Unleashing a novel function of endonuclease G in mitochondrial genome instability

  1. Sumedha Dahal
  2. Humaira Siddiqua
  3. Shivangi Sharma
  4. Ravi K Babu
  5. Diksha Rathore
  6. Sheetal Sharma
  7. Sathees C Raghavan  Is a corresponding author
  1. Indian Institute of Science Bangalore, India
  2. Post Graduate Institute of Medical Education and Research, India

Abstract

Having its genome makes the mitochondrion a unique and semiautonomous organelle within cells. Mammalian mitochondrial DNA (mtDNA) is a double-stranded closed circular molecule of about 16 kb coding for 37 genes. Mutations, including deletions in the mitochondrial genome, can culminate in different human diseases. Mapping the deletion junctions suggests that the breakpoints are generally seen at hotspots. '9-bp deletion' (8271-8281), seen in the intergenic region of cytochrome c oxidase II/tRNALys, is the most common mitochondrial deletion. While it is associated with several diseases like myopathy, dystonia, and hepatocellular carcinoma, it has also been used as an evolutionary marker. However, the mechanism responsible for its fragility is unclear. In the current study, we show that Endonuclease G, a mitochondrial nuclease responsible for nonspecific cleavage of nuclear DNA during apoptosis, can induce breaks at sequences associated with '9-bp deletion' when it is present on a plasmid or in the mitochondrial genome. Through a series of in vitro and intracellular studies, we show that Endonuclease G binds to G-quadruplex structures formed at the hotspot and induces DNA breaks. Therefore, we uncover a new role for Endonuclease G in generating mtDNA deletions, which depends on the formation of G4 DNA within the mitochondrial genome. In summary, we identify a novel property of Endonuclease G, besides its role in apoptosis and the recently described elimination of paternal mitochondria during fertilisation.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Source data for each data is provided along with the figures

Article and author information

Author details

  1. Sumedha Dahal

    Department of Biochemistry, Indian Institute of Science Bangalore, Bangalore, India
    Competing interests
    The authors declare that no competing interests exist.
  2. Humaira Siddiqua

    Department of Biochemistry, Indian Institute of Science Bangalore, Bangalore, India
    Competing interests
    The authors declare that no competing interests exist.
  3. Shivangi Sharma

    Department of Biochemistry, Indian Institute of Science Bangalore, Bangalore, India
    Competing interests
    The authors declare that no competing interests exist.
  4. Ravi K Babu

    Department of Biochemistry, Indian Institute of Science Bangalore, Bangalore, India
    Competing interests
    The authors declare that no competing interests exist.
  5. Diksha Rathore

    Department of Biochemistry, Indian Institute of Science Bangalore, Bangalore, India
    Competing interests
    The authors declare that no competing interests exist.
  6. Sheetal Sharma

    Department of Experimental Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
    Competing interests
    The authors declare that no competing interests exist.
  7. Sathees C Raghavan

    Department of Biochemistry, Indian Institute of Science Bangalore, Bangalore, India
    For correspondence
    sathees@iisc.ac.in
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3003-1417

Funding

Council of Scientific and Industrial Research, India (37(1692)/17/EMR-11)

  • Sathees C Raghavan

Department of Atomic Energy, Government of India (21/01/2016-BRNS/35074)

  • Sathees C Raghavan

Department of Biotechnology, Ministry of Science and Technology, India (BT/PR/3458/COE/34/33/2015)

  • Sathees C Raghavan

IISc-DBT partnership programme (BT/PR27952-INF/22/212/2018)

  • Sathees C Raghavan

Indian Institute of Science

  • Sumedha Dahal

Indian Institute of Science

  • Humaira Siddiqua

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

Ethics

Animal experimentation: This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the Indian National Law on animal care and use. All of the animals were handled according to approved institutional animal care and use committee protocols (CAF-SOP) of the Indian Institute of Science, Bangalore. The protocol was approved by the Committee on the Ethics of Animal Experiments of the Central Animal Facility (CAF/Ethics/526/2016).

Copyright

© 2022, Dahal 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

  • 1,337
    views
  • 197
    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. Sumedha Dahal
  2. Humaira Siddiqua
  3. Shivangi Sharma
  4. Ravi K Babu
  5. Diksha Rathore
  6. Sheetal Sharma
  7. Sathees C Raghavan
(2022)
Unleashing a novel function of endonuclease G in mitochondrial genome instability
eLife 11:e69916.
https://doi.org/10.7554/eLife.69916

Share this article

https://doi.org/10.7554/eLife.69916

Further reading

    1. Cell Biology
    Fatima Tleiss, Martina Montanari ... C Leopold Kurz
    Research Article

    Multiple gut antimicrobial mechanisms are coordinated in space and time to efficiently fight foodborne pathogens. In Drosophila melanogaster, production of reactive oxygen species (ROS) and antimicrobial peptides (AMPs) together with intestinal cell renewal play a key role in eliminating gut microbes. A complementary mechanism would be to isolate and treat pathogenic bacteria while allowing colonization by commensals. Using real-time imaging to follow the fate of ingested bacteria, we demonstrate that while commensal Lactiplantibacillus plantarum freely circulate within the intestinal lumen, pathogenic strains such as Erwinia carotovora or Bacillus thuringiensis, are blocked in the anterior midgut where they are rapidly eliminated by antimicrobial peptides. This sequestration of pathogenic bacteria in the anterior midgut requires the Duox enzyme in enterocytes, and both TrpA1 and Dh31 in enteroendocrine cells. Supplementing larval food with hCGRP, the human homolog of Dh31, is sufficient to block the bacteria, suggesting the existence of a conserved mechanism. While the immune deficiency (IMD) pathway is essential for eliminating the trapped bacteria, it is dispensable for the blockage. Genetic manipulations impairing bacterial compartmentalization result in abnormal colonization of posterior midgut regions by pathogenic bacteria. Despite a functional IMD pathway, this ectopic colonization leads to bacterial proliferation and larval death, demonstrating the critical role of bacteria anterior sequestration in larval defense. Our study reveals a temporal orchestration during which pathogenic bacteria, but not innocuous, are confined in the anterior part of the midgut in which they are eliminated in an IMD-pathway-dependent manner.

    1. Cell Biology
    2. Developmental Biology
    Heungjin Ryu, Kibum Nam ... Jung-Hoon Park
    Research Article

    In most murine species, spermatozoa exhibit a falciform apical hook at the head end. The function of the sperm hook is not yet clearly understood. In this study, we investigate the role of the sperm hook in the migration of spermatozoa through the female reproductive tract in Mus musculus (C57BL/6), using a deep tissue imaging custom-built two-photon microscope. Through live reproductive tract imaging, we found evidence indicating that the sperm hook aids in the attachment of spermatozoa to the epithelium and facilitates interactions between spermatozoa and the epithelium during migration in the uterus and oviduct. We also observed synchronized sperm beating, which resulted from the spontaneous unidirectional rearrangement of spermatozoa in the uterus. Based on live imaging of spermatozoa-epithelium interaction dynamics, we propose that the sperm hook plays a crucial role in successful migration through the female reproductive tract by providing anchor-like mechanical support and facilitating interactions between spermatozoa and the female reproductive tract in the house mouse.