结核分枝杆菌PPE32蛋白的生物信息学分析
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摘要
目的应用生物学软件预测结核分枝杆菌PPE32基因编码蛋白的结构和功能。方法从NCBI中获得PPE32基因及其编码序列,通过ORF Finder、ProtParam、ProtScaleon Expasy、TMHMM Server v.2.0、SignalP 4.1 Server、TargetP 1.1 Server、NetPhos 3.1 Server、BLAST、SOPMA、SWISS-MODEL、ABCpred、SYFPEITHI、STRING等工具预测分析PPE32蛋白的相关生物学信息。结果 Rv1808基因全长为1 230 bp,有8个开放阅读框架,其编码蛋白为PPE32,由409个氨基酸组成,等电点4.35,为亲水性蛋白,无跨膜区域及信号肽;有31个磷酸化位点,1个保守域;蛋白二级结构中α-螺旋占52.81%,β-折叠占8.31%,β-转角占5.62%,无规则卷曲占33.25%;有38个(得分>0.5)B细胞抗原表位和12个(得分>15)T细胞抗原表位。讨论 PPE32蛋白为亲水性蛋白,具有潜在的T、B细胞抗原表位,可作为研发结核病疫苗的候选蛋白。
Objective To using biological software to predict the structure and function of the PPE32 gene encoding a protein in Mycobacterium tuberculosis. Methods The Rv1808 gene and its coding sequence were obtained from the NCBI database. Open reading frames of the Rv1808 gene were analyzed using the tool ORF Finder. The physical and chemical properties and hydrophobicity of the PPE32 protein were predicted using ProtParam and ProtScale on Expasy. The transmembrane region of the PPE32 protein was analyzed with TMHMM Server v.2.0. The tools Signal P 4.1 Server and TargetP 1.1 Server were used to predict signal peptides and subcellular localization in PPE32. Netphos 3.1 server was used to predict phosphorylation sites in ppe32. Conserved domains in the ppe32 protein and its homology were analyzed using BLAST. The secondary and tertiary structures of the protein were analyzed using the tools SOPMA and Swiss-Model. Protein epitopes were predicted with ABCpred and SYFPEITHI to find the best B-and T-cell epitopes. Results The Rv1808 gene is 1,230 bp in length and has 8 open reading frames. The protein it encodes is PPE32, which consists of 409 amino acids. The protein's isoelectric point is 4.35. It is a hydrophilic protein with no transmembrane regions or signal peptides. The protein has 31 phosphorylation sites and 1 conserved domain. Alpha helices account for 52.81% of the protein's secondary structure, beta bridges account for 8.31%, beta turns account for 5.62%, and random coils account for 33.25%. The protein has 38(Score >0.5) B-cell epitopes and 12(Score >5) T-cell epitopes. Conclusion The PPE32 protein is a hydrophilic protein with potential T-and B-cell epitopes, and it can potentially be used to develop tuberculosis vaccines.
Objective To using biological software to predict the structure and function of the PPE32 gene encoding a protein in Mycobacterium tuberculosis. Methods The Rv1808 gene and its coding sequence were obtained from the NCBI database. Open reading frames of the Rv1808 gene were analyzed using the tool ORF Finder. The physical and chemical properties and hydrophobicity of the PPE32 protein were predicted using ProtParam and ProtScale on Expasy. The transmembrane region of the PPE32 protein was analyzed with TMHMM Server v.2.0. The tools Signal P 4.1 Server and TargetP 1.1 Server were used to predict signal peptides and subcellular localization in PPE32. Netphos 3.1 server was used to predict phosphorylation sites in ppe32. Conserved domains in the ppe32 protein and its homology were analyzed using BLAST. The secondary and tertiary structures of the protein were analyzed using the tools SOPMA and Swiss-Model. Protein epitopes were predicted with ABCpred and SYFPEITHI to find the best B-and T-cell epitopes. Results The Rv1808 gene is 1,230 bp in length and has 8 open reading frames. The protein it encodes is PPE32, which consists of 409 amino acids. The protein's isoelectric point is 4.35. It is a hydrophilic protein with no transmembrane regions or signal peptides. The protein has 31 phosphorylation sites and 1 conserved domain. Alpha helices account for 52.81% of the protein's secondary structure, beta bridges account for 8.31%, beta turns account for 5.62%, and random coils account for 33.25%. The protein has 38(Score >0.5) B-cell epitopes and 12(Score >5) T-cell epitopes. Conclusion The PPE32 protein is a hydrophilic protein with potential T-and B-cell epitopes, and it can potentially be used to develop tuberculosis vaccines.
引文
[1] 袁秋露, 付玉荣, 伊正君. 结核分枝杆菌BfrB蛋白的生物信息学分析[J]. 中国病原生物学杂志, 2018, 13(2): 131-4.
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[5] Brennan MJ. The enigmatic PE/PPE multigene family of mycobacteria and tuberculosis vaccination[J]. Infect Immun, 2017, 85(6): e00969-16.
[6] Deng W, Li W, Zeng J, et al. Mycobacterium tuberculosis PPE family protein Rv1808 manipulates cytokines profile via co-activation of MAPK and NF-u03baB signaling pathways [J]. Cell Physiol Biochem, 2014, 33(2): 273-88.
[7] Oliver GR, Hart SN, Klee EW. Bioinformatics for clinical next generation sequencing[J]. Clin Chem, 2015, 61(1): 124-35.
[8] Wani WY, Boyer-Guittaut M, Dodson M, et al. Regulation of autophagy by protein post-translational modification[J]. Lab Invest, 2015, 95(1): 14-25.
[9] 张西燕, 付玉荣, 伊正君. 结核分枝杆菌eis基因及其编码蛋白的生物信息学分析[J]. 中国病原生物学杂志, 2018, 13(2): 140-5, 151.
[10] Betts JC, Lukey PT, Robb LC, et al. Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling[J]. Mol Microbiol, 2002, 43(3): 717-31.
[11] Ocampo M, Patarroyo MA, Vanegas M, et al. Functional, biochemical and 3D studies of Mycobacterium tuberculosis protein peptides for an effective anti-tuberculosis vaccine[J].Crit Rev Microbiol, 2014, 40(2): 117.
[12] Delogu G, Provvedi R, Sali M, et al. Mycobacterium tuberculosis virulence: insights and impact on vaccine development[J]. Future Microbiol, 2015, 10(7): 1177-94.
[13] Cornaby C, Gibbons L, Mayhew V, et al. B cell epitope spreading: mechanisms and contribution to autoimmune diseases[J]. Immunol Lett, 2015, 163(1): 56-68.
[14] Coscolla M, Copin R, Sutherland J, et al. M. tuberculosis T cell epitope analysis reveals paucity of antigenic variation and identifies rare variable TB antigens[J]. Cell Host Microbe, 2015, 18(5): 538-48.
[15] Deng W, Yang W, Zeng J, et al. Mycobacterium tuberculosis PPE32 promotes cytokines production and host cell apoptosis through caspase cascade accompanying with enhanced ER stress response[J]. Oncotarget, 2016, 7(41): 67347-59.
[16] Cui Y, Zhao D, Barrow PA, et al. The endoplasmic reticulum stress response: A link with tuberculosis?[J]. Tuberculosis, 2016, 97(7): 52-6.
[2] Ekiert DC, Cox JS. Structure of a PE-PPE-EspG complex from Mycobacterium tuberculosis reveals molecular specificity of ESX protein secretion[J]. Proc Natl Acad Sci USA, 2014, 111(41): 14758-63.
[3] Grover S, Sharma T, Singh Y, et al. The PGRS domain of Mycobacterium tuberculosis PE_ PGRS protein Rv0297 is involved in endoplasmic reticulum stress-mediated apoptosis through Toll-Like receptor 4[J]. MBio, 2018, 9(3): e0107-18.
[4] Ahmed A, Das A, Mukhopadhyay S. Immunoregulatory functions and expression patterns of PE/PPE family members: roles in pathogenicity and impact on anti-tuberculosis vaccine and drug design[J]. IUBMB Life, 2015, 67(6): 414-27.
[5] Brennan MJ. The enigmatic PE/PPE multigene family of mycobacteria and tuberculosis vaccination[J]. Infect Immun, 2017, 85(6): e00969-16.
[6] Deng W, Li W, Zeng J, et al. Mycobacterium tuberculosis PPE family protein Rv1808 manipulates cytokines profile via co-activation of MAPK and NF-u03baB signaling pathways [J]. Cell Physiol Biochem, 2014, 33(2): 273-88.
[7] Oliver GR, Hart SN, Klee EW. Bioinformatics for clinical next generation sequencing[J]. Clin Chem, 2015, 61(1): 124-35.
[8] Wani WY, Boyer-Guittaut M, Dodson M, et al. Regulation of autophagy by protein post-translational modification[J]. Lab Invest, 2015, 95(1): 14-25.
[9] 张西燕, 付玉荣, 伊正君. 结核分枝杆菌eis基因及其编码蛋白的生物信息学分析[J]. 中国病原生物学杂志, 2018, 13(2): 140-5, 151.
[10] Betts JC, Lukey PT, Robb LC, et al. Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling[J]. Mol Microbiol, 2002, 43(3): 717-31.
[11] Ocampo M, Patarroyo MA, Vanegas M, et al. Functional, biochemical and 3D studies of Mycobacterium tuberculosis protein peptides for an effective anti-tuberculosis vaccine[J].Crit Rev Microbiol, 2014, 40(2): 117.
[12] Delogu G, Provvedi R, Sali M, et al. Mycobacterium tuberculosis virulence: insights and impact on vaccine development[J]. Future Microbiol, 2015, 10(7): 1177-94.
[13] Cornaby C, Gibbons L, Mayhew V, et al. B cell epitope spreading: mechanisms and contribution to autoimmune diseases[J]. Immunol Lett, 2015, 163(1): 56-68.
[14] Coscolla M, Copin R, Sutherland J, et al. M. tuberculosis T cell epitope analysis reveals paucity of antigenic variation and identifies rare variable TB antigens[J]. Cell Host Microbe, 2015, 18(5): 538-48.
[15] Deng W, Yang W, Zeng J, et al. Mycobacterium tuberculosis PPE32 promotes cytokines production and host cell apoptosis through caspase cascade accompanying with enhanced ER stress response[J]. Oncotarget, 2016, 7(41): 67347-59.
[16] Cui Y, Zhao D, Barrow PA, et al. The endoplasmic reticulum stress response: A link with tuberculosis?[J]. Tuberculosis, 2016, 97(7): 52-6.