DONG Lu,YANG Chun-hong,CHEN Lin,et al.Bioinformatics Analysis of Soybean Catalase Family and the Response to Abiotic Stress[J].Soybean Science,2022,41(06):663-671.[doi:10.11861/j.issn.1000-9841.2022.06.0663]
大豆CAT基因家族生物信息学分析及非生物逆境胁迫响应研究
- Title:
- Bioinformatics Analysis of Soybean Catalase Family and the Response to Abiotic Stress
- Keywords:
- soybean; catalase; gene family; expression quantity; abiotic stress
- 文献标志码:
- A
- 摘要:
- 过氧化氢酶(catalase，CAT)是一种清除需氧生物体中羟基自由基的酶，能减轻氧化伤害。为探究大豆CAT家族基因特性及其在逆境响应中的作用，以拟南芥和水稻CATs基因序列为参考序列，利用大豆基因组数据库进行全基因组鉴定，采用生物信息学方法对其蛋白特性、进化关系、亚细胞定位、组织特异性表达情况、共表达基因以及互作蛋白进行预测分析，并采用荧光定量PCR方法对盐、干旱及缺氧胁迫下不同时间和部位的基因表达模式进行分析。结果显示：在大豆基因组中共鉴定到4个CAT家族同源基因GmCAT1/2、GmCAT3、GmCAT4和GmCAT5。大豆CATs均为亲水性非跨膜蛋白，其氨基酸编码序列均为492 aa，分子量为56 736~56 911 Da，均定位于过氧化物酶体中；GmCATs与拟南芥亲缘关系较近，与水稻亲缘关系较远；GmCATs蛋白以α-螺旋和无规则卷曲为主要结构。基因表达模式预测表明，大豆CAT家族成员在叶和开放的花中的表达量较高；互作蛋白预测表明，GmCATs蛋白与谷胱甘肽氧化酶、酰基辅酶A氧化酶蛋白相互作用；基因共表达预测表明，GmCATs基因与植物能量代谢、氧化还原酶及氧化酶等多个途径的相关基因共表达。荧光定量PCR分析表明，在盐、干旱及缺氧胁迫后GmCATs基因表达量升高，且盐和干旱胁迫下根中的响应较叶片更显著。结果表明GmCATs可能参与大豆对这些逆境胁迫的应答反应，可作为大豆非生物胁响应的重要候选基因。
- Abstract:
- 、Catalase (CAT) is an enzyme that scavenge the hydroxyl radicals in all aerobic organisms in order to reduce oxidative damage. To explore the characteristics of soybean CAT genes and their role in stress response， we carried out the whole genome identification by using Glycine max genome database with the Arabidopsis and rice CAT genes as reference sequences， predicted and analyzed the protein characteristics， evolutionary relationship， subcellular localization， gene expression pattern， co-expressed genes and interacting proteins by bioinformatics methods. Then we took qPCR method to analyze the soybean CAT genes expression pattern in leaf and root tissues under drought， salt and hypoxia stress， respectively. The results showed that four soybean CAT genes were identified， which named as GmCAT1/2， GmCAT3， GmCAT4 and GmCAT5. GmCATs encoded hydrophilic and non-transmembrane proteins， which contained 492 amino acid and their molecular weights ranged from 56 736 to 56 911 Da. They were located in peroxisome. GmCATs were more closely related to Arabidopsis. The main structures of GmCATs consist of α-spiral and irregular curl. Gene expression pattern analysis showed GmCATs were highly expressed in leaves and open flowers. Interaction protein analysis showed that GmCATs interacted with glutathione oxidase and acyl CoA oxidase. Gene co-expression analysis showed that GmCATs were co-expressed with multiple energy metabolism pathways in plants. Fluorescent quantitative PCR analysis showed that the expression levels of GmCATs genes increased after salt， drought or hypoxia stress， and the response in root was more significant than that in leaf under salt and drought stress. The above results showed that GmCATs might participate in the response of soybean to these stresses， and may as important candidate genes for soybean abiotic stress response.
参考文献/References:
［1］毛爽， 周万里， 杨帆， 等. 植物根系应答盐碱胁迫机理研究进展[J]. 浙江农业学报， 2021， 33(10): 1991-2000. (MAO S， ZHOU W L， YANG F， et al. Rserach progress on mechanism ofplant roots response to salt-alkali stress[J]. Acta Agriculturae Zhejiangensis， 2021， 33(10): 1991-2000.)[2]张仟雨， 李萍， 宗毓铮， 等. 干旱对大豆生理及产量影响的研究[J]. 华北农学报， 2016， 31(5): 140-145. (ZHANG Q Y， LI P， ZONG Y Z， et al. Effects of drought on physiology and yield of soybean[J]. Acta Agriculturae Boreali-Sinica， 2016， 31(5): 140-145.)[3]张威， 廖锡良， 喻德跃， 等. 大豆耐盐性研究进展[J]. 土壤与作物， 2018， 7(3): 284-292. (ZHANG W， LIAO X L， YU D Y， et al. A review of salt tolerance in soybean (Glycine max L. Merill)[J]. Soils and Crops， 2018， 7(3): 284-292.)[4]ZHANG Y， ZHENG L， YUN L， et al. Catalase (CAT) gene family in wheat (Triticum aestivum L.): Evolution， expression pattern and function analysis[J]. International Journal of Molecular Sciences， 2022， 23(1): 542.[5]刘健喆. 水稻过氧化氢酶互作蛋白NCA1的功能及作用机理研究[D]. 广州: 华南农业大学， 2018. (LIU J Z. Function and Mechanism of catalase interacting protein NCA in rice[D]. Guangzhou:South China Agricultural University， 2018.)[6]HU L， YANG Y， JIANG L， et al. The catalase gene family in cucumber:Genome-wide identification and organization[J]. Genetics and Molecular Biology， 2016， 39: 408-415.[7]南芝润， 范月仙. 植物过氧化氢酶的研究进展[J]. 安徽农学通报， 2008， 14(5): 27-29. (NAN Z R， FAN Y X. Advance of researchs on catalase in plants[J]. Anhui Agricultural Science Bulletin， 2008， 14(5): 27-29.)[8]YANG〖KG(0.4mm〗 T， POOVAIAH B W. Hydrogen peroxide homeostasis: activation of plant catalase by calcium/calmodulin[J]. Proceedings of the National Academy of Sciences， 2002， 99(6): 4097-4102.[9]宋新华， 赵凤云. 植物体内过氧化氢酶的研究进展[J]. 安徽农业科学， 2007， 35(31): 9824-9827. (SONG X H， ZAHO F Y. Research progress on catalase in plants[J]. Journal of Anhui Agricultural Sciences， 2007， 35(31): 9824-9827.)〖ZK)〗[10]李恩义. 导入小麦过氧化氢酶培育耐低温水稻[J]. 生物技术通报， 2001(3): 48-49. (LI E Y. Cultivation of low temperature tolerant rice by introducing wheat catalase[J]. Biotechnology Information， 2001(3): 48-49.)[11]葛菲. 火龙果CAT基因在烟草中的遗传转化及功能分析[D]. 贵阳: 贵州大学， 2016. (GE F. Genetic transformation and functional characterization of pitaya CAT gene in tobacco[D]. Guiyang: Guizhou University， 2016.)[12]杨芳. 豌豆过氧化氢酶基因在玉米中的转化[D]. 济南: 山东师范大学， 2006. (YANG F. Genetic transformation with the pea catalase gene in maize[D]. JiNan: Shandong Nornal University， 2006.)[13]蔡永智， 祝建波， 郝晓云， 等. 转过氧化氢酶基因KatG棉花的抗旱性[J]. 西北农业学报， 2013， 22(12): 56-61. (CAI Y Z， ZHU J B， HAO X Y， et al. Drought resistance of KatG transgenic cotton[J]. Acta Agriculturae Boreali-occidentalis Sinica， 2013， 22(12): 56-61.)[14]KWON S I， LEE HAN C S. Differential expression of three catalase genes in the small radish (Rhaphanus sativus L. var. sativus)[J]. Molecules and Cells， 2007， 24(1): 37-44.[15]〖KG(0.25mm〗刘仲慧. 烟草过氧化氢酶基因的鉴定与对非生物胁迫响应的功能研究[D]. 泰安: 山东农业大学， 2021. (LIU Z H. Identification of catalase genes in Nicotiana tabacum and functional studies in response to abiotic stress[D]. Taian: Shandong Agricultural University， 2021.)[16]ALAM N B， GHOSH A. Comprehensive analysis and transcript profiling of Arabidopsis thaliana and Oryza sativa catalase gene family suggests their specific roles in development and stress responses[J]. Plant Physiology and Biochemistry， 2018， 123: 54-64.[17]WANG X Y， WU Z H， ZHOU Q， et al. Physiological response of soybean plants to water deficit[J]. Frontiers in Plant Science， 2022， 12: 809692.[18]HAO L， WANG Y， ZHANG J， et al. Coronatine enhances drought tolerance via improving antioxidative capacity to maintaining higher photosynthetic performance in soybean[J]. Plant Science， 2013， 210: 1-9.[19]FAN X D， WANG J Q， YANG N， et al. Gene expression profiling of soybean leaves and roots under salt， saline-alkali and drought stress by high-throughput Illumina sequencing[J]. Gene， 2013， 512(2): 392-402.[20]GOODSTEIN D M， SHU S， HOWSON R， et al. Phytozome: A comparative platform for green plant genomics[J]. Nucleic Acids Research， 2011， 40: D1178-D1186.[21]MISTRY J， CHUGURANSKY S， WILLIAMS L， et al. Pfam: The protein families database in 2021[J]. Nucleic Acids Research， 2021， 49: D412-D419.[22]TAMURA〖KG(0.15mm〗 K， STECHER G， KUMAR S. MEGA11: Molecular evolutionary genetics analysis version 11[J]. Molecular Biology and Evolution， 2021， 38(7): 3022-3027.[23]CHEN C J， CHEN H， ZHANG Y， et al. TBtools: An integrative toolkit developed for interactive analyses of big biological data[J]. Molecular Plant， 2020， 13(8): 1194-1202.[24]HU B， JIN J， GUO A Y， et al. GSDS 2.0:An upgraded gene feature visualization server[J]. Bioinformatics， 2014， 31(8): 1296-1297.[25]GASTEIGER E， HOOGLAND C， GATTIKER A， et al. Protein identification and analysis tools on the ExPASy server[M]. The proteomics protocols handbook， Springer Protocols Handbooks. Humana Press. 2005， 571-607.[26]盖胜男， 魏玉磊， 张今杰， 等. 拟南芥及玉米过氧化氢酶基因家族生物信息学分析[J]. 分子植物育种， 2022， 20(15): 4891-4899. (GAI S N， WEI Y L， ZHANG J J， et al. Bioinformatics analysis of catalase gene family of Arabidopsis and maize[J]. Molecular Plant Breeding， 2022， 20(15): 4891-4899.)[27]KELLEY L A， MEZULIS S， YATES C M， et al. The Phyre2 web portal for protein modeling， prediction and analysis[J]. Nature Protocols， 2015， 10(6): 845-858.[28]KROGH A， LARSSON B， VON HEIJNE G， et al. Predicting transmembrane protein topology with a hidden Markov model:Application to complete genomes[J]. Journal of Molecular Biology， 2001， 305(3): 567-580.[29]SZKLARCZYK D， GABLE A L， NASTOU K C， et al. The STRING database in 2021:Customizable protein-protein networks， and functional characterization of user-uploaded gene/measurement sets[J]. Nucleic Acids Research， 2021， 49: D605-D612.[30]KOHL M， WIESE S， WARSCHEID B.Cytoscape: Software for visualization and analysis of biological networks[J]. Data Mining in Proteomics， 2011， 696: 291-303.[31]WANG M， CHEN B， ZHOU W， et al. Genome-wide identification and expression analysis of the AT-hook Motif Nuclear Localized gene family in soybean[J]. BMC Genomics， 2021， 22(1): 1-26.[32]KABIR M H， WANG M H. Functional studies on two catalase genes from tomato (Solanum lycopersicum L.) [J]. Journal of Pomology & Horticultural Science， 2011， 86(1): 84-90.[33]侯含， 王升平， 张超群， 等. 烟草过氧化氢酶基因CAT2克隆与表达特征分析[J]. 中国烟草科学， 2019， 40(1): 1-8. (HOU H， WANG S P， ZAHNG C Q， et al. Cloning of Catalase 2 (CAT) gene and study on its expression pattern in Nicotiana tabacum L.[J]. Chinese Tobacco Science， 2019， 40(1): 1-8.)[34]谢宗旺. 水稻叶片中过氧化氢酶酶学特性及其互作蛋白NCA的研究[D].广州: 华南农业大学， 2016. (XIE Z W. Enzymatic characterization of catalase and studies on its interaction protein NCA in rice leaves[D]. Guangzhou: South China Agricultural University， 2016.)[35]肖佳琪. 甘蓝型油菜酰基辅酶A氧化酶BnACX的基因编辑对种子萌发和幼苗活力的影响[D]. 沈阳: 沈阳农业大学， 2020. (XIAO J Q. Effects on seed germination and seeding vigor by gene editing of BnACX in Brassica napus L.[D]. Shenyang: Shenyang Agricultural University， 2020.)[36]GRAHAM I A. Seed storage oil mobilization[J]. Annual Review of Plant Biology， 2008， 59: 115-142.[37]MILLER G， SUZUKI N， CIFTCI-YILMAZ S， et al. Reactive oxygen species homeostasis and signaling during drought and salinity stresses[J]. Plant， Cell & Environment， 2010， 33(4): 453-467.[38]马艳丽， 王鹏. 植物在干旱中的适应机制研究进展[J]. 河北林果研究， 2010， 25(4): 359-361. (MA Y L， WANG P. Research progresses of plant adaptation mechanism to drought stress[J]. Hebei Journal of Forestry and Orchard Research， 2010， 25(4): 359-361.)[39]MITTOVA V， GUY M， TAL M， et al. Salinity up-regulates the antioxidative system in root mitochondria and peroxisomes of the wild salt-tolerant tomato species Lycopersicon pennellii[J]. Journal of Experimental Botany， 2004， 55(399): 1105-1113.
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备注/Memo
收稿日期：2022-05-09