Bioinformatic Analysis of Insulin-Like Growth Factor I Gene of Three Avain Species

ABSTRACT 

A lot of attention has been paid to the study of Insulin-like Growth factor 1 (IGF1) due to its function in stimulating systemic body growth and regulating cell growth and development. A bioinformatics study was carried out to investigate the Insulin-like Growth Factor 1 gene of turkey, chicken and quail. A total of 15 insulin-like growth factor 1 nucleotide sequence and their corresponding protein were obtained from the Genebank (a public domain protein database) and were analyzed using various software tools (Clustal W, MEGA 6, dnaSP, BLAST, phyre2, ExPASy GORIV and Rasmol software) to determine the percent identity and similarities in function of IGF 1 gene, genetic diversity, evolutionary relationship, protein structure prediction and physiochemical properties. The result obtained showed that percent identity and similarity of IGF1 gene in avians ranged from 86-99% and were similar in function. Observed genetic diversity was high within each avian (1.000 in turkey, 0.900 in chicken and 0.900 in quail). However chicken had the highest haplotype number value (4), this showed that chicken has more variation than turkey and quail IGF1 gene sequence. Phylogenetic analysis showed that the IGF1 in gene sequence of avian were grouped into the same taxon, chicken and quail shared a most recent common ancestor and were closely related than the IGF1 gene of turkey. The secondary structure analyzed by GORIV (Garnier-Osguthorpe-Robson IV) software tool showed that the alpha helix structure of chicken, turkey and quail occupied (20.92%), (21.57%) and (20.92%) of the IGF1 gene sequences respectively. The results from the secondary and tertiary structure of IGF1 protein predictions showed that the IGF genes of avian are stable and properly formed. The physiochemical properties showed that chicken, turkey and quail IGF1protein had isoelectric potential (theoretical pI) of 9.25, estimated half-life of 30 hours. In conclusion, the high percent identity and similarity in function, high genetic diversity observed, a relative relatedness in the phylogentic study and high alpha helix in the protein structure of IGF1 gene seen in this study make the gene highly effective in improving growth, and regulating cellular activities.

TABLE OF CONTENT

Title page………………………………….……………………………………….. i

Certification……………………………………………………………………….. ii

Dedication………………………………………………………………………… .iii

Acknowledgement ………………………………………………………………... iv

Table of content……………………………………………………………………. v

List of tables……………………………………………………………………….. viii

List of figures………………………………………………………………………. ix

List of plates………………………………………………………………………... x

Abstract…………………………………………………………………………….. xi

CHAPTER ONE: GENERAL INTRODUCTION

1.1 Introduction………………………………………………….………………….. 1

1.2 Objectives of the study……………………………………….………………… 3

1.3 Justification…………………………………………….………………………… 3

CHAPTER TWO: LITERATURE REVIEW

2.1 Insulin-like growth factor……………………………………………………….. 4

2.2 Basic biochemistry and physiologic functions………………………………….. 5

2.2.1 Structure and synthesis…………………………….………………………….. 5

2.2.2 Physiologic role and mechanism of action………………………….………… 5

2.2.3 Regulation and differentiation of function……………………………….…... 6

2.3 Pathologic conditions associated with alteration in the IGF system……………. 6

2.3.1 Insulin-like growth factor I……………………………………………............ 6

2.3.2 Insulin-like growth factor II…………………………………………………... 8

2.4 Insulin-like growth factor I as a therapeutic agent…………………………….... 8

2.5 The IGF system and muscle development in birds……………………………... 8

2.6 Species specificities of the avian IGF system ……………………………….... 9

2.7 Structure of IGF I peptide and gene transcript ………………………………. 10

2.8 IGF1 as a local regulator of muscle growth …………………………………... 11

2.9 Genetic diversity………………………………………………………………. 12

2.10 Protein structure ……………………………………………………………... 12

2.11 Levels of protein Structure …………………………………………............... 13

2.11.1 Primary structure………………………………………………………....… 13

2.11.2 Secondary structure………………………………………………………… 13

2.11.3 Tertiary structure ……………………………………………………........... 14

2.11.4 Quaternary structure ……………………………………………………….. 14

2.12 Protein structure prediction…………………………………………………… 14

2.13 Bioinformatics ………………………………………………………………... 15

2.13.1 Application of bioinformatics to biotechnology and biomedical sciences...... 15

2.14 Phylogenetics ……………………………………………………………….... 18

2.15 Comparative genomics ……………………………………………….............. 19

CHAPTER THREE: MATERIALS AND METHOD

3.1 Location of study and retrieval of IGF I gene sequence …………………………. 21

3.2 Multiple sequence alignment ………………………………………………….. 21

3.3 Determination of genetic diversity of IGF I gene of turkey, chicken and quail.. 21

3.4 Determination of evolutionary relationship…………………………………….. 21

3.4.1 Determination of percent identity and similarity……………………………... 21

3.4.2 Phylogenetic analysis…………………………………………………............. 22

3.5 Prediction of protein structure …………………………………………………. 22

3.6 Determination of physiochemical properties …………………………………... 22

CHAPTER FOUR: RESULT AND DISCUSSION

4.1 Retrieval of nucleotide and amino acid sequences of IGF I gene…………….. 23

4.2 Percentage identity and similarities of IGF I gene among avian species……… 24

4.2.1 Percentage identity of IGF I gene among avian species ……………….…… 24

4.2.2 Percentage similarities of IGF I gene among avian species…………………. 25

4.3 Genetic diversity of IGF I gene on three avian species……………………….. 26

4.4 Evolutionary relationship study of IGF I gene on three avian species ………. 28

4.5 Secondary and tertiary protein structure IGF I protein of three avian species... 30

4.5.1 Secondary protein structure of IGF I protein……………………………….. 30

4.5.2 Tertiary protein structures of IGF I protein of chicken, turkey and quail...… 31

4.6 Physiochemical properties of chicken, turkey and quail IGF I protein………. 36

CHAPTER FIVE: CONCLUSION AND RECOMMENDATION

5.1 Conclusion and recommendation ……………………………………………. 38

References ……………………………………………………………………….. 39