R.V., Yule,R., Elo,A., Christensen,A.C., Meyer-Gauen,G. and Mackenzie,S.A. (2003) Substoichiometric shifting in the plant mitochondrial genome is influenced by a gene homologous to MutS. Proc. Natl Acad. Sci. USA, 100, 5968-5973.
41. Janska,H., Sarria,R., Woloszynska,M., Arrieta-Montiel,M. and Mackenzie,S.A. (1998) Stoichiometric shifts in the common bean mitochondrial genome leading to male sterility and spontaneous reversion to fertility. Plant Cell, 10, 1163-1180.
42. Mackenzie,S. and McIntosh,L. (1999) Higher plant mitochondria. Plant Cell, 11, 571-586.
43. Ullrich,H., Lattig,K., Brennicke,A. and Knoop,V. (1997) Mitochondrial DNA variations and nuclear RFLPs reflect different genetic similarities among 23 Arabidopsis thaliana ecotypes. Plant Mol. Biol., 33, 37-45.
44. Marker,C., Zemann,A., Terhorst,T., Kiefmann,M., Kastenmayer,J.P., Green,P., Bachellerie,J.P., Brosius,J. and Huttenhofer,A. (2002) Experimental RNomics: Identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana. Curr. Biol., 12, 2002-2013.