木薯泛素结合酶的生物信息学分析

贾利强

doi:10.13417/j.gab.040.002765

木薯泛素结合酶的生物信息学分析

贾利强^,

贵州师范学院生物科学学院

基金项目:

贵州师范学院博士科研启动基金项目(2019BS004)资助

详细信息

通讯作者:
贾利强,liqiangj@zju.edu.cn

中图分类号: S533
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出版历程
- 刊出日期: 2021-08-24

Bioinformatic Analysis of the Ubiquitin Conjugating Enzyme Gene Family in Cassava

JIA Li-qiang^,

School of Biological Sciences, Guizhou Normal College

摘要

摘要: 泛素结合酶(ubiquitin conjugating enzyme, E2)在植物蛋白质的泛素化降解系统中处于中心地位，广泛参与调控植物的生长发育以及对逆境胁迫的响应信号途径。木薯(Manihot esculenta Crantz)是许多热带国家主要的粮食作物。随着木薯全基因组序列的公布，木薯功能基因的研究进入了快车道，但有关木薯E2基因的研究尚未有报道。本研究从Phytozome木薯数据库中获得了62个木薯E2基因，并对其进行了生物信息学分析。结果表明，62个木薯E2基因散布在18条染色体上，并且chr2上定位的E2基因最多。进化树分析结果表明，这62个木薯E2基因分成16个亚家族，包括两个UEV亚家族。基因结构分析结果也支持这一结果。利用半定量PCR的方法，检测了部分E2基因在木薯不同组织器官中的表达模式，以及应答模拟盐和干旱胁迫条件下的表达模式，结果表明，3个E2基因(MeUBC14, MeUBC33和MeUBC56)表现出组织特异性表达，而所选的其他E2基因呈现组成性表达模式。在模拟盐和干旱胁迫条件下，分别有10个和11个木薯E2基因表达上调，其中有8个基因同时受到模拟盐和干旱的诱导上调表达。在这两种胁迫条件下，MeUBC8基因的表达不受影响。这些结果表明木薯E2基因可能广泛参与木薯生长发育及抗逆胁迫途径。
- 木薯 /
- 泛素结合酶 /
- 基因家族 /
- 胁迫 /
- 基因表达
Abstract: Ubiquitin binding enzymes（E2） play a central role in the ubiquitination and degradation system of plant proteins and are widely involved in regulating the growth and development of plants and signaling pathways in response to stress. Cassava is a staple food crop and the main income source in many tropical countries. With cassava whole genome sequencing, functional gene research in cassava entered in fast lane. However, the study about cassava E2 genes has not been reported yet. In this study, 62 MeE2 s were obtained from the the publicly available database Phytozome and performed bioinformatic analysis. The results showed that 62 MeE2 s were widely but unevenly distributed on 18 chromosomes and chr2 contains the largest number of MeE2 s with a total of six genes. The phylogenetic analysis revealed that MeE2 s can be divided into 16 groups with two UEV subfamily. The analysis of MeE2 gene structure indicated that MeE2 members in the same subfamilies shared a similar exon/intron structure. Using semi RT-PCR technic, the expression pattern of some MeE2 s in different cassava tissues or in responsive to salt/drought stress was detected. The results showed that three E2 genes（MeUBC14, MeUBC33 and MeUBC56） had tissue specific expression pattern, while the other genes had constitutive expression pattern. Under salt and drought stress conditions, 10 and 11 MeE2 expression were upregulated, respectively, and 8 MeE2 s were induced by two stress conditions at the same time. However, the expression of MeUBC8 was not altered under the two stress conditions. The results indicated that MeE2 gene family is widely involved in cassava growth and abiotic tolerance.
- Manihot esculenta Crantz /
- Ubiquitin conjugating enzyme /
- Gene family /
- Stress /
- Gene expression

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参考文献(22)

[1]	Burns A.,Gle a dow R.,Cliff J.,Zacarias A.,and Cavagnaro T.,2010,Cassava:the drought,war and famine crop in a changing world,Sustainability,2(11):3572-3607.
[2]	Cui F.,Liu L.J.,Zhao Q.Z.,Zhang Z.H.,Li Q.L.,Lin B.Y.,Wu Y.R.,Tang S.Y.,and Xie Q.,2012,Arabidipsis ubiquitin conjugase UBC32 is an ERAD component that functions in brassinosteroid-mediated salt stress tolerance,Plant Cell,24(1):233-244.
[3]	Dong C.,Hu H.G.,Jue D.W.,Zhao Q.F.,Chen H.L.,Xie J.H.,and Jia L.Q.,2016,The banana E2 gene family:genomic identification,characterization,expression profiling analysis,Plant Sci.,245:11-24.
[4]	E Z.G.,Zhang Y.P.,Li T.T.,Wang L.,and Zhao H.M.,2015,Characterization of the ubiquitin-conjugating enzyme gene family in rice and evaluation of expression profiles underabiotic stresses and hormone treatments,PLoS ONE,10(4):e0122621.
[5]	Jeon E.H.,Pak J.H.,Kim M.J.,Kim H.J.,Shin S.H.,Lee J.H.,Kim D.H.,Oh J.S.,Oh B.J.,Jung H.W.,and Chung Y.S.,2012,Ectopic expression of ubiquitin conjugating enzyme gene from wild rice,OgUBC1,confers resistance against UV-B radiation and Botrytis infection in Arabidopsis thaliana,Biochem.Biophys.Res.Commun.,427(2):309-314.
[6]	Jones D.,Crowe E.,Stevens T.A.,and Candido E.P.M.,2002,Functional and phylogenetic analysis of the ubiquitylation system in Caenorhabditis elegans:ubiquitin-conjugating enzymes,ubiquitin-activating enzymes,and ubiquitin-like proteins,Genome.Biol.,3(1):RESEARCH0002.
[7]	Jue D.W.,Sang X.L.,Lu S.Q.,Dong C.,Zhao Q.F.,Chen H.L,and Jia L.Q.,2015,Genome-wide identification,phylogenetic and expression analyses of the ubiquitin-conjugating enzyme gene family in maize,PLoS ONE,10(11):e0143488.
[8]	Kraft E.,Stone S.L.,Ma L.,Su N.,Gao Y.,Lau O.S.,Deng X.W.,and Callis J.,2005,Genome analysis and functional characterization of the E2 and RING-type E3 ligase ubiquitination enzymes of Arabidopsis,Plant Physiol.,139(4):1597-1611.
[9]	Li W.,and Schmidt W.,2010,A lysine-63-linked ubiquitin chainforming conjugase,UBC13,promotes the developmental responses to iron deficiency in Arabidopsis roots,Plant J.,62(2):330-343.
[10]	Nandi D.,Tahiliani P.,Kumar A.,and Chandu D.,2006,The ubiquitin-proteasome system,J.Biosci.,31(1):137-155.
[11]	Park B.S.,Seo J.S.,and Chua N.H.,2014,Nitrogen limitation adaptation recruits phosphate2 to target the phosphate transporter PT2 for degradation during the regulation of Arabidopsis phosphate homeostasis,Plant Cell,26 (1):454-464.
[12]	Park C.H.,Chen S.,Shirsekar G.,Zhou B.,Khang C.H.,Songkumarn P.,Afzal A.J.,Ning Y.,Wang R.,Bellizzi M.,Valent B.,and Wang G.L.,2012,The Magnaporthe oryzae effector Avr Piz-t targets the RING E3 ubiquitin ligase APIP6 to suppress pathogen-associated molecular pattern-triggered immunity in rice,Plant Cell,24(11):4748-4762.
[13]	Sadanandom A.,Bailey M.,Ewan R.,Lee J.,and Nelis S.,2012,The ubiquitin-proteasome system:central modifier of plant signaling,New Phytol.,196(1):13-28.
[14]	Santner A.,and Estelle M.,2010,The ubiquitin-proteasome system regulates plant hormone signaling,Plant J.,61(6):1029-1040.
[15]	Smalle J.,and Vierstra R.D.,2004,The ubiquitin 26S proteasome proteolytic pathway,Ann.Rev.Plant Biol.,55:555-590.
[16]	Wang Y.Y.,Wang W.H.,Cai J.H.,Zhang Y.R.,Qin G.Z.,and Tian S.P.,2014,Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening,Genome Biol.,15(12):548.
[17]	Welchman R.L.,Gordon C.,and Mayer R.J.,2005,Ubiquitin and ubiquitin like proteins as multifunctional signals,Nat.Rev.Mol.Cell Biol.,6(8):599-609.
[18]	Xu L.,Menard R.,Berr A.,Fuchs J.,Cognat V.,Meyer D.,and Shen W.H.,2009,The E2 ubiquitin-conjugating enzymes,At UBC1 and At UBC2,play redundant roles and are involved in activation of FLC expression and repression of flowering in Arabidopsis thaliana,Plant J.,57(2):279-288.
[19]	Yanagawa Y.,Sullivan J.A.,Komatsu S.,Gusmaroli G.,Suzuki G.,Yin J.,Ishibashi T.,Saijo Y.,Rubio V.,Kimura S.,Wang J.,and Deng X.W.,2004,Arabidopsis COP10 forms a complex with DDB1 and DET1 in vivo and enhances the activity of ubiquitin conjugating enzymes,Genes Dev.,18(17):2172-2181.
[20]	Yang S.,Arguello J.R.,Li X.,Ding Y.,Zhou Q.,Chen Y.,Zhang Y.,Zhao R.P.,Brunet F.,Peng L.X.,Long M.Y.,and Wang W.,2008,Repetitive element-mediated recombination as a mechanism for new gene origination in Dorsophila,PLoSGenet.,4(1):e3.
[21]	Zhao Q.F.,Dong C.,Jue D.W.,Chen H.L.,and Jia L.Q.,2016,Bioinformatics preliminary analysis of ubiquitin conjugating enzyme gene family in cacao,Redai Zuowu Xuebao(Chinese Journal of Tropical Crops),37(9):1732-1740.(赵秋芳,董晨,决登伟,陈宏良,贾利强,2016,可可泛素结合酶基因家族的生物信息学初步分析,热带作物学报,37(9):1732-1740.)
[22]	Zhou G.A.,Chang R.Z.,and Qiu L.J.,2010,Overexpression of soybean ubiquitin-conjugating enzyme gene GmUBC2 confers enhanced drought and salt tolerance through modulating abiotic stress-responsive gene expression in Arabidopsis,Plant Mol.Biol.,72(4-5):357-367.