Dataset Information

Rapid Evolution of Gained Essential Developmental Functions of a Young Gene via Interactions with Other Essential Genes.

ABSTRACT: New genes are of recent origin and only present in a subset of species in a phylogeny. Accumulated evidence suggests that new genes, like old genes that are conserved across species, can also take on important functions and be essential for the survival and reproductive success of organisms. Although there are detailed analyses of the mechanisms underlying new genes' gaining fertility functions, how new genes rapidly become essential for viability remains unclear. We focused on a young retro-duplicated gene (CG7804, which we named Cocoon) in Drosophila that originated between 4 and 10 Ma. We found that, unlike its evolutionarily conserved parental gene, Cocoon has evolved under positive selection and accumulated many amino acid differences at functional sites from the parental gene. Despite its young age, Cocoon is essential for the survival of Drosophila melanogaster at multiple developmental stages, including the critical embryonic stage, and its expression is essential in different tissues from those of its parental gene. Functional genomic analyses found that Cocoon acquired unique DNA-binding sites and has a contrasting effect on gene expression to that of its parental gene. Importantly, Cocoon binding predominantly locates at genes that have other essential functions and/or have multiple gene-gene interactions, suggesting that Cocoon acquired novel essential function to survival through forming interactions that have large impacts on the gene interaction network. Our study is an important step toward deciphering the evolutionary trajectory by which new genes functionally diverge from parental genes and become essential.

SUBMITTER: Lee YCG

PROVIDER: S-EPMC6759199 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Rapid Evolution of Gained Essential Developmental Functions of a Young Gene via Interactions with Other Essential Genes.

Lee Yuh Chwen G YCG Ventura Iuri M IM Rice Gavin R GR Chen Dong-Yuan DY Colmenares Serafin U SU Long Manyuan M

Molecular biology and evolution 20191001 10

New genes are of recent origin and only present in a subset of species in a phylogeny. Accumulated evidence suggests that new genes, like old genes that are conserved across species, can also take on important functions and be essential for the survival and reproductive success of organisms. Although there are detailed analyses of the mechanisms underlying new genes' gaining fertility functions, how new genes rapidly become essential for viability remains unclear. We focused on a young retro-dup ...[more]

PMID: 31187122

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Project description:New genes are those that originated relatively recently and are only present in a subset of species in a phylogeny. Evidence from humans and other species has demonstrated that, despite their young age, new genes can exhibit novel functions that are essential for the survival of an organism. One potential mechanism by which new genes gain essential functions is through the acquisition of many new interactions with pre-existing genes. This hypothesis is consistent with well-established observations that genes with many interaction partners are more likely to have essential functions. However, the accumulation of gene-gene interactions is, on average, a slow evolutionary process. This raises the question of how, in a short evolutionary time, new genes can acquire multiple novel interactions and how this might lead to their essential roles in the survival of an organism. In this study, we characterized the evolutionary history and function of a young duplicated gene that quickly became essential for the survival of Drosophila melanogaster. This young gene (CG7804) duplicated from another essential gene (TBPH) through retrotransposition less than four million years ago (Zhang et al. 2010), and is present in few Drosophila species. We found that unlike its evolutionarily conserved, broadly expressed parental gene, CG7804 has evolved rapidly under positive selection since its birth. Despite its young age, functional analyses show that CG7804 is essential for the survival of D. melanogaster. In particular, its expression is essential at different tissues from its parental gene. RNA-seq and ChIP-seq analysis suggests that CG7804 acquired essential function to survival through gaining new DNA binding targets that influence the expression of a suite of genes with other essential function and large number of protein-protein interaction. Our study is an important step towards deciphering the evolutionary trajectory by which duplicated genes functionally diverge from the parental gene and become essential.

Dataset Information

Rapid Evolution of Gained Essential Developmental Functions of a Young Gene via Interactions with Other Essential Genes.

Publications

Rapid Evolution of Gained Essential Developmental Functions of a Young Gene via Interactions with Other Essential Genes.

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