Limits...
Strong purifying selection in transmission of mammalian mitochondrial DNA.

Stewart JB, Freyer C, Elson JL, Wredenberg A, Cansu Z, Trifunovic A, Larsson NG - PLoS Biol. (2008)

Bottom Line: Purifying selection is thought to be important in shaping mtDNA sequence evolution, but the strength of this selection has been debated, mainly due to the threshold effect of pathogenic mtDNA mutations and an observed excess of new mtDNA mutations in human population data.These data show strong purifying selection against mutations within mtDNA protein-coding genes.To our knowledge, our study presents the first direct experimental observations of the fate of random mtDNA mutations in the mammalian germ line and demonstrates the importance of purifying selection in shaping mitochondrial sequence diversity.

View Article: PubMed Central - PubMed

Affiliation: Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden. Jim.Stewart@ki.se

ABSTRACT
There is an intense debate concerning whether selection or demographics has been most important in shaping the sequence variation observed in modern human mitochondrial DNA (mtDNA). Purifying selection is thought to be important in shaping mtDNA sequence evolution, but the strength of this selection has been debated, mainly due to the threshold effect of pathogenic mtDNA mutations and an observed excess of new mtDNA mutations in human population data. We experimentally addressed this issue by studying the maternal transmission of random mtDNA mutations in mtDNA mutator mice expressing a proofreading-deficient mitochondrial DNA polymerase. We report a rapid and strong elimination of nonsynonymous changes in protein-coding genes; the hallmark of purifying selection. There are striking similarities between the mutational patterns in our experimental mouse system and human mtDNA polymorphisms. These data show strong purifying selection against mutations within mtDNA protein-coding genes. To our knowledge, our study presents the first direct experimental observations of the fate of random mtDNA mutations in the mammalian germ line and demonstrates the importance of purifying selection in shaping mitochondrial sequence diversity.

Show MeSH

Related in: MedlinePlus

Distribution of Mutations by Gene for mtDNA Mutator Lines and Human mtDNA Sequence DataPlot of observed minus expected ratio of 4-fold degenerate sites versus all other protein-coding sites.(A) For mtDNA mutator mouse lines, the ratio of observed to expected sites is plotted for third codon position mutations at 4-fold degenerate sites (filled bars), and for all other protein-coding gene mutations observed (open bars). The line represents the observed expected values normalized to 1.0.(B) The same plot for observed human variants found on the mtDB database.(C) Plot of observed minus expected for non–4-fold degenerate sites for mouse (filled bar) and human (open bars). Genes are grouped by mitochondrial respiratory chain complexes. Expected values are derived from an assumption of equal distribution of the observed mutations in the dataset, and observed values are derived from a count of the detected mutations for that gene (see Material and Methods).
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2214808&req=5

pbio-0060010-g003: Distribution of Mutations by Gene for mtDNA Mutator Lines and Human mtDNA Sequence DataPlot of observed minus expected ratio of 4-fold degenerate sites versus all other protein-coding sites.(A) For mtDNA mutator mouse lines, the ratio of observed to expected sites is plotted for third codon position mutations at 4-fold degenerate sites (filled bars), and for all other protein-coding gene mutations observed (open bars). The line represents the observed expected values normalized to 1.0.(B) The same plot for observed human variants found on the mtDB database.(C) Plot of observed minus expected for non–4-fold degenerate sites for mouse (filled bar) and human (open bars). Genes are grouped by mitochondrial respiratory chain complexes. Expected values are derived from an assumption of equal distribution of the observed mutations in the dataset, and observed values are derived from a count of the detected mutations for that gene (see Material and Methods).

Mentions: We further investigated the observed selection on protein-coding genes in the mtDNA mutator lines by separating the mutations at 4-fold degenerate sites (third codon positions for amino acids L2, V, A, T, P, S1, R, and G) from all other protein-coding mutations. The 4-fold degenerate sites can mutate to any nucleotide without changing the encoded amino acid and should therefore be subject to less selective constraint than other protein-coding sites. Expected values were calculated based on an assumption of an equal distribution of the observed mutations of these two classes, across the genes and corrected for their coding size. The ratios between observed and expected mutation frequencies at 4-fold degenerate sites were approximately equal in all of the protein-coding genes except for mt-ND2 and mt-ATP8 (Figure 3A and Table S3A). In contrast, mutations at the non–4-fold degenerate sites deviated profoundly from the ratios predicted by equal distribution of mutations (Figure 3A). Contingency table analysis was carried out to detect changes in the proportion of 4-fold degenerate site mutations to other sites within the protein-coding genes. The 13 protein-coding subunits were grouped by the oxidative phosphorylation (OXPHOS) enzyme complex to which they belong. Only complexes III (containing mt-CYTB) and complex IV (containing mt-CO1–3) showed statistically significant changes in the ratio of 4-fold to non–4-fold sites (see Table 2). After correcting for multiple tests, only the complex IV data remained significant. Interestingly, the mt-ATP8 and mt-ATP6 subunits appear to allow for excess changes at all sites relative to the expected values, though the ratio of 4-fold to non–4-fold sites did not vary significantly (Figure 3A). Analyses of human mtDNA sequences have shown a similar occurrence of excess sequence variation in the mt-ATP8 and mt-ATP6 genes, particularly evident for the mt-ATP6 gene [23–25,28]. These previous reports lead us to investigate available human sequence data, and we found a strong selection against non–4-fold degenerate changes in mt-CO1 versus the weaker selection in mt-ATP6, mt-ATP8, and mt-CYTB (Figure 3B and Table S3B). Observed mutations for each protein gene for mtDNA mutator lines and human population showed the same variation from expected in 11 of 13 cases (Figure 3C). Thus, sequence variation in protein-coding genes of this experimental mouse model demonstrates similar patterns to those seen in human populations.


Strong purifying selection in transmission of mammalian mitochondrial DNA.

Stewart JB, Freyer C, Elson JL, Wredenberg A, Cansu Z, Trifunovic A, Larsson NG - PLoS Biol. (2008)

Distribution of Mutations by Gene for mtDNA Mutator Lines and Human mtDNA Sequence DataPlot of observed minus expected ratio of 4-fold degenerate sites versus all other protein-coding sites.(A) For mtDNA mutator mouse lines, the ratio of observed to expected sites is plotted for third codon position mutations at 4-fold degenerate sites (filled bars), and for all other protein-coding gene mutations observed (open bars). The line represents the observed expected values normalized to 1.0.(B) The same plot for observed human variants found on the mtDB database.(C) Plot of observed minus expected for non–4-fold degenerate sites for mouse (filled bar) and human (open bars). Genes are grouped by mitochondrial respiratory chain complexes. Expected values are derived from an assumption of equal distribution of the observed mutations in the dataset, and observed values are derived from a count of the detected mutations for that gene (see Material and Methods).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2214808&req=5

pbio-0060010-g003: Distribution of Mutations by Gene for mtDNA Mutator Lines and Human mtDNA Sequence DataPlot of observed minus expected ratio of 4-fold degenerate sites versus all other protein-coding sites.(A) For mtDNA mutator mouse lines, the ratio of observed to expected sites is plotted for third codon position mutations at 4-fold degenerate sites (filled bars), and for all other protein-coding gene mutations observed (open bars). The line represents the observed expected values normalized to 1.0.(B) The same plot for observed human variants found on the mtDB database.(C) Plot of observed minus expected for non–4-fold degenerate sites for mouse (filled bar) and human (open bars). Genes are grouped by mitochondrial respiratory chain complexes. Expected values are derived from an assumption of equal distribution of the observed mutations in the dataset, and observed values are derived from a count of the detected mutations for that gene (see Material and Methods).
Mentions: We further investigated the observed selection on protein-coding genes in the mtDNA mutator lines by separating the mutations at 4-fold degenerate sites (third codon positions for amino acids L2, V, A, T, P, S1, R, and G) from all other protein-coding mutations. The 4-fold degenerate sites can mutate to any nucleotide without changing the encoded amino acid and should therefore be subject to less selective constraint than other protein-coding sites. Expected values were calculated based on an assumption of an equal distribution of the observed mutations of these two classes, across the genes and corrected for their coding size. The ratios between observed and expected mutation frequencies at 4-fold degenerate sites were approximately equal in all of the protein-coding genes except for mt-ND2 and mt-ATP8 (Figure 3A and Table S3A). In contrast, mutations at the non–4-fold degenerate sites deviated profoundly from the ratios predicted by equal distribution of mutations (Figure 3A). Contingency table analysis was carried out to detect changes in the proportion of 4-fold degenerate site mutations to other sites within the protein-coding genes. The 13 protein-coding subunits were grouped by the oxidative phosphorylation (OXPHOS) enzyme complex to which they belong. Only complexes III (containing mt-CYTB) and complex IV (containing mt-CO1–3) showed statistically significant changes in the ratio of 4-fold to non–4-fold sites (see Table 2). After correcting for multiple tests, only the complex IV data remained significant. Interestingly, the mt-ATP8 and mt-ATP6 subunits appear to allow for excess changes at all sites relative to the expected values, though the ratio of 4-fold to non–4-fold sites did not vary significantly (Figure 3A). Analyses of human mtDNA sequences have shown a similar occurrence of excess sequence variation in the mt-ATP8 and mt-ATP6 genes, particularly evident for the mt-ATP6 gene [23–25,28]. These previous reports lead us to investigate available human sequence data, and we found a strong selection against non–4-fold degenerate changes in mt-CO1 versus the weaker selection in mt-ATP6, mt-ATP8, and mt-CYTB (Figure 3B and Table S3B). Observed mutations for each protein gene for mtDNA mutator lines and human population showed the same variation from expected in 11 of 13 cases (Figure 3C). Thus, sequence variation in protein-coding genes of this experimental mouse model demonstrates similar patterns to those seen in human populations.

Bottom Line: Purifying selection is thought to be important in shaping mtDNA sequence evolution, but the strength of this selection has been debated, mainly due to the threshold effect of pathogenic mtDNA mutations and an observed excess of new mtDNA mutations in human population data.These data show strong purifying selection against mutations within mtDNA protein-coding genes.To our knowledge, our study presents the first direct experimental observations of the fate of random mtDNA mutations in the mammalian germ line and demonstrates the importance of purifying selection in shaping mitochondrial sequence diversity.

View Article: PubMed Central - PubMed

Affiliation: Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden. Jim.Stewart@ki.se

ABSTRACT
There is an intense debate concerning whether selection or demographics has been most important in shaping the sequence variation observed in modern human mitochondrial DNA (mtDNA). Purifying selection is thought to be important in shaping mtDNA sequence evolution, but the strength of this selection has been debated, mainly due to the threshold effect of pathogenic mtDNA mutations and an observed excess of new mtDNA mutations in human population data. We experimentally addressed this issue by studying the maternal transmission of random mtDNA mutations in mtDNA mutator mice expressing a proofreading-deficient mitochondrial DNA polymerase. We report a rapid and strong elimination of nonsynonymous changes in protein-coding genes; the hallmark of purifying selection. There are striking similarities between the mutational patterns in our experimental mouse system and human mtDNA polymorphisms. These data show strong purifying selection against mutations within mtDNA protein-coding genes. To our knowledge, our study presents the first direct experimental observations of the fate of random mtDNA mutations in the mammalian germ line and demonstrates the importance of purifying selection in shaping mitochondrial sequence diversity.

Show MeSH
Related in: MedlinePlus