Actinidia DRM1 - An Intrinsically Disordered Protein Whose mRNA Expression Is Inversely Correlated with Spring Budbreak in Kiwifruit

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Wood, Marion ^a   Rae, Georgina M ^a   Wu, Rong Mei ^a   Walton, Eric F ^b   Xue, Bin ^c   Hellens, Roger P ^a   Uversky, Vladimir N ^c,d  

^a THE NEW ZEALAND INSTITUTE FOR PLANT AND FOOD RESEARCH LIMITED   (New Zealand)

^b UNIVERSITY OF OTAGO   (New Zealand)

^c UNIVERSITY OF SOUTH FLORIDA   (United States)

^d INSTITUTE FOR BIOLOGICAL INSTRUMENTATION   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

DORMANCY ASSOCIATED GENE 1 PROTEIN; MESSENGER RNA; UNCLASSIFIED DRUG; VEGETABLE PROTEIN;

ALPHA HELIX; AMINO ACID COMPOSITION; ARTICLE; BUD DORMANCY; DORMANCY ASSOCIATED GENE 1; GENE EXPRESSION; KIWIFRUIT; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENE; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN SECONDARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; UNINDEXED SEQUENCE;

ACTINIDIA; AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; FRUIT; GENE EXPRESSION REGULATION, PLANT; GENETIC ASSOCIATION STUDIES; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT PROTEINS; PROTEIN STRUCTURE, SECONDARY; RNA, MESSENGER; SEASONS; SEQUENCE ALIGNMENT;

EID: 84874836745     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0057354     Document Type: Article

References (48)

1. Fennel A, Hoover E, (1991) Photoperiod influences growth, bud dormancy and cold acclimation in Vitis labruscana and Vitis riparia. J Amer Soc Hort Sci 116: 270-273.
2. Li C, Junttila O, Ernstsen A, Heino P, Palva ET, (2003) Photoperiodic control of growth, cold acclimation and dormancy development in silver birch (Betula pendula) ecotypes. Physiol Plant 117: 206-212.
3. Heide OM, Prestrud AK, (2005) Low temperature, but not photoperiod controls growth cessation and dormancy induction and release in apple and pear. Tree Physiol(Oxford, U. K.). 25: 109-114.
4. Rhode A, Bhalerao RP, (2007) Plant dormancy in the perennial context. TIPS 12: 217-223.
5. Horvath DP, (2009) Common mechanisms regulate flowering and dormancy. Plant Science 177: 523-531.
6. McPherson HG, Snelgar WP, Manson PJ, Snowball AM, (1997) Bud respiration and dormancy of kiwifruit (Actinidia deliciosa). Ann BotOxford, U. K. 80: 411-418.
7. Faust M, Erez A, Rowland LJ, Wang SY, Norman HA, (1997) Bud dormancy in perennial fruit trees: physiological basis for dormancy induction, maintenance and release. HortScience 32: 623-629.
8. Brundell DJ, (1976) The effect of chilling on the termination of rest and flower development of the Chinese gooseberry. Sci Hortic (Amsterdam, Neth.) 4: 175-182.
9. Welling A, Pavla ET, (2006) Molecular control of cold acclimation in trees. Physiol Plant 127: 167-181.
10. McPherson HG, Richardson AC, Snelgar WP, Currie MB, (2001) Effects of hydrogen cyanamide on budbreak and flowering in kiwifruit (Actinidia deliciosa 'Hayward'). N Z J Crop Hortic Sci 29: 277-285.
11. Arora R, Rowland LJ, Tanino K, (2003) Induction and release of bud dormancy in woody perennials: A science comes of age. HortScience 38: 911-921.
12. Pang X, Halaly T, Crane O, Keilin T, Keren-Keiserman A, et al. (2007) Involvement of calcium signalling in dormancy release of grape buds. J Exp Bot 58: 3249-3262.
13. Halaly T, Pang X, Batikoff T, Crane O, Keren A, et al. (2008) Similar mechanisms might be triggered by alternative external stimuli that induce dormancy release in grape buds. Planta 228: 79-88.
14. Tatematsu K, Ward S, Leyser O, Kamiya Y, Nambara E, (2005) Identification of cis-elements that regulate gene expression during initiation of axillary bud outgrowth in Arabidopsis. Plant Physiol 138: 757-766.
15. Kebrom TH, Brutnell TP, Finlayson SA, (2010) Suppression of sorghum axillary bud outgrowth by shade, PhyB and defoliation signalling pathways. Plant Cell Environ 33: 48-58.
16. Strafstrom JP, Ripley BD, Devitt ML, Drake B, (1998) Dormancy-associated gene expression in pea axillary buds. Planta 205: 547-552.
17. Park S, Han KH, (2003) An auxin-repressed gene (RpARP) from black locust (Robinia pseudoacacia) is posttranscriptionally regulated and negatively associated with shoot elongation. Tree PhysiolOxford, U. K. 23: 815-823.
18. Steiner C, Bauer J, Amrhein N, Bucher M, (2003) Two novel genes are differentially expressed during early germination of the male gametophyte of Nicotiana tabacum. Biochim Biophys Acta 1625: 123-133.
19. Kim HB, Lee H, Oh CJO, An CS, (2007) Expression of EuNOD-ARP1 encoding auxin-repressed protein homolog is upregulated by auxin and localized to the fixation zone in root nodules of Elaeagnus umbellate. Mol Cells 23: 115-121.
20. Finlayson SA, (2007) Arabidopsis TEOSINTE BRANCHED1-LIKE 1 regulates axillary bud outgrowth and is homologous to monocot TEOSINTE BRANCHED1. Plant Cell Physiol 48(5): 667-677.
21. Xie H, Vucetic S, Iakoucheva LM, Oldfield CJ, Dunker AK, et al. (2007) Functional anthology of intrinsic disorder 1. Biological processes and functions of proteins with long disordered regions. J Proteome Res 6(5): 1882-1898.
22. Walton EF, Wu RM, Richardson AC, Davy M, Hellens RP, et al. (2009) A rapid transcriptional activation is induced by the dormancy-breaking chemical hydrogen cyanamide in kiwifruit (Actinidia deliciosa) buds. J Exp Bot 60: 3835-3848.
23. Crowhurst RN, Gleave AP, MacRae EA, Ampomah-Dwamena C, Atkinson RG, et al. (2008) Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening. BMC Genomics 9: 351-376.
24. Rozen S, Helen J, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In Bioinformatics Methods and Protocols: Methods in Molecular Biology (Krawetz, S. and Misener, SS., eds.). 365-386, Humana Press, Totowa, NJ.
25. Sickmeier M, Hamilton JA, LeGall T, Vacic V, Cortese MS, et al. (2007) DisProt: the Database of Disordered Proteins. Nucleic Acids Res 35: 786-793.
26. Vacic V, Uversky VN, Dunker AK, Lonardi S, (2007) Composition Profiler: A tool for discovery and visualization of amino acid composition differences. BMC Bioinformatics 8: 211-217.
27. Oldfield CJ, Cheng Y, Cortese MS, Brown CJ, Uversky VN, et al. (2005) Comparing and combining predictors of mostly disordered proteins. Biochemistry 44(6): 1989-2000.
28. Xue B, Oldfield CJ, Dunker AK, Uversky VN, (2009) CDF it all: consensus prediction of intrinsically disordered proteins based in various cumulative distribution functions. FEBS Lett 583: 1469-1474.
29. Huang F, Oldfield CJ, Meng J, Hsu WL, Xue B, et al. (2012) Subclassifying disordered proteins by the CH-CDF plot method. Pacific Symposium on Biocomputing 128-139.
30. Xue B, Dunbrack RL, Williams RW, Dunker AK, Uversky VN, (2010) PONDR® FIT: A meta-predictor of intrinsically disordered amino acids. BBA Proteins and Proteomics 1804 (4): 996-1010.
31. Cole C, Barber JD, Barton GJ, (2008) The Jpred secondary structure prediction server. Nucleic Acids Res. 36: W197-W201.
32. Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ, (2009) Jalview Version 2-A multiple sequence alignment editor and analysis workbench. Bioinformatics 25(9): 1189-91.
33. Oldfield CJ, Cheng Y, Cortese MS, Romero P, Uversky VN, et al. (2005) Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry 44 (37): 12454-12470.
34. Cheng Y, Oldfield CJ, Meng J, Romero P, Uversky VN, et al. (2007) Mining alpha-helix-forming molecular recognition features with cross species sequence alignments. Biochemistry 46(47): 13468-13477.
35. Liu C, Liu C, Wang H, Shen Z, Yang C, et al. (2011) Identification and analysis of phosphorylation status of proteins in dormant terminal buds of poplar. BMC Plant Biol 11: 158-173.
36. Emes MJ, (2009) Oxidation of methionine residues: the missing link between stress and signalling responses in plants. Biochem J 422: e1-e2.
37. Rousseau F, Serrano L, Schymkowitzm JW, (2006) How evolutionary pressure against protein aggregation helped shape chaperone specificity. J Mol Biol 355(5): 1037-1047.
38. Radivojac P, Iakoucheva LM, Oldfield CJ, Obradovic Z, Dunker AK, (2007) Intrinsic disorder and functional proteomics. Biophys J 92: 1439-1456.
39. Rechsteiner M, Rogers SW, (1996) PEST sequences and regulation by proteolysis. Trends Biochem Sci 21: 267-271.
40. Ner-Gaon H, Halachmi R, Savaldi-Goldstein S, Rubin E, Ophir R, et al. (2004) Intron retention is a major phenomenon in alternative splicing in Arabidopsis. The Plant Journal 39: 877-885.
41. Schranz ME, Mitchell-Olds T, (2006) Independent Ancient Polyploidy Events in the Sister Families Brassicaceae and Cleomaceae. Plant Cell 18: 1152-1165.
42. Tóth-Petróczy A, Mészéros B, Simon I, Dunker AK, Uversky VN, et al. (2008) Assessing conservation of disordered regions in plants. The Open Proteomics Journal 1: 46-53.
43. Sun X, Jones WT, Harvey D, Edwards PJB, Pascal SM, et al. (2010) N-terminal domains of DELLA proteins are intrinsically unstructured in the absence of interaction with GID1/gibberellic acid receptors. J Biol Chem 285: 11557-11571.
44. Vergara R, Parada F, Rubio S, Pérez FJ, (2012) Hypoxia induces H2O2 production and activates antioxidant defence system in grapevine buds through mediation of H2O2 and ethylene. J Exp Bot 63 (11): 4123-4131.
45. Hwang EW, Kim KA, Park SC, Jeong MJ, Byun MO, et al. (2005) Expression profiles of hot pepper (Capsicum annuum) genes under cold stress conditions. J Biosci New Delhi, India. 30: 101-111.
46. Chakravarthy S, Velasquez AC, Ekengren SK, Collmer A, Martin GB, (2010) Identification of Nicotiana benthamiana genes involved in pathogen-associated molecular pattern-triggered immunity. Mol Plant-Microbe Interact 23: 715-726.
47. Gill SS, Tuteja N, (2010) Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol Biochem 48 (12): 909-930.
48. Kovalchuk I (2010) Multiple roles of radicles in plants. In Gupta DS editor. Reactive Oxygen Species and Antioxidants in Higher Plants, CRC Press, New York. pp.31-44.