1. Genetics and Genomics
  2. Microbiology and Infectious Disease

A single synonymous nucleotide change impacts the male-killing phenotype of prophage WO gene wmk

  1. Jessamyn I Perlmutter  Is a corresponding author
  2. Jane E Meyers
  3. Seth R Bordenstein  Is a corresponding author
  1. University of Kansas, United States
  2. Vanderbilt University, United States
https://doi.org/10.7554/eLife.67686
Share this article
Cite this article
  1. Jessamyn I Perlmutter
  2. Jane E Meyers
  3. Seth R Bordenstein
(2021)
A single synonymous nucleotide change impacts the male-killing phenotype of prophage WO gene wmk
eLife 10:e67686.
https://doi.org/10.7554/eLife.67686
  2. Download BibTeX
  3. Download .RIS

Abstract

Wolbachia are the most widespread bacterial endosymbionts in animals. Within arthropods, these maternally-transmitted bacteria can selfishly hijack host reproductive processes to increase the relative fitness of their transmitting females. One such form of reproductive parasitism called male killing, or the selective killing of infected males, is recapitulated to degrees by transgenic expression of the WO-mediated killing (wmk) gene. Here, we characterize the genotype-phenotype landscape of wmk-induced male killing in D. melanogaster using transgenic expression. While phylogenetically distant wmk homologs induce no sex-ratio bias, closely-related homologs exhibit complex phenotypes spanning no death, male death, or death of all hosts. We demonstrate that alternative start codons, synonymous codons, and notably a single synonymous nucleotide in wmk can ablate killing. These findings reveal previously unrecognized features of transgenic wmk-induced killing and establish new hypotheses for the impacts of post-transcriptional processes in male killing variation. We conclude that synonymous sequence changes are not necessarily silent in nested endosymbiotic interactions with life-or-death consequences.

Data availability

All data generated or analyzed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 3-6.

Article and author information

Author details

  1. Jessamyn I Perlmutter

    Molecular Biosciences, University of Kansas, Lawrence, United States
    For correspondence
    jessamyn.perlmutter@ku.edu
    Competing interests
    Jessamyn I Perlmutter, J. Perlmutter and S. Bordenstein are listed as authors on a patent related to the use of wmk in vector control. US Patent 20210000092 16/982708.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9789-4674

  2. Jane E Meyers

    Biological Sciences, Vanderbilt University, Nashville, United States
    Competing interests
    No competing interests declared.

  3. Seth R Bordenstein

    Biological Sciences and Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, United States
    For correspondence
    s.bordenstein@vanderbilt.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7346-0954

Funding

National Institutes of Health (R21 AI133522)

  • Seth R Bordenstein

National Institutes of Health (F31 AI143152)

  • Jessamyn I Perlmutter

Vanderbilt Microbiome Initiative (VMI General Funds)

  • Seth R Bordenstein

National Institutes of Health (P20 GM103418)

  • Jessamyn I Perlmutter

National Science Foundation (DBI 2109772)

  • Jessamyn I Perlmutter

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2021, Perlmutter et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 1,143
    views
  • 149
    downloads
  • 13
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Jessamyn I Perlmutter
  2. Jane E Meyers
  3. Seth R Bordenstein
(2021)
A single synonymous nucleotide change impacts the male-killing phenotype of prophage WO gene wmk
eLife 10:e67686.
https://doi.org/10.7554/eLife.67686

Share this article

https://doi.org/10.7554/eLife.67686

Categories and tags

Research organism

Further reading

    1. Computational and Systems Biology
    2. Genetics and Genomics

    Discovering root causal genes with high-throughput perturbations

    Eric V Strobl, Eric Gamazon
    Research Article

    Root causal gene expression levels – or root causal genes for short – correspond to the initial changes to gene expression that generate patient symptoms as a downstream effect. Identifying root causal genes is critical towards developing treatments that modify disease near its onset, but no existing algorithms attempt to identify root causal genes from data. RNA-sequencing (RNA-seq) data introduces challenges such as measurement error, high dimensionality and non-linearity that compromise accurate estimation of root causal effects even with state-of-the-art approaches. We therefore instead leverage Perturb-seq, or high-throughput perturbations with single-cell RNA-seq readout, to learn the causal order between the genes. We then transfer the causal order to bulk RNA-seq and identify root causal genes specific to a given patient for the first time using a novel statistic. Experiments demonstrate large improvements in performance. Applications to macular degeneration and multiple sclerosis also reveal root causal genes that lie on known pathogenic pathways, delineate patient subgroups and implicate a newly defined omnigenic root causal model.

    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Transcription: The plusses and minuses of DNA torsion

    Steven Henikoff, David L Levens
    Insight

    A new method for mapping torsion provides insights into the ways that the genome responds to the torsion generated by RNA polymerase II.

    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Improved base editing and functional screening in Leishmania via co-expression of the AsCas12a ultra variant, a T7 RNA polymerase, and a cytosine base editor

    Nicole Herrmann May, Anh Cao ... Tom Beneke
    Research Advance

    The ability to analyze the function of all genes in a genome is highly desirable, yet challenging in Leishmania due to a repetitive genome, limited DNA repair mechanisms, and lack of RNA interference in most species. While our introduction of a cytosine base editor (CBE) demonstrated potential to overcome these limitations (Engstler and Beneke, 2023), challenges remained, including low transfection efficiency, variable editing rates across species, parasite growth effects, and competition between deleterious and non-deleterious mutations. Here, we present an optimized approach addressing these issues. We identified a T7 RNAP promoter variant ensuring high editing rates across Leishmania species without compromising growth. A revised CBE single-guide RNAs (sgRNAs) scoring system was developed to prioritize STOP codon generation. Additionally, a triple-expression construct was created for stable integration of CBE sgRNA expression cassettes into a Leishmania safe harbor locus using AsCas12a ultra-mediated DNA double-strand breaks, increasing transfection efficiency by ~400-fold to 1 transfectant per 70 transfected cells. Using this improved system for a small-scale proof-of-principle pooled screen, we successfully confirmed the essential and fitness-associated functions of CK1.2, CRK2, CRK3, AUK1/AIRK, TOR1, IFT88, IFT139, IFT140, and RAB5A in Leishmania mexicana, demonstrating a significant improvement over our previous method. Lastly, we show the utility of co-expressing AsCas12a ultra, T7 RNAP, and CBE for hybrid CRISPR gene replacement and base editing within the same cell line. Overall, these improvements will broaden the range of possible gene editing applications in Leishmania species and will enable a variety of loss-of-function screens in the near future.