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 CONTENTS
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
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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
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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
CHAPTER ONE
1.1 INTRODUCTION
Insulin-like growth factors (IGF1) are naturally occurring protein capable of stimulating
cellular growth, proliferation and differentiation. According to Hegarty et al. (2006), IGF1
are proteins which are important for regulating a variety of cellular processes. Insulin-like
growth factor-1 is a mediator of many biological effects; it increases the absorption of
glucose, stimulates myogenesis, inhibits cell cycle genes, increases the synthesis of lipids,
and stimulates the production of progesterone in the synthesis of DNA, RNA and protein
(Etherton, 2004). Due to these biological functions, IGF1 is being considered as a candidate
gene for predicting growth and meat quality traits in the animal genetic development scheme
(Andrade et al., 2008).
IGF1 is produced primarily by the liver as an endocrine hormone as well as in target tissues
in a paracrine or autocrine manner (Kemp, 2007). Its production is stimulated by growth
hormone and can be retarded by under-nutrition, growth insensitivity or lack of growth
hormone receptors (Flier and Underhill, 2006). Growth hormone is made in the anterior
pituitary gland and released into the blood stream and then stimulates the liver to produce
IGF1 (Akinfenwa et al., 2011). Then IGF1 stimulates systemic body growth and has growthpromoting
effects on almost every cell in the body system (Yilmaz et al., 2011). Deficiency
of either growth hormone or IGF1 therefore results in diminished stature (Akinfenwa et al.,
2011).
Different researchers have established a link between the concentration of the circulating
IGF1 and growth trait in many livestock species and laboratory animals (Bertlett and Tom,
2005; Bunter et al., 2005; Hegarty et al., 2006).
Bioinformatics involves discovery, development and implementation of computational
algorithms and software tools that facilitates an understanding of the biological processes
with the goal to serve primarily agriculture and health care sectors with several spinoffs
(Albert et al., 2011). In a developing country like Nigeria, bioinformatics has a key role to
play in areas like agriculture where it can be used to analyze livestock genomic and
proteomic data that can be very useful in making genetic improvements.
Computational analysis greatly helps in understanding the molecular basis of the biological
function of proteins through the use of available information to understand the biological
function of unknown proteins. Technical progress in computational methods offers the
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potential to make many improvements far faster and more efficient than would be possible by
laboratory methods (Zimin et al., 2009). Bioinformatics is a branch of biological science
which deals with the study of methods for storing, retrieving and analysis biological data,
such as nucleic acid (Deoxyribonucleic acid/ribonucleic acids/ and protein sequences,
structures, function, pathways and genetic interaction) (www.wikipeadia.com). Ribonucleic
acids (RNA) and deoxyribonucleic acids (DNA) are the molecules that store the hereditary
information about an organism. These macro-molecules have a fixed structure, which can be
analysed by biologists with the help of bioinformatics tools and databases. A few popular
data bases are gene Bank from NCBI (National Centre for Biotechnology Information), Swiss
port from the Swiss institution of Bioinformatics and protein information Resources (PIR)
(www.ncbi.nlm.nih.gov).
One of the major challenges of animal breeding is to understand the genetic basis of
phenotypic diversity within and among species. Thousands of years of relative breeding of
domestic animals has created a diversity of phenotypes among breeds that is only matched by
that observed among species in nature. Selection of most livestock in Nigeria has been
carried out with little or no knowledge of series of reactions at the molecular and cellular
level. Selection has been on the effect of the gene rather than directly on the gene themselves
(Akinbiyi, 2014). Traits are controlled by single or combination of many gene actions. The
study of IGF1gene on avian using bioinformatics aim at enlightening the farmers and
breeders more in understanding the importance of molecular components of genes in
selection, especially in a developing country like Nigeria where molecular genetics and
bioinformatics is still under study and not well documented.
According to Mahmoud et al. (2014), chicken IGF1have been seen to serve as better
candidate gene for growth and other metabolic process (proliferation and cellular
differentiation) when compared to most species. In this study, the role of IGF1in three avian
species was identified and a comparison made to help researchers and farmers know which
specie IGF1gene can best serve as a molecular maker and also as a growth promoter to
improve production traits in farm animals. Toro et al., (2008) reported that molecular data on
within and between breed genetic diversity are essential for effective management of farm
animal genetic resources. FAO (2000) reported that genetic diversity in livestock allows
farmers to select stocks or develop new breeds in response to environmental changes, threat
of disease, new knowledge of human nutrition requirement, changing market conditions and
societal needs.
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1.2 OBJECTIVES OF THE STUDY
The general objective of the study was to obtain information on the insulin-like growth factor
1 gene of three avian species using bioinformatics.
The specific objectives of the study are:
I. To determine the percent identity and similarities in function between the insulin-like
growth factor 1 gene protein sequences of three avian species;
II. To determine the genetic diversity of IGF1 gene among three avian species;
III. To investigate an evolutionary relationship between the species;
IV. To determine the secondary and tertiary structures of insulin like growth factor 1
protein of the three avian species;
V. To determine the physicochemical properties of IGF1 of turkey, chicken and quail
species.
1.3 JUSTIFICATION
The genetics of the diversity of the IGF1 gene in avian is a pertinent study given its abundant
occurrence among species, among individuals of the same species and among cells of single
multi-cellular organisms. Knowledge of the morphological characterization of IGF 1 gene,
will lead to the understanding of its genetic diversity will provide an insight on which avian
species IGF1 gene has been subjected to mutation, has undergone high natural selection, and
high genetic variation (allowing species to change over time thereby surviving changing
environmental conditions). In other words, that having greater genetic diversity can offer
greater resilience.
The study of IGF1 gene of avian through bioinformatics in Nigeria is important to ascertain if
the variation and polymorphism among Gallus gallus, Meleagris gallopavo, and Coturnix
coturnix are as a result of convergent or divergent evolution or by chance and predict the
secondary and tertiary structure of the insulin-like growth factor 1 gene of avians, and also if
a particular mutation in IGF1gene that encodes for IGF1protein can lead to changes in the
behavior of the protein among the different species, which will affect their fitness level for a
particular trait either positively or negatively.
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