Cloning and Expression Analysis of Two NAC Transcription Factors in Bambusa emeiensis

doi:10.7525/j.issn.1673-5102.2016.06.013

Abstract

Abstract: Based on the transcriptome database of Bambusa emeiensis and genome information of Phyllostachys heterocycla, the two NAC genes were cloned by homology cloning technology from the shoots of B.emeiensis, named as BeNAC1(GenBank:KU550706) and BeNAC2(GenBank:KU821586), encoding 313 and 389 amino acids, respectively. By protein function prediction and conserved domain multiple alignment, both of BeNAC1 and BeNAC2 contained NAM conserved region. By protein structure prediction, the putatived three-dimensional structure of BeNAC1 and BeNAC2 protein was similar to a rice protein with known crystal structure. By subcellular localization prediction analysis, BeNAC1 was mainly concentrated in the cytoplasm, and BeNAC2 was mainly concentrated in the nucleus. Tissue expression pattern analysis showed that BeNAC1 and BeNAC2 displayed similar tissue-specific, both having the highest expression on stems, whereas in addition to the bamboo shoots, the expression of BeNAC1 in each tissue tested was higher than that of BeNAC2.

Key words: Bambusa emeiensis, NAC transcription factors, clone, bioinformatics analysis, tissue expression pattern

CLC Number:

S795.5

LI Hui-Ping, LI Bang-Yong, HU Shang-Lian, CAO Ying. Cloning and Expression Analysis of Two NAC Transcription Factors in Bambusa emeiensis[J]. Bulletin of Botanical Research, 2016, 36(6): 895-901.

References

1. 周宗昌.全慈竹浆生产纸袋纸研究[J].西南造纸,1989(2):30-31. Zhou C Z.Study on the production of paper bags from Bambusa emeiensis pulp[J].Southwest Pulpand Paper,1989(2):30-31.
2. 谢寅峰,张春霞,丁雨龙.竹子开花人工诱导与逆转研究现状及前景[J].浙江农林学院学报,2000,17(4):436-440. Xie Y F,Zhang C X,Ding Y L.Research status and Prospect of artificial induction and reversion of bamboo flowering[J].Journal of Zhejiang A &F University,2000,17(4):436-440.
3. 刘庆,何海,沈昭萍.成都地区慈竹生长状况及其与环境因子关系的初步分析[J].四川环境,2001,20(4):43-46. Liu Q,He H,Shen S P.Study on the Growth Status and Correlative Environment Factors of Bamboo,Bambusa emeiensis from Chengdu Region[J].Sichuan Environment,2001,20(4):43-46.
4. 胡尚连,蒋瑶,陈其兵,等.四川2种丛生竹理化特性及纤维形态研究[J].植物研究,2010,30(6):708-712. Hu S L,Jiang Y,Chen Q B,et al.Physical and Chemical Properties of 2 Species in Bamboos from the Different Regions in Sichuan Province[J].Bulletin of Botanical Research,2010,30(6):708-712.
5. 陈其兵,蒋瑶,卢学琴,等.四川不同地区慈竹的遗传多样性研究[J].西北农林科技大学学报:自然科学版,2009,37(6):187-193. Chen Q B,Jiang Y,Lu X Q,et al.Assessment of genetic diversity in Neosinocalamus affinis from different regions of Sichuan province[J] Journal of Northwest A&F University:Natural Science Edition,2009,37(6):187-193.
6. 胡尚连,曹颖,黄胜雄,等.慈竹4CL基因的克隆及其生物信息学分析[J].西北农林科技大学学报:自然科学版,2009,37(8):204-210. Hu S L,Cao Y,Huang S X,et al.Cloning and bioinformation analysis of 4CL gene in Neosinocalamus affinis[J].ournal of Northwest A&F University:Natural Science Edition,2009,37(8):204-210.
7. Olsen A N,Ernst H A,Leggio L L,et al.NAC transcription factors:structurally distinct,functionally diverse[J].Trends in Plant Science,2005,10(2):79-87.
8. Riechmann J L,Heard J,Martin G,et al.Arabidopsis transcription factors:genome-wide comparative analysis among eukaryotes[J].Science,2000,290(5499):2105-2110.
9. Souer E,van Houwelingen A,Kloos D,et al.The no apical meristem gene of Petunia is required for pattern formation in embryos and flowers and is expressed at meristem and primordia boundaries[J].Cell,1996,85(2):159-170.
10. Huang D,Wang S,Zhang B,et al.A gibberellin-mediated DELLA-NAC signaling cascade regulates cellulose synthesis in rice[J].Plant Cell,2015,27(6):1681-1696.
11. Xie Q,Frugis G,Colgan D,et al.Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development[J].Genes & Development,2000,14(23):3024-3036.
12. Takasaki H,Maruyama K,Kidokoro S,et al.The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice[J].Molecular Genetics and Genomics,2010,284(3):173-183.
13. 杨传凤,曹颖,胡尚连,等.基于慈竹转录组MYB基因的克隆及胁迫诱导表达[J].森林与环境学报,2015,35(1):60-66. Yang C F,Cao Y,Hu S L,et al.Cloning of MYB gene based on Bambusa emeiensis transcriptome and their induced expression under stresses[J].Journal of Forest and Environment,2015,35(1):60-66.
14. Xia X H,Xie Z,Salemi M,et al.An index of substitution saturation and its application[J].Molecular Phylogenetics and Evolution,2003,26(1):1-7.
15. Xia X,Lemey P.Assessing substitution saturation with DAMBE[M].//Lemey P,Salemi M,Vandamme A M.The phylogenetic handbook.Cambridge:Cambridge University Press,2009:611-626.
16. Keane T M,Creevey C J,Pentony M M,et al.Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified[J].BMC Evolutionary Biology,2006,6:29.
17. Briesemeister S,Rahnenführer J,Kohlbacher O.Going from where to why-interpretable prediction of protein subcellular localization[J].Bioinformatics,2010,26(9):1232-1238.
18. Briesemeister S,Rahnenführer J,Kohlbacher O.YLoc-an interpretable web server for predicting subcellular localization[J].Nucleic Acids Research,2010,38(S2):W497-W502.
19. Pfaffl M W.A new mathematical model for relative quantification in real-time RT-PCR[J].Nucleic Acids Research,2001,29(9):e45.
20. Marchler-Bauer A,Derbyshire M K,Gonzales N R,et al.CDD:NCBI's conserved domain database[J].Nucleic Acids Research,2015,43(D1):D222-D226.
21. Ooka H,Satoh K,Doi K,et al.Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana[J].DNA Research,2009,34(6):239-247.
22. 钟慧.两个油菜NAC基因的鉴定及其表达和功能的初步研究[D].武汉:华中师范大学,2011. Zhong H,Idengtification of two NAC genes and their expression and function in Brassica napus[D].Wuhan:Huazhong Normal Universiry,2011.
23. Bailey T L,Elkan C.Fitting a mixture model by expectation maximization to discover motifs in biopolymers[C].//Proceedings of the international conference on intelligent systems for molecular biology.Stanford,CA,1994.2:28-36
24. Chen Q F,Wang Q,Xiong L Z,et al.A structural view of the conserved domain of rice stress-responsive NAC1[J].Protein & Cell,2011,2(1):55-63.
25. Kelley L A,Mezulis S,Yates C M,et al.The Phyre2 web portal for protein modeling,prediction and analysis[J].Nature Protocols,2015,10(6):845-858.
26. 张进艳.玉米NAC转录因子家族特性分析及与水分胁迫相关性[D].兰州:甘肃农业大学,2014. Zhang J Y.Characteristic analysis of NAC transcription factor family and correlation with water stress in Zea mays L.[D].Lanzhou:Gansu Agricultural University,2014.
27. Fang Y J,Liao K F,Du H,et al.A stress-responsive NAC transcription factor SNAC3 confers heat and drought tolerance through modulation of reactive oxygen species in rice[J].Journal of Experimental Botany,2015,66(21):6803-6817.
28. Hussey S G,Mizrachi E,Spokevicius A V,et al.SND2,a NAC transcription factor gene,regulates genes involved in secondary cell wall development in Arabidopsis fibres and increases fibre cell area in Eucalyptus[J].Bmc Plant Biology,2011,11:173.

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