菠菜高迁移率族基因家族鉴定及表达分析

doi:10.13560/j.cnki.biotech.bull.1985.2024-0420

摘要/Abstract

摘要：

【目的】高迁移率族蛋白（high mobility group, HMG）参与DNA结构/染色质的调节，在基因转录调控中起重要作用。鉴定菠菜（Spinacia oleracea L.）HMG基因家族，为菠菜HMG蛋白生物学功能研究提供理论依据。【方法】从全基因组水平对菠菜SoHMG家族成员进行鉴定，并对家族成员进行理化性质、基因结构、保守基序、启动子元件及水杨酸响应表达谱等分析。【结果】菠菜基因组含有16个SoHMG基因家族成员，编码区长度为240-4 029 bp，编码氨基酸79-1 342，分散在6条染色体上。进化树分析将SoHMG划分为2个亚家族，包括3个A亚族和13个B亚族成员，同一亚家族成员具有类似的保守结构域。在B亚家族启动子中发现了水杨酸等激素响应元件。SoHMG基因在菠菜根、茎、叶中均有表达，其中4个基因在叶中表达量较高。绝大多数SoHMG基因表达量在水杨酸处理下表达上调，其中，SoHMGB1（SOV1g000250.1）、SoHMGB7（SOV5g026260.1）、SoHMGB2（SOV1g027200.1）上调幅度最为显著，上调倍数10倍以上。【结论】菠菜HMG基因家族注释得到16个成员，分为2个亚族，其中3个基因（SoHMGB1、SoHMGB7和SoHMGB2）在水杨酸处理下显著上调，可能在水杨酸信号响应中发挥重要作用。

关键词: 菠菜, HMG, 鉴定, 水杨酸, 基因表达

Abstract:

【Objective】High mobility group（HMG）proteins participate in the regulation of DNA structure and chromatin, which play an important role in gene transcription regulation. Identifying the family of HMG genes in spinach（Spinacia oleracea L.）may provide a theoretical basis for studying the biological functions of spinach HMG proteins.【Method】The members of the spinach SoHMG family were identified at the whole genome level, and their physicochemical properties, gene structure, conserved motifs, promoter elements, and salicylic acid-responsive expression profiles were analyzed. 【Result】The spinach genome contained 16 members of the SoHMG gene family, with a coding region length of 240-4 029 bp and a coding amino acid number between 79-1 342. The 16 SoHMG genes were scattered across six chromosomes. By evolutionary tree analysis, SoHMG members were divided into two subfamilies, including three members in A subfamily and 13 in B subfamily. The members of the same subfamily have similar conserved domains. Some hormone-responsive elements, such as salicylic acid（SA）, were found in the promoter of the SoHMGB subfamily. The SoHMG genes were expressed in the roots, stems, and leaves of spinach. Most of genes had higher expressions in the leaves. SA treatment induced the expressions of most of the SoHMG genes. Among them, the expressions of SoHMGB1（SOV1g000250.1）, SoHMGB7（SOV5g026260.1）, and SoHMGB2（SOV1g027200.1）were more than 10 times higher than those in control. 【Conclusion】There are 16 members of HMG gene family in spinach genome, which is divided into 2 subfamilies. Three genes（（SoHMGB1, SoHMGB7, and SoHMGB2））are significantly upregulated under SA treatment, which may play an important role in the SA signal response.

Key words: spinach, HMG, identification, salicylic acid, gene expression

邹婷婷, 杨莉, 曲茜彤, 陈子航, 潘曦, 邵鸿旭, 王小丽. 菠菜高迁移率族基因家族鉴定及表达分析[J]. 生物技术通报, 2024, 40(12): 84-92.

ZOU Ting-ting, YANG Li, QU Xi-tong, CHEN Zi-hang, PAN Xi, SHAO Hong-xu, WANG Xiao-li. Identification and Expression Analysis of High Mobility Gene Families in Spinach[J]. Biotechnology Bulletin, 2024, 40(12): 84-92.

图/表 8

表1 实时荧光定量PCR引物序列

Table 1 Primer sequences for real-time fluorescence quantitative PCR

基因编号Gene ID	正向引物Forward primer（5'-3'）	反向引物Reverse primer（5'-3'）
SOV1g000250.1	TGGTGAACTCTGGAACAAA	CTCGTCTTCATCAGTCTCG
SOV1g027200.1	TCAACTACGGAGCGATGGC	TCCACATAGCAGAAACAGC
SOV2g035530.1	GCAACGACCGTGGAAAAAC	CCTTGACACCCTTGGAATC
SOV3g013500.1	GTTGCTATTACTGATGCTGC	AGGAATGTGATACAAGATGC
SOV4g023910.1	AAAAGAGAACCCAAATGCAG	CGCGCTTTCTTTGCTGACA
SOV5g003140.1	CTGCATCTTTCATTCTTACGTC	TTCAACAACATAGTCGGTCT
SOV5g026260.1	CATCAAAGAGGTCAAAATCG	TATTCTGCCATTGCCCTGT
SOV5g034730.1	TTTTATGCCTCGGGTATTAGCC	TGCCTGCTGCTTCATCTGA
SOV5g037650.1	CCAAGTGCCTTCTTCGTCT	GCCATCTTCATCATCCTCA
SOV6g009370.1	AAGACTCAGACTCACTCGG	GGGACTATTGCTAACCTAA
SOV6g009420.1	CACACGAAAGAGTTGAAGA	GGGACTATTGCTAACCTAA
SOV6g043170.1	AAGCCTACTATGACTCTGCC	CACTTTGCACCCATTATGTT
SOV4g034920.1	CCCAACTTCATCCGTCGTG	AAACCCCTTCACCCCCAAT
SOV2g030330.1	GCCTACTAAGGGGATTGTGTGGA	TCATTGGCGGTTCATCAGG
SOV4g003160.1	TCTGTTGGGCTGGATTCGC	CTCTTCCTTGGACGACCTCT

图1 菠菜与拟南芥、玉米HMG家族进化树构建

Fig. 1 Construction of evolutionary tree for HMG family in spinach, Arabidopsis and maize

图2 SoHMG基因家族保守结构域（A）及保守基序（B）分析

Fig. 2 Analysis of conserved domains (A) and conserved motifs (B) in the SoHMG gene family

图3 SoHMG基因家族成员基因结构分析

Fig. 3 Analysis of gene structure of SoHMG gene family members

图4 菠菜与拟南芥HMG家族成员共线性分析

Fig. 4 Collinearity analysis of spinach and Arabidopsis HMG family members

图5 SoHMG基因家族顺式作用元件分析

Fig. 5 Analysis of cis-acting elements in the SoHMG gene family

图6 菠菜根茎叶中SoHMG基因相对表达量

Fig. 6 Relative expressions of SoHMG genes in spinach's roots, stems, and leaves

图7 菠菜水杨酸处理后SoHMG基因相对表达量不同小写字母表示处理间差异显著（Tukey’test, P<0.05）

Fig. 7 Relative expressions of SoHMG gene in spinach after SA treatment Different lower-case letters indicate significant differences between treatments（Tukey’test, P<0.05）

参考文献 30

[1]	Cai XF, Sun XP, Xu CX, et al. Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits[J]. Nat Commun, 2021, 12(1): 7246.
[2]	Bianchi ME, Beltrame M, Paonessa G. Specific recognition of cruciform DNA by nuclear protein HMG1[J]. Science, 1989, 243(4894Pt1): 1056-1059.
[3]	Grasser KD, Launholt D, Grasser M. High mobility group proteins of the plant HMGB family: Dynamic chromatin modulators[J]. Biochim Biophys Acta, 2007, 1769(5/6): 346-357.
[4]	Antosch M, Mortensen SA, Grasser KD. Plant proteins containing high mobility group box DNA-binding domains modulate different nuclear processes[J]. Plant Physiol, 2012, 159(3): 875-883. doi: 10.1104/pp.112.198283 pmid: 22585776
[5]	Hu LS, Yang XY, Yuan DJ, et al. GhHmgB3 deficiency deregulates proliferation and differentiation of cells during somatic embryogenesis in cotton.[J]. Plant Biotechnol J, 2011, 9(9): 1038-1048. doi: 10.1111/j.1467-7652.2011.00617.x pmid: 21554528
[6]	Hamilton DJ, Hein AE, Wuttke DS, et al. The DNA binding high mobility group box protein family functionally binds RNA[J]. Wiley Interdiscip Rev RNA, 2023, 14(5): e1778.
[7]	Stemmer C, Schwander A, Bauw G, et al. Protein kinase CK2 differentially phosphorylates maize chromosomal high mobility group B(HMGB)proteins modulating their stability and DNA interactions[J]. J Biol Chem, 2002, 277(2): 1092-1098.
[8]	王春瑶, 雷晓锦, 刘中原. 逆境胁迫下山新杨PdbHMGs基因表达模式分析[J]. 植物研究, 2023, 43(6): 932-942. doi: 10.7525/j.issn.1673-5102.2023.06.015
	Wang CY, Lei XJ, Liu ZY. Expression pattern analysis of PdbHMGs genes in Populus davidiana × P. bolleana under abiotic stress[J]. Bull Bot Res, 2023, 43(6): 932-942.
[9]	Kwak KJ, Kim JY, Kim YO, et al. Characterization of transgenic arabidopsis plants overexpressing high mobility group B proteins under high salinity, drought or cold stress[J]. Plant and Cell Physiol, 2007, 48(2): 221-231.
[10]	Villano C, D'Amelia V, Esposito S, et al. Genome-wide HMG family investigation and its role in glycoalkaloid accumulation in wild tuber-bearing Solanum commersonii[J]. Life, 2020, 10(4): 37.
[11]	Xu K, Chen SJ, Li TF, et al. Overexpression of OsHMGB707, a high mobility group protein, enhances rice drought tolerance by promoting stress-related gene expression[J]. Front Plant Sci, 2021, 12: 711271.
[12]	Jang JY, Kwak KJ, Kang H. Expression of a high mobility group protein isolated from Cucumis sativus affects the germination of Arabidopsis thaliana under abiotic stress conditions[J]. J Integr Plant Biol, 2008, 50(5): 593-600. doi: 10.1111/j.1744-7909.2008.00650.x
[13]	Choi HW, Manohar M, Manosalva P, et al. Activation of plant innate immunity by extracellular high mobility group box 3 and its inhibition by salicylic acid[J]. PLoS Pathog, 2016, 12(3): e1005518.
[14]	张小茜, 全先庆, 单雷, 等. 高迁移率族蛋白A的特征及其在转录中的调控[J]. 生命的化学, 2006, 26(5): 414-417.
	Zhang XQ, Quan XQ, Shan L, et al. Characteristics of high mobility group protein A and its regulation in transcription[J]. Chem Life, 2006, 26(5): 414-417.
[15]	Zhao J, Paul LK, Grafi G. The maize HMGA protein is localized to the nucleolus and can be acetylated in vitro at its globular domain, and phosphorylation by CDK reduces its binding activity to AT-rich DNA[J]. Biochim Biophys Acta, 2009, 1789(11/12): 751-757.
[16]	Chen CJ, Wu Y, Li JW, et al. TBtools-II: A “One for All, All for One” bioinformatics platform for biological big-data mining[J]. Mol Plant, 2023, 16(11): 1733-1742.
[17]	Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2^-ΔΔCtmethod[J]. Methods, 2001, 25(4): 402-408. doi: 10.1006/meth.2001.1262 pmid: 11846609
[18]	Wang XL, Cai XF, Xu CX, et al. Identification and characterization of the NPF, NRT2 and NRT3in spinach[J]. Plant Physiol Biochem, 2021, 158: 297-307.
[19]	Wu Q, Zhang WS, Pwee KH, et al. Cloning and characterization of rice HMGB1 gene[J]. Gene, 2003, 312: 103-109. pmid: 12909345
[20]	Tang HB, Wang XY, Bowers JE, et al. Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps[J]. Genome Res, 2008, 18(12): 1944-1954. doi: 10.1101/gr.080978.108 pmid: 18832442
[21]	Luthringer R, Raphalen M, Guerra C, et al. Repeated co-option of HMG-box genes for sex determination in brown algae and animals[J]. Science, 2024, 383(6689): eadk5466.
[22]	Young Jang J, Jin Kwak K, Kang H. Molecular cloning of a cDNA encoding a high mobility group protein in Cucumis sativus and its axpression by abiotic stress treatments[J]. J Plant Physiol, 2007, 164(2): 205-208.
[23]	时明坤. TaHMGB家族的生物信息学分析与TaHMGB11-7A功能的初步鉴定[D]. 郑州: 河南农业大学, 2021.
	Shi MK. Bioinformatics analysis of TaHMGB family and preliminary functional identification of TaHMGB11-7A function[D]. Zhengzhou: Henan Agricultural University, 2021.
[24]	Kaya C, Ugurlar F, Ashraf M, et al. Salicylic acid interacts with other plant growth regulators and signal molecules in response to stressful environments in plants[J]. Plant Physiol Biochem, 2023, 196: 431-443.
[25]	Ullah C, Schmidt A, Reichelt M, et al. Lack of antagonism between salicylic acid and jasmonate signalling pathways in poplar[J]. New phytol, 2022, 235(2): 701-717.
[26]	Rastegar S, Shojaie A, Koy RAM. Foliar application of salicylic acid and calcium chloride delays the loss of chlorophyll and preserves the quality of broccoli during storage[J]. J Food Biochem, 2022, 46(8): e14154.
[27]	Puthusseri B, Divya P, Lokesh V, et al. Salicylic acid-induced elicitation of folates in coriander(Coriandrum sativum L.) improves bioaccessibility and reduces pro-oxidant status[J]. Food Chem, 2013, 136(2): 569-575. doi: 10.1016/j.foodchem.2012.09.005 pmid: 23122099
[28]	王惠宇, 门艺涵, 樊婕, 等. 外源水杨酸影响苦荞类黄酮生物合成及相关基因表达模式[J]. 植物生理学报, 2024, 60(1): 117-129.
	Wang HY, Men YH, Fan J, et al. Effects of exogenous salicylic acid on flavonoid biosynthesis and expression patterns of related genes in tartary buckwheat[J]. Plant Physiol J, 2024, 60(1): 117-129
[29]	张云秀, 蒋旭, 尉春雪, 等. 紫花苜蓿高迁移率族蛋白基因MsHMG-Y调控花期的功能分析[J]. 中国农业科学, 2022, 55(16): 3082-3092. doi: 10.3864/j.issn.0578-1752.2022.16.002
	Zhang YX, Jiang X, Yu CX, et al. The functional analysis of high mobility group MsHMG-Y involved in flowering regulation in Medicago sativa L[J]. Sci Agric Sin, 2022, 55(16): 3082-3092.
[30]	Mollah MMI, Choi HW, Yeam I, et al. Salicylic acid, a plant hormone, suppresses phytophagous insect immune response by interrupting HMG-like DSP1[J]. Front Physiol, 2021, 12: 744272.

编辑推荐 0

Metrics

阅读次数

全文

HTML			PDF

最新录用	在线预览	正式出版	最新录用	在线预览	正式出版
0	0	13	0	0	61

来源	本网站	其他网站

次数	67	7
比例	91%	9%

摘要

最新录用	在线预览	正式出版

0	0	98

	来源	本网站

	次数	98
	比例	100%