Identification and Expression Analysis of NAC Gene Family in Andrographis paniculate

doi:10.11924/j.issn.1000-6850.casb2024-0755

Abstract

Abstract:

NAC (NAM, ATAF, and CUC) transcription factors play a crucial role in plant growth and development, as well as in responses to various abiotic and biotic stresses. This study aims to identify and analyze the NAC gene family in Andrographis paniculata. Using bioinformatics methods, NAC genes were identified from the A.paniculata genome, followed by analysis of their phylogenetic relationships, cis-acting elements, chromosome distribution, collinearity, and expression profiles under drought stress and MeJA treatment. A total of 91 NAC genes were identified in A.paniculata, with protein lengths ranging from 139 to 715 amino acids, unevenly distributed at both ends of the chromosomes. Subcellular localization predictions revealed that most of the genes were located in the nucleus. Phylogenetic analysis, based on the construction of a phylogenetic tree with Arabidopsis NAC proteins, divided these genes into 16 subfamilies. Intraspecies collinearity analysis identified 4 tandem duplication groups and 36 segmental duplication gene pairs within the A.paniculata NAC family. Based on the functional conservation of subfamilies, analysis of cis-acting elements, and transcriptome analysis under drought stress and MeJA treatment, NAC genes responsive to drought and andrographolide synthesis were identified. This study identified and analyzed the NAC gene family in A.paniculata, predicting genes related to drought response and andrographolide synthesis, laying the foundation for further functional research on NAC genes.

Key words: Andrographis paniculata, NAC gene family, drought stress, MeJA treatment, whole-genome identification, bioinformatics, physicochemical properties, phylogenetic tree, cis-acting elements, chromosome distribution, collinearity analysis, expression profiles analysis

XU Shiqiang, LI Jingyu, SUN Mingyang, GU Yan, WANG Jihua. Identification and Expression Analysis of NAC Gene Family in Andrographis paniculate[J]. Chinese Agricultural Science Bulletin, 2024, 40(36): 117-125.

Figures/Tables 6

References 39

[1]	吴征镒, 彭华, 李德铢, 等. 中国植物志(第一卷)[J]. 中国西南野生生物种质资源库, 2004.
[2]	药品标准化工作《中华人民共和国药典》2020版颁布实施[Z]. 2023.000435.
[3]	曾吴静, 许玲, 何秋伶, 等. 穿心莲农艺性状及其与二萜内酯成分相关性研究[J]. 中国中药杂志, 2019(15):6.
[4]	闫婕, 卫莹芳, 胡慧玲, 等. 穿心莲药用植物资源调查[J]. 时珍国医国药, 2013, 24(8):1997-1999.
[5]	KIM H J, NAM H G, LIM P O. Regulatory network of NAC transcription factors in leaf senescence[J]. Current opinion in plant biology, 2016,33:48-56.
[6]	OOKA H, SATOH K, DOI K, et al. Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana[J]. DNA research, 2003, 10(6):239-247.
[7]	NURUZZAMAN M, MANIMEKALAI R, SHARONI A M, et al. Genome-wide analysis of NAC transcription factor family in rice[J]. Gene, 2010, 465(1-2):30-44. doi: 10.1016/j.gene.2010.06.008 pmid: 20600702
[8]	LE D T, NISHIYAMA R, WATANABE Y, et al. Genome-wide survey and expression analysis of the plant-specific NAC transcription factor family in soybean during development and dehydration stress[J]. DNA research, 2011, 18(4):263-276. doi: 10.1093/dnares/dsr015 pmid: 21685489
[9]	LI W, LI X X, CHAO J T, et al. NAC family transcription factors in tobacco and their potential role in regulating leaf senescence[J]. Frontiers in plant science, 2018,9:1-8.
[10]	FAN K, WANG M, MIAO Y, et al. Molecular evolution and expansion analysis of the NAC transcription factor in Zea mays[J]. Plos one, 2014, 9(11):e111837.
[11]	ZHANG H, XU J, CHEN H, et al. Characterization of NAC family genes in Salvia miltiorrhiza and NAC2 potentially involved in the biosynthesis of tanshinones[J]. Phytochemistry, 2021,191:112932.
[12]	WANG Z, ZHANG Z, WANG P, et al. Genome-wide identification of the NAC transcription factors family and regulation of metabolites under salt stress in Isatis indigotica[J]. International journal of biological macromolecules, 2023,240:124436.
[13]	HE H, LI Q, FANG L, et al. Comprehensive analysis of NAC transcription factors in Scutellaria baicalensis and their response to exogenous ABA and GA3[J]. International journal of biological macromolecules, 2023: 244(2):125290-125306.
[14]	SUN H, HU M L, LI J Y, et al. Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cotton[J]. BMC plant biology, 2018, 18(1):150-154. doi: 10.1186/s12870-018-1367-5 pmid: 30041622
[15]	AN J P, LI R, QU F J, et al. An apple NAC transcription factor negatively regulates cold tolerance via CBF-dependent pathway[J]. Journal of plant physiology, 2018,221:74-80.
[16]	SAKURABA Y, KIM Y S, HAN S H, et al. The Arabidopsis transcription factor NAC016 promotes drought stress responses by repressing AREB1 transcription through a trifurcate feed-forward regulatory loop involving NAP[J]. Plant cell, 2015, 27(6):1771-1787.
[17]	HUANG Y, LI T, XU Z S, et al. Six NAC transcription factors involved in response to TYLCV infection in resistant and susceptible tomato cultivars[J]. Plant physiology and biochemistry, 2017,120:61-74.
[18]	REN T T, WANG J W, ZHAO M M, et al. Involvement of NAC transcription factor SiNAC1 in a positive feedback loop via ABA biosynthesis and leaf senescence in foxtail millet[J]. Planta, 2018, 247(1):53-68. doi: 10.1007/s00425-017-2770-0 pmid: 28871431
[19]	YAMAGUCHI-SHINOZAKI K, SHINOZAKI K. Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses[J]. Annual review of plant biology, 2006, 57:781-803.
[20]	SHAO H, WANG H, TANG X. NAC transcription factors in plant multiple abiotic stress responses: progress and prospects[J]. Front plant sci, 2015, 6: 902. doi: 10.3389/fpls.2015.00902 pmid: 26579152
[21]	XU Z Y, KIM S Y, HYEON D Y, et al. The Arabidopsis NAC transcription factor ANAC096 cooperates with bZIP-Type transcription factors in dehydration and osmotic stress responses[J]. Plant cell, 2013, 25(11):4708-4724.
[22]	JENSEN M K, SKRIVER K. NAC transcription factor gene regulatory and protein-protein interaction networks in plant stress responses and senescence[J]. Iubmb life, 2014, 66(3):156-166. doi: 10.1002/iub.1256 pmid: 24659537
[23]	WANG G, ZHANG S, MA X, et al. A stress-associated NAC transcription factor (SlNAC35) from tomato plays a positive role in biotic and abiotic stresses[J]. Physiologia plantarum, 2016, 158(1):45-64.
[24]	CHEN J, GONG Y, GAO Y, et al. TaNAC48 positively regulates drought tolerance and ABA responses in wheat (Triticum aestivum L.)[J]. Crop journal, 2021, 9(4):785-793.
[25]	TRAN L S P, NAKASHIMA K, SAKUMA Y, et al. 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[J]. Plant cell, 2004, 16(9):2481-2498.
[26]	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, 2010,284:173-183.
[27]	ZHENG H, FU X, SHAO J, et al. Transcriptional regulatory network of high-value active ingredients in medicinal plants[J]. Trends in plant science, 2023, 28(4):429-446. doi: 10.1016/j.tplants.2022.12.007 pmid: 36621413
[28]	DIAO W, SNYDER J C, WANG S, et al. Genome-wide analyses of the NAC transcription factor gene family in pepper (Capsicum annuum L.): chromosome location, phylogeny, structure, expression patterns, cis-elements in the promoter, and interaction network[J]. Int j mol sci, 2018, 19(4):1-6.
[29]	MENGARELLI D A, ZANOR M I. Genome-wide characterization and analysis of the CCT motif family genes in soybean (Glycine max)[J]. Planta, 2021, 253(1):15. doi: 10.1007/s00425-020-03537-5 pmid: 33392793
[30]	李静宇, 孙铭阳, 徐世强, 等. 穿心莲R2R3-MYB基因家族的鉴定与表达分析[J]. 中国中药杂志, 2022, 47(1):72-84.
[31]	SHAN Z, JIANG Y, LI H, et al. Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stress[J]. BMC genomics, 2020, 21(1):96.
[32]	GUO Y F, GAN S S. AtNAP, a NAC family transcription factor, has an important role in leaf senescence[J]. Plant Journal, 2006, 46(4):601-612. doi: 10.1111/j.1365-313X.2006.02723.x pmid: 16640597
[33]	YU M X, LIU J L, DU B S, et al. NAC transcription factor PwNAC11 activates ERD1 by interaction with ABF3 and DREB2A to enhance drought tolerance in transgenic Arabidopsis[J]. International journal of molecular sciences, 2021, 22(13):1-9.
[34]	HEGEDUS D, YU M, BALDWIN D, et al. Molecular characterization of Brassica napus NAC domain transcriptional activators induced in response to biotic and abiotic stress[J]. Plant molecular biology, 2003, 53(3):383-397.
[35]	YANG Q, LI B, RIZWAN H M, et al. Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression analysis under Fusarium kyushuense and drought stress conditions in Passiflora edulis[J]. Frontiers in plant science, 2022,13:1-7.
[36]	温砚, 王莹敏, 曾广莹, 等. 三七NAC基因家族全基因组鉴定与表达分析[J]. 植物保护学报, 2023, 50(1):187-196.
[37]	LIU Y C, SUN J, WU Y R. Arabidopsis ATAF1 enhances the tolerance to salt stress and ABA in transgenic rice[J]. Journal of plant research, 2016, 129(5):955-962.
[38]	JENSEN M K, KJAERSGAARD T, NIELSEN M M, et al. The Arabidopsis thaliana NAC transcription factor family: structure-function relationships and determinants of ANAC019 stress signalling[J]. Biochemical journal, 2010,426:183-196.
[39]	HU H, DAI M, YAO J, et al. Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice[J]. Proceedings of the national academy of sciences, 2006, 103(35):12987-12992.