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.

1.1       INTRODUCTION

CHAPTER ONE

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 growth- promoting 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 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.

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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