Factors influencing codon usage of mitochondrial ND1 gene in pisces, aves and mammals

Highlights

• Our result suggests that the ND1 is AT rich in pisces, aves and mammals.

• Most of the nucleotides differ significantly among pisces, aves and mammals as revealed from t-test.

• The codon usage bias was low in ND1gene.

• Codon usage bias is mainly influenced by natural selection and mutation pressure.

• t-Test analysis showed that the MT-ND1 gene has a wide significant discrepancy in codon choices in pisces, aves and mammals.

Abstract

Animal mitochondrial genome harbours 13 protein coding genes which regulate the process of respiration. The mitochondrial NADH dehydrogenase 1 (MT-ND1) gene, one of the 13 protein-coding genes, encodes the NADH dehydrogenase 1 enzyme of the respiratory chain. Analysis of codon usage bias (CUB) acquires importance for better understanding of the molecular biology, new gene discovery, design of transgenes and gene evolution. The MT-ND1 gene seems to be a good candidate for analyzing codon usage pattern, since no work has yet been reported. Moreover, it is still not clear which factors significantly influence the codon usage pattern. In the present study, comparative analysis of codon usage pattern, expression level and influencing factors for MT-ND1 gene from 100 different species each of pisces, aves and mammals were used for CUB analysis. Our result suggests that the gene is AT rich in pisces, aves and mammals and most of the nucleotides significantly differ among them as revealed from t-test. CUB was not remarkable as reflected by high value of effective number of codons and it also significantly differs among pisces, aves and mammals. Although we found that CUB is mainly influenced by natural selection and mutation pressure for MT-ND1 gene as suggested by correlation and correspondence analysis but neutrality plot further revealed that natural selection played a major role and mutation pressure played a minor role in codon usage pattern. Additionally, t-test analysis showed that the MT-ND1 gene has a wide significant discrepancy in codon choices in pisces, aves and mammals. This study has contributed to boost our understanding about the mechanism of distribution of the codons and the factors that may influence the evolution of the MT-ND1 gene.

Introduction

The MT-ND1 gene is one of the 13 protein-coding genes in mitochondrial DNA involved in respiration. It encodes the NADH dehydrogenase 1 enzyme and forms a subunit of complex I of the mitochondrial respiratory chain (Hauptmann et al., 2009). The mitochondrial DNA is covalently closed, double stranded structure with nearly 16.6 kb size, which encodes 2 rRNA, 22 tRNAs and 13 polypeptides (Chen et al., 2009). Each polypeptide encoded by mitochondrial gene is a subunit of one of four respiratory complexes in the electron transport chain (ETC) localized in the inner membrane of mitochondria (Braun et al., 1992). The mitochondrial DNA is maternally inherited and harbours higher rates of mutation (Taylor and Turnbull, 2005). The lack of introns in the mitochondrial genes and histones in packaging of mitochondrial genome makes mitochondrial DNA more prone to mutation due to the presence of reactive oxygen species (ROS) generated by oxidative phosphorylation in the mitochondria (Kunkel and Loeb, 1981, Matsukage et al., 1975, Modica-Napolitano and Singh, 2004, Shay and Werbin, 1992, Singh et al., 2001, Torri and Englund, 1995). Mutation rate in mitochondrial DNA is tenfold higher than nuclear DNA (Shoubridge, 2000, Wilson and Roof, 1997). Mitochondrial DNA is an excellent tool for evolutionary study due to its small size and relatively conserved gene content and high mutation rate (Clark et al., 2007). Unlike nuclear genetic code, mitochondrial genetic code in vertebrates is composed of 60 sense codons that represent 20 standard amino acids, and the remaining four codons that act as termination signals are TAA, TAG, AGA and AGG (Knight et al., 2001). The genetic code is universal with a few exceptions in mitochondrial DNA. In animal mitochondrial DNA only six codons have been reported which vary in the process of evolution and these codons are TGA, ATA, AAA, AGA, AGG and TAA. The codon TGA acts as termination codon in standard genetic code but in animal mitochondrial DNA, TGA encodes Trp. The codon ATA encodes Ile in standard genetics code but Met in most of the mitochondrial DNA of metazoans (Watanabe and Yokobori, 2011).

Codon usage bias (CUB) is the phenomenon of unequal usage of codons during translation of genes. In protein-coding genes, some codons are used more often than other synonymous codons which create such bias. These codons are called optimal or preferred codons. CUB is a common trend in an extensive variety of organisms, including prokaryotes as well as eukaryotes (Akashi, 1997, Sharp et al., 1993). The codon usage pattern is a unique property of a genome (Grantham et al., 1980). Furthermore, within the same organism, different tissues may exhibit different codon usage pattern (Plotkin et al., 2004). The mutations in the third codon position generally changes the synonymous codons without altering the encoded amino acid and thereby retaining the primary sequence of the protein (Biro, 2008). Generally, compositional properties under mutational pressure and natural selection have been considered to be the two main forces influencing the codon usage bias among genes (Sharp et al., 1993, Shields et al., 1988, Stenico et al., 1994). In some organisms, the codon usage bias is influenced by the mutation pressure and genetic drift while in other organisms, it is due to the balance between natural selection and mutational pressure (Bulmer, 1991). In certain genes, the mutation pressure plays an important role in influencing the synonymous codon usage bias due to very high content of any of the four nucleotides (Karlin and Mrázek, 1996, Sharp et al., 1993, Zhao et al., 2007, Zhong et al., 2007). Mutational bias arises from extremely high or low G or C nucleotide in the wobble position in an open reading frame (Sueoka, 1988). Previous studies on the highly expressed genes suggested that the phenomenon of translational selection is responsible for codon usage bias. The preferred codons are easily recognized by the abundant tRNA molecules in highly expressed genes (Bibb et al., 1984, McEwan and Gatherer, 1999).

The mitochondrial electron transport chain plays a vital role in fulfilling energy requirements of an organism. Analysis of codon usage patterns in MT-ND1 gene is of great interest to understand how the energy requirement of pisces, aves and mammals, influences the codon usage pattern against rapid environmental changes during the course of evolution. These three groups namely pisces, aves and mammals live in three different habitats and so their mode of respiration and energy requirement are also different (Ellington, 2001). Therefore, the study of synonymous codon usage helps in understanding the factors influencing gene evolution. Some previous studies on codon usage pattern of nuclear and mitochondrial genomes have been conducted on some invertebrates and vertebrates (Karlin and Mrázek, 1996, Wei et al., 2014). However, no work was reported for MT-ND1 gene. Since all the protein-coding mitochondrial genes play a crucial role in the electron transport chain, so the study of their codon usage will be interesting to generate biologically useful information. Mitochondrial genome is a suitable tool to study the evolutionary relationship due to its small size, relatively conserved gene content, maternal inheritance pattern and high mutation rate. Herein, we investigated the mitochondrial MT-ND1 gene to understand the codon usage pattern among 100 species each of pisces, aves and mammals belonging to aquatic, aerial and terrestrial environments, respectively. Understanding the synonymous codon usage patterns in MT-ND1 gene among pisces, aves and mammals would improve our knowledge on the distribution of codons, their variation and eventuallyelucidate the factors influencing the codon usage pattern.