Genome-wide investigation and expression analyses of WD40 protein family in the model plant foxtail millet (Setaria italica L.)

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Mishra, Awdhesh Kumar ^a   Muthamilarasan, Mehanathan ^a   Khan, Yusuf ^a   Parida, Swarup Kumar ^a   Prasad, Manoj ^a  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

UNCLASSIFIED DRUG; VEGETABLE PROTEIN; WD40 PROTEIN;

ABIOTIC STRESS; ARTICLE; CHROMOSOME INVERSION; CHROMOSOME REARRANGEMENT; CONTROLLED STUDY; FOXTAIL MILLET; GENE DELETION; GENE DUPLICATION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENE MAPPING; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME ANALYSIS; MAIZE; MOLECULAR DYNAMICS; NONHUMAN; PLANT GENE; PLANT GENOME; PREDICTION; PROTEIN DETERMINATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; RICE; SEQUENCE HOMOLOGY; SORGHUM; SPECIES DIFFERENCE; WD40 GENE;

BIOLOGICAL MARKERS; CHROMOSOME MAPPING; GENE EXPRESSION PROFILING; GENES, PLANT; GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; MICRORNAS; MOLECULAR SEQUENCE ANNOTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORYZA SATIVA; PHYLOGENY; PROMOTER REGIONS, GENETIC; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SETARIA PLANT; SORGHUM; ZEA MAYS;

EID: 84899784816     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0086852     Document Type: Article

References (64)

1. Li P, Brutnell TP (2011) Setaria viridis and Setaria italica, model genetic systems for Panicoid grasses. J Exp Bot 62: 3031-3037.
2. Lata C, Gupta S, Prasad M (2013) Foxtail millet, a model crop for genetic and genomic studies in bioenergy grasses. Crit Rev Biotechnol 33: 328-343.
3. Lata C, Prasad M (2013) Setaria genome sequencing: an overview. J Plant Biochem Biotechnol 22: 257-260.
4. Doust AN, Kellogg EA, Devos KM, Bennetzen JL (2009) Foxtail millet, a sequence-driven grass model system. Plant Physiol 149: 137-141.
5. Zhang G, Liu X, Quan Z, Cheng S, Xu X, et al. (2012) Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nature Biotechnol 30: 549-554.
6. Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, et al. (2012) Reference genome sequence of the model plant Setaria. Nature Biotechnol 30: 555-561.
7. Muthamilarasan M, Theriappan P, Prasad M (2013) Recent advances in crop genomics for ensuring food security. Curr Sci 105: 155-158.
8. Gupta S, Kumari K, Das J, Lata C, Puranik S, et al. (2011) Development and utilization of novel intron length polymorphic markers in foxtail millet [Setaria italica (L.) P. Beauv.]. Genome 54: 586-602.
9. Gupta S, Kumari K, Sahu PP, Vidapu S, Prasad M (2012) Sequence based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [Setaria italica (L.) P. Beauv.]. Plant Cell Rep 31: 323-337.
10. Pandey G, Misra G, Kumari K, Gupta S, Parida SK, et al. (2013) Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)]. DNA Res 20: 197-207.
11. Gupta S, Kumari K, Muthamilarasan M, Subramanian A, Prasad M (2013) Development and utilization of novel SSRs in foxtail millet [Setaria italica (L.) P. Beauv.]. Plant Breed doi: 10.1111/pbr.12070.
12. Kumari K, Muthamilarasan M, Misra G, Gupta S, Subramanian A, et al. (2013) Development of eSSR-markers in Setaria italica and their applicability in studying genetic diversity, cross-transferability and comparative mapping in millet and non-millet species. PLoS ONE 8: e67742.
13. Muthamilarasan M, Venkata Suresh B, Pandey G, Kumari K, Parida SK, et al. (2013) Development of 5123 intron-length polymorphic markers for large-scale genotyping applications in foxtail millet. DNA Res doi: 10.1093/dnares/dst039.
14. Jayaraman A, Puranik S, Rai NK, Vidapu S, Sahu PP, et al. (2008) cDNA-AFLP analysis reveals differential gene expression in response to salt stress in foxtail millet (Setaria italica L.). Mol Biotechnol 40: 241-251.
15. Lata C, Sahu PP, Prasad M (2010) Comparative transcriptome analysis of differentially expressed genes in foxtail millet (Setaria italica L.) during dehydration stress. Biochem Biophy Res Commun 393: 720-727.
16. Puranik S, Bahadur RP, Srivastava PS, Prasad M (2011) Molecular cloning and characterization of a membrane associated NAC family gene, SiNAC from foxtail millet [Setaria italica (L.) P. Beauv.]. Mol Biotechnol 49: 138-150.
17. Lata C, Bhutty S, Bahadur RP, Majee M, Prasad M (2011) Association of an SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet [Setaria italica (L.)]. J Exp Bot 62: 3387-3401.
18. Lata C, Jha S, Dixit V, Sreenivasulu N, Prasad M (2011) Differential antioxidative responses to dehydration-induced oxidative stress in core set of foxtail millet cultivars [Setaria italica (L.)]. Protoplasma 248: 817-828.
19. Puranik S, Kumar K, Srivastava PS, Prasad M (2011) Electrophoretic Mobility Shift Assay reveals a novel recognition sequence for Setaria italica NAC protein. Plant Signal Behav 6: 1588-1590.
20. Mishra AK, Puranik S, Bahadur RP, Prasad M (2012) The DNA-binding activity of an AP2 protein is involved in transcriptional regulation of a stress-responsive gene, SiWD40, in foxtail millet. Genomics 100: 252-263.
21. Puranik S, Sahu PP, Mandal SN, B VS, Parida SK, et al. (2013) Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italica L.). PLoS ONE 8: e64594.
22. Kumar K, Muthamilarasan M, Prasad M (2013) Reference genes for quantitative Real-time PCR analysis in the model plant foxtail millet (Setaria italica L.) subjected to abiotic stress conditions. Plant Cell Tiss Organ Cult 115: 13-22.
23. Mishra AK, Puranik S, Prasad M: (2012) Structure and regulatory networks of WD40 protein in plants. J Plant Biochem Biotechnol 21: 32-39.
24. Neer EJ, Schmidt CJ, Nambudripad R, Smith TF (1994) The ancient regulatory-protein family of WD-repeat proteins. Nature 371: 297-300. (Pubitemid 24300613)
25. Smith TF, Gaitatzes C, Saxena K, Neer EJ (1999) The WD repeat: a common architecture for diverse functions. Trends Biochem Sci 24: 181-185. (Pubitemid 29348450)
26. Andrade MA, Perez-Iratxeta C, Ponting CP (2001) Protein repeats: structures, functions, and evolution. J Struct Biol 134: 117-131.
27. Lee JH, Terzaghi W, Gusmaroli G, Charron JB, Yoon HJ, et al. (2008) Characterization of Arabidopsis and rice DWD proteins and their roles as substrate receptors for CUL4-RING E3 ubiquitin ligases. Plant Cell 20: 152-167. (Pubitemid 352844040)
28. Angers S, Li T, Yi X, MacCoss MJ, Moon RT, Zheng N (2006) Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery. Nature 443: 590-593. (Pubitemid 44527296)
29. Hua Z, Vierstra RD (2011) The cullin-RING ubiquitin-protein ligases. Annu Rev Plant Biol 62: 299-334.
30. Van Nocker S, Ludwig P (2003) The WD-repeat protein superfamily in Arabidopsis: conservation and divergence in structure and function. BMC Genomics 4: 50.
31. Ouyang Y, Huang X, Lu Z, Yao J (2012) Genomic survey, expression profile and co-expression network analysis of OsWD40 family in rice. BMC Genomics 13: 100.
32. Lecharny A, Boudet N, Gy I, Aubourg S, Kreis M (2003) Introns in, introns out in plant gene families: a genomic approach of the dynamics of gene structure. J Struct Funct Genomics 3: 111-116. (Pubitemid 36460249)
33. Jain M, Khurana P, Tyagi AK, Khurana JP (2008) Genome-wide analysis of intronless genes in rice and Arabidopsis. Funct Integr Genomics 8: 69-78.
34. Puranik S, Sahu PP, Srivastava PS, Prasad M (2012) NAC proteins: regulation and role in stress tolerance. Trends Plant Sci 17: 1360-1385.
35. Han Z, Guo L, Wang H, Shen Y, Deng XW, Chai J (2006) Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5. Mol Cell 22: 137-144.
36. Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, et al. (2007) F-Box Proteins in Rice. genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143: 1467-1483. (Pubitemid 46849461)
37. Cannon SB, Mitra A, Baumgarten A, Young ND, May G (2004) The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol 4: 10.
38. Söding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21: 951-960.
39. Jefferys BR, Kelley LA, Sternberg MJE (2010) Protein folding requires crowd control in a simulated cell. J Mol Biol 397: 1329-1338.
40. Stirnimann CU, Petsalaki E, Russell RB, Müller CW (2010) WD40 proteins propel cellular networks. Trends Biochem Sci 35: 565-574.
41. Letunic I, Doerks T, Bork P (2012) SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res 40: D302-D305.
42. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93: 77-78.
43. Tang H, Bowers JE, Wang X, Ming R, Alam M, et al. (2008) Synteny and collinearity in plant genomes. Science 320: 486-488. (Pubitemid 351590631)
44. Du D, Zhang Q, Cheng T, Pan H, Yang W, Sun L (2012) Genome-wide identification and analysis of late embryogenesis abundant (LEA) genes in Prunus mume. Mol Biol Rep 40: 1937-1946.
45. Shiu S-H, Bleecker AB (2003) Expansion of the Receptor-Like Kinase/Pelle Gene Family and Receptor-Like Proteins in Arabidopsis. Plant Physiol 132: 530-543. (Pubitemid 36715055)
46. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639-1645.
47. Guo AY, Zhu QH, Chen X, Luo JC (2007) GSDS: a gene structure display server. Yi Chuan 29: 1023-1026.
48. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
49. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL-X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882. (Pubitemid 28022245)
50. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
51. Conesa A, Götz S (2008) Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics 2008: 619832.
52. Chang WC, Lee TY, Huang HD, Huang HY, Pan RL (2008) PlantPAN: Plant Promoter Analysis Navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene group. BMC Genomics 9: 561.
53. Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39: W155-159.
54. Suyama M, Torrents D, Bork P (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34: W609-W612. (Pubitemid 44529842)
55. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
56. Yang Z, Gu S, Wang X, Li W, Tang Z, Xu C (2008) Molecular evolution of the cpp-like gene family in plants: insights from comparative genomics of Arabidopsis and rice. J Mol Evol 67: 266-277.
57. Cochrane G, Alako B, Amid C, Bower L, Cerdeño-Tárraga A, et al. (2013) Facing growth in the European Nucleotide Archive. Nucleic Acids Res 41: D30-D35.
58. Patel RK, Jain M (2012) NGS QC Toolkit: A toolkit for quality control of next generation sequencing data. PLoS ONE 7: e30619.
59. Saeed AI, Sharov V, White J, Li J, Liang W, et al. (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34: 374-378. (Pubitemid 36184095)
60. Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, et al. (2006) TM4 microarray software suite. Methods Enzymol 411: 134-193.
61. Longeman J, Schell J, Willmitzer L (1987) Improved method for the isolation of RNA from plant tissues. Anal Biochem 163: 16-20.
62. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The protein data bank. Nucleic Acids Res 28: 235-242. (Pubitemid 30047768)
63. Kelley LA, Sternberg MJE (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nature Protocols 4: 363-371.
64. Laurie AT, Jackson RM (2005) Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 21: 1908-1916. (Pubitemid 40668026)