Genetic background and environmental effects on single nucleotide polymorphisms in the NADPH pathway

Abstract

A major focus in modern genomics is determining the connection between genotypes and quantifying phenotypes. In this connection, many factors come into play including different genetic backgrounds, genetic variation at a locus, and environmental conditions. Genetic variation in Drosophila melanogaster, and specifically the simple polymorphisms within Malic enzyme (Men), can provide insight into the pathways between genotypes and phenotypes. Globally, there are two polymorphic sites in the malic enzyme gene. On site is near the protein (MEN) active site and found at an allelic frequency of 50% glycine amino acid and 50% alanine amino acid. The second polymorphism is buried within the protein and found at an allelic frequency of 90% methionine amino acid and 10% leucine amino acid. To determine the complexity of the pathway between genotypes and phenotypes, multiple genetic backgrounds for each genotype, using multiple D. melanogaster lines, were included to explore and quantify genetic background effects, and paraquat was used to induce oxidative stress. The biochemical characteristics of the alleles varied significantly between the genotypes under benign conditions and both polymorphic sites effected some phenotypes. The first site played a role in the MEN Vmax and Km; the glycine allele had 14% higher Vmax activity than the alanine allele and the glycine allele had 8% higher Km than the alanine allele. The second site influenced the Km and Vmax/Km ratio (relative activity); the methionine allele had 34% higher malate Km than the leucine allele the leucine allele had 52% higher relative activity than the methionine allele. Interestingly, the protein product encoded by the rarer allele, leucine, had a higher relative activity and lower Km concentration, having a large impact on the enzymatic phenotype. These extreme phenotypes of that allele may be an indication of the why the allele is maintained at 10% across populations. Different lines with the same genotype had different biochemical phenotypes, indicating the importance of backgrounds effects influencing the final phenotype. Further, the flies’ phenotypes differed between benign and oxidative stress conditions. Flies exposed to paraquat had a decrease in MEN Vmax, and the MEN alleles did not significantly differ from each other. Overall, the findings from this study suggest that the final phenotype are strongly influenced by the polymorphisms found in MEN, the interactions between genetic background and environmental conditions.