植物IPP基因的生物信息学分析

doi:10.7525/j.issn.1673-5102.2024.05.014

摘要/Abstract

摘要：

异戊烯基焦磷酸异构酶（IPP）催化异戊烯焦磷酸与二甲基丙烯基焦磷酸（DMAPP）的可逆异构化反应，对下游萜类产物的合成发挥重要作用。该研究利用生物信息学方法，从稻（Oryza sativa）与拟南芥（Arabidopsis thaliana）等单、双子叶植物基因组中鉴定获得31条IPP基因。系统进化树将IPP分为3簇，其中单子叶植物单独形成一簇，同簇的IPP成员具有相似的结构域，可能执行相似的生物学功能；以稻与拟南芥IPP基因为代表，顺式调控元件分析显示它们含有干旱等响应元件；定量PCR结果显示，稻与拟南芥IPP转录水平的表达模式较为多样化。研究结果为系统认识IPP基因的生物学作用及可能的应用研究提供了理论依据。

关键词: 异戊烯基焦磷酸异构酶, 生物信息学, 干旱胁迫, 脱落酸, 表达模式

Abstract:

Isopentenyl pyrophosphate isomerase（IPP） is responsible for the reversible isomerization of isopentenyl pyrophosphate and dimethylallylpyrophosphate（DMAPP）， playing an important role in the biosynthesis of downstream terpenoid products. In this paper， 31 IPP genes were identified from genomes of various mono- and dicotyledonous plants such as Oryza sativa and Arabidopsis thaliana by bioinformatics method. Phylogenetic analysis indicated that these IPPs were divided into three clades， in which those from monocotyledon plants formed a monophyletic clade. IPPs within the same clade shared similar domains and might have similar biological functions. The analysis on cis-regulatory elements of O. sativa and A. thaliana IPP genes exhibited multiple response elements such as drought response elements. Finally， quantitative PCR results showed that the expression patterns of IPP transcription levels in O. sativa and A. thaliana were diversified. These above results provided theoretical basis for systematic understanding and further application of IPPs.

Key words: isopentenyl pyrophosphate isomerase, bioinformatics, drought stress, abscisic acid, expression pattern

中图分类号:

Q945.78

喻心怡, 冀慧玥, 路萍萍, 周嘉裕, 廖海. 植物IPP基因的生物信息学分析[J]. 植物研究, 2024, 44(5): 774-782.

Xinyi YU, Huiyue JI, Pingping LU, Jiayu ZHOU, Hai LIAO. The Bioinformatic Analysis on the Plant Isopentenyl Pyrophosphate Isomerase[J]. Bulletin of Botanical Research, 2024, 44(5): 774-782.

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物种 Species	IPP基因序列号 IPP gene number
拟南芥 Arabidopsis thaliana	transcript：AT5G16440.1
	transcript：AT3G02780.1
	transcript：AT3G02780.2
稻 Oryza sativa	transcript：Os05g0413400-01
	transcript：Os07g0546000-01
	transcript：Os05g0413400-02

基因 Gene	引物 Primer	序列（5′→3′） Sequence（5′→3′）
AT5G16440	AtIPP1-F	AGAAGGCTGATGCTGGAGATGAAG
AT5G16440	AtIPP1-R	CCCTTTTCAACATGATCCCACCAC
AT3G02780	AtIPP2-F	TCGCTTGAATCTCCTTCGCTGTATG
AT3G02780	AtIPP2-R	TTAGGGTTAGGGTTAGGGCTTCTCC
NC_003074.8	At18s-F	CAGTCGGGGGCATTCGTATTT
NC_003074.8	At18s-R	CAGCCTTGCGACCATACTCC
Os05g0413400	OsIPP1-F	CCACAGAGCGTTCAGTGTTTTT
Os05g0413400	OsIPP1-R	GTTCATGTTCGCCCCATTTTCC
Os07g0546000	OsIPP2-F	CGAGAAAGGCACCCTCAACGA
Os07g0546000	OsIPP2-R	CCAAGCTCCAAACCCAGAAAC
NM_001418593.1	OsACT-F	AGGAAGGCTGGAAGAGGACC
NM_001418593.1	OsACT-R	CGGGAAATTGTGAGGGACAT

蛋白质 Protein	氨基酸长度 Number of amino acids/aa	相对分子质量 Relative molecular mass	等电点 Isoelectric point	相对疏水性 Gravy
D7KZL1	283	32 469.32	6.10	-0.267
D7M847	289	33 103.88	5.72	-0.256
A0A1I9LM15	237	27 550.78	5.71	-0.281
A0A5S9X8V2	284	32 607.49	6.10	-0.264
A0A5S9Y4N3	291	33 213.95	5.69	-0.298
A0A0Q3G4K6	296	33 266.11	5.86	-0.241
I1GTN8	236	27 253.05	4.82	-0.374
A0A0A0LHK1	286	32 466.14	5.84	-0.165
A0A0A0M046	235	27 025.92	5.00	-0.307
A0A165WP97	234	27 066.85	5.06	-0.366
A0A2C9UNS0	303	34 303.98	5.82	-0.300
A0A2C9USD6	302	34 024.76	5.62	-0.251
A0A0N7KKS3	301	34 220.17	6.07	-0.255
A0A0P0X7B7	238	27 341.20	4.90	-0.330
A0A2T7EDT1	298	33 051.92	5.94	-0.175
A0A2T7EX19	234	26 812.49	5.06	-0.412
A0A2T7EX32	237	27 259.10	5.01	-0.384
V7D3U4	301	34 171.89	5.75	-0.300
A0A2K1WQ15	309	34 896.81	5.78	-0.293
K3Z8E5	297	32 873.71	5.94	-0.136
K3ZWJ9	237	27 269.04	4.93	-0.433
K4A2A8	233	26 535.25	5.19	-0.368
A0A4U6VF90	297	32 907.73	5.94	-0.140
A0A4V6DBX0	237	27 269.04	4.93	-0.433
M1AB35	302	34 658.83	6.17	-0.322
M1C547	235	27 168.10	5.06	-0.289
A0A1Z5R2L3	296	32 862.54	6.01	-0.228
C5XAU4	237	27 271.11	4.86	-0.357
A0A438BYS2	191	22 326.46	5.86	-0.572
A0A3L6DPN5	296	33 028.79	5.94	-0.199
A0A3L6E2U3	237	27 242.02	4.84	-0.356

物种 Species	基因 Gene	染色体定位 Gene localization
琴叶拟南芥 Arabidopsis lyrata	ARALYDRAFT_477520	3
琴叶拟南芥 Arabidopsis lyrata	ARALYDRAFT_488496	6
拟南芥 Arabidopsis thaliana	AT3G02780	3
拟南芥 Arabidopsis thaliana	AT5G16440	5
菜豆 Phaseolus vulgaris	PHAVU_L002800g	未确定
毛果杨 Populus trichocarpa	POPTR_019G053700	19
黄瓜 Cucumis sativus	Csa_2G074290	2
黄瓜 Cucumis sativus	Csa_1G656460	1
胡萝卜 Daucus carota var. sativa	DCAR_015080	4
木薯 Manihot esculenta	MANES_13G005300	13
木薯 Manihot esculenta	MANES_12G005500	12
马铃薯 Solanum tuberosum	PGSC0003DMG400007268	4
马铃薯 Solanum tuberosum	PGSC0003DMG400023359	5
葡萄 Vitis vinifera	Vitvi04g01175	4
二穗短柄草 Brachypodium distachyon	BRADI_2g25360v3	2
二穗短柄草 Brachypodium distachyon	BRADI_1g25350v3	1
稻 Oryza sativa	Os05g0413400	5
稻 Oryza sativa	Os07g0546000	7
粱 Setaria italica	SETIT_022815mg	3
	SETIT_030981mg	2
	SETIT_033005mg	2
狗尾草 Setaria viridis	SEVIR_3G247700v2	3
狗尾草 Setaria viridis	SEVIR_2G354200v2	2
高粱 Sorghum bicolor	SORBI_3009G137700	9
高粱 Sorghum bicolor	SORBI_3002G330500	2
霍尔稷草 Panicum hallii var. hallii	GQ55_3G269900	3
	GQ55_2G389900	2
	GQ55_2G390000	2
玉蜀黍 Zea mays	Zm00001eb349410	8
玉蜀黍 Zea mays	Zm00001eb323510	7

顺式作用元件 Cis-acting elements	AT3G02780	AT5G16440	Os05t0413400	Os07t0546000
脱落酸响应元件 ABRE	3	1	4	7
抗氧化响应元件 ARE	2	3	2	3
防御和应激响应元件 Defense and stress responsive	0	1	0	0
干旱响应元件 Drought induced-responsive	2	1	0	1
雌激素响应元件 ERE	2	0	2	0
光响应元件 Light responsive	10	8	15	12
低温响应元件 LTR	1	0	1	1
茉莉酸甲酯响应元件 MeJA-responsive	0	2	6	4
分生组织表达 Meristem expression	1	1	0	0
氧化应激响应元件 As-1	0	1	0	0
水杨酸响应元件 Salicylic acid-responsive	2	1	0	0
盐应激响应元件 Salt stress-responsive	5	10	0	0
压力响应元件 Stress-responsive	6	7	5	3
伤口响应元件 Wounding responsive	1	1	4	0
玉米醇溶蛋白代谢响应元件 Zein metabolism regulation	1	0	0	0