Der p 1 gene sequence polymorphism in house dust mite Dermatophagoides pteronyssinus
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Abstract. Adji A, Niode NJ, Memah VV, Posangi J, Wahongan GJP, Tallei TE. 2021. Der p 1 gene sequence polymorphism in house dust mite Dermatophagoides pteronyssinus. Biodiversitas 22: 72-78. Gene polymorphisms in Dermatophagoides pteronyssinus (DP) mite can affect the immune response that plays a role in atopic disease. This study aimed to determine the polymorphisms of Der p 1 gene from DP. House dust containing DP was used as a source of DNA containing the Der p 1 gene. The gene was amplified using specific primers DP Der 1 P 108F and DP Der 1 P 1509R. The amplified fragments were cloned using the Toyobo pTA2 vector and sorted then compared with the Gene Bank database. The result shows that there are 8 polymorphism sites in the Der p 1 gene positioned at 190 (GR), 463 (CT), 645 (AR), 751 (CY, CT), 787 (CG), 827 (TA; TW), and 1084 (CG). In the Der p 1 gene, there are 5 silent mutations and 3 nonsynonymous substitutions, resulting in amino acid polymorphisms as follows: Histidine H146 to Tyrosine Y146, Alanine A220 to Valine V220 and amino acid X220, and Tyrosine T232 to Serine S232. Polymorphisms in these amino acids lead to a polarity change, from polar to polar and non-polar to non-polar. These dynamics in polarity does not change the structure or function of the allergen protein. So that they can be used for vaccine design strategies.
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References
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Chruszcz M, Pomés A, Glesner J, Vailes LD, Osinski T. 2012. Molecular determinants for antibody binding on group 1 house dust mite allergens. J Biol Chem 287:7388–7398.
Clancy S. 2008. Genetic mutation. Nature Education 1(1) .
Corpet F. 1988. Multalin (Multiple Sequence Alignment with Hierarchical Clustering). Nucl. Acids Res 16(22):10881-890. http://multalin.toulouse.inra.fr/multalin/
Cui Y, Gao C, Zhou Y, Zhou P, Peng M, Lin Y, Peng J. 2010. Phylogenetic analysis of house dust mites. Cent Eur J Med 5(1): 69-74.
Cui, Y, Wang Q. & Jia H. 2018. Consideration of methods for identifying mite allergens. Clin Transl Allergy 8:14. https://doi.org/10.1186/s13601-018-0200-4
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Hizawa N, Freidhoff LR, Chiu YF, Ehrlich E. 1998. Genetic regulation of Dermatophagoides pteronyssinus–specific IgE responsiveness: A genome-wide multipoint linkage analysis in families recruited through 2 asthmatic sibs. J Allergy Clin Immunol 102(3):436-42.
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Tallei TE, Kolondam BJ. 2015. DNA barcoding of Sangihe nutmeg (Myristica fragrans) using matK gene. Hayati J Biosciences 22(1):41-47. DOI:10.4308/hjb.22.1.41
Thomas WR. 2010. Geography of house dust mite allergens. Asian Pac J Allergy Immunol 28:211–224.
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Verma S, Dixit R, Pandey KC. 2016. Der p 1 proteins: modes of activation and future prospects as pharmacological targets. Front Pharmacol 7:107.
Waldron R, Mc Gowan J, Gordon N, Mc Carthy C, Mitchell EB, Fitzpatrick DA. 2019. Proteonom and allergenome of the European house dust mite Dermatophagoides pteronyssinus. PLoS ONE 14(5):e0216171. https://doi.org/10.1371/ journal.pone.0216171
Zymobiomics DNA mini kit. (D4300). Zymo Research Corp. www.zymoresearch.com.
Zymoclean gel DNA recovery kit. Zymo Research Corp. www.zymoresearch.com.
Cao R, Shi Y, Chen S, Ma Y, Chen J, Yang J, Chen G and Shi T. 2017. dbSAP: single amino-acid polymorphism database for protein variation detection. Nucleic Acids Res 45: D827–D832. DOI: 10.1093/nar/gkw1096
Chevigne A, Jacquet A. 2018. Emerging roles of the protease allergen Der p 1 in house dust mite-induced airway inflammation. J. Allergy Clin Immunol 142:398–400.
Chruszcz M, Pomés A, Glesner J, Vailes LD, Osinski T. 2012. Molecular determinants for antibody binding on group 1 house dust mite allergens. J Biol Chem 287:7388–7398.
Clancy S. 2008. Genetic mutation. Nature Education 1(1) .
Corpet F. 1988. Multalin (Multiple Sequence Alignment with Hierarchical Clustering). Nucl. Acids Res 16(22):10881-890. http://multalin.toulouse.inra.fr/multalin/
Cui Y, Gao C, Zhou Y, Zhou P, Peng M, Lin Y, Peng J. 2010. Phylogenetic analysis of house dust mites. Cent Eur J Med 5(1): 69-74.
Cui, Y, Wang Q. & Jia H. 2018. Consideration of methods for identifying mite allergens. Clin Transl Allergy 8:14. https://doi.org/10.1186/s13601-018-0200-4
Herman J. 2014. Der p 1 is the primary activator of Der p 3, Der p 6 and Der p 9 the proteolytic allergens produced by the house dust mite Dermatophagoides pteronyssinus. Biochim Biophys Acta 1840:1117–1124.
Hizawa N, Freidhoff LR, Chiu YF, Ehrlich E. 1998. Genetic regulation of Dermatophagoides pteronyssinus–specific IgE responsiveness: A genome-wide multipoint linkage analysis in families recruited through 2 asthmatic sibs. J Allergy Clin Immunol 102(3):436-42.
International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
Izquierdo-Alvarez A. 2012. Differential redox proteomics allows identification of proteins reversibly oxidized at cysteine residues in endothelial cells in response to acute hypoxia. J Proteom75:5449–5462.
Jeong KY, Lee IY, Yong TS, Lee JH, Kim EJ. 2012. Sequence polymorphisms of Der f 1, Der p 1, Der f 2 and Der p 2 from Korean house dust mite isolates. Exp Appl Acarol 58:35–42.
Jia X, Han B, Onengut-Gumuscu S, Chen W-M, Concannon PJ, Rich SS, Raychaudhuri S, de Bakker PIW. 2013. Imputing Amino Acid Polymorphisms in Human Leukocyte Antigens. PLoS ONE 8(6): e64683,. https://doi.org/10.1371/journal.pone.0064683
Karki R, Pandya D, Elston RC, and Ferlini C. 2015. Defining “mutation” and “polymorphism” in the era of personal genomics. BMC Med Genomics 8: 37. DOI: 10.1186/s12920-015-0115-z
Liao EC, Hsieh CW, Chang CY, Yu SJ, Sheu ML, Wu SM, and Tsai JJ. 2015. Enhanced Allergic Inflammation of Der p 2 Affected by Polymorphisms of MD-2 Promoter. Allergy Asthma Immunol Res 7(5): 497–506, DOI: 10.4168/aair.2015.7.5.497.
López-Rodríguez JC, Manosalva J, Cabrera-García JD, Escribese M, Villalba MM, Barber D, Martínez-Ruiz A, Batanero E. 2019. Human glutathione-S-transferase pi potentiates the cysteine-protease activity of the Der p 1 allergen from house dust mite through a cysteine redox mechanism. Redox Biology 26: 101256. https://doi.org/10.1016/j.redox.2019.101256.
Lusiastuti AM, Seeger H, Sugiani D, Mufidah T, Novita H. 2015. Deteksi polymorphisme dengan substitusi nukleotida tunggal pada Streptococcus agalactiae isolat lokal Indonesia. Media Akuakultur 10(2): 91-95, .
Mix & Go E. coli Transformation Kit. Zymo Research Corp. www.zymoresearch.com.
Piboonpocanun S, Jirapongsananuruk O, Thomas WR, Malainual N, Vichnayond P. 2006. Genetic polymorphism of major house dust mite allergens. Clinical & Experimental Allergy 36(4):510-6. DOI: 10.1111/j.1365-2222.2006.02464.x
Resende RO, Ynoue LH, Miranda JS, de Almeida KC, de Oliveira Silva DA, Sopelete MC, Alves R, Gennari-Cardoso ML, Taketomi EA. 2019. IgE, IgG1, and IgG4 Reactivity to Dermatophagoides pteronyssinus Glycosylated Extract in Allergic Patients. Biomed Res Int Article ID 9840890. https://doi.org/10.1155/2019/9840890
Saitou M. and Mei M. 1987. The neighbor-joining method: A new method for constructing phylogenetic trees. Mol Biol Evol 4:406 – 425.
Shafique RH, Klimov PB, Inam M, Chaudhary FR, O’Connor BM. 2014. Group 1 Allergen Genes in Two Species of House Dust Mites, Dermatophagoides farinae and D. pteronyssinus (Acari: Pyroglypidae): Direct Sequencing, Characterization an Polymorphism. PLoS One 9(12):114636. DOI:0.1371/journal.pone.0114636.
Tallei TE, Kolondam BJ. 2015. DNA barcoding of Sangihe nutmeg (Myristica fragrans) using matK gene. Hayati J Biosciences 22(1):41-47. DOI:10.4308/hjb.22.1.41
Thomas WR. 2010. Geography of house dust mite allergens. Asian Pac J Allergy Immunol 28:211–224.
Toyobo Kod FX Neo (KFX-201). Target clone/Target clone plus. www.toyobo.co.jp/e/bio.
Toyobo. Target clone/Target clone plus. www.toyobo.co.jp/e/bio.
Twyman R. 2003. Mutation or polymorphism? Wellcome Trust website. http://genome.wellcome. ac.uk/doc_WTD020780.html
Verma S, Dixit R, Pandey KC. 2016. Der p 1 proteins: modes of activation and future prospects as pharmacological targets. Front Pharmacol 7:107.
Waldron R, Mc Gowan J, Gordon N, Mc Carthy C, Mitchell EB, Fitzpatrick DA. 2019. Proteonom and allergenome of the European house dust mite Dermatophagoides pteronyssinus. PLoS ONE 14(5):e0216171. https://doi.org/10.1371/ journal.pone.0216171
Zymobiomics DNA mini kit. (D4300). Zymo Research Corp. www.zymoresearch.com.
Zymoclean gel DNA recovery kit. Zymo Research Corp. www.zymoresearch.com.
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