An evolutionarily conserved translation initiation mechanism regulates nuclear or mitochondrial targeting of DNA ligase 1 in Arabidopsis thaliana

Plant Journal

Volumn 47, Issue 3, 2006, Pages 356-367

  Sunderland, Paul A ^a   West, Christopher E ^a,b   Waterworth, Wanda M ^a   Bray, Clifford M ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

Arabidopsis; DNA ligase; Mitochondria; Targeting; Translational control

Indexed keywords

FLUORESCENCE; LASERS; MICROSCOPIC EXAMINATION; PROTEINS; SCANNING; SYNTHESIS (CHEMICAL);

ARABIDOPSIS; DNA LIGASE; MITOCHONDRIA; TARGETING; TRANSLATIONAL CONTROL;

DNA;

ARABIDOPSIS PROTEIN; GREEN FLUORESCENT PROTEIN; HYBRID PROTEIN; ISOPROTEIN; MESSENGER RNA; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE (ATP); SIGNAL PEPTIDE;

ARABIDOPSIS; ARTICLE; BIOSYNTHESIS; CELL NUCLEUS; CHEMISTRY; CHLOROPLAST; ENZYMOLOGY; GENETICS; METABOLISM; MITOCHONDRION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEAR LOCALIZATION SIGNAL; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PROTEIN SECONDARY STRUCTURE; PROTEIN TRANSPORT; RNA TRANSLATION; START CODON; ULTRASTRUCTURE;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; BASE SEQUENCE; CELL NUCLEUS; CHLOROPLASTS; CODON, INITIATOR; DNA LIGASES; EVOLUTION, MOLECULAR; GREEN FLUORESCENT PROTEINS; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; NUCLEAR LOCALIZATION SIGNALS; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; PROTEIN ISOFORMS; PROTEIN SORTING SIGNALS; PROTEIN STRUCTURE, SECONDARY; PROTEIN TRANSPORT; RECOMBINANT FUSION PROTEINS; RNA, MESSENGER;

NUCLEIC ACIDS;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 33745808015     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2006.02791.x     Document Type: Article

References (38)

1. van Attikum, H., Bundock, P., Overmeer, R.M., Lee, L.-Y., Gelvin, S.B. and Hooykaas, P.J.J. (2003) The Arabidopsis AtLIG4 gene is required for the repair of DNA damage, but not for the integration of Agrobacterium T-DNA. Nucleic Acids Res. 31, 4247-4255.
2. Babiychuk, E., Cottrill, P.B., Storozhenko, S., Fuanthong, M., Chen, Y., O'Farrell, M.K., Inzé, D. and Kushnin, S. (1998) Higher plants possess two structurally different poly (ADP-ribose) polymerases. Plant J. 15, 635-645.
3. Bonatto, D., Revers, L.F., Brendel, M. and Henriques, J.A.P. (2005) The eukaryotic Pso2/Snm1/Atremis proteins and their function as genomic and cellular caretakers. Braz. J. Med. Biol. Res. 38, 321-334.
4. Caldecott, K.W. (2001) Mammalian single strand break repair: an X-ra(y)ted affair. Bioessays, 23, 447-455.
5. Chabregas, S.M., Luche, D.D., Van Sluys, M.-A., Menck, C.F.M. and Silva-Filho, M.C. (2003) Differential usage of two in-frame translational start codons regulates subcellular localisation of Arabidopsis thaliana THI1. J. Cell Sci. 116, 285-291.
6. Christophe, D., Christophe-Hobertus, C. and Pichon, B. (2000) Nuclear targeting of proteins: how many different signals? Cell. Signal. 12, 337-341.
7. Claros, M.G. and Vincens, P. (1996) Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur. J. Biochem. 241, 779-786.
8. Clough, S.J. and Bent, A.F. (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735-743.
9. Kip1 gene is conserved in human and mouse and produces a long 5′-UTR. BMC Mol. Biol. 2, 12 (http://www.biomedcentral.eom/1471-2199/2/12).
10. Davis, S.J. and Vierstra, R.D. (1998) Soluble highly fluorescent variants of green fluorescent protein (GFP) for use in higher plants. Plant Mol. Biol. 36, 521-528.
11. Donahue, S.L., Corner, B.E., Bordone, L. and Campbell, C. (2001) Mitochondrial DNA ligase function in Saccharomyces cerevisiae. Nucleic Acids Res. 29, 1582-1589.
12. Friesner, J. and Britt, A.B. (2003) Ku80- and DNA ligase IV-deficient plants are sensitive to ionizing radiation and defective in T-DNA integration. Plant J. 34, 427-440.
13. Hasseloff, J., Siemering, K.R., Prasher, D.C. and Hodge, S. (1997) Removal of a cryptic intron and subcellular localization of green fluorescent protein are required to mark transgenic Arabidopsis plants brightly. Proc. Natl Acad. Sci. USA, 94, 2122-2127.
14. Hedtke, B., Borner, T. and Weihe, A. (2000) One RNA polymerase serving two genomes. EMBO Rep. 1, 435-440.
15. Jiang, Q. (2001) The role of Arabidopsis photolyases and DNA ligases in the repair of DNA damage. PhD Thesis. The University of Manchester, Manchester, UK.
16. Jones, D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202.
17. Kozak, M. (1987) An analysis of 5′ non-coding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res. 15, 8125-8148.
18. Kozak, M. (1997) Recognition of AUG and alternative initiator codons is augmented by a G in position +4 but is not generally affected by the nucleotides in positions +5 and +6. EMBO J. 16, 2482-2492.
19. Kozak, M. (2002) Pushing the limits of the scanning mechanism for initiation of translation. Gene, 299, 1-34.
20. Lakshmipathy, U. and Campbell, C. (1999) The human DNA ligase III gene encodes nuclear and mitochondrial proteins. Mol. Cell. Biol. 19, 3869-3876.
21. Lindahl, T. (1993) Instability and decay of the primary structure of DNA. Nature, 362, 709-715.
22. Martin, I.V. and MacNeill, S.A. (2004) Functional analysis of subcellular localisation and protein-protein interaction sequences in the essential DNA ligase I protein of fission yeast. Nucleic Acids Res. 32, 632-642.
23. Maruyama, K. and Sugano, S. (1994) Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene, 138, 171-174.
24. Merkle, T. (2001) Nuclear import and export of proteins in plants: a tool for the regulation of signalling. Planta, 213, 499-517.
25. Murashige, T. and Skoog, F. (1962) A revised medium for rapid growth and bioassays with tobacco tissue culture. Physiol. Plant. 18, 100-127.
26. Nakai, K. and Kanehisa, M. (1991) Expert system for predicting protein localization sites in Gram-negative bacteria. Proteins, 11, 95-110.
27. Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
28. Schaefer, B.C. (1995) Revolutions in rapid amplification of cDNA ends: new strategies for polymerase chain reaction cloning of full length cDNA ends. Anal. Biochem. 227, 255-273.
29. Small, I., Wintz, H., Akashi, K. and Mireau, M. (1998) Two birds with one stone: genes that encode products targeted to two or more compartments. Plant Mol. Biol. 38, 265-277.
30. Sunderland, P.A., West, C.E., Waterworth, W.M. and Bray, C.M. (2004) Choice of start codon in a single transcript determines DNA ligase 1 isoform production and intracellular targeting in Arabidopsis thaliana. Biochem. Soc. Trans. 32, 614-616.
31. Taylor, R.M., Hamer, M.J., Rosamond, J. and Bray, C.M. (1998) Molecular cloning and functional analysis of the Arabidopsis thaliana DNA ligase I homologue. Plant J. 15, 75-81.
32. The Arabidopsis genome initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
33. Tomkinson, A.E. and Mackey, Z.B. (1998) Structure and function of mammalian DNA ligases. Mutat. Res. 407, 1-9.
34. Von Heijne, G. (1986) Mitochondrial targeting sequences may form amphiphilic helices. EMBO J. 5, 1335-1342.
35. Wang, L. and Wessler, S.R. (2001) Role of mRNA secondary structure in translational repression of the maize transcriptional activator Lc. Plant Physiol. 125, 1380-1387.
36. Watanabe, N., Che, F.-S., Iwano, M., Takayama, S., Yoshida, S. and Isogai, A. (2001) Dual targeting of spinach proteporphyrinogen oxidase II to mitochondria and chloroplasts by alternative use of two in-frame initiation codons. J. Biol. Chem. 276, 20474-20481.
37. West, C.E., Waterworth, W.M., Jiang, Q. and Bray, C.M. (2000) Arabidopsis DNA ligase IV is induced by γ-irradiation and interacts with an Arabidopsis homologue of the double strand break repair protein XRCC4. Plant J. 24, 67-78.
38. Willer, M., Rainey, M., Pullen, T. and Stirling, C.J. (1999) The yeast CDC9 gene encodes both a nuclear and mitochondrial form of DNA ligase I. Curr. Biol. 9, 1085-1094.