生菜bHLH转录因子家族的鉴定与生物信息学分析

doi:10.11924/j.issn.1000-6850.casb2022-0214

摘要/Abstract

摘要：

本研究旨在对生菜(Lactuca sativa L.)bHLH转录因子进行全基因组鉴定与系统分析，以期为生菜bHLH家族基因的生物学功能的研究提供理论基础。通过Pfam下载bHLH结构域的隐马氏模型，利用HMMER3.0和SMART鉴定生菜bHLH基因。使用ExPASy ProtParam tool、DNAMAN 5.0、ClustalX和MEGA 7.0等软件对bHLH的蛋白序列进行生物信息学分析。在生菜全基因组中共鉴定出135个bHLH转录因子，其编码蛋白的相对分子量为17843.82~75409.15 Da，理论等电点为0.63~9.51，其中有92个酸性蛋白，43个碱性蛋白。123个bHLH蛋白为不稳定蛋白，135个bHLH蛋白均为亲水性蛋白。各家族成员均含有N端碱性结构域和C端HLH结构域，其中N端可结合特定的DNA顺式元件，C端可维持bHLH蛋白二级结构的稳定。系统进化分析将生菜中135个bHLH蛋白分为10个亚家族。通过全基因组分析，共鉴定出135个生菜bHLH转录因子，为生菜bHLH家族基因的功能研究提供借鉴。

关键词: 生菜, bHLH, 进化树分析, 序列比对, 全基因组鉴定

Abstract:

The aim of this study is to conduct genome-wide identification and systematic analysis of lettuce (Lactuca sativa L.) bHLH transcription factors in order to provide a theoretical basis for studying the biological function of lettuce bHLH gene family. The Hidden Markov Model profiles of the bHLH domains downloaded from Pfam were used to search the database using HMMER ver. 3.0. and SMART. The obtained amino acid sequences were analyzed by bioinformatics using software such as ExPASy ProtParam tool, DNAMAN 5.0, ClustalX and MEGA 7.0. In this study, 135 bHLH transcription factors were identified from lettuce and the relative molecular weight of the encoding proteins ranged from 17843.82 Da to 75409.15 Da with theoretical isoelectric points of 0.63-9.51, among which there were 92 acidic proteins and 43 basic proteins. In addition, 123 bHLH proteins were unstable proteins and all 135 bHLH proteins were hydrophilic proteins. Each family member contained an N-terminal basic structural domain and a C-terminal HLH structural domain, where the N-terminal could bind specific DNA cis-elements and the C-terminal could maintain the stability of the bHLH protein secondary structure. The 135 bHLH proteins could be divided into 10 sub-families by phylogenetic analysis. In conclusion, 135 bHLH transcription factors in lettuce are identified by genome-wide screening, and the study can provide reference for exploring the biological function of lettuce bHLH gene family.

Key words: lettuce, bHLH, phylogeny analysis, sequence alignment, genome-wide identification

隋心意, 赵小刚, 毛欣, 李亚灵, 温祥珍. 生菜bHLH转录因子家族的鉴定与生物信息学分析[J]. 中国农学通报, 2023, 39(3): 104-110.

SUI Xinyi, ZHAO Xiaogang, MAO Xin, LI Yaling, WEN Xiangzhen. Identification and Bioinformatics Analysis of bHLH Transcription Factor Family in Lactuca sativa L.[J]. Chinese Agricultural Science Bulletin, 2023, 39(3): 104-110.

图/表 5

图1. 生菜bHLH结构域的氨基酸序列比对

图2. 生菜bHLH转录因子家族的保守结构域不同位点上氨基酸字母的高度代表保守性的高低

图3. 生菜中bHLH蛋白家族的系统进化树

图4. 生菜中bHLH蛋白家族的系统进化树

图5. 生菜bHLH家族基因外显子与内含子基因结构分布

参考文献 32

[1]	BUCK M J, ATCHLEY W R. Phylogenetic analysis of plant basic helix-loop-helix proteins[J]. Journal of molecular evolution, 2003, 56(6):742-750. doi: 10.1007/s00239-002-2449-3 pmid: 12911037
[2]	刘文文, 李文学. 植物bHLH转录因子研究进展[J]. 生物技术进展, 2013, 3(1):7-11.
[3]	ATCHLEY W R, FITCH W M. A natural classification of the basic helix-loop-helix class of transcription factors[J]. Proceedings of the national academy of sciences of the United States of America, 1997, 94(10):5172-5176. doi: 10.1073/pnas.94.10.5172 pmid: 9144210
[4]	PIRES N, DOLAN L. Origin and diversification of basic-helix-loop-helix proteins in plants[J]. Molecular biology and evolution, 2010, 27(4):862-874. doi: 10.1093/molbev/msp288 pmid: 19942615
[5]	王勇, 姚勤, 陈克平. 动物bHLH转录因子家族成员及其功能[J]. 遗传, 2010, 32(4):307-330.
[6]	刘晓月, 王文生, 傅彬英. 植物bHLH转录因子家族的功能研究进展[J]. 生物技术进展, 2011, 1(6):391-397.
[7]	TOLEDO-ORTIZ G, HUQ E, QUAIL P H. The Arabidopsis basic/helix-loop-helix transcription factor family[J]. Plant cell, 2003, 15(8):1749-1770. doi: 10.1105/tpc.013839 URL
[8]	BAILEY P C, MARTIN C, TOLEDO-ORTIZ G, et al. Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana[J]. The plant cell, 2003, 15(11):2497-2502. doi: 10.1105/tpc.151140 URL
[9]	LI X, DUAN X, JIANG H, et al. Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis[J]. Plant physiology, 2006, 141(4):1167-1184. doi: 10.1104/pp.106.080580 URL
[10]	HEIM M A, JAKOBY M, WERBER M, et al. The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity[J]. Molecular biology and evolution, 2003, 20(5):735-747. doi: 10.1093/molbev/msg088 pmid: 12679534
[11]	PIRES N, DOLAN L. Early evolution of bHLH proteins in plants[J]. Plant signaling & behavior, 2010, 5(7):911-912.
[12]	王翠, 兰海燕. 植物bHLH转录因子在非生物胁迫中的功能研究进展[J]. 生命科学研究, 2016, 20(4):358-364.
[13]	HUQ E, QUAIL P H. PIF4, a phytochrome-interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in Arabidopsis[J]. The EMBO journal, 2002, 21(10):2441-2450. doi: 10.1093/emboj/21.10.2441 URL
[14]	BERNHARDT C, ZHAO M, GONZALEZ A, et al. The bHLH genes GL3 and EGL3 participate in an intercellular regulatory circuit that controls cell patterning in the Arabidopsis root epidermis[J]. Development (Cambridge, England), 2005, 132(2):291-298.
[15]	KONDOU Y, NAKAZAWA M, KAWASHIMA M, et al. RETARDED GROWTH OF EMBRYO1, a new basic helix-loop-helix protein, expresses in endosperm to control embryo growth[J]. Plant physiology, 2008, 147(4):1924-1935. doi: 10.1104/pp.108.118364 pmid: 18567831
[16]	顾敬楠. 拟南芥绒毡层发育重要转录因子DYT1转录调控研究[D]. 上海: 上海师范大学, 2014.
[17]	HEISLER M G, ATKINSON A, BYLSTRA Y H, et al. SPATULA, a gene that controls development of carpel margin tissues in Arabidopsis, encodes a bHLH protein[J]. Development (Cambridge, England), 2001, 128(7):1089-1098.
[18]	LIU Y, JI X, NIE X, et al. Arabidopsis AtbHLH112 regulates the expression of genes involved in abiotic stress tolerance by binding to their E-box and GCG-box motifs[J]. The new phytologist, 2015, 207(3):692-709. doi: 10.1111/nph.13387 URL
[19]	WANG W S, ZHU J, LU Y T. Overexpression of AtbHLH112 suppresses lateral root emergence in Arabidopsis[J]. Functional plant biology, 2014, 41(4):342-352. doi: 10.1071/FP13253 URL
[20]	NI M, TEPPERMAN J M, QUAIL P H. PIF3, a phytochrome-interacting factor necessary for normal photoinduced signal transduction, is a novel basic helix-loop-helix protein[J]. Cell, 1998, 95(5):657-667. doi: 10.1016/s0092-8674(00)81636-0 pmid: 9845368
[21]	杨攀, 杨诗雯, 李磊, 等. 生菜研究进展综述[J]. 现代园艺, 2020, 43(15):34-36.
[22]	王力伟, 房永雨, 刘红葵, 等. bHLH转录因子的研究进展[J]. 畜牧与饲料科学, 2020, 41(1):23-27.
[23]	何开平, 吴楚. bHLH转录因子对植物形态发生的影响[J]. 安徽农业科学, 2010, 38(35):19957-19959.
[24]	CHU Y, XIAO S, SU H, et al. Genome-wide characterization and analysis of bHLH transcription factors in Panax ginseng[J]. Acta pharmaceutica sinica B, 2018, 8(4):666-677. doi: 10.1016/j.apsb.2018.04.004 URL
[25]	何洁, 顾秀容, 魏春华, 等. 西瓜bHLH转录因子家族基因的鉴定及其在非生物胁迫下的表达分析[J]. 园艺学报, 2016, 43(02):281-294.
[26]	CUI X, WANG Y-X, LIU Z-W, et al. Transcriptome-wide identification and expression profile analysis of the bHLH family genes in Camellia sinensis[J]. Functional & integrative genomics, 2018, 18(5):489-503.
[27]	WANG P, SU L, GAO H, et al. Genome-wide characterization of bHLH genes in grape and analysis of their potential relevance to abiotic stress tolerance and secondary metabolite biosynthesis[J]. Frontiers in plant science, 2018, 9:64. doi: 10.3389/fpls.2018.00064 pmid: 29449854
[28]	MAO K, DONG Q, LI C, et al. Genome wide identification and characterization of apple bHLH transcription factors and expression analysis in response to drought and salt stress[J]. Frontiers in plant science, 2017, 8:480. doi: 10.3389/fpls.2017.00480 pmid: 28443104
[29]	FERRÉ-D'AMARÉ A R, POGNONEC P, ROEDER R G, et al. Structure and function of the b/HLH/Z domain of USF[J]. The EMBO journal, 1994, 13(1):180-189. doi: 10.1002/j.1460-2075.1994.tb06247.x URL
[30]	MURRE C, MCCAW P S, BALTIMORE D. A new DNA binding and dimerization motif in immunoglobulin enhancer binding, daughterless, MyoD, and myc proteins[J]. Cell, 1989, 56(5):777-783. doi: 10.1016/0092-8674(89)90682-x pmid: 2493990
[31]	HUDSON K A, HUDSON M E. The basic helix-loop-helix transcription factor family in the sacred lotus, Nelumbo Nucifera[J]. Tropical plant biology, 2014, 7(2):65-70. doi: 10.1007/s12042-014-9138-4 URL
[32]	郑斌, 文定青, 武红霞, 等. 芒果果实bHLH家族转录因子的生物信息学分析[J]. 热带作物学报, 2019, 40(2):289-299.