Identification of Novel Mutations in IL-2 Gene in Khorasan Native Fowls

Document Type: Original Paper

Authors

1 Department of Animal Science, Faculty of Agriculture, Torbat-e Jam University of Agriculture, Torbat-e Jam, Iran

2 Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran

Abstract

The intron-exon structure of Khorasan native fowl interleukin-2 (IL-2) was investigated. For this purpose, twenty chickens were selected from the Native Fowl Breeding Station of Khorasan province, and genomic DNA was extracted using a modified conventional DNA extraction protocol. An 875 bp fragment of IL-2 was successfully amplified, including a small part of the promoter, exon 1, intron 1, and exon 2. To report a novel mutation in IL-2, PCRsequencing techniques were applied to the gene obtained from Khorasan native fowls. Then, the sequences were compared to evaluate gene mutations using CLC Main Workbench V. 5.5. The I-TASSER server was used to predict the 3-dimensional structure and function of protein molecules from amino acid sequences. The results of the comparison showed mutations in the DNA fragments of the sample birds, which caused changes in the amino acid content of IL-2. Substitutions at points 733, 738, 744, and 794 bp in the sequence were for C/A, A/T, C/A, and C/T, respectively. The translation of nucleotide to protein using BLASTx in the NCBI revealed that nucleotide substitutions caused three amino acid substitutions including A/E, R/W, and P/T.

Keywords


Betts MJ & Russell RB. 2003. Amino acid properties and consequences of substitutions. In: Michael R. Barnes MR & Gray CI. (Eds). Bioinformatics for Geneticists, John Wiley and Sons, Ltd.

Chen WT, Huang WY, Chen T, Salawu EO, Wang D, Lee YZ, Chang YY, Yang LW, Sue SC, Wang X, Yin HS. 2016. Structure and function of chicken interleukin-1 beta mutants: uncoupling of receptor binding and in vivo biological activity. Scientific Reports, 6: 27729. DOI: 10.1038/srep27729

Chorev M & Carmel L. 2012. The Function of introns. Frontiers in Genetics, 3: 55. DOI: 10.3389/fgene.2012.00055

Dakshinamurthi AK, Chidambaram MV, Manivel VA & Detchanamurthy S. 2009. Site-directed mutagenesis of human Interleukin-2 gene to increase the stability of the gene product- A bioinformatics approach. International Journal of Bioinformatics Research, 1: 4-13. DOI: 10.9735/0975-3087

FAO (Food and Agriculture Organization). 2007. The State of the World’s Animal Genetic Resources for Food and Agriculture. Edi: Barbara Rischkowsky & Dafydd Pilling. Rome. Italy; Available: http://www. fao.org/docrep/010/a1250e/a1250e00.htm.

Flori L, Gao Y, Oswald IP, Lefevre F, Bouffaud M, Mer-cat M.-J, Bidanel J-P &Rogel-Gaillard C. 2011. Deciphering the genetic control of innate and adaptive immune responses in the pig: A combined genetic and genomic study. BMC Proceedings, 4: S32. DOI: 10.1186/1753-6561-5-S4-S32

Gaffen SL & Liu KD. 2004. Overview of interleukin-2 function, production, and clinical applications. Cytokine, 28: 109-123. DOI: 10.1016/j.cyto.2004.06.010

Griffin DK, Robertson LB, Tempest HG, Vignal A, Fillon V, Crooijmans RPMA, Groenen MAM, Deryusheva S, Gaginskaya E, Carre W, Waddington D, Talbot R, Volker M, Masabanda JS, & Burt DW. 2008. Whole-genome comparative studies between chicken and turkey and their implications for avian genome evolution. BMC Genomics, 168. DOI: 10.1186/1471-2164-9-168

Haan C, Hermanns HM, Heinrich PC & Behrmann I. 2000. A single amino acid substitution (Trp (666)-->Ala) in the interbox1/2 region of the interleukin-6 signal transducer gp130 abrogates binding of JAK1, and dominantly impairs signal transduction. The Biochemical journal, 349: 261–266. DOI: 10.1042/0264-6021:3490261

Hu P, Mizokami M, Ruoff G, Khawli LA, & Epstein AL. 2003. Generation of low-toxicity interleukin-2 fusion proteins devoid of vaso-permeability activity. Blood, 101: 4853-4861. DOI: 10.1182/blood-2002-10-3089

Kaiser P & Mariani P. 1999. Promoter sequence, exon: intron structure and synteny of genetic location show that a chicken cytokine with T-cell proliferative activity is IL2 and not IL15. Immunogenetics, 49: 26–35. DOI: 10.1007/s002510050460

Kolodsick JE, Stepaniak JA, Hu W &Sundick RS. 2001. Mutational analysis of chicken interleukin 2. Cytokine, 13: 317-324. DOI: 10.1006/cyto.2001.0846

Kramer J, Malek M & Lamont SJ. 2003. Association of twelve candidate gene polymorphisms and response to challenge with Salmonella enteritidis poultry. Animal Genetics, 34: 339-348. DOI: 10.1046/j.1365-2052.2003.01027.x

Li D, Li Y, Li M, Che T & Tian S. 2019. Population genomics identifies patterns of genetic diversity and selection in chicken. BMC Genomics, 20: 263-275. DOI: 10.1186/s12864-019-5622-4

Liang SM, Thatcher DR, Liang CM & Allet B. 1986. Studies of structure-activity relationships of human interleukin-2. Journal of Biological Chemistry, 261: 334-337.

Mengesha M. 2012. The issue of feed-food competition and chicken production for the demands of foods of animal origin. Asian Journal of Poultry Science, 6: 31-43. DOI: 10.3923/ajpsaj.2012.31.43

Miller SA, Dykes DD & Polesky HF. 1988. A simple salting out procedure for extracting DNA from human nucleated cell. Nucleic Acids Research, 16: 1215. DOI: 10.1093/nar/16.3.1215

Muir WM & Aggrey SE. 2003. Poultry genetics, breeding and biotechnology. CABI Publ., Cambridge, MA.

Ng PC & Kirkness EF. 2010. Whole genome sequencing. In: Barnes MR & Breen G. (eds.), Genetic Variation: Methods and Protocols, Methods in Molecular Biology, vol. 628. DOI 10.1007/978-1-60327-367-1

Oh D, Son B, Mun S, Oh MH, Oh S, Ha J, Yi J, Lee S & Han K. 2016. Whole genome re-sequencing of three domesticated chicken breeds. BioOne, 33: 73-77. DOI: 10.2108/zs150071

Roy A, Kucukural A & Zhang Y. 2010. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocol, 5: 725-738. DOI: 10.1038/nprot.2010.5

Scepanovic P, Alanio C, Hammer C, Hodel F, Bergstedt J, Patin E, Thorball CW, Chaturvedi N, Charbit B, Abel L, Quintana-Mercy L, Duffy D, Albert ML, Fellay J & Milieu Intérieur Consortium. 2018. Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines. Genome Medicine,10: 59-72. DOI:  10.1186/s13073-018-0568-8

Sundick RS & Gill-Dixon C. 1997. A cloned chicken lymphokine homologous to both mammalian IL-2 and IL-15. The Journal of Immunology, 159: 720-725.

Thompson-Crispi K, Sewalem A, Miglior F &Mallard BA. 2012. Genetic parameters of adaptive immune response traits in Canadian Holsteins. Journal of Dairy Science, 95: 401-409. DOI:10.3168/jds.2011-4452

Tohidi R, Idris I, Malar Panandam J & Hair Bejo M. 2012. The effects of polymorphisms in IL-2, IFNg, TGF-β2, IgL, TLR-4, MD-2, and iNOS genes on resistance to Salmonella enteritidis in indigenous chickens. Avian Pathology, 41: 605–612. DOI: 10.1080/03079457.2012.739680

Wang A, Lu S& Mark D. 1984. Site-specific mutagenesis of the human interleukin-2 gene: structure-function analysis of the cysteine residues. Science, 224: 1431-1433. DOI: 10.1126/science.6427925

Wigley P & Kaiser P. 2003. Avian cytokines in health and disease. Revista Brasileira de Ciência Avícola, 5: 1-14. DOI: 10.1590/S1516-635X2003000100001

Wijga S, Parmentier HK, Nieuwland MG & Bovenhuis H. 2009. Genetic parameters for levels of natural antibodies in chicken lines divergently selected for specific antibody response. Poultry Science, 88:1805-1810. DOI: 10.3382/ps.2009-00064

Zekarias B, Ter Huurne AA, Landman WJ, Rebel JM, Pol JM & Gruys E. 2002. Immunological basis of differences in disease resistance in the chicken. Veterinary Research, 33: 109-125. DOI: 10.1051/vetres: 2002001

Zelus D, Robinson-Rechavi M, Delacre M, Auriault C & Laudet V. 2000. Fast evolution of interleukin-2 in mammals and positive selection in ruminants. Journal of Molecular Evolution, 51: 234-244. DOI: 10.1007/s002390010085

Zhang DY, Zhou JY, Chen WQ & Chen JG. 2009. Co-expression of IBV structural proteins and chicken interleukin-2 for DNA immunization. Veterinarni Medicina, 54: 169-174. DOI: 10.17221/23/2009-vetmed

Zhang DP, Zhao HJ, Luo YZ &Han JL. 2011. Characterization of haplotype diversity defined by discontinuous insertions/deletions within the intron 2 of interleukin 2 in different domestic chicken populations. Journal of Biological Sciences, 11: 261-267. DOI: 10.3923/jbs.2011.261.267

Zhang T, Zhao N & Liu Q. 2013. The effects of artificial selection on genetic variation of some immune genes in Gallus gallus. Archives Animal Breeding, 56: 691-699. DOI: 10.7482/0003-9438-56-069

Zhou H, Buitenhuis A, Weigend S & Lamont S. 2001. Candidate gene promoter polymorphisms and antibody response kinetics in chickens: interferon-gamma, interleukin-2, and immunoglobulin light chain. Poultry Science, 80: 1679-1689. DOI: 10.1093/ps/80.12.1679

Zurawski SM, Vega Jr F, Doyle EL, Huyghe B, Flaherty K, McKay DB& Zurawski G. 1993. Definition and spatial location of mouse interleukin-2 residues that interact with its heterotrimeric receptor. EMBO, 12: 5113-5119. DOI: 10.1002/j.1460-2075.1993.tb06206.x