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PucACO、PucACS基因家族鉴定及其生物信息学分析
刘亚龙,欧春青,张艳杰,李舒然,王晨,吝茹雪,姜淑苓,王斐
1.中国农业科学院 果树研究所 农业农村部园艺作物种质资源利用重点实验室,辽宁 兴城 125100;2.沈阳农业大学 园艺学院, 辽宁 沈阳110866
摘要:
【目的】对梨PucACO、PucACS基因家族进行生物信息学分析,为进一步研究PucACO、PucACS基因家族在梨生长发育过程中的功能奠定基础。【方法】在‘中矮1号’基因组中鉴定出梨PucACO、PucACS基因家族,利用ExPASy、Plant-mPLo、NetPhos等软件分析PucACO、PucACS蛋白的理化性质,使用TBtools分析PucACO、PucACS基因家族的基因结构、构建进化树及共线性分析,使用Swiss-Model、I-TASSER、ROBETTA预测PucACS、PucACO蛋白的3D模型,并使用SAVEs6.0对其进行质量评估,再使用VMD对PucACO、PucACS蛋白的三级结构进行美化。【结果】共鉴定出8个梨PucACO基因和8个梨PucACS基因,其中梨PucACO基因编码蛋白长度为226~322个氨基酸,核苷酸序列一致性及氨基酸序列同源性分别为38.05%~99.78%和29.39%~99.70%,相对分子质量为25.75~36.54 ku,等电点为5.07~5.84;所有PucACO基因编码的蛋白质均为亲水性蛋白质,部分为不稳定蛋白,亚细胞均位于细胞质中,脂肪系数为76.13~89.25,热稳定性比较好。梨PucACS基因编码的蛋白长度为432~794个氨基酸,核苷酸序列一致性及氨基酸序列同源性分别为31.79%~100%和30.00%~100%,相对分子质量为48.41~89.77 ku,等电点为5.48~8.41;不稳定系数均大于40,为不稳定蛋白质;PucACS2位于细胞质中,其余均位于叶绿体中;脂肪系数为77.17~84.40,热稳定性较好,均为亲水性蛋白质。PucACS和PucACO蛋白生物学功能主要以丝氨酸磷酸化修饰为主,均不含信号肽位点,无跨膜结构,且不含GPI锚定蛋白位点。二级结构预测结果表明,PucACS、PucACO蛋白质结构均以α-螺旋和无规则卷曲为主,PucACS中包含多个保守的脯氨酸,PucACO中包含多个保守的组氨酸。梨PucACS基因家族分为3类,PucACO基因家族可以分为2类,PucACS、PucACO家族各成员的基因结构和保守基序差异较小,内含子数量和所包含的基序大致相同。梨PucACS、PucACO基因家族启动子顺式作用元件分析结果表明,该启动子中存在多种与植物生长调控、植物激素调节、逆境诱导等相关的作用元件。拟南芥与梨共存在24对共线性关系,其中PucACS家族与拟南芥构建了16对共线性关系,PucACO家族与拟南芥构建了8对共线性关系。梨物种内部的共线性分析结果表明,PucACO家族之间存在3对共线性关系,PucACS家族之间存在4对共线性关系。【结论】鉴定出8个梨PucACS基因和8个梨PucACO基因,其生物信息学分析结果丰富了梨PucACSPucACO基因的分子生物学理论。
关键词:  梨遗传育种  PucACS  PucACO  生物信息学  基因结构  蛋白质结构
DOI:DOI:10.13207/j.cnki.jnwafu.2024.12.011
分类号:
基金项目:中国农业科学院创新工程项目(CAAS-ASTIP);国家重点研发计划项目(2019YFD1001404)
Protein prediction and bioinformatics analysis of pear PucACO and PucACS gene families
LIU Yalong1, OU Chunqing1, ZHANG Yanjie2,3, LI Shuran1, WANG Chen1, LIN Ruxue1, JIANG Shuling1, ,WANG Fei1
1.Key Laboratory of Biology and Genetic Improvement of Horticultural Crops,Germplasm Resources Utilization,Ministry of Agriculture and Rural Areas,Research Institute of Pomology,Chinese Academy of Agricultural Sciences,Xingcheng,Liaoning 125100,China;2.Key Laboratory of Biology and Genetic Improvement of Horticultural Crops,Germplasm Resources Utilization,Ministry of Agriculture and Rural Areas,Research Institute of Pomology,Chinese Academy of Agricultural Sciences,Xingcheng,Liaoning 125100,China;3.College of Horticulture,Shenyang Agricultural University,Shenyang,Liaoning 110866,China
Abstract:
【Objective】Bioinformatics analysis of pear PucACO and PucACS gene families was carried out to lay foundation for further research on functions of PucACO and PucACS gene families in pear growth and development.【Method】Pear PucACO and PucACS gene families were identified in ‘Zhongai 1’, and physicochemical properties of PucACO and PucACS proteins were analyzed using software including ExPASy,Plant-mPLo and NetPhos.Structures of PucACO and PucACS gene families were analyzed using TBtools,evolutionary tree was constructed and covariance analysis was conducted.The 3D model was predicted using Swiss-Model,I-TASSER and ROBETTA,the quality was assessed using SAVEs6.0,and the final tertiary structures of PucACO and PucACS proteins were beautified using VMD.【Result】A total of eight PucACO genes and eight PucACS genes were identified.PucACO genes encoded protein lengths of 226-322 aa,with nucleotide sequence identity and amino acid sequence homology of 38.05%-99.78% and 29.39%-99.70%,respectively.The relative molecular masses were 25.75-36.54 ku,and isoelectric points were 5.07-5.84.All proteins encoded by PucACO genes are hydrophilic proteins,with some being unstable proteins.Subcellular are all located in the cytoplasm,with fat coefficient were 76.13-89.25 and good thermal stability.PucACS genes encoded protein lengths of 432-794 aa,with nucleotide sequence identity and amino acid sequence homology of 31.79%-100% and 30.00%-100%respectively.The relative molecular masses were 48.41-89.77 ku and isoelectric points were 5.48-8.41.The instability coefficients are all greater than 40,indicating an unstable protein.PucACS2 is located in the cytoplasm,while the rest are located in the chloroplast.The fat coefficient were 77.17-84.40,and it has good thermal stability,all of which are hydrophilic proteins.The biological functions of proteins were mainly dominated by serine phosphorylation modification,none of them contained signal peptide sites,and there were no transmembrane structures and GPI-anchored protein sites.Predicted secondary structure showed that PucACS and PucACO structures were dominated by α-helix and irregular coiling,PucACS contained multiple conserved prolines,and PucACO contained multiple conserved histidines.The PucACS gene family was categorized into three groups,and PucACO gene family was categorized into two groups.The gene structures and conserved motifs of different members of PucACO and PucACS families had relatively small differences,and numbers of introns and inclusion motifs were approximately same.The cisacting element analysis of promoters of PucACS and PucACO gene families showed that there were a variety of promoters with plant growth regulation,phytohormone regulation and adversity induction.A total of 24 covariate pairs existed between Arabidopsis and pear,of which 16 were constructed between PucACS family and Arabidopsis and 8 were constructed between PucACO family and Arabidopsis.The covariance analysis within pear species showed that three covariance pairs existed between PucACO family and four pairs existed between PucACS family.【Conclusion】Eight PucACS genes and eight PucACO genes were identified,and the bioinformatic analyses enriched their molecular biology theory.
Key words:  genetic breeding of pear  PucACS  PucACO  bioinformatics  gene structure  protein structure