Bioinformatics analysis of small G protein CaROP in pepper

doi:10.6048/j.issn.1001-4330.2024.01.018

Abstract

Abstract:

【Objective】 To clarify the biological function,physicochemical properties,protein structure and phylogenetic relationship of small G protein CaROP in pepper. 【Methods】 In this study,the physicochemical properties of nine CaROP proteins were analyzed by using bioinformatics software such as ProtParam,ProtScale,SignalP5.0,TMHMM,NetPhos3.1 and NetCGlyc1.0; The structures of 9 CaROP proteins were predicted and analyzed by using SOPMA,SWISS-MODEL and other bioinformatics software; The phylogenetic relationship of 9 CaROP proteins was analyzed by using bioinformatics software MEGA11. 【Results】 The results of protein physicochemical properties analysis showed that the total average hydrophilicity of 9 CaROP proteins was less than 0,which were all hydrophilic proteins,and 6 of them were stable hydrophilic proteins; None of the 9 CaROP proteins had signal peptide,namely,they were non secretory proteins; Nine CaROP proteins had no transmembrane domain,namely,none of them were membrane proteins; All 9 CaROP proteins had phosphorylation sites and none had glycosylation sites. The results of protein structure prediction and analysis showed that the main secondary structural elements of 9 CaROP proteins were irregular curls and α- Spiral,followed by β- Fold,finally β- Corner. Phylogenetic analysis showed that nine CaROP proteins were clustered into four branches,of which each of branch I and branch III contained one CaROP protein,branch II contained two CaROP proteins,and the other five CaROP proteins were clustered in branch IV. 【Conclusion】 Nine CaROP proteins have the Rhoa domain and are all non-secretory hydrophilicproteins.The nine CaROP proteins were clustered into four branches in thephylogenetic tree,and the prediction results of their tertiary structure modeling were also ideal.The structure of the nine CaROP proteins was relatively stable.

Key words: pepper; small G protein ROP; physical and chemical properties of protein; protein structure; phylogenetic relationship

摘要：

【目的】研究辣椒内小G蛋白CaROP的生物学功能、蛋白理化性质、蛋白结构及系统发育关系。【方法】运用ProtParam、ProtScale、SignalP5.0、TMHMM、NetPhos3.1和NetCGlyc1.0等生物信息学软件分析9个CaROP蛋白的蛋白理化特性;运用SOPMA和SWISS-MODEL等生物信息学软件预测分析9个CaROP蛋白的结构;运用生物信息学软件MEGA11分析9个CaROP蛋白的系统发育关系。【结果】9个CaROP蛋白的亲水性总平均值均小于0,均为亲水蛋白,其中6个为稳定的亲水蛋白;9个CaROP蛋白均无信号肽,即均为非分泌性蛋白;9个CaROP蛋白无跨膜结构域,即均非膜蛋白;9个CaROP蛋白均存在磷酸化位点,均无糖基化位点。9个CaROP蛋白的主要二级结构原件为无规则卷曲和α-螺旋,其次是β-折叠,最后是β-转角。9个CaROP蛋白聚为4个分支,其中分支Ⅰ和分支Ⅲ各包括1个CaROP蛋白。分支Ⅱ包括2个CaROP蛋白,其余5个CaROP蛋白均聚于分支Ⅳ中。【结论】9个CaROP蛋白具有完整的Rho功能域,均为非分泌性亲水蛋白。9个CaROP蛋白在系统进化树中共聚为了4个分支,其三级结构建模的预测结果也均较为理想,9个CaROP蛋白结构较稳定。

关键词: 辣椒, 小G蛋白ROP, 蛋白理化特性, 蛋白结构, 系统发育关系

CLC Number:

S641.3
S188

MA Sijie, ZHU Tiansheng, HE Lu, YANG Shuqing. Bioinformatics analysis of small G protein CaROP in pepper[J]. Xinjiang Agricultural Sciences, 2024, 61(1): 165-175.

马思洁, 朱天生, 何璐, 杨叔青. 辣椒小G蛋白CaROP的生物信息学分析[J]. 新疆农业科学, 2024, 61(1): 165-175.

Figures/Tables 13

References 25

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基因登录号 Gene ID	蛋白长度 Protein length (aa)	分子式 Molecular formula	分子量 Molecular weight	原子总数 Total number of atoms	带负电荷氨基酸残基总数 Total number of negatively Charged amino acid residues (Asp + Glu)	带正电荷氨基酸残基总数 Total number of positively Charged amino acid residues (Arg + Lys)	理论等电点PI
CA01g27430	210	C₁₀₃₇H₁₆₄₈N₂₈₂O₃₀₉S₆	23 202.56	3 282	19	28	9.33
CA03g28070	174	C₈₆₁H₁₃₃₃N₂₂₅O₂₅₆S₆	19 124.77	2 681	17	16	6.28
CA02g04310	197	C₉₈₆H₁₅₇₅N₂₆₃O₂₈₆S₇	21 914.36	3 117	18	26	9.32
CA00g84620	197	C₉₇₁H₁₅₄₃N₂₅₅O₂₈₃S₅	21 477.77	3 057	17	25	9.3
CA02g05500	197	C₉₆₉H₁₅₃₈N₂₅₆O₂₈₄S₅	21 478.72	3 052	18	25	9.21
CA02g21300	197	C₉₇₃H₁₅₄₆N₂₅₆O₂₈₄S₅	21 534.82	3 064	17	25	9.3
CA04g05500	210	C₁₀₅₀H₁₆₄₉N₂₇₁O₃₀₁S₅	23 045.58	3 276	18	25	9.17
CA08g19280	198	C₉₈₂H₁₅₆₆N₂₆₂O₂₈₃S₅	21 731.12	3 098	18	27	9.39
CA00g82910	224	C₁₁₃₀H₁₇₇₅N₃₀₅O₃₂₄S₁₃	25 234.15	3 547	21	28	9.04

基因登录号 Gene ID	蛋白长度 Protein length (aa)	分子式 Molecular formula	分子量 Molecular weight	原子总数 Total number of atoms	带负电荷氨基酸残基总数 Total number of negatively Charged amino acid residues (Asp + Glu)	带正电荷氨基酸残基总数 Total number of positively Charged amino acid residues (Arg + Lys)	理论等电点PI
CA01g27430	210	C₁₀₃₇H₁₆₄₈N₂₈₂O₃₀₉S₆	23 202.56	3 282	19	28	9.33
CA03g28070	174	C₈₆₁H₁₃₃₃N₂₂₅O₂₅₆S₆	19 124.77	2 681	17	16	6.28
CA02g04310	197	C₉₈₆H₁₅₇₅N₂₆₃O₂₈₆S₇	21 914.36	3 117	18	26	9.32
CA00g84620	197	C₉₇₁H₁₅₄₃N₂₅₅O₂₈₃S₅	21 477.77	3 057	17	25	9.3
CA02g05500	197	C₉₆₉H₁₅₃₈N₂₅₆O₂₈₄S₅	21 478.72	3 052	18	25	9.21
CA02g21300	197	C₉₇₃H₁₅₄₆N₂₅₆O₂₈₄S₅	21 534.82	3 064	17	25	9.3
CA04g05500	210	C₁₀₅₀H₁₆₄₉N₂₇₁O₃₀₁S₅	23 045.58	3 276	18	25	9.17
CA08g19280	198	C₉₈₂H₁₅₆₆N₂₆₂O₂₈₃S₅	21 731.12	3 098	18	27	9.39
CA00g82910	224	C₁₁₃₀H₁₇₇₅N₃₀₅O₃₂₄S₁₃	25 234.15	3 547	21	28	9.04

基因登录号 Gene ID	不稳定系数 Instability coefficient	不稳定/ 稳定蛋白 Instability/ stable protein	脂肪系数 Fat coefficient	亲水性总平均值 Total average hydrophilicity	非亲水/ 亲水蛋白 Non hydrophilic/ hydrophilic protein
CA01g27430	47.19	不稳定蛋白	82.14	-0.277	亲水蛋白
CA03g28070	43.18	不稳定蛋白	85.69	-0.04	亲水蛋白
CA02g04310	38.96	稳定蛋白	90.56	-0.138	亲水蛋白
CA00g84620	33.45	稳定蛋白	88.53	-0.096	亲水蛋白
CA02g05500	36.01	稳定蛋白	87.56	-0.121	亲水蛋白
CA02g21300	37.31	稳定蛋白	88.53	-0.122	亲水蛋白
CA04g05500	29.96	稳定蛋白	91.43	-0.029	亲水蛋白
CA08g19280	42.05	不稳定蛋白	90.61	-0.12	亲水蛋白
CA00g82910	33.89	稳定蛋白	33.89	-0.054	亲水蛋白

基因登录号 Gene ID	不稳定系数 Instability coefficient	不稳定/ 稳定蛋白 Instability/ stable protein	脂肪系数 Fat coefficient	亲水性总平均值 Total average hydrophilicity	非亲水/ 亲水蛋白 Non hydrophilic/ hydrophilic protein
CA01g27430	47.19	不稳定蛋白	82.14	-0.277	亲水蛋白
CA03g28070	43.18	不稳定蛋白	85.69	-0.04	亲水蛋白
CA02g04310	38.96	稳定蛋白	90.56	-0.138	亲水蛋白
CA00g84620	33.45	稳定蛋白	88.53	-0.096	亲水蛋白
CA02g05500	36.01	稳定蛋白	87.56	-0.121	亲水蛋白
CA02g21300	37.31	稳定蛋白	88.53	-0.122	亲水蛋白
CA04g05500	29.96	稳定蛋白	91.43	-0.029	亲水蛋白
CA08g19280	42.05	不稳定蛋白	90.61	-0.12	亲水蛋白
CA00g82910	33.89	稳定蛋白	33.89	-0.054	亲水蛋白

基因代码 Gene ID	丝氨酸 Serine	苏氨酸 Threonine	络氨酸 Tyrosine
CA01g27430	11	5	2
CA03g28070	5	4	4
CA02g04310	8	6	6
CA00g84620	9	4	4
CA02g05500	11	5	4
CA02g21300	10	3	4
CA04g05500	10	4	3
CA08g19280	10	2	4
CA00g82910	9	5	5