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Molecular trajectories leading to the alternative fates of duplicate genes.

Marotta M, Piontkivska H, Tanaka H - PLoS ONE (2012)

Bottom Line: The alternative fates are associated with expression divergence between these species, and reduced expression in humans is regulated by silencing mutations that have been propagated between duplicates by gene conversion.The difference in evolutionary processes left a unique DNA footprint in which dying duplicates are significantly more similar to each other (99.4%) than preserved ones.Such molecular trajectories could provide insights for the mechanisms underlying duplicate life and death in extant genomes.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America.

ABSTRACT
Gene duplication generates extra gene copies in which mutations can accumulate without risking the function of pre-existing genes. Such mutations modify duplicates and contribute to evolutionary novelties. However, the vast majority of duplicates appear to be short-lived and experience duplicate silencing within a few million years. Little is known about the molecular mechanisms leading to these alternative fates. Here we delineate differing molecular trajectories of a relatively recent duplication event between humans and chimpanzees by investigating molecular properties of a single duplicate: DNA sequences, gene expression and promoter activities. The inverted duplication of the Glutathione S-transferase Theta 2 (GSTT2) gene had occurred at least 7 million years ago in the common ancestor of African great apes and is preserved in chimpanzees (Pan troglodytes), whereas a deletion polymorphism is prevalent in humans. The alternative fates are associated with expression divergence between these species, and reduced expression in humans is regulated by silencing mutations that have been propagated between duplicates by gene conversion. In contrast, selective constraint preserved duplicate divergence in chimpanzees. The difference in evolutionary processes left a unique DNA footprint in which dying duplicates are significantly more similar to each other (99.4%) than preserved ones. Such molecular trajectories could provide insights for the mechanisms underlying duplicate life and death in extant genomes.

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Propagation of a regulatory mutation by gene conversion.A. A 17-bp duplication mutation at the GSTT2 promoter. Sequences from PCR-clones are shown for the promoter with 17-bp duplication (shaded in orange) and the promoter without 17-bp duplication. B. The 17-bp duplication is a hypomorphic mutation, judged by the reduced luciferase activity associated with the mutation. Either a promoter harboring 17-bp duplication (an orange rectangle) or without the duplication was cloned into pGL3-basic vector (Promega). Each vector was co-transfected with the control vector encoding Renilla luciferase into three human cell lines (a human kidney epithelial cell line HEK293T and human colorectal cancer cell lines HCT116 and HT29) for measuring luciferase activity. Relative activities of luciferase (Firefly/Renilla) to the activities from 17-bp dup promoters are shown. C. Propagation of the 17-bp duplication in humans. (left) PCR was used to amplify the genomic region containing the 17-bp duplication. Note that most of the human DNA samples show only one PCR product, the duplicate with 17-bp duplication (drawn schematically at the bottom). (right) The numbers of PCR clones for the duplicate without 17-bp duplication (red) and the one with 17-bp duplication (blue) are shown.
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pone-0038958-g004: Propagation of a regulatory mutation by gene conversion.A. A 17-bp duplication mutation at the GSTT2 promoter. Sequences from PCR-clones are shown for the promoter with 17-bp duplication (shaded in orange) and the promoter without 17-bp duplication. B. The 17-bp duplication is a hypomorphic mutation, judged by the reduced luciferase activity associated with the mutation. Either a promoter harboring 17-bp duplication (an orange rectangle) or without the duplication was cloned into pGL3-basic vector (Promega). Each vector was co-transfected with the control vector encoding Renilla luciferase into three human cell lines (a human kidney epithelial cell line HEK293T and human colorectal cancer cell lines HCT116 and HT29) for measuring luciferase activity. Relative activities of luciferase (Firefly/Renilla) to the activities from 17-bp dup promoters are shown. C. Propagation of the 17-bp duplication in humans. (left) PCR was used to amplify the genomic region containing the 17-bp duplication. Note that most of the human DNA samples show only one PCR product, the duplicate with 17-bp duplication (drawn schematically at the bottom). (right) The numbers of PCR clones for the duplicate without 17-bp duplication (red) and the one with 17-bp duplication (blue) are shown.

Mentions: The three-fold reduction of GSTT2 mRNA in humans (Figure 2B) would indicate additional underlying mechanisms for repression. We identified a human-specific, 17-bp duplication in the promoter region (Figure 4A). Such a mutation could function as a regulatory mutation and repress transcription. Indeed, the promoter with the 17-bp duplication (17bp dup-Luc) showed a considerably reduced level of luciferase activity than the promoter without the 17-bp duplication (no dup-Luc) (Figure 4B). In all three cell lines tested, we observed an almost 70% reduction of luciferase activity from the promoter with 17-bp duplication.


Molecular trajectories leading to the alternative fates of duplicate genes.

Marotta M, Piontkivska H, Tanaka H - PLoS ONE (2012)

Propagation of a regulatory mutation by gene conversion.A. A 17-bp duplication mutation at the GSTT2 promoter. Sequences from PCR-clones are shown for the promoter with 17-bp duplication (shaded in orange) and the promoter without 17-bp duplication. B. The 17-bp duplication is a hypomorphic mutation, judged by the reduced luciferase activity associated with the mutation. Either a promoter harboring 17-bp duplication (an orange rectangle) or without the duplication was cloned into pGL3-basic vector (Promega). Each vector was co-transfected with the control vector encoding Renilla luciferase into three human cell lines (a human kidney epithelial cell line HEK293T and human colorectal cancer cell lines HCT116 and HT29) for measuring luciferase activity. Relative activities of luciferase (Firefly/Renilla) to the activities from 17-bp dup promoters are shown. C. Propagation of the 17-bp duplication in humans. (left) PCR was used to amplify the genomic region containing the 17-bp duplication. Note that most of the human DNA samples show only one PCR product, the duplicate with 17-bp duplication (drawn schematically at the bottom). (right) The numbers of PCR clones for the duplicate without 17-bp duplication (red) and the one with 17-bp duplication (blue) are shown.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3375281&req=5

pone-0038958-g004: Propagation of a regulatory mutation by gene conversion.A. A 17-bp duplication mutation at the GSTT2 promoter. Sequences from PCR-clones are shown for the promoter with 17-bp duplication (shaded in orange) and the promoter without 17-bp duplication. B. The 17-bp duplication is a hypomorphic mutation, judged by the reduced luciferase activity associated with the mutation. Either a promoter harboring 17-bp duplication (an orange rectangle) or without the duplication was cloned into pGL3-basic vector (Promega). Each vector was co-transfected with the control vector encoding Renilla luciferase into three human cell lines (a human kidney epithelial cell line HEK293T and human colorectal cancer cell lines HCT116 and HT29) for measuring luciferase activity. Relative activities of luciferase (Firefly/Renilla) to the activities from 17-bp dup promoters are shown. C. Propagation of the 17-bp duplication in humans. (left) PCR was used to amplify the genomic region containing the 17-bp duplication. Note that most of the human DNA samples show only one PCR product, the duplicate with 17-bp duplication (drawn schematically at the bottom). (right) The numbers of PCR clones for the duplicate without 17-bp duplication (red) and the one with 17-bp duplication (blue) are shown.
Mentions: The three-fold reduction of GSTT2 mRNA in humans (Figure 2B) would indicate additional underlying mechanisms for repression. We identified a human-specific, 17-bp duplication in the promoter region (Figure 4A). Such a mutation could function as a regulatory mutation and repress transcription. Indeed, the promoter with the 17-bp duplication (17bp dup-Luc) showed a considerably reduced level of luciferase activity than the promoter without the 17-bp duplication (no dup-Luc) (Figure 4B). In all three cell lines tested, we observed an almost 70% reduction of luciferase activity from the promoter with 17-bp duplication.

Bottom Line: The alternative fates are associated with expression divergence between these species, and reduced expression in humans is regulated by silencing mutations that have been propagated between duplicates by gene conversion.The difference in evolutionary processes left a unique DNA footprint in which dying duplicates are significantly more similar to each other (99.4%) than preserved ones.Such molecular trajectories could provide insights for the mechanisms underlying duplicate life and death in extant genomes.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America.

ABSTRACT
Gene duplication generates extra gene copies in which mutations can accumulate without risking the function of pre-existing genes. Such mutations modify duplicates and contribute to evolutionary novelties. However, the vast majority of duplicates appear to be short-lived and experience duplicate silencing within a few million years. Little is known about the molecular mechanisms leading to these alternative fates. Here we delineate differing molecular trajectories of a relatively recent duplication event between humans and chimpanzees by investigating molecular properties of a single duplicate: DNA sequences, gene expression and promoter activities. The inverted duplication of the Glutathione S-transferase Theta 2 (GSTT2) gene had occurred at least 7 million years ago in the common ancestor of African great apes and is preserved in chimpanzees (Pan troglodytes), whereas a deletion polymorphism is prevalent in humans. The alternative fates are associated with expression divergence between these species, and reduced expression in humans is regulated by silencing mutations that have been propagated between duplicates by gene conversion. In contrast, selective constraint preserved duplicate divergence in chimpanzees. The difference in evolutionary processes left a unique DNA footprint in which dying duplicates are significantly more similar to each other (99.4%) than preserved ones. Such molecular trajectories could provide insights for the mechanisms underlying duplicate life and death in extant genomes.

Show MeSH
Related in: MedlinePlus