Genome-wide analysis of the RNA helicase gene family in Gossypium raimondii

International Journal of Molecular Sciences

Volumn 15, Issue 3, 2014, Pages 4635-4656

  Chen, Jie ^a   Zhang, Yujuan ^a   Liu, Jubo ^a   Xia, Minxuan ^a   Wang, Wei ^a   Shen, Fafu ^a  

^a SHANDONG AGRICULTURAL UNIVERSITY   (China)

Author keywords

Cotton; Fiber; Gene expansion; RNA helicase; Structure

Indexed keywords

RNA HELICASE; TRANSCRIPTOME; VEGETABLE PROTEIN;

ARTICLE; CHROMOSOME POSITIONING; COTTON; DIPLOIDY; GENE; GENE DUPLICATION; GENE EXPRESSION; GENE SEQUENCE; GENE STRUCTURE; GENOME ANALYSIS; GOSSYPIUM; GOSSYPIUM RAIMONDII; MOLECULAR WEIGHT; NONHUMAN; PHYLOGENY; RNA HELICASE GENE; RNA METABOLISM; CHROMOSOME MAP; CLASSIFICATION; CLUSTER ANALYSIS; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MULTIGENE FAMILY; PLANT CHROMOSOME; PLANT GENOME; PLANT LEAF; SYNTENY; TOMATO;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; CLUSTER ANALYSIS; COTTON FIBER; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; GOSSYPIUM; LYCOPERSICON ESCULENTUM; MULTIGENE FAMILY; PHYLOGENY; PLANT LEAVES; PLANT PROTEINS; RNA HELICASES; SYNTENY; TRANSCRIPTOME;

EID: 84896484003     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms15034635     Document Type: Article

References (61)

1. Umate, P.; Tuteja, R.; Tuteja, N. Genome-wide analysis of helicase gene family from rice and Arabidopsis: A comparison with yeast and human. Plant Mol. Biol. 2010, 73, 449-465.
2. Lohman, T. M.; Bjornson, K. P. Mechanisms of helicase-catalyzed DNA unwinding. Annu. Rev. Biochem. 1996, 65, 169-214.
3. Owttrim, G. W. RNA helicases and abiotic stress. Nucleic Acids Res. 2006, 34, 3220-3230.
4. Schmid, S.; Linder, P. D-E-A-D protein family of putative RNA helicases. Mol. Microbiol. 1992, 6, 283-292.
5. Xu, R.; Zhang, S.; Lu, L.; Cao, H.; Zheng, C. A genome-wide analysis of the RNA helicase gene family in Solanum lycopersicum. Gene 2013, 513, 128-140.
6. Xu, R.; Zhang, S.; Huang, J.; Zheng, C. Genome-wide comparative in silico analysis of the RNA helicase gene family in Zea mays and Glycine max: A comparison with arabidopsis and Oryza sativa. PLoS One 2013, 8, e78982.
7. Gong, Z.; Dong, C. H.; Lee, H.; Zhu, J.; Xiong, L.; Gong, D.; Stevenson, B.; Zhu, J. K. A DEAD box RNA helicase is essential for mrna export and important for development and stress responses in Arabidopsis. Plant Cell Online 2005, 17, 256-267.
8. Gong, Z.; Lee, H.; Xiong, L.; Jagendorf, A.; Stevenson, B.; Zhu, J. K. RNA helicase-like protein as an early regulator of transcription factors for plant chilling and freezing tolerance. Proc. Natl. Acad. Sci. USA 2002, 99, 11507-11512.
9. Kant, P.; Kant, S.; Gordon, M.; Shaked, R.; Barak, S. STRESS RESPONSE SUPPRESSOR1 and STRESS RESPONSE SUPPRESSOR2, two DEAD-Box RNA helicases that attenuate Arabidopsis responses to multiple abiotic stresses. Plant Physiol. 2007, 145, 814-830.
10. Guan, Q.; Wu, J.; Zhang, Y.; Jiang, C.; Liu, R.; Chai, C.; Zhu, J. A DEAD vox RNA helicase is critical for pre-mrna splicing, cold-responsive gene regulation, and cold tolerance in Arabidopsis. Plant Cell Online 2013, 25, 342-356.
11. Wang, Y.; Duby, G.; Purnelle, B.; Boutry, M. Tobacco VDL gene encodes a plastid DEAD box RNA Helicase and is involved in chloroplast differentiation and plant morphogenesis. Plant Cell Online 2000, 12, 2129-2142.
12. Gendra, E.; Moreno, A.; Albà, M. Interaction of the plant glycine-rich RNA-binding protein MA16 with a novel nucleolar DEAD box RNA helicase protein from Zea mays. Plant J. 2004, 38, 875-886.
13. Macovei, A.; Vaid, N.; Tula, S.; Tuteja, N. A new DEAD-box helicase ATP-binding protein (OsABP) from rice is responsive to abiotic stress. Plant Signal. Behav. 2012, 7, 1138-1143.
14. Liu, H.; Liu, J.; Fan, S.; Song, M.; Han, X.; Liu, F.; Shen, F. Molecular cloning and characterization of a salinity stress-induced gene encoding DEAD-box helicase from the halophyte Apocynum venetum. J. Exp. Bot. 2008, 59, 633-644.
15. Lange, H.; Sement, F. M.; Gagliardi, D. MTR4, a putative RNA helicase and exosome co-factor, is required for proper rRNA biogenesis and development in Arabidopsis thaliana. Plant J. 2011, 68, 51-63.
16. Kobayashi, K.; Otegui, M. S.; Krishnakumar, S.; Mindrinos, M.; Zambryski, P. INCREASED SIZE EXCLUSION LIMIT2 encodes a putative DEVH Box RNA helicase involved in plasmodesmata function during Arabidopsis embryogenesis. Plant Cell Online 2007, 19, 1885-1897.
17. + deprivation responses and tolerance in Arabidopsis thaliana. FEBS J. 2011, 278, 2296-2306.
18. Ohtani, M.; Demura, T.; Sugiyama, M. Arabidopsis ROOT INITIATION DEFECTIVE1, a DEAH-Box RNA helicase involved in pre-mrna splicing, is essential for plant development. Plant Cell Online 2013, doi: 10. 1105/tpc. 113. 111922.
19. Aubourg, S.; Kreis, M.; Lecharny, A. The DEAD box RNA helicase family in Arabidopsis thaliana. Nucleic Acids Res. 1999, 27, 628-636.
20. Rathore, K. S. Cotton. In Genetic Modification of Plants; Springer: Berlin/Heidelberg, Germany, 2010; pp. 269-285.
21. Wendel, J. F.; Brubaker, C.; Alvarez, I.; Cronn, R.; Stewart, J. M. Evolution and natural history of the cotton genus. In Genetics and Genomics of Cotton; Springer: New York, NY, USA, 2009; pp. 3-22.
22. Hovav, R.; Udall, J. A.; Hovav, E.; Rapp, R.; Flagel, L.; Wendel, J. F. A majority of cotton genes are expressed in single-celled fiber. Planta 2008, 227, 319-329.
23. Hovav, R.; Udall, J. A.; Chaudhary, B.; Hovav, E.; Flagel, L.; Hu, G.; Wendel, J. F. The evolution of spinnable cotton fiber entailed prolonged development and a novel metabolism. PLoS Genet. 2008, 4, e25.
24. Yao, D.; Zhang, X.; Zhao, X.; Liu, C.; Wang, C.; Zhang, Z.; Zhang, C.; Wei, Q.; Wang, Q.; Yan, H. Transcriptome analysis reveals salt-stress-regulated biological processes and key pathways in roots of cotton (Gossypium hirsutum L.). Genomics 2011, 98, 47-55.
25. Wang, K.; Wang, Z.; Li, F.; Ye, W.; Wang, J.; Song, G.; Yue, Z.; Cong, L.; Shang, H.; Zhu, S.; et al. The draft genome of a diploid cotton Gossypium raimondii. Nat. Genet. 2012, 44, 1098-1103.
26. NCBI. Available online: http://www. ncbi. nlm. nih. gov/(accessed on 1 October 2013).
27. Marchat, L. A.; Orozco, E.; Guillen, N.; Weber, C.; Lopez-Camarillo, C. Putative DEAD and DExH-box RNA helicases families in Entamoeba histolytica. Gene 2008, 424, 1-10.
28. Rocak, S.; Linder, P. DEAD-box proteins: the driving forces behind RNA metabolism. Nat. Rev. Mol. Cell Biol. 2004, 5, 232-241.
29. Zou, J.; Chang, M.; Nie, P.; Secombes, C. Origin and evolution of the RIG-I like RNA helicase gene family. BMC Evol. Biol. 2009, 9, 85.
30. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32, 1792-1797.
31. Holub, E. B. The arms race is ancient history in Arabidopsis, the wildflower. Nat. Rev. Genet. 2001, 2, 516-527.
32. Zhang, C.; Zhang, H.; Zhao, Y.; Jiang, H.; Zhu, S.; Cheng, B.; Xiang, Y. Genome-wide analysis of the CCCH zinc finger gene family in Medicago truncatula. Plant Cell Rep. 2013, 1-13.
33. Altenhoff, A. M.; Dessimoz, C. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput. Biol. 2009, 5, e1000262.
34. Linder, P.; Owttrim, G. W. Plant RNA helicases: Linking aberrant and silencing RNA. Trends Plant Sci. 2009, 14, 344-352.
35. Asakura, Y.; Galarneau, E.; Watkins, K. P.; Barkan, A.; van Wijk, K. J. Chloroplast RH3 DEAD box RNA helicases in maize and Arabidopsis function in splicing of specific group II introns and affect chloroplast ribosome biogenesis. Plant Physiol. 2012, 159, 961-974.
36. He, J.; Duan, Y.; Hua, D.; Fan, G.; Wang, L.; Liu, Y.; Chen, Z.; Han, L.; Qu, L. J.; Gong, Z. DEXH Box RNA helicase-mediated mitochondrial reactive oxygen species production in Arabidopsis mediates crosstalk between abscisic acid and auxin signaling. Plant Cell Online 2012, 24, 1815-1833.
37. Shang, H.; Li, W.; Zou, C.; Yuan, Y. Analyses of the NAC transcription factor gene family in Gossypium raimondii Ulbr.: Chromosomal location, structure, phylogeny, and expression patterns. J. Integr. Plant Biol. 2013, 55, 663-676.
38. Cannon, S. B.; Mitra, A.; Baumgarten, A.; Young, N. D.; May, G. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol. 2004, 4, 10.
39. Du, D.; Hao, R.; Cheng, T.; Pan, H.; Yang, W.; Wang, J.; Zhang, Q. Genome-wide analysis of the AP2/ERF gene family in Prunus mume. Plant Mol. Biol. Rep. 2013, 31, 741-750.
40. Tanner, N. K.; Cordin, O.; Banroques, J.; Doère, M.; Linder, P. The Q motif: A newly identified motif in DEAD Box helicases may regulate ATP binding and hydrolysis. Mol. Cell 2003, 11, 127-138.
41. Ilsleya, J. L.; Sudolb, M.; Windera, S. J. The WW domain: Linking cell signalling to the membrane cytoskeleton. Cell. Signal. 2002, 14, 183-189.
42. Klostermeier, D.; Rudolph, M. G. A novel dimerization motif in the C-terminal domain of the Thermus thermophilus DEAD box helicase Hera confers substantial flexibility. Nucleic Acids Res. 2009, 37, 421-430.
43. Menges, M.; de Jager, S. M.; Gruissem, W.; Murray, J. A. Global analysis of the core cell cycle regulators of Arabidopsis identifies novel genes, reveals multiple and highly specific profiles of expression and provides a coherent model for plant cell cycle control. Plant J. 2005, 41, 546-566.
44. Lucas, W. J.; Ham, B. K.; Kim, J. Y. Plasmodesmata-Bridging the gap between neighboring plant cells. Trends Cell Biol. 2009, 19, 495-503.
45. CottonGen. Available online: http://www. cottongen. org/(accessed on 1 October 2013).
46. Altschul, S. F.; Gish, W.; Miller, W.; Myers, E. W.; Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 1990, 215, 403-410.
47. The Arabidopsis Information Resource. Available online: http://www. arabidopsis. org/(accessed on 6 October 2013).
48. PlantGDB. Available online: http://www. plantgdb. org/(accessed on 6 October 2013).
49. PROSITE Program. Available online: http://www. expasy. ch/prosite/(accessed on 25 October 2013).
50. Compute pI/Mw Tool. ExPASy Server. Available online: http://web. expasy. org/compute_pi/(accessed on 25 October 2013).
51. CELLO v2. 5. Available online: http://cello. life. nctu. edu. tw/(accessed on 25 October 2013).
52. Guindon, S.; Lethiec, F.; Duroux, P.; Gascuel, O. PHYML Online-A web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res. 2005, 33, W557-W559.
53. Tang, H.; Bowers, J. E.; Wang, X.; Ming, R.; Alam, M.; Paterson, A. H. Synteny and collinearity in plant genomes. Science 2008, 320, 486-488.
54. Wang, Y.; Tang, H.; DeBarry, J. D.; Tan, X.; Li, J.; Wang, X.; Lee, T.-H.; Jin, H.; Marler, B.; Guo, H. MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012, 40, e49-e49.
55. Krzywinski, M.; Schein, J.; Birol, İ.; Connors, J.; Gascoyne, R.; Horsman, D.; Jones, S. J.; Marra, M. A. Circos: An information aesthetic for comparative genomics. Genome Res. 2009, 19, 1639-1645.
56. Bairoch, A. PROSITE: A dictionary of sites and patterns in proteins. Nucleic Acids Res. 1991, 19, 2241.
57. Gasteiger, E.; Gattiker, A.; Hoogland, C.; Ivanyi, I.; Appel, R. D.; Bairoch, A. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 2003, 31, 3784-3788.
58. GSDS v2. 0. Available online: http://gsds. cbi. pku. edu. cn/(accessed on 25 October 2013).
59. Li, H.; Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25, 1754-1760.
60. Mortazavi, A.; Williams, B. A.; McCue, K.; Schaeffer, L.; Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 2008, 5, 621-628.
61. Yin, Z.; Wang, J.; Wang, D.; Fan, W.; Wang, S.; Ye, W. The MAPKKK gene family in Gossypium raimondii: Genome-wide identification, classification and expression analysis. Int. J. Mol. Sci. 2013, 14, 18740-18757.