Protein intrinsic disorder in plants

Frontiers in Plant Science

Volumn 4, Issue SEP, 2013, Pages

  Pazos, Florencio ^a   Pietrosemoli, Natalia ^a   García Martín, Juan A ^a,b   Solano, Roberto ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b BOSTON COLLEGE   (United States)

Author keywords

Biological networks; Plant environmental responses; Protein function; Protein interactions; Protein intrinsic disorder; Protein structure

Indexed keywords

EID: 84896351549     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2013.00363     Document Type: Article

References (40)

1. Buljan, M., Chalancon, G., Dunker, A. K., Bateman, A., Balaji, S., Fuxre-iter, M., et al. (2013). Alternative splicing of intrinsically disordered regions and rewiring of protein interactions. Curr. Opin. Struct. Biol. 23, 443-450. doi: 10.1016/j.sbi.2013. 03.006
2. Cozzetto, D., and Jones, D. T. (2013). The contribution of intrinsic disorder prediction to the elicidation of protein function. Curr. Opin. Struct. Biol. 23, 467-472. doi: 10.1016/j.sbi.2013.02.001
3. Diella, F., Haslam, N., Chica, C., Budd, A., Michael, S., Brown, N. P., et al. (2008). Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front. Biosci. 13:6580-6603. doi: 10.2741/3175
4. Dosztanyi, Z., Csizmok, V., Tompa, P., and Simon, I. (2005). IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 21, 3433-3434. doi: 10.1093/bioinformatics/bti541
5. Dunker, A. K., Brown, C. J., Law-son, J. D., Iakoucheva, L. M., and Obradovic, Z. (2002). Intrinsic disorder and protein function. Biochemistry 41, 6573-6582. doi: 10.1021/bi012159+
6. Dunker, A. K., and Obradovic, Z. (2001). The protein trinity - linking function and disorder. Nat. Biotechnol. 19, 805-806. doi: 10.1038/nbt0901-805
7. Dyson, H. J., and Wright, P. E. (2005). Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol. 6, 197-208. doi: 10.1038/nrm1589
8. Fuxreiter, M., Simon, I., Friedrich, P., and Tompa, P. (2004). Preformed structural elements feature in partner recognition by intrinsically unstructured proteins. J. Mol. Biol. 338, 1015-1026. doi: 10.1016/j.jmb.2004.03.017
9. Gould, C. M., Diella, F., Via, A., Pun-tervoll, P., Gemund, C., Chabanis-Davidson, S., et al. (2010). ELM: the status of the 2010 eukary-otic linear motif resource. Nucleic Acids Res. 38, D167-D180. doi: 10.1093/nar/gkp1016
10. Haynes, C., Oldfield, C. J., Ji, F., Klit-gord, N., Cusick, M. E., Radivojac, P., et al. (2006). Intrinsic disorder is a common feature of hub proteins from four eukaryotic interac-tomes. PLoS Comp. Biol. 2:e100. doi: 10.1371/journal.pcbi.0020100
11. Iakoucheva, L. M., Brown, C. J., Law-son, J. D., Obradovic, Z., and Dunker, A. K. (2002). Intrinsic disorder in cell-signaling and cancer-associated proteins. J. Mol. Biol. 323, 573-584. doi: 10.1016/S0022-2836(02)00 969-5
12. Jensen, M. K., Kjaersgaard, T., Nielsen, M. M., Galberg, P., Petersen, K., O'Shea, C., et al. (2010). The Arabidopsis thaliana NAC transcription factor family: structure-function relationships and determinants of ANAC019 stress signalling. Biochem. J. 426, 183-196. doi: 10.1042/BJ20091234
13. Jeong, H., Mason, S. P., Barabási, A. L., and Oltvai, Z. N. (2001). Lethality and centrality in protein networks. Nature 411, 41-42. doi: 10.1038/35075138
14. Kovacs, B., and Tompa, P. (2012). Diverse functional manifestations of intrinsic structural disorder in molecular chaperones. Biochem. Soc. Trans. 4, 963-968. doi: 10.1042/BST20120108
15. Kovacs, D., Kalmar, E., Torok, Z., and Tompa, P. (2008). Chaperone activity of ERD10 and ERD14, two disordered stress-related plant proteins. Plant Physiol. 147, 381-390. doi: 10.1104/pp.108.118208
16. Midic, U., Oldfield, C. J., Dunker, A. K., Obradovic, Z., and Uversky, V. N. (2009). Protein disorder in the human diseasome: unfoldomics of human genetic diseases. BMC Genomics 10:S12. doi: 10.1186/1471-2164-10-S1-S12
17. Mohan, A., Oldfield, C. J., Radivojac, P., Vacic, V., Cortese, M. S., Dunker, A. K., et al. (2006). Analysis of molecular recognition features (MoRFs). J. Mol. Biol. 362, 1043-1059. doi: 10.1016/j.jmb.2006.07.087
18. Mouillon, J.-M., Gustafsson, P., and Harryson, P. (2006). Structural investigation of disordered stress proteins. Comparison of full-length dehy-drins with isolated peptides of their conserved segments. Plant Physiol. 141, 638-650. doi: 10.1104/pp.106. 079848
19. Oldfield, C. J., Meng, J., Yang, J. Y., Yang, M. Q., Uversky, V. N., and Dunker, A. K. (2008). Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC Genomics 9:S1. doi: 10.1186/1471-2164-9-S1-S1
20. Pietrosemoli, N., García-Martín, J. A., Solano, R., and Pazos, F. (2013). Genome-wide analysis of protein disorder in Arabidopsis thaliana: implications for plant environmental adaptation. PLoS ONE 8:e55524. doi: 10.1371/journal.pone.0055524
21. Prilusky, J., Felder, C. E., Zeev-Ben-Mordehai, T., Rydberg, E. H., Man, O., Beckmann, J. S., et al. (2005). FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics 21, 3435-3438. doi: 10.1093/bioin-formatics/bti537
22. Romero, P., Obradovic, Z., Kissinger, C., Villafranca, J. E., and Dunker, A. K. (1997). Identifying disordered regions in proteins from amino acid sequence. Proc. Int. Conf. Neural Netw. 1, 90-95.
23. Romero, P., Obradovic, Z., Li, X., Garner, E. C., Brown, C. J., and Dunker, A. K. (2001). Sequence complexity of disordered protein. Proteins 42, 38-48. doi: 10.1002/ 1097-0134(20010101)42:1
24. Romero, P. R., Zaidi, S., Fang, Y. Y., Uversky, V. N., Radivojac, P., Oldfield, C. J., et al. (2006). Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. Proc. Natl. Acad. Sci. U.S.A. 103, 8390-8395. doi: 10.1073/pnas.05079 16103
25. Schad, E., Tompa, P., and Hegyi, H. (2011). The relationship between proteome size, structural disorder and organism complexity. Genome Biol. 12, R120. doi: 10.1186/gb-2011-12-12-r120
26. Sun, X., Jones, W. T., and Rikkerink, E. H. A. (2012). GRAS proteins: the versatile roles of intrinsically disordered proteins in plant signalling. Biochem. J. 442, 1-12. doi: 10.1042/BJ20111766
27. Sun, X., Rikkerink, E. H. A., Jones, W. T., and Uversky, V. N. (2013). Multifarious roles of intrinsic disorder in proteins illustrate its broad impact on plant biology. Plant Cell 25, 38-55. doi: 10.1105/tpc.112.106062
28. Sun, X., Xue, B., Jones, W. T., Rikkerink, E., Dunker, A. K., and Uversky, V. N. (2011). A functionally required unfoldome from the plant kingdom: intrinsically disordered N-terminal domains of GRAS proteins are involved in molecular recognition during plant development. Plant Mol. Biol. 77, 205-223. doi: 10.1007/s11103-011-9803-z
29. Tompa, P. (2002). Intrinsically unstructured proteins. Trends Biochem. Sci. 27, 527-533. doi: 10.1016/S0968-0004(02)02169-2
30. Tompa, P. (2005). The interplay between structure and function in intrinsically unstructured proteins. FEBS Lett. 579, 3346-3354. doi: 10.1016/j.febslet.2005.03.072
31. Tompa, P., Dosztanyi, Z., and Simon, I. (2006). Prevalent structural disorder in E. coli and S. cerevisiae proteomes. J. Proteome Res. 5, 1996-2000. doi: 10.1021/pr0600881
32. Tompa, P., and Kovacs, D. (2010). Intrinsically disordered chaperones in plants and animals. Biochem. Cell Biol. 88, 167-174. doi: 10.1139/O09-163
33. Tompa, P., Szász, C., and Buday, L. (2005). Structural disorder throws new light on moonlighting. Trends Biochem. Sci. 30, 484-489. doi: 10.1016/j.tibs.2005.07.008
34. Uversky, V. N. (2013). A decade and a half of protein intrinsic disorder: biology still waits for physics. Protein Sci. 6, 693-724. doi: 10.1002/pro.2261
35. Uversky, V. N., Oldfield, C. J., and Dunker, A. K. (2005). Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling. J. Mol. Recognit. 18, 343-384. doi: 10.1002/jmr.747
36. Vucetic, S., Brown, C. J., Dunker, A. K., and Obradovic, Z. (2003). Flavors of protein disorder. Proteins 52, 573-584. doi: 10.1002/prot.10437
37. Ward, J. J., Sodhi, J. S., McGuffin, L. J., Buxton, B. F., and Jones, D. T. (2004). Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J. Mol. Biol. 337, 635-645. doi: 10.1016/j.jmb.2004. 02.002
38. Xie, H., Vucetic, S., Iakoucheva, L. M., Oldfield, C. J., Dunker, A. K., Uversky, V. N., et al. (2007). Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 6, 1882-1898. doi: 10.1021/pr06 0392u
39. Yoon, M. K., Shin, J., Choi, G., and Choi, B. S. (2006). Intrinsically unstructured N-terminal domain of bZIP transcription factor HY5. Proteins 65, 856-866. doi: 10.1002/prot. 21089
40. Yruela, I., and Contreras-Moreira, B. (2012). Protein disorder in plants: a view from the chloroplast. BMC Plant Biol. 12:165. doi: 10.1186/1471-2229-12-165