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Towards reconstructing the dipteran demise of an ancient essential gene: E3 ubiquitin ligase Murine double minute

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Abstract

Genome studies have uncovered many examples of essential gene loss, raising the question of how ancient genes transition from essentiality to dispensability. We explored this process for the deeply conserved E3 ubiquitin ligase Murine double minute (Mdm), which is lacking in Drosophila despite the conservation of its main regulatory target, the cellular stress response gene p53. Conducting gene expression and knockdown experiments in the red flour beetle Tribolium castaneum, we found evidence that Mdm has remained essential in insects where it is present. Using bioinformatics approaches, we confirm the absence of the Mdm gene family in Drosophila, mapping its loss to the stem lineage of schizophoran Diptera and Pipunculidae (big-headed flies), about 95–85 million years ago. Intriguingly, this gene loss event was preceded by the de novo origin of the gene Companion of reaper (Corp), a novel p53 regulatory factor that is characterized by functional similarities to vertebrate Mdm2 despite lacking E3 ubiquitin ligase protein domains. Speaking against a 1:1 compensatory gene gain/loss scenario, however, we found that hoverflies (Syrphidae) and pointed-wing flies (Lonchopteridae) possess both Mdm and Corp. This implies that the two p53 regulators have been coexisting for ~ 150 million years in select dipteran clades and for at least 50 million years in the lineage to Schizophora and Pipunculidae. Given these extensive time spans of Mdm/Corp coexistence, we speculate that the loss of Mdm in the lineage to Drosophila involved further acquisitions of compensatory gene activities besides the emergence of Corp. Combined with the previously noted reduction of an ancestral P53 contact domain in the Mdm homologs of crustaceans and insects, we conclude that the loss of the ancient Mdm gene family in flies was the outcome of incremental functional regression over long macroevolutionary time scales.

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Acknowledgments

We thank the two anonymous reviewers for their attentive, thoughtful, and in the end crucially stimulating comments, high school intern Johanan Isaac for help with analyses in the gene knockdown experiments, and Lori Pile for proofreading comments.

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Authors and Affiliations

  1. Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA

    Naveen Jasti, Dylan Sebagh, Mohammed Riaz, Xin Wang, Bharat Koripella, Vasanth Palanisamy, Nabeel Mohammad, Qing Chen & Markus Friedrich

  2. Institute for Protein Design, Washington University, 1959 NE Pacific Street, Seattle, WA, 98195, USA

    Naveen Jasti

  3. Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, 540 East Canfield Avenue, Detroit, MI, 48201, USA

    Markus Friedrich

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  1. Naveen Jasti
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Correspondence to Markus Friedrich.

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Communicated by Claude Desplan

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Jasti, N., Sebagh, D., Riaz, M. et al. Towards reconstructing the dipteran demise of an ancient essential gene: E3 ubiquitin ligase Murine double minute. Dev Genes Evol 230, 279–294 (2020). https://doi.org/10.1007/s00427-020-00663-8

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