Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes

Abstract

Background: Model organisms have contributed substantially to our understanding of the etiology of human disease as well as having assisted with the development of new treatment modalities. The availability of the human, mouse and, most recently, the rat genome sequences now permit the comprehensive investigation of the rodent orthologs of genes associated with human disease. Here, we investigate whether human disease genes differ significantly from their rodent orthologs with respect to their overall levels of conservation and their rates of evolutionary change.

Results: Human disease genes are unevenly distributed among human chromosomes and are highly represented (99.5%) among human-rodent ortholog sets. Differences are revealed in evolutionary conservation and selection between different categories of human disease genes. Although selection appears not to have greatly discriminated between disease and non-disease genes, synonymous substitution rates are significantly higher for disease genes. In neurological and malformation syndrome disease systems, associated genes have evolved slowly whereas genes of the immune, hematological and pulmonary disease systems have changed more rapidly. Amino-acid substitutions associated with human inherited disease occur at sites that are more highly conserved than the average; nevertheless, 15 substituting amino acids associated with human disease were identified as wild-type amino acids in the rat. Rodent orthologs of human trinucleotide repeat-expansion disease genes were found to contain substantially fewer of such repeats. Six human genes that share the same characteristics as triplet repeat-expansion disease-associated genes were identified; although four of these genes are expressed in the brain, none is currently known to be associated with disease.

Conclusions: Most human disease genes have been retained in rodent genomes. Synonymous nucleotide substitutions occur at a higher rate in disease genes, a finding that may reflect increased mutation rates in the chromosomal regions in which disease genes are found. Rodent orthologs associated with neurological function exhibit the greatest evolutionary conservation; this suggests that rodent models of human neurological disease are likely to most faithfully represent human disease processes. However, with regard to neurological triplet repeat expansion-associated human disease genes, the contraction, relative to human, of rodent trinucleotide repeats suggests that rodent loci may not achieve a 'critical repeat threshold' necessary to undergo spontaneous pathological repeat expansions. The identification of six genes in this study that have multiple characteristics associated with repeat expansion-disease genes raises the possibility that not all human loci capable of facilitating neurological disease by repeat expansion have as yet been identified.

Figure 1

K_A/K_S, K_S, and K_A distributions of ortholog pairs for disease versus non-disease genes. (a) The K_A/K_S ratio, (b) K_S, the number of synonymous substitutions per synonymous site, and (c) K_A, the number of non-synonymous substitutions per non-synonymous sites, were calculated for 1:1 human:rat orthologs for a set containing human genes associated with disease and a set containing human genes not known to be associated with disease.

Figure 2

Human disease gene distribution across pathophysiology systems. The horizontal axis represents different disease systems. The vertical axis represents the number of genes present in each disease systems; these numbers are provided at the top of each bar. IDE, insufficient disease evidence.

Figure 3

Median K_A/K_S ratios for rat and mouse orthologs of human disease genes. Median K_A/K_S values for each disease category are depicted for rat (color) and mouse (grey) demonstrating differences by disease category. The disease categories exhibiting the greatest purifying selection, the neurological and malformation-syndrome disease systems, show the lowest median K_A/K_S ratios.

Figure 4

K_A/K_S differences by disease system. Significance of K_A/K_S differences determined by Wilcoxon analysis indicate that both rat (color) and mouse (grey) demonstrate significantly strong purifying selection for the orthologs of the neurological and malformation-syndrome disease categories. The immunological, hematological, and pulmonary disease systems demonstrated significantly lower conservation. Disease categories are listed along the vertical axis in the order of standardized score from low to high. The P value is indicated above the bars in the figure; P values of less than 0.05 are considered statistically significant.

Figure 5

Functional annotation distribution by disease system. Over-representation of gene ontology annotation in different disease systems. Only records with P value ≤0.05 and both expected and observed frequency ≥2%, and with number of records ≥5, are shown. Over-represented functions are labeled red with the color gradient representing the deviation in value. The darker the color, the greater the deviation observed.

Figure 6

Disease gene system conservation in model organisms. The five disease systems in which significant conservation differences are found (hematological, immune, malformation syndrome, metabolic and neurological) are plotted on the horizontal axis for the six different model organisms (mouse, rat, fish, fly, nematode and yeast). The vertical axis represents standardized score from Wilcoxon analyses for conservation index. The greater the score, the more conserved the disease system.

Figure 7

Poly-glutamine repeat length comparison between human-rat and human-mouse orthologous proteins. Comparison of the poly-glutamine length between human-rat orthologous proteins (light orange, dark orange) and human-mouse orthologous proteins (light blue, dark blue). Dark orange and dark blue correspond to repeats in genes associated with repeat-expansion disease in humans: SCA1, spinocerebellar ataxia 1 protein, or ataxin1; SCA2, spinocerebellar ataxia 2 protein; SCA7, spinocerebellar ataxia 7 protein; MJD, Machado-Joseph disease protein, or voltage-dependent calcium channel gamma-1 subunit; CACNA1A, spinocerebellar ataxia 6 protein, or calcium channel alpha 1A subunit isoform 1; DRPLA, dentatorubro-pallidoluysian atrophy protein; HD, Huntington's disease protein, or huntingtin; TBP, TATA binding protein or spinocerebellar ataxia 17 protein. In the case of SCA2 the rat orthologous sequence did not contain the human amino-terminal region, wherein the repeat is located. Points below the diagonal line correspond to a repeat length that is more than double in humans versus rodents.