مطالعه بیوانفورماتیک پپتید ضد باکتریایی آتاسین a1 از حشرهTenebrio molitor
محورهای موضوعی :
زیست فناوری میکروبی
محمدحسین کریمی گرجی
1
,
مهدی گلستانی نسب
2
,
شکیبا درویش علیپور
3
1 - دانشکده بیوتکنولوژی، پردیس علوم و فناوری نوین، دانشگاه سمنان، سمنان، ایران
2 - گروه آموزشی زیست شناسی، دانشکده علوم پایه، دانشگاه سمنان، سمنان، ایران
3 - گروه میکروبیولوژی، دانشکده بیوتکنولوژی، پردیس علوم و فناوری نوین، دانشگاه سمنان
تاریخ دریافت : 1401/03/19
تاریخ پذیرش : 1401/08/15
تاریخ انتشار : 1401/09/15
کلید واژه:
آتاسین,
T. molitor,
آنالیز بیوانفورماتیک,
پپتید ضد باکتریایی,
چکیده مقاله :
سابقه و هدف: امروزه پپتید های ضد میکروبی تولید شده از حشرات به دلیل تاثیر ضد باکتری های بیماری زا با اثرات جانبی کمتر، مورد توجه هستند. هدف از این مطالعه، بررسی خواص فیزیکی-شیمیایی آتاسین 1a به عنوان ترکیب ضد باکتریایی برای انجام پژوهش های آزمایشگاهی بر پایه ی تولید حامل های دارو رسانی و طراحی واکسن، با استفاده از روش های بیوانفورماتیک است.مواد و روش ها: در این پژوهش توالی ژن کد کننده پپتید ضد میکروبی آتاسین 1a تولید شده از حشره T. molitor، از پایگاه داده NCBI، با نشانی www.ncbi.nlm.nih.gov، در فرمت FASTA دریافت شد. وزن مولکولی، میزان مشابهت و تفاوت میان توالی های آتاسین1a با سایر پپتید های همولوگ، و مشخصات فیزیکی-شیمیایی مولکول بررسی گردید. همچنین ساختار دوم و شکل فضایی پپتید آتاسین1a، با استفاده از نرم افزار‌های بیوانفورماتیک پیشگویی و میزان عملکرد و ایمنی زایی پپتید مطالعه شد.یافته ها: توالی آمینو اسیدی پپتید آتاسین1a، با پپتید های مشابه در 10 عضو از زیر راسته Polyphaga، در نواحی مرکزی و انتهایی (-cترمینال) مشابه است. ویژگی های ساختاری و بیوشیمیایی آتاسین1a، 51% آمینو اسید های غیر قطبی با شاخص بی نظمی %61 و انعطاف پذیری 53% را نشان می دهد. ساختار دوم آتاسین1a، شامل 52/60% پیچ های تصادفی، 1/43% صفحات بتا و 21/43% مارپیچ آلفا است. پیشگویی ساختار سوم در پایگاه Phyre2، 32% هم پوشانی و 31/1% اعتبار سنجی به پروتین متعلق به بتا شبه ایمونوگلوبولین (d2aw2a1) را نشان می دهد. این پپتید توانایی بالایی در تحریک سیستم ایمنی ندارد.نتیجه گیری: فراوانی صفحات بتا در ساختار آتاسین 1a، دلیلی بر پایداری مولکول و افزایش توانایی آن در عبور از غشای سلولی باکتری ها است.
چکیده انگلیسی:
Background & Objectives: Nowadays, antimicrobial peptides produced from insects are considered for their antibacterial activity against pathogens and the fewer side effects. The aim of this study is a bioinformatics analysis of attacin1a as an antibacterial compound and the investigation of its physicochemical properties for laboratory research based on the production of drug delivery carriers and vaccine design.Materials & methods: The sequence of attacin1a gene belonged to T. molitor, was extracted in FASTA format from the NCBI database; www.ncbi.nlm.nih.gov. The Molecular weight, similarity and physicochemical characteristics were investigated in the attacin1a and their homologous peptides. In addition, the second and tertiary structures of the attacin1a were predicted using bioinformatics software’s, and the function and immunogenicity of the peptide were studied.Results: Bioinformatics studies showed that the amino acid sequences of the attacin1a were conserved in the central and c-terminal regions between 10 members of the suborder Polyphaga. The assessment of structural and biochemical properties showed that the attacin1a structure contains 51% of non-polar amino acids with a disorder index of 61% and flexibility of 53%. The second structure of attacin1a consisted of 52.60% Random coils, 21.43% beta-strands and 21.43% alpha helices. The prediction of the tertiary structure in the Phyre2 showed 32% confidence and 31.1% identity to a beta-immunoglobulin protein (d2aw2a1). This peptide doesn’t have a high ability to stimulate the immune system.Conclusion: The abundance of beta strands in the attacin 1a structure increased the molecule's stability and its ability to cross through the cell membrane in bacteria.
منابع و مأخذ:
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Manniello MD, Moretta A, Salvia R, Scieuzo C, Lucchetti D, Vogel H, Sgambato A, Falabella P. Insect antimicrobial peptides: Potential weapons to counteract the antibiotic resistance. Cell. Life Sci. 2021;78(9):4259-82.
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Yi HY, Chowdhury M, Huang YD, Yu XQ. Insect antimicrobial peptides and their applications. Microbiol. Biotechnol. 2014; 98(13):5807-22.
Lu A, Zhang Q, Zhang J, Yang B, Wu K, Xie W, Luan YX, Ling E. Insect prophenoloxidase: the view beyond immunity. physiol. 2014; 11; 5:252.
Buonocore F, Fausto AM, Pelle GD, Roncevic T, Gerdol M, Picchietti S. Attacins: A promising class of insect antimicrobial peptides. Antibiotics. 2021;10(2):212.
Naafs MA. The antimicrobial peptides: ready for clinical trials. J. Sci. Tech. Res. 2018; 7:6038-42.
Jo YH, Kim YJ, Park KB, Seong JH, Kim SG, Park S, Noh MY, Lee YS, Han YS. TmCactin plays an important role in Gram-negative and-positive bacterial infection by regulating expression of 7 AMP genes in Tenebrio molitor. Rep. 2017; 18;7(1):1-2.
Yi L, Lakemond CM, Sagis LM, Eisner-Schadler V, van Huis A, van Boekel MA. Extraction and characterisation of protein fractions from five insect species. Food chem. 2013; 141(4):3341-8.
Jo YH, Park S, Park KB, Noh MY, Cho JH, Ko HJ, Kim CE, Patnaik BB, Kim J, Won R, Bang IS. In silico identification, characterization and expression analysis of attacin gene family in response to bacterial and fungal pathogens in Tenebrio molitor. Res. 2018; 48(1):45-54.
Ratcliffe NA, Mello CB, Garcia ES, Butt TM, Azambuja P. Insect natural products and processes: new treatments for human disease. Insect Biochem. Mol. Biol. 2011; 41(10):747-69.
Moretta A, Salvia R, Scieuzo C, Di Somma A, Vogel H, Pucci P, Sgambato A, Wolff M, Falabella P. A bioinformatic study of antimicrobial peptides identified in the Black Soldier Fly (BSF) Hermetia illucens (Diptera: Stratiomyidae). Rep. 2020;10(1):1-4.
Elhag O, Zhou D, Song Q, Soomro AA, Cai M, Zheng L, Yu Z, Zhang J. Screening, expression, purification and functional characterization of novel antimicrobial peptide genes from Hermetia illucens (L.). PloS one. 2017 Jan 5;12(1):e0169582.
Wu Q, Patočka J, Kuča K. Insect antimicrobial peptides, a mini review. Toxins. 2018;10(11):461.
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Sudha R, Murthy GN, Awasthi AK, Ponnuvel KM. Attacin gene sequence variations in different ecoraces of tasar silkworm Antheraea mylitta. Bioinformation. 2015;11(10):481.
Van Moll L, De Smet J, Paas A, Tegtmeier D, Vilcinskas A, Cos P, Van Campenhout L. In vitro evaluation of antimicrobial peptides from the black soldier fly (Hermetia Illucens) against a Selection of Human Pathogens. Spectr. 2022;10(1):e01664-21.
Brady D, Grapputo A, Romoli O, Sandrelli F. Insect cecropins, antimicrobial peptides with potential therapeutic applications. J. Mol. Sci. 2019; 20(23):5862.
Rahbar MR, Rasooli I, Gargari SL, Amani J, Fattahian Y. In silico analysis of antibody triggering biofilm associated protein in Acinetobacter baumannii. Theor. Biol. 2010; 266(2):275-90.
Di Somma A, Moretta A, Cané C, Scieuzo C, Salvia R, Falabella P, Duilio A. Structural and functional characterization of a novel recombinant antimicrobial peptide from Hermetia illucens. Biol. 2021; 44(1):1-3.
Skorupka K, Han SK, Nam HJ, Kim S, Faham S. Protein design by fusion: implications for protein structure prediction and evolution. Acta Crystallogr D Biol Crystallogr. 2013; 69(12):2451-60.
Wiederstein M, Sippl MJ. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 2007; 35(suppl_2):W407-10.
Benkert P, Tosatto SC, Schomburg D. QMEAN: A comprehensive scoring function for model quality assessment. Proteins: Struct., Funct., Genet. 2008; 71(1):261-77.
Holm L, Rosenstrï¿ ½m P½. Dali server: conservation mapping in 3D. Nucleic Acids Res. 2010; 38(suppl_2):W545-9.
Yao B, Zhang L, Liang S, Zhang C. SVMTriP: A Method to Predict Antigenic Epitopes Using Support Vector Machine to Integrate Tri-Peptide Similarity and Propensity. PLoS ONE. 2012; 7(9): e45152.
Ansari HR, Raghava GP. Identification of conformational B-cell Epitopes in an antigen from its primary sequence. Immunome Res. 2010; 6(1):1-9.
Rashki M, Mortazavi M. Modeling and determining the structures and characteristics of cytochrome P450 enzymes in the entomopathogenic fungus, Beauveria bassiana. JMW. 2020; 42(1):47-57 [In Persion].
Javid H. Antigenic properties of Finegoldia magna protein L and Type IV Pilin (PilA) for in-silico multi epitope peptide vaccine designing. JMW. 2020; 42(1):78-98 [In Persion].
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Liao YY, Zuo YH, Tsai CL, Hsu CM, Chen ME. cDNA cloning and transcriptional regulation of the cecropin and attacin from the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae), Insect Biochem. Physiol. 2015; 89(2):111-26.
Manniello MD, Moretta A, Salvia R, Scieuzo C, Lucchetti D, Vogel H, Sgambato A, Falabella P. Insect antimicrobial peptides: Potential weapons to counteract the antibiotic resistance. Cell. Life Sci. 2021;78(9):4259-82.
Muthuirulan P, Paramasamy G, Jeyaprakash R. Antimicrobial peptides: versatile biological properties. J. Pept. 2013; 23935642.
Ntwasa M, Goto A, Kurata S. Coleopteran antimicrobial peptides: prospects for clinical applications. J. Microbiol. 2012; ID 101989.
Kim SG, Jo YH, Seong JH, Park KB, Noh MY, Cho JH, Ko HJ, Kim CE, Tindwa H, Patnaik BB, Bang IS. TmSR-C, scavenger receptor class C, plays a pivotal role in antifungal and antibacterial immunity in the coleopteran insect Tenebrio molitor. Insect Biochem. Mol. Biol. 2017;1: 89:31-42.
6- Rosales C, Vonnie S. Cellular and molecular mechanisms of insect immunity. Insect physiology and ecology. IntechOpen Book Series. 2017; 179-212.
Yi HY, Chowdhury M, Huang YD, Yu XQ. Insect antimicrobial peptides and their applications. Microbiol. Biotechnol. 2014; 98(13):5807-22.
Lu A, Zhang Q, Zhang J, Yang B, Wu K, Xie W, Luan YX, Ling E. Insect prophenoloxidase: the view beyond immunity. physiol. 2014; 11; 5:252.
Buonocore F, Fausto AM, Pelle GD, Roncevic T, Gerdol M, Picchietti S. Attacins: A promising class of insect antimicrobial peptides. Antibiotics. 2021;10(2):212.
Naafs MA. The antimicrobial peptides: ready for clinical trials. J. Sci. Tech. Res. 2018; 7:6038-42.
Jo YH, Kim YJ, Park KB, Seong JH, Kim SG, Park S, Noh MY, Lee YS, Han YS. TmCactin plays an important role in Gram-negative and-positive bacterial infection by regulating expression of 7 AMP genes in Tenebrio molitor. Rep. 2017; 18;7(1):1-2.
Yi L, Lakemond CM, Sagis LM, Eisner-Schadler V, van Huis A, van Boekel MA. Extraction and characterisation of protein fractions from five insect species. Food chem. 2013; 141(4):3341-8.
Jo YH, Park S, Park KB, Noh MY, Cho JH, Ko HJ, Kim CE, Patnaik BB, Kim J, Won R, Bang IS. In silico identification, characterization and expression analysis of attacin gene family in response to bacterial and fungal pathogens in Tenebrio molitor. Res. 2018; 48(1):45-54.
Ratcliffe NA, Mello CB, Garcia ES, Butt TM, Azambuja P. Insect natural products and processes: new treatments for human disease. Insect Biochem. Mol. Biol. 2011; 41(10):747-69.
Moretta A, Salvia R, Scieuzo C, Di Somma A, Vogel H, Pucci P, Sgambato A, Wolff M, Falabella P. A bioinformatic study of antimicrobial peptides identified in the Black Soldier Fly (BSF) Hermetia illucens (Diptera: Stratiomyidae). Rep. 2020;10(1):1-4.
Elhag O, Zhou D, Song Q, Soomro AA, Cai M, Zheng L, Yu Z, Zhang J. Screening, expression, purification and functional characterization of novel antimicrobial peptide genes from Hermetia illucens (L.). PloS one. 2017 Jan 5;12(1):e0169582.
Wu Q, Patočka J, Kuča K. Insect antimicrobial peptides, a mini review. Toxins. 2018;10(11):461.
Emr SD, Silhavy TJ. Importance of secondary structure in the signal sequence for protein secretion. Natl. Acad. Sci. 1983; 80(15):4599-603.
Mylonakis E, Podsiadlowski L, Muhammed M, Vilcinskas A. Diversity, evolution and medical applications of insect antimicrobial peptides. Philos Trans R Soc Lond B Biol Sci. 2016; 371(1695):20150290.
Grau T, Vilcinskas A, Joop G. Sustainable farming of the mealworm Tenebrio molitor for the production of food and feed. Naturforsch. C. 2017;72(9-10):337-49.
Petersen TN, Brunak S, Von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Methods. 2011; 8(10):785-6.
Combet C, Blanchet C, Geourjon C, Deleage G. NPS@: network protein sequence analysis. Trends Biochem. Sci. 2000; 25(3):147-50.
Dey J, Mahapatra SR, Patnaik S, Lata S, Kushwaha GS, Panda RK, Misra N, Suar M. Molecular characterization and designing of a novel multiepitope vaccine construct against Pseudomonas aeruginosa. Int J Pept Res Ther. 2022; 28(2):1-9.
Sudha R, Murthy GN, Awasthi AK, Ponnuvel KM. Attacin gene sequence variations in different ecoraces of tasar silkworm Antheraea mylitta. Bioinformation. 2015;11(10):481.
Van Moll L, De Smet J, Paas A, Tegtmeier D, Vilcinskas A, Cos P, Van Campenhout L. In vitro evaluation of antimicrobial peptides from the black soldier fly (Hermetia Illucens) against a Selection of Human Pathogens. Spectr. 2022;10(1):e01664-21.
Brady D, Grapputo A, Romoli O, Sandrelli F. Insect cecropins, antimicrobial peptides with potential therapeutic applications. J. Mol. Sci. 2019; 20(23):5862.
Rahbar MR, Rasooli I, Gargari SL, Amani J, Fattahian Y. In silico analysis of antibody triggering biofilm associated protein in Acinetobacter baumannii. Theor. Biol. 2010; 266(2):275-90.
Di Somma A, Moretta A, Cané C, Scieuzo C, Salvia R, Falabella P, Duilio A. Structural and functional characterization of a novel recombinant antimicrobial peptide from Hermetia illucens. Biol. 2021; 44(1):1-3.
Skorupka K, Han SK, Nam HJ, Kim S, Faham S. Protein design by fusion: implications for protein structure prediction and evolution. Acta Crystallogr D Biol Crystallogr. 2013; 69(12):2451-60.
Wiederstein M, Sippl MJ. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 2007; 35(suppl_2):W407-10.
Benkert P, Tosatto SC, Schomburg D. QMEAN: A comprehensive scoring function for model quality assessment. Proteins: Struct., Funct., Genet. 2008; 71(1):261-77.
Holm L, Rosenstrï¿ ½m P½. Dali server: conservation mapping in 3D. Nucleic Acids Res. 2010; 38(suppl_2):W545-9.
Yao B, Zhang L, Liang S, Zhang C. SVMTriP: A Method to Predict Antigenic Epitopes Using Support Vector Machine to Integrate Tri-Peptide Similarity and Propensity. PLoS ONE. 2012; 7(9): e45152.
Ansari HR, Raghava GP. Identification of conformational B-cell Epitopes in an antigen from its primary sequence. Immunome Res. 2010; 6(1):1-9.
Rashki M, Mortazavi M. Modeling and determining the structures and characteristics of cytochrome P450 enzymes in the entomopathogenic fungus, Beauveria bassiana. JMW. 2020; 42(1):47-57 [In Persion].
Javid H. Antigenic properties of Finegoldia magna protein L and Type IV Pilin (PilA) for in-silico multi epitope peptide vaccine designing. JMW. 2020; 42(1):78-98 [In Persion].
