DIP2 is a unique regulator of diacylglycerol lipid homeostasis in eukaryotes

Abstract

Chain-length specific subsets of diacylglycerol (DAG) lipids are proposed to regulate differential physiological responses ranging from signal transduction to modulation of the membrane properties. However, the mechanism or molecular players regulating the subsets of DAG species remains unknown. Here, we uncover the role of a conserved eukaryotic protein family, DISCO-interacting protein 2 (DIP2) as a homeostatic regulator of a chemically distinct subset of DAGs using yeast, fly and mouse models. Genetic and chemical screens along with lipidomics analysis in yeast reveal that DIP2 prevents the toxic accumulation of specific DAGs in the logarithmic growth phase, which otherwise leads to endoplasmic reticulum stress. We also show that the fatty acyl-AMP ligase-like domains of DIP2 are essential for the redirection of the flux of DAG subspecies to storage lipid, triacylglycerols. DIP2 is associated with vacuoles through mitochondria-vacuole contact sites and such modulation of selective DAG abundance by DIP2 is found to be crucial for optimal vacuole membrane fusion and consequently osmoadaptation in yeast. Thus, the study illuminates an unprecedented DAG metabolism route and provides new insights on how cell fine-tunes DAG subspecies for cellular homeostasis and environmental adaptation.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting file; Source Data files have been provided for all figures in the manuscript.

Article and author information

Author details

  1. Sudipta Mondal

    Structural Biology, Centre for Cellular and Molecular Biology, Hyderabad, India
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3923-7449
  2. Priyadarshan Kinatukara

    Structural Biology, Centre for Cellular and Molecular Biology, Hyderabad, India
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2210-2369
  3. Shubham Singh

    Department of Biology, Indian Institute of Science Education and Research Pune, Pune, India
    Competing interests
    No competing interests declared.
  4. Sakshi Shambhavi

    Structural Biology, Centre for Cellular and Molecular Biology, Hyderabad, India
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8852-1542
  5. Gajanan S Patil

    Structural Biology, Centre for Cellular and Molecular Biology, Hyderabad, India
    Competing interests
    No competing interests declared.
  6. Noopur Dubey

    Structural Biology, Centre for Cellular and Molecular Biology, Hyderabad, India
    Competing interests
    No competing interests declared.
  7. Salam Herojeet Singh

    Structural Biology, Centre for Cellular and Molecular Biology, Hyderabad, India
    Competing interests
    No competing interests declared.
  8. Biswajit Pal

    Structural Biology, Centre for Cellular and Molecular Biology, Hyderabad, India
    Competing interests
    No competing interests declared.
  9. P Chandra Shekar

    Structural Biology Laboratory, Centre for Cellular and Molecular Biology, Hyderabad, India
    Competing interests
    No competing interests declared.
  10. Siddhesh S Kamat

    Department of Biology, Indian Institute of Science Education and Research Pune, Pune, India
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6132-7574
  11. Rajan Sankaranarayanan

    Structural Biology Laboratory, Centre for Cellular and Molecular Biology, Hyderabad, India
    For correspondence
    sankar@ccmb.res.in
    Competing interests
    Rajan Sankaranarayanan, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4524-9953

Funding

Council for Scientific and Industrial Research , India

  • Sudipta Mondal

Department of Biotechnology, Ministry of Science and Technology, India

  • Priyadarshan Kinatukara

University Grants Commission

  • Sakshi Shambhavi

DBT/Wellcome Trust India Alliance Fellowship (IA/I/15/2/502058)

  • Siddhesh S Kamat

Department of Science and Technology, Ministry of Science and Technology, India (SR/FST/LSII-043/2016)

  • Siddhesh S Kamat

J.C. Bose Fellowship

  • Rajan Sankaranarayanan

NCP under health care theme project

  • Rajan Sankaranarayanan

Centre of Excellence Project

  • Rajan Sankaranarayanan

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 carried out in strict accordance with the recommendations in the Committee for the Purpose of Control and Supervision of Experiments on Animals (CPCSEA), India. The protocols were approved by the Institutional Animal Ethics Committee (IAEC) of CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India (20/ GO/RBi/99/CPCSEA). All terminal experiments were performed by cervical dislocation after anesthetizing with isoflurane. All efforts were made to minimize suffering during all experiments.

Copyright

© 2022, Mondal 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

  • 3,698
    views
  • 652
    downloads
  • 8
    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. Sudipta Mondal
  2. Priyadarshan Kinatukara
  3. Shubham Singh
  4. Sakshi Shambhavi
  5. Gajanan S Patil
  6. Noopur Dubey
  7. Salam Herojeet Singh
  8. Biswajit Pal
  9. P Chandra Shekar
  10. Siddhesh S Kamat
  11. Rajan Sankaranarayanan
(2022)
DIP2 is a unique regulator of diacylglycerol lipid homeostasis in eukaryotes
eLife 11:e77665.
https://doi.org/10.7554/eLife.77665

Share this article

https://doi.org/10.7554/eLife.77665

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Jie Luo, Jeff Ranish
    Tools and Resources

    Dynamic conformational and structural changes in proteins and protein complexes play a central and ubiquitous role in the regulation of protein function, yet it is very challenging to study these changes, especially for large protein complexes, under physiological conditions. Here, we introduce a novel isobaric crosslinker, Qlinker, for studying conformational and structural changes in proteins and protein complexes using quantitative crosslinking mass spectrometry. Qlinkers are small and simple, amine-reactive molecules with an optimal extended distance of ~10 Å, which use MS2 reporter ions for relative quantification of Qlinker-modified peptides derived from different samples. We synthesized the 2-plex Q2linker and showed that the Q2linker can provide quantitative crosslinking data that pinpoints key conformational and structural changes in biosensors, binary and ternary complexes composed of the general transcription factors TBP, TFIIA, and TFIIB, and RNA polymerase II complexes.

    1. Biochemistry and Chemical Biology
    2. Stem Cells and Regenerative Medicine
    Alejandro J Brenes, Eva Griesser ... Angus I Lamond
    Research Article

    Human induced pluripotent stem cells (hiPSCs) have great potential to be used as alternatives to embryonic stem cells (hESCs) in regenerative medicine and disease modelling. In this study, we characterise the proteomes of multiple hiPSC and hESC lines derived from independent donors and find that while they express a near-identical set of proteins, they show consistent quantitative differences in the abundance of a subset of proteins. hiPSCs have increased total protein content, while maintaining a comparable cell cycle profile to hESCs, with increased abundance of cytoplasmic and mitochondrial proteins required to sustain high growth rates, including nutrient transporters and metabolic proteins. Prominent changes detected in proteins involved in mitochondrial metabolism correlated with enhanced mitochondrial potential, shown using high-resolution respirometry. hiPSCs also produced higher levels of secreted proteins, including growth factors and proteins involved in the inhibition of the immune system. The data indicate that reprogramming of fibroblasts to hiPSCs produces important differences in cytoplasmic and mitochondrial proteins compared to hESCs, with consequences affecting growth and metabolism. This study improves our understanding of the molecular differences between hiPSCs and hESCs, with implications for potential risks and benefits for their use in future disease modelling and therapeutic applications.