Genomewide identification, classification and analysis of NAC type gene family in maize

Journal of Genetics

Volumn 94, Issue 3, 2015, Pages 377-390

  Peng, Xiaojian ^a   Zhao, Yang ^a   Li, Xiaoming ^a   Wu, Min ^a   Chai, Wenbo ^a   Sheng, Lei ^a   Wang, Yu ^a   Dong, Qing ^a   Jiang, Haiyang ^a   Cheng, Beijiu ^a  

^a ANHUI AGRICULTURAL UNIVERSITY   (China)

Author keywords

abiotic stress; expression; maize; NAC transcription factor

Indexed keywords

VEGETABLE PROTEIN;

AMINO ACID SEQUENCE; CONSERVED SEQUENCE; DROUGHT; EXON; GENE DUPLICATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; INTRON; MAIZE; METABOLISM; MOLECULAR GENETICS; MULTIGENE FAMILY; PHYLOGENY; PHYSIOLOGICAL STRESS; PLANT CHROMOSOME; PLANT GENE; PROMOTER REGION; PROTEIN MOTIF; SEGMENTAL DUPLICATION;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; CHROMOSOMES, PLANT; CONSERVED SEQUENCE; DROUGHTS; EXONS; GENE DUPLICATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; INTRONS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; PLANT PROTEINS; PROMOTER REGIONS, GENETIC; SEGMENTAL DUPLICATIONS, GENOMIC; STRESS, PHYSIOLOGICAL; ZEA MAYS;

EID: 84945466973     PISSN: 00221333     EISSN: 09737731     Source Type: Journal    
DOI: 10.1007/s12041-015-0526-9     Document Type: Article

References (57)

1. Aida M., Ishida T., Fukaki H., Fujisawa H. and Tasaka M. 1997 Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. Plant Cell 9, 841–857.
2. Bailey T. L. and Elkan C. 1995 The value of prior knowledge in discovering motifs with MEME. Proc. Int. Conf. Intell. Syst. Mol. Biol. 3, 21–29.
3. Benson D. A., Karsch-Mizrachi I., Lipman D. J., Ostell J. and Sayers E. W. 2010 GenBank. Nucleic Acids Res. 38, D46–D51.
4. Daimon Y., Takabe K. and Tasaka M. 2003 The CUP-SHAPED COTYLEDON genes promote adventitious shoot formation on calli. Plant Cell Physiol. 44, 113–121.
5. Duval M., Hsieh T.-F., Kim S. Y. and Thomas T. L. 2002 Molecular characterization of AtNAM: a member of the Arabidopsis NAC domain superfamily. Plant Mol. Biol. 50, 237–248.
6. Fang Y. J., You J., Xie K. B., Xie W. B. and Xiong L. Z. 2008 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. Finn R. D., Mistry J., Schuster-Böckler B., Griffiths-Jones S., Hollich V., Lassmann T. et al. 2006 Pfam: clans, web tools and services. Nucleic Acids Res. 34, D247–D251.
8. Fujita M., Fujita Y., Maruyama K., Seki M., Hiratsu K., Ohme-Takagi M. et al. 2004 A dehydration-induced NAC protein, RD26, is involved in a novel ABA-dependent stress-signaling pathway. Plant J. 39, 863–876.
9. Gaut B. S. 2002 Evolutionary dynamics of grass genomes. New Phytol. 154, 15–28.
10. Gaut B. S., Morton B. R., McCaig B. C. and Clegg M. T. 1996 Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc. Natl. Acad. Sci. USA 93, 10274–10279.
11. Greve K., La Cour T., Jensen M., Poulsen F. and Skriver K. 2003 Interactions between plant RING-H2 and plant-specific NAC (NAM/ATAF1/2/CUC2) proteins: RING-H2 molecular specificity and cellular localization. Biochem. J. 371, 97–108.
12. Guo A. Y., Zhu Q. H., Chen X. and Luo J. C. 2007 GSDS: a gene structure display server. Yi Chuan 29, 1023–1026.
13. He X. J., Mu R. L., Cao W. H., Zhang Z. G., Zhang J. S. and Chen S. Y. 2005 AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development. Plant J. 44, 903–916.
14. Hibara Ki., Karim M. R., Takada S., Taoka Ki., Furutani M., Aida M. and Tasaka M. 2006 Arabidopsis CUP-SHAPED COTYLEDON3 regulates postembryonic shoot meristem and organ boundary formation. Plant Cell 18, 2946–2957.
15. Hibara Ki, Takada S. and Tasaka M. 2003 CUC1 gene activates the expression of SAM-related genes to induce adventitious shoot formation. Plant J. 36, 687–696.
16. Higo K., Ugawa Y., Iwamoto M. and Korenaga T. 1999 Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res. 27, 297–300.
17. Hu H., Dai M., Yao J., Xiao B., Li X., Zhang Q. and 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.
18. Kikuchi K., Ueguchi-Tanaka M., Yoshida K., Nagato Y., Matsusoka M. and Hirano H. Y. 2000 Molecular analysis of the NAC gene family in rice. Mol. Genet. Genomics 262, 1047–1051.
19. Kubo M., Udagawa M., Nishikubo N., Horiguchi G., Yamaguchi M., Ito J. et al. 2005 Transcription switches for protoxylem and metaxylem vessel formation. Gene Dev. 19, 1855–1860.
20. Letunic I., Doerks T. and Bork P. 2009 SMART 6: recent updates and new developments. Nucleic Acids Res. 37, D229–D232.
21. Lin Y. X., Jiang H. Y., Chu Z. X., Tang X. L., Zhu S. W. and Cheng B. J. 2011 Genome-wide identification, classification and analysis of heat shock transcription factor family in maize. BMC Genomics 12, 76.
22. Liu Y. Z., Baig M., Fan R., Ye J. L., Cao Y. C. and Deng X. X. 2009 Identification and expression pattern of a novel NAM, ATAF, and CUC-like gene from Citrus sinensis Osbeck. Plant Mol. Biol. Rep. 27, 292–297.
23. Mitsuda N., Iwase A., Yamamoto H., Yoshida M., Seki M., Shinozaki K. and 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.
24. Mitsuda N. and Ohme-Takagi M. 2008 NAC transcription factors NST1 and NST3 regulate pod shattering in a partially redundant manner by promoting secondary wall formation after the establishment of tissue identity. Plant J. 56, 768–778.
25. Mitsuda N., Seki M., Shinozaki K. and Ohme-Takagi M. 2005 The NAC transcription factors NST1 and NST2 of Arabidopsis regulate secondary wall thickenings and are required for anther dehiscence. Plant Cell 17, 2993–3006.
26. Moore R. C. and Purugganan M. D. 2003 The early stages of duplicate gene evolution. Proc. Natl. Acad. Sci. USA 100, 15682–15687.
27. Narusaka Y., Nakashima K., Shinwari Z. K., Sakuma Y., Furihata T., Abe H. et al. 2003 Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant J. 34, 137–148.
28. Ooka H., Satoh K., Doi K., Nagata T., Otomo Y., Murakami K. et al. 2003 Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res. 10, 239–247.
29. Peng X., Zhao Y., Cao J., Zhang W., Jiang H., Li X. et al. 2012 CCCH-type zinc finger family in maize: genome-wide identification, classification and expression profiling under abscisic acid and drought treatments. PLoS One 7, e40120.
30. Pla M., Vilardell J., Guiltinan M. J., Marcotte W. R., Niogret M. F., Quatrano R. S. and Pagès M. 1993 The cis-regulatory element CCACGTGG is involved in ABA and water-stress responses of the maize gene rab28. Plant Mol. Biol. 21, 259–266.
31. Quraishi U. M., Abrouk M., Murat F., Pont C., Foucrier S., Desmaizieres G. et al. 2011 Cross-genome map based dissection of a nitrogen use efficiency ortho-meta QTL in bread wheat unravels concerted cereal genome evolution. Plant J. 65, 745–756.
32. Ren T., Qu F. and Morris T. J. 2000 HRT gene function requires interaction between a NAC protein and viral capsid protein to confer resistance to turnip crinkle virus. Plant Cell 12, 1917–1925.
33. Rogozin I. B., Wolf Y. I., Sorokin A. V., Mirkin B. G. and Koonin E. V. 2003 Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr. Biol. 13, 1512–1517.
34. Rozas J., Sánchez-DelBarrio J. C., Messeguer X. and Rozas R. 2003 DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496–2497.
35. Sablowski R. W. and Meyerowitz E. M. 1998 A homolog of NO APICAL MERISTEM is an immediate target of the floral homeotic genes APETALA3/PISTILLATA. Cell 92, 93–103.
36. Salse J., Bolot S., Throude M., Jouffe V., Piegu B., Quraishi U. M. et al. 2008 Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell 20, 11–24.
37. Schnable P. S., Ware D., Fulton R. S., Stein J. C., Wei F., Pasternak S. et al. 2009 The B73 maize genome: complexity, diversity, and dynamics. Science 326, 1112–1115.
38. Sekhon R. S., Lin H., Childs K. L., Hansey C. N., Buell C. R., de Leon N. and Kaeppler S. M. 2011 Genome-wide atlas of transcription during maize development. Plant J. 66(4), 553–563.
39. Takada S., Hibara K.-i., Ishida T. and Tasaka M. 2001 The CUP-SHAPED COTYLEDON1 gene of Arabidopsis regulates shoot apical meristem formation. Development 128, 1127–1135.
40. Takasaki H., Maruyama K., Kidokoro S., Ito Y., Fujita Y., Shinozaki K. et al. 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.
41. Tamura K., Dudley J., Nei M. and Kumar S. 2007 MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596–1599.
42. Thompson J. D., Higgins D. G. and Gibson T. J. 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680.
43. Tran L.-S. P., Nakashima K., Sakuma Y., Simpson S. D., Fujita Y., Maruyama K. et al. 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.
44. Tran L. S. P., Nakashima K., Sakuma Y., Osakabe Y., Qin F., Simpson S. D. et al. 2007 Co-expression of the stress-inducible zinc finger homeodomain ZFHD1 and NAC transcription factors enhances expression of the ERD1 gene in Arabidopsis. Plant J. 49, 46–63.
45. Vroemen C. W., Mordhorst A. P., Albrecht C., Kwaaitaal M. A. and de Vries S. C. 2003 The CUP-SHAPED COTYLEDON3 gene is required for boundary and shoot meristem formation in Arabidopsis. Plant Cell 15, 1563–1577.
46. Wang Xe, Basnayake B. V. S., Zhang H., Li G., Li W., Virk N., Mengiste T. and Song F. 2009 The Arabidopsis ATAF1, a NAC transcription factor, is a negative regulator of defense responses against necrotrophic fungal and bacterial pathogens. Mol. Plant Microbe. Interact. 22, 1227–1238.
47. Wei F., Coe E., Nelson W., Bharti A. K., Engler F., Butler E. et al. 2007 Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet. 3, e123.
48. Xie Q., Frugis G., Colgan D. and Chua N. H. 2000 Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development. Gene Dev. 14, 3024–3036.
49. Xie Q., Guo H. S., Dallman G., Fang S., Weissman A. M. and Chua N. H. 2002 SINAT5 promotes ubiquitin-related degradation of NAC1 to attenuate auxin signals. Nature 419, 167–170.
50. Xie Q., Sanz-Burgos A. P., Guo H., García J. A. and Gutiérrez 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. Xiong Y. Q., Liu T. Y., Tian C. G., Sun S. H., Li J. Y. and Chen M. S. 2005 Transcription factors in rice: a genome-wide comparative analysis between monocots and eudicots. Plant Mol. Biol. 59, 191–203.
52. Zhang W., Ruan J., Ho T.-hD., You Y., Yu T. and Quatrano R. S. 2005 Cis-regulatory element based targeted gene finding: genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana. Bioinformatics 21, 3074–3081.
53. Zhao Y., Zhou Y., Jiang H., Li X., Gan D., Peng X. et al. 2011 Systematic analysis of sequences and expression patterns of drought-responsive members of the HD-Zip gene family in maize. PLoS One 6, e28488.
54. Zheng X., Chen B., Lu G. and Han B. 2009 Overexpression of a NAC transcription factor enhances rice drought and salt tolerance. Biochem. Biophys. Res. 379, 985–989.
55. Zhong R., Demura T. and Ye Z. H. 2006 SND1, a NAC domain transcription factor, is a key regulator of secondary wall synthesis in fibres of Arabidopsis. Plant Cell 18, 3158–3170.
56. Zhong R., Lee C., Zhou J., McCarthy R. L. and Ye Z. H. 2008 A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis. Plant Cell 20, 2763–2782.
57. Zhong R., Richardson E. A. and Ye Z. H. 2007 Two NAC domain transcription factors, SND1 and NST1, function redundantly in regulation of secondary wall synthesis in fibres of Arabidopsis. Planta 225, 1603–1611.