Identification of 32 full-length NAC transcription factors in ramie (Boehmeria nivea L. Gaud) and characterization of the expression pattern of these genes

Molecular Genetics and Genomics

Volumn 289, Issue 4, 2014, Pages 675-684

  Liu, Touming ^a   Zhu, Siyuan ^a   Tang, Qingming ^a   Tang, Shouwei ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

Expression pattern; NAC transcription factor; Phylogenetic analysis; Ramie; Stress responsive genes

Indexed keywords

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BOEHMERIA; CADMIUM; DROUGHTS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; MOLECULAR SEQUENCE DATA; NEMATODA; OPEN READING FRAMES; ORGAN SPECIFICITY; PHYLOGENY; PLANT COMPONENTS, AERIAL; PLANT PROTEINS; PLANT ROOTS; RNA, PLANT; SEEDLING; SEQUENCE ANALYSIS, DNA; STRESS, PHYSIOLOGICAL; TRANSCRIPTION FACTORS;

EID: 84905098732     PISSN: 16174615     EISSN: 16174623     Source Type: Journal    
DOI: 10.1007/s00438-014-0842-4     Document Type: Article

References (62)

1. Aida M, Ishida T, Fukaki H, Fujisawa H, Tasaka M (1997) Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. Plant Cell 9:841-857 (Pubitemid 28173836)
2. Balazadeh S, Siddiquil H, Allu A, Matallana-Ramirez L, Caldana C, Mehrnia M, Zanor M, hler B, Mueller-Roeber B (2010) A gene regulatory network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence. Plant J 62:250-264
3. 2-responsive NAC transcription factor, controls senescence in Arabidopsis thaliana. Mol Plant 4:346-360
4. Chen J, Guo Q, Zhang X (2006) Cloning full length of Ramie Caffeoyl-CoA 3-O-methyltransferase cDNA and sequence analysis. Scientia Agricultura Sinica 39:1058-1063
5. Ernst H, Olsen A, Larsen S, Leggio L (2004) Structure of the conserved domain of ANAC, a member of the NAC family of transcription factors. EMBO Rep 5:297-303 (Pubitemid 38500111)
6. Fang Y, You J, Xie K, Xie W, Xiong L (2006) Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice. Mol Genet Genomics 280:547-563
7. Gao F, Xiong A, Peng R, Jin X, Xu J, Zhu B, Chen J, Yao Q (2010) OsNAC52, a rice NAC transcription factor, potentially responds to ABA and confers drought tolerance in transgenic plants. Plant Cell Tiss Organ Cult 100:255-262
8. Hu H, Dai M, Yao J, Xiao B, Li X, Zhang Q, Xiong L (2006) Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc Natl Acad Sci USA 103:12987-12992 (Pubitemid 44338904)
9. Hu R, Qi G, Kong Y, Kong D, Gao Q, Zhou G (2010) Comprehensive analysis of NAC domain transcription factor gene family in Populus trichocarpa. BMC Plant Biol 10:145
10. Ishida T, Aida M, Takada S, Tasaka M (2000) Involvement of CUPSHAPED COTYLEDON genes in gynoecium and ovule development in Arabidopsis thaliana. Plant Cell Physiol 41:60-67 (Pubitemid 30097494)
11. Jeong J, Kim Y, Baek K, Jung H, Ha S, Do Choi Y, Kim M, Reuzeau C, Kim J (2010) Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. Plant Physiol 153:187-195
12. Jin J, Zhang H, Kong L, Gao G, Luo J (2013a) PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res. doi:10.1093/nar/gkt1016
13. Jin H, Huang F, Cheng H, Song H, Yu D (2013b) Overexpression of the GmNAC2 gene, an NAC transcription factor, reduces abiotic stress tolerance in Tobacco. Plant Mol Biol Rep 31:435-442
14. John I, Hackett R, Cooper W, Drake R, Farrell A, Grierson D (1997) Cloning and characterization of tomato leaf senescence-related cDNAs. Plant Mol Biol 33:641-651 (Pubitemid 27155922)
15. Kaneda T, Taga Y, Takai R, Iwano M, Matsui H, Takayama S, Isogai A, Che F (2009) The transcription factor OsNAC4 is a key positive regulator of plant hypersensitive cell death. EMBO J 28:926-936
16. Kato H, Motomura T, Komeda Y, Saito T, Kato A (2010) Overexpression of the NAC transcription factor family gene ANAC036 results in adwarf phenotype in Arabidopsis thaliana. J Plant Physiol 167:571-577
17. Kim Y, Kim S, Park J, Park H, Lim M, Chua N, Parka C (2006) A membrane-bound NAC transcription factor regulates cell division in Arabidopsis. Plant Cell 18:3132-3144 (Pubitemid 46013281)
18. Kim S, Kim S, Park C (2007) A membrane-associated NAC transcription factor regulates salt-responsive flowering via FLOWERING LOCUS T in Arabidopsis. Planta 226:647-654 (Pubitemid 47038013)
19. Kim M, Park M, Seo P, Song J, Kim H, Park C (2012) Controlled nuclear import of NTL6 transcription factor reveals a cytoplasmic role of SnRK2.8 in drought stress response. Biochem J 448:353-363
20. Kou X, Watkins C, Gan S (2012) Arabidopsis AtNAP regulates fruit senescence. J Exp Bot 63:6139-6147
21. Kubo M, Udagawa M, Nishikubo N, Horiguchi G, Yamaguchi M, Ito J, Mimura T, Fukuda H, Demura T (2005) Transcription switches for protoxylem and metaxylem vessel formation. Genes Dev 19:1855-1860 (Pubitemid 41186986)
22. Kunieda T, Mitsuda N, Ohme-Takagi M, Takeda S, Aida M, Tasaka M, Kondo M, Nishimura M, Hara-Nishimura I (2008) NAC family proteins NARS1/NAC2 and NARS2/NAM in the outer integument regulate embryogenesis in Arabidopsis. Plant Cell 20:2631-2642 (Pubitemid 352844581)
23. Lee S, Seo P, Lee H, Park C (2012) A NAC transcription factor NTL4 promotes reactive oxygen species production during drought-induced leaf senescence in Arabidopsis. Plant J 70:831-844
24. Li P, Windb J, Shi X, Zhang H, Hanson J, Smeekens S, Teng S (2011) Fructose sensitivity is suppressed in Arabidopsis by the transcription factor ANAC089 lacking the membrane-bound domain. Proc Natl Acad Sci USA 108:3436-3441
25. Li Q, Lina Y, Sun Y, Song J, Chen H, Zhang X, Sederoff R, Chiang V (2012) Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa. Proc Natl Acad Sci USA 109:14699-14704
26. Liu J, Yu C, Tang S, Zhu A, Wang Y, Zhu S, Ma X, Xiong H (2008) Cloning and tissue expression of important enzyme gene UGlcAE in ramie pectin biosynthesis. ACTA AGRONOMICA SINICA 34:1938-1945
27. Liu T, Zhu S, Tang Q, Chen P, Yu Y, Tang S (2013a) De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L.Gaud). BMC Genomics 14:125
28. Liu T, Zhu S, Tang Q, Yu Y, Tang S (2013b) Identification of drought stress-responsive transcription factors in ramie (Boehmeria nivea L. Gaud). BMC Plant Biol 13:130
29. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25:402-408 (Pubitemid 34164012)
30. Mao X, Zhang H, Qian X, Li A, Zhao G, Jing R (2012) TaNAC2, a NAC-type wheat transcription factor conferring enhanced multiple abiotic stress tolerances in Arabidopsis. J Exp Bot 63:2933-2946
31. Mitsuda N, Seki M, Shinozaki K, Ohme-Takagi M (2005) The NAC transcription factors NST1 and NST2 of Arabidopsis regulate secondary wall thickening and are required for anther dehiscence. Plant Cell 17:2993-3006
32. Mitsuda N, IwaseA Yamamoto H, Yoshida M, Seki M, Shinozaki K, Ohme-Takagi M (2007) NAC transcription factors, NST1 and NST3, are key regulators of the formation of secondary walls in woody tissues of Arabidopsis. Plant Cell 19:270-280 (Pubitemid 46852716)
33. Nakashima K, Tran LS, Van Nguyen D, Fujita M, Maruyama K, Todaka D, Ito Y, Hayashi N, Shinozaki K, Yamaguchi-Shinozaki K (2007) Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Plant J 51:617-630 (Pubitemid 47231189)
34. Nuruzzaman M, Manimekalai R, Sharoni A, Satoh K, Kondoh H, Ooka H, Kikuchi S (2010) Genome-wide analysis of NAC transcription factor family in rice. Gene 465:30-44
35. Olsen A, Ernst H, Leggio L, Skriver K (2005) NAC transcription factors: structurally distinct, functionally diverse. Trends Plant Sci 10:79-87 (Pubitemid 40234483)
36. Park J, Kim Y, Kim S, Jung J, Woo J, Park C (2011) Integration of auxin and salt signals by the NAC transcription factor NTM2 during seed germination in Arabidopsis. Plant Physiol 156:537-549
37. Pinheiro G, Marques C, Costa M, Reis P, Alves M, Carvalho C, Fietto L, Fontes E (2009) Complete inventory of soybean NAC transcription factors: sequence conservation and expression analysis uncover their distinct roles in stress response. Gene 444:10-23
38. Ren T, Qu F, Morris TJ (2000) HRT gene function requires interaction between a NAC protein and viral capsid protein to confer resistance to turnip crinkle virus. Plant Cell 12:1917-1926
39. She W, Jie Y, Xing H, Luo Z, Kang W, Huang M, Zhu S (2011) Absorption and accumulation of cadmium by ramie (Boehmeria nivea) cultivars: a field study. ACTA AGR SCAND B-S P 61:641-647
40. Souer E, van Houwelingen A, Kloos D, Mol J, Koes R (1996) The no apical meristem gene of Petunia is required for pattern formation in embryos and flowers and is expressed at meristem and primordia boundaries. Cell 85:159-170 (Pubitemid 26118159)
41. Sun H, Huang X, Xu X, Lan H, Huang J, Zhang H (2012) ENAC1, a NAC transcription factor, is an early and transient response regulator induced by abiotic stress in rice (Oryza sativa L.). Mol Biotechnol 52:101-110
42. Takasaki H, Maruyama K, Kidokoro S, Ito Y, Fujita Y, Shinozaki K, Yamaguchi-Shinozaki K, Nakashima K (2010) The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice. Mol Genet Genomics 284:173-183
43. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599 (Pubitemid 47236692)
44. 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)
45. Tian Z, Yi R, Chen J, Guo Q, Zhang X (2008) Cloning and expression of cellulose synthase gene in Ramie [Boehmeria nivea (Linn.) Gaud.]. ACTA AGRONOMICA SINICA 34:76-83
46. Tran L, Nakashima K, Sakuma Y, Simpson S, Fujita Y, Maruyama K, Fujita M, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2004) Isolation and functional analysis of Arabidopsis stress inducible NAC transcription factors that bind to a drought responsive cis-element in the early responsive to dehydration stress 1 promoter. Plant Cell 16:2481-2498 (Pubitemid 39247086)
47. Vandesompele J, de Preter K, Pattyn F, Poppe B, Roy N, Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3:RESEARCH0034
48. Vroemen CW, Mordhorst AP, Albrecht C, Kwaaitaal MA, de Vries SC (2003) The CUP-SHAPED COTYLEDON3 gene is required for boundary and shoot meristem formation in Arabidopsis. Plant Cell 15:1563-1577 (Pubitemid 36872597)
49. Wu A, Allu A, Garapati P, Siddiqui H, Dortay H et al (2012) JUNGBRUNNEN1, a reactive oxygen species-responsive NAC transcription factor, regulates longevity in Arabidopsis. Plant Cell 24:482-506
50. Xie Q, Sanz-Burgos A, Guo H, Garcia J, Gutierrez C (1999) GRAB proteins, novel members of the NAC domain family, isolated by their interaction with a geminivirus protein. Plant Mol Biol 39:647-656
51. Xie Q, Frugis G, Colgan D, Chua N (2000) Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development. Genes Dev 14:3024-3036
52. Xiong L, Yang Y (2003) Disease resistance and abiotic stress tolerance in rice are inversely modulated by an abscisic acid-inducible mitogen-activated protein Kinase. Plant Cell 15:745-759 (Pubitemid 36345491)
53. Yamaguchi M, Mitsuda N, Ohtani M, Ohme-Takagi M, Kato K, Demura T (2011) VASCULAR-RELATED NAC-DOMAIN 7 directly regulates the expression of a broad range of genes for xylem vessel formation. Plant J 66:579-590
54. Yang B, Zhou M, Shu W, Lan C, Ye Z, Qiu R, Jie Y, Cui G, Wong M (2010) Constitutional tolerance to heavy metals of a fiber crop, ramie (Boehmeria nivea), and its potential usage. Environ Pollut 158:551-558
55. Yang S, Seo P, Yoon H, Park C (2011) The Arabidopsis NAC transcription factor VNI2 integrates abscisic acid signals into leaf senescence via the COR/RD genes. Plant Cell 23:2155-2168
56. Yoshii M, Shimizu T, Yamazaki M, Higashi T, Miyao A, Hirochika H, Omura T (2009) Disruption of a novel gene for a NAC-domain protein in rice confers resistance to Rice dwarf virus. Plant J 57:615-625
57. Zélicourt A, Diet A, Marion J, Laffont C, Ariel F, Moison M, Zahaf O, Crespi M, Gruber V, Frugier F (2012) Dual involvement of a Medicago truncatula NAC transcription factor in root abiotic stress response and symbiotic nodule senescence. Plant J 70:220-230
58. Zhao C, Avci U, Grant E, Haigler C, Beers E (2008) XND1, a member of the NAC domain family in Arabidopsis thaliana, negatively regulates lignocellulose synthesis and programmed cell death in xylem. Plant J 53:425-436 (Pubitemid 351172015)
59. Zheng X, Chen B, Lu G, Han B (2009) Overexpression of a NAC transcription factor enhances rice drought and salt tolerance. Biochem Biophy Res Commun 379:985-989
60. Zhong R, Lee C, Ye Z (2010) Functional characterization of poplar wood associated NAC domain transcription factors. Plant Physiol 152:1044-1055
61. Zhu Q, Huang D, Liu S, Luo Z, Rao Z, Cao X, Ren X (2013) Accumulation and subcellular distribution of cadmiumin ramie (Boehmeria nivea L. Gaud.). Plant Soil Environ 59:57-61
62. Zhu S, Tang S, Tang Q and Liu T (2014) Genome-wide transcriptional changes of ramie (Boehmeria nivea L. Gaud) in response to the infection of root-lesion nematode. BMC Genomics (in press)