Characterization and Prediction of Protein Structures of Interferon Regulatory Factor 3 (Irf 3) Gene in three Nigerian Cattle Breeds

Authors

  • Abubakar A. M. Federal College of Education, (Special), Oyo, Oyo State, Nigeria.
  • Micheal O. O. Federal University of Agriculture, Abeokuta
  • Alaka F. A. Federal College of Education, (Special), Oyo, Oyo State, Nigeria.
  • Salami S. O. Federal College of Education, (Special), Oyo, Oyo State, Nigeria.
  • Christian O. I. Federal University of Agriculture, Abeokuta
  • Adewale O. T. Federal University of Agriculture, Abeokuta
  • Samuel O. D. Federal University of Agriculture, Abeokuta
  • John S. D. Federal University of Agriculture, Abeokuta

Keywords:

Cattle, IRF 3, Proteins, Nigeria, Exons 1 and 2, Exons 5 and 6

Abstract

The study was conducted to characterize and predict the secondary and tertiary protein structures of exons 1to 2 and exons 5 to 6 of the IRF 3 gene in three Nigerian cattle breeds, namely; the White Fulani, Muturu and N’Dama breeds. Blood samples for deoxyribonucleic acid (DNA) and studies were collected from 90 animals (30 White Fulani, 30 Muturu and 30 N’Dama). DNA was extracted from the blood samples using the Zymo-spin extraction kit. Primers were designed and DNA amplification was carried out using the specified PCR protocols. The purified PCR products were subjected to sequencing using BigDye® terminator cycle sequencing kit on ABI 3730xl (Applied Biosystems) DNA analyzer. The nucleotide sequences of the IRF3 gene of each breed were translated to amino acid sequence using NCBI ORF finder, Primary and secondary protein structures were predicted using GOR IV and Phyre 2 software, respectively, while the tertiary structures were viewed with Rasmol. Findings of the study revealed that the predicted secondary and tertiary protein structures and physico-chemical properties of exons 1 to 2 of the candidate gene in the three cattle breeds were identical, while for exons 5 to 6, the structures and physico-chemical properties were different. It was concluded that the prediction of secondary protein structures of the loci under consideration showed mixed folding proteins, which contained alpha helices, extended strand and random coils. It was recommended that; the roles of IRF3 gene in animal reproduction and development should be further explored and Polymorphism in the IRF3 gene and their association with diseases of economic importance in Nigerian cattle should also be studied.

 

 

 

 

L’étude a été menée pour caractériser et prédire les structures protéiques secondaires et tertiaires des exons 1 à 2 et des exons 5 à 6 du gène IRF 3 chez trois races de bovins nigérianes, à savoir; les races White Fulani, Muturu et N’Dama. Des échantillons de sang pour l’acide ésoxyribonucléique (ADN) et les études ont été collectés auprès de 90 animaux (30 White Fulani, 30 Muturu et 30 N’Dama). L’ADN a été extrait des échantillons de sang en utilisant le kit d’extraction Zymo-spin. Des amorces ont été conçues et l’amplification de l’ADN a été réalisée en utilisant les protocoles de PCR spécifiés. Les produits de PCR purifiés ont été soumis à un séquençage utilisant le kit de séquençage par cycle BigDye® terminator sur l’analyseur d’ADN ABI 3730xl (Applied Biosystems). Les séquences nucléotidiques du gène IRF3 de chaque race ont été traduites en séquence d’acides aminés à l’aide de l’outil NCBI ORF finder. Les structures protéiques primaires et secondaires ont été prédites en utilisant respectivement les logiciels GOR IV et Phyre 2, tandis que les structures tertiaires ont été visualisées avec Rasmol. Les résultats de l’étude ont révélé que les structures protéiques secondaires et tertiaires prédites et les propriétés physico-chimiques des exons 1 à 2 du gène candidat chez les trois races de bovins étaient identiques, tandis que pour les exons 5 à 6, les structures et les propriétés physicochimiques étaient différentes. Il a été conclu que la prédiction des structures protéiques secondaires des loci étudiés montrait des protéines à pliage mixte, contenant des hélices alpha, des brins étendus et des bobines aléatoires. Il a été recommandé que les rôles du gène IRF3 dans la reproduction et le développement des animaux soient davantage explorés et que le polymorphisme du gène IRF3 et son association avec les maladies d’importance économique chez les bovins nigérians soient également étudiés. 

 

 

 

Author Biographies

Abubakar A. M. , Federal College of Education, (Special), Oyo, Oyo State, Nigeria.

Department of Agricultural Education, Federal College of Education, (Special), Oyo, Oyo State,
Nigeria.

Micheal O. O. , Federal University of Agriculture, Abeokuta

Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun
State, Nigeria.

Alaka F. A. , Federal College of Education, (Special), Oyo, Oyo State, Nigeria.

Department of Agricultural Education, Federal College of Education, (Special), Oyo, Oyo State,
Nigeria.

Salami S. O. , Federal College of Education, (Special), Oyo, Oyo State, Nigeria.

Department of Agricultural Education, Federal College of Education, (Special), Oyo, Oyo State,
Nigeria.

Christian O. I. , Federal University of Agriculture, Abeokuta

Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun
State, Nigeria.

Adewale O. T., Federal University of Agriculture, Abeokuta

Department of Veterinary Medicine and Surgery, Federal University of Agriculture, Abeokuta, Ogun
State, Nigeria.

Samuel O. D. , Federal University of Agriculture, Abeokuta

2Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun
State, Nigeria.

John S. D., Federal University of Agriculture, Abeokuta

Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun
State, Nigeria.

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Published

2024-10-09

How to Cite

A. M. , A., O. O. , M., F. A. , A., S. O. , S., O. I. , C., O. T., A., O. D. , S., & S. D., J. (2024). Characterization and Prediction of Protein Structures of Interferon Regulatory Factor 3 (Irf 3) Gene in three Nigerian Cattle Breeds. Nigerian Journal of Animal Production, 50(4), 108–120. Retrieved from https://njap.org.ng/index.php/njap/article/view/8022