NAD依赖型去乙酰化酶SRT在植物表观遗传调控中的作用

doi:10.13560/j.cnki.biotech.bull.1985.2022-0971

摘要/Abstract

摘要：

SRT（sirtuin）是一类与酵母沉默信息调节蛋白2（yeast silent information regulator 2, Sir2）高度同源的烟酰胺腺嘌呤二核苷酸（nicotinamide adenine dinucleotide, NAD）依赖型蛋白质去乙酰化酶。真核生物中，SRT通过催化特异组蛋白或非组蛋白赖氨酸（Lys）残基的去乙酰化反应，调控染色体稳定、基因转录及相关蛋白的活性状态。研究表明，SRT介导的去乙酰化在植物代谢、生长发育和逆境胁迫响应等过程中起重要作用。本文对植物SRT的鉴定、结构与分类、生物进化、表观遗传调控机制和生物学过程调控方面的研究加以综述，并对该蛋白未来研究方向进行展望，以期为今后SRT介导的表观遗传学生物过程的研究提供基础。

关键词: NAD, 去乙酰化酶, 表观遗传, 生长发育, 胁迫响应

Abstract:

Sirtuin（SRT）is one of nicotinamide adenine dinucleotide（NAD）-dependent protein deacetylases being highly homologous to yeast silencing information regulator 2（Sir2）. In eukaryotes, SRT regulates chromosome stability, gene transcription and the activity status of related proteins by catalyzing the deacetylation of specific or non-histone lysine（Lys）residues. Studies have shown that SRT-mediated deacetylation plays an important role in plant metabolism, growth and development, and stress response. In this review, the identification, structure and classification, biological evolution, epigenetic regulation mechanism and biological processes of SRT in plants are summarized, and its future research directions are also prospected, aiming to provide a basis for future research on SRT-mediated epigenetic biological processes in plant.

Key words: NAD, deacetylase, epigenetics, growth and development, stress response

魏明, 王欣玉, 伍国强, 赵萌. NAD依赖型去乙酰化酶SRT在植物表观遗传调控中的作用[J]. 生物技术通报, 2023, 39(4): 59-70.

WEI Ming WANG Xin-yu WU Guo-qiang ZHAO Meng. The Role of NAD-dependent Deacetylase SRT in Plant Epigenetic Inheritance Regulation[J]. Biotechnology Bulletin, 2023, 39(4): 59-70.

图/表 4

表1 不同植物的SRT基因家族

Table 1 SRT gene families in different plant species

物种 Species	基因名称Gene name	蛋白长度 Protein length/aa	分子量 Mw/kD	等电点 pI	亚细胞定位 Subcellular localization	参考文献 Reference
拟南芥Arabidopsis thaliana	AtSRT1	473	52.64	8.54	Nucleus	[22]
拟南芥Arabidopsis thaliana	AtSRT2	376	41.87	9.08	Mitochondria	[22]
水稻Oryza sativa	OsSRT1	483	53.90	9.38	Nucleus	[23-24]
水稻Oryza sativa	OsSRT2	393	43.47	8.79	Mitochondria	[23-24]
葡萄Vitis vinifera	VvSRT1	467	52.04	9.24	/	[25]
葡萄Vitis vinifera	VvSRT2	382	41.99	9.09	/	[25]
番茄Solanum lycopersicum	SlSRT1	472	52.50	9.10	Nucleus	[26-27]
番茄Solanum lycopersicum	SlSRT2	389	43.06	8.97	Mitochondria	[26-27]
大豆Glycine max	GmSRT1	393	43.46	9.40	Mitochondria chloroplast	[28-29]
	GmSRT2	392	43.21	9.32	Mitochondria chloroplast
	GmSRT3	434	48.21	9.11	Nucleus chloroplast
	GmSRT4	479	53.20	9.15	Nucleus cytoplasm
地钱Marchantia polymorpha	MpSIRT4	377	41.22	8.36	Mitochondria	[30]
	MpSIRT5	285	30.75	7.02	/
	MpSIRT6	379	41.39	7.60	Nucleus cytosol
玉米Zea mays	ZmSRT1	437	49.05	9.31	/	[31]
玉米Zea mays	ZmSRT2	351	39.19	8.91	/	[31]
茶树Camellia sinensis	CsSRT1	566	63.46	9.29	Nucleus	[32]
	CsSRT2	460	51.36	8.82	Chloroplast
	CsSRT3	479	53.39	9.11	Chloroplast
	CsSRT4	177	19.77	9.58	Nucleus
石斛Dendrobium officinale	DoSRT1	409	45.50	8.19	Nucleus	[33]
石斛Dendrobium officinale	DoSRT2	279	30.82	7.04	Nucleus	[33]
白梨Pyrus bretschneideri	PbSRT1	484	54.13	9.27	Nucleus cytoplasm	[34]
白梨Pyrus bretschneideri	PbSRT2	394	43.46	8.80	Chloroplast vacuole	[34]
大麻Cannabis sativa	CsSRT1	484	53.61	9.04	Nucleus chloroplast	[35]
大麻Cannabis sativa	CsSRT2	397	43.49	8.37	Nucleus chloroplast	[35]
高粱Sorghum bicolor	SbSRT1	476	53.24	8.88	Chloroplast	[36]
高粱Sorghum bicolor	SbSRT2	484	53.66	9.17	Chloroplast	[36]
甜菜Beta vulgaris	BvSRT1	496	55.64	9.22	/	Unpublished data
甜菜Beta vulgaris	BvSRT2	389	43.37	8.89	/	Unpublished data

图1 植物SRTs三维空间结构利用SWISS-MODEL同源建模工具预测水稻SRT1（A）和SRT2（B）蛋白SIR2结构域三维结构[38]。将SRTs SIR2结构域蛋白序列在SWISS-MODEL模板库比对并基于GMQE和QMEANZ分析分别从智人（Homo sapiens, SRT1 SMTL ID：3k35.1）和非洲蟾蜍（Xenopus tropicalis, SRT2 SMTL ID: 5oj7.1）两个物种中获得两个高得分SRT1/2晶体模板[43⇓-45]。最后通过Swiss PDB和PyMOL软件对SRT1和SRT2蛋白的SIR2结构域进行可视化和比较[46]

Fig. 1 Three-dimensional structure of SRTs in plants The three-dimensional structure of SIR2 domain in SRT1（A）and SRT2（B）proteins from Oryza sativa was predicted by homology modeling using SWISS-MODEL workspace[38]. The protein sequences of SRTs SIR2 domain were applied to search for a suitable template in the SWISS-MODEL Template Library（SMTL）and two crystal structures of SIR2（SRT1/2）from Homo sapiens（SMTL ID: 3k35.1 for SRT1）and Xenopus tropicalis（SMTL ID: 5oj7.1 for SRT2）were selected as the templates by the Global Model Quality Estimation（GMQE）values and the QMEANZ-scores[43-45]. Visualization and comparison of the SIR2 domains from SRT1 and SRT2 protein were performed through the Swiss PDB viewer and PyMOL program[46]

图2 不同物种SRTs系统发育分析

Fig. 2 Phylogenetic analysis of SRTs in different species SRTs基因的来源、名称及蛋白登录号如下: 拟南芥（Arabidopsis thaliana）AtSRT1（NP_200387.1）, AtSRT2（NP_001078550.1）；水稻（Oryza sativa）OsSRT1（XP_015636502.1）, OsSRT2（XP_015618411.1）；葡萄（Vitis riparia）VrSRT1（XP_034679101.1）, VrSRT2（XP_010652926.1）；番茄（Solanum lycopersicum）SlSRT1（XP_004244044.1）, SlSRT2（XP_004236824.1）；大豆（Glycine max）GmSRT1（XP_003522478.1）, GmSRT1（XP_003528059.2）, GmSRT3（KHN11152.1）, GmSRT4（XP_003551434.1）；地钱（Marchantia polymorpha）MpSIRT（PTQ32963.1）, MpSIRT5（PTQ31328.1）, MpSIRT6（PTQ40866.1）；玉米（Zea mays）ZmSRT1（NP_001105577.1）, ZmSRT2（XP_020400867.1）；白梨（Pyrus bretschneideri）PbSRT1（XP_009375070.1）, PbSRT2（XP_009375792.1）；大麻（Cannabis sativa）CsSRT1（XP_030478610.1）, CsSRT2（XP_030499415.1）；高粱（Sorghum bicolor）SbSRT1（XP_021318881.1）, SbSRT2（XP_002442918.2）；甜菜（Beta vulgaris）BvSRT1（XP_019104724.1）, BvSRT2（XP_010674411.1）；菠菜（Spinacia oleracea）SoSRT1（XP_021842668.1）, SoSRT2（XP_021835887.1）；油菜（Brassica napus）BnSRT1（XP_022570011.1）, BnSRT2（XP_013675778.1）；芜菁（Brassica rapa）BrSRT1（XP_009132354.1）, BrSRT2（XP_033140955.1）；荠菜（Capsella rubella）CrSRT1（XP_023641545.1）, CrSRT2（XP_023637530.1）；烟草（Nicotiana tabacum）NtSRT1（XP_016490271.1）, NtSRT2（XP_016482509.1）；小麦（Triticum aestivum）TaSRT1（XP_044455034.1）, TaSRT2（XP_044380222.1）；谷子（Setaria italica）SiSRT1（XP_004975166.1）, SiSRT2（XP_004977219.1）；狗尾草（Setaria viridis）SvSRT1（XP_034603198.1）, SvSRT2（XP_034606073.1）；花生（Arachis hypogaea）AhSRT1（XP_025626741.1）, AhSRT2（XP_025615786.1）；木豆（Cajanus cajan）CcSRT1（XP_020232854.1）, CcSRT2（XP_020234960.1）；鹰嘴豆（Cicer arietinum）CaSRT1（XP_004516096.2）, CaSRT2（XP_004502971.1）；大叶栎（Quercus lobata）QlSRT1（XP_030931433.1）, QlSRT2（XP_030940716.1）；番木瓜（Carica papaya）CpSRT1（XP_021906115.1）, CpSRT2（XP_021900464.1）；南瓜（Cucurbita moschata）CmSRT1（XP_022936498.1）, CmSRT2（XP_022948086.1）；蒺藜苜蓿（Medicago truncatula）MtSRT1（XP_013460060.1）, MtSRT2（XP_003602659.1）；豇豆（Vigna unguiculata）VuSRT1（XP_027930984.1）, VuSRT2（XP_027901777.1）；冬瓜（Benincasa hispida）BhSRT1（XP_038900035.1）, BhSRT1（XP_038902560.1）；盐芥（Eutrema salsugineum）EsSRT1（XP_006401417.1）, EsSRT2（XP_006399395.1）

图2 不同物种SRTs系统发育分析

图3 组蛋白（去）乙酰化与基因转录的动态调控

Fig. 3 Diagram of histone acetylation/deacetylation modif-ication and dynamic regulation of gene transcription HAT：组蛋白乙酰转移酶 Histone acetyltransferase；HDACs：组蛋白去乙酰化酶 Histone deacetylases；Ac：乙酰基 Acetyl；TF：转录因子 Transcription factor

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