Quantitative H2S-mediated protein sulfhydration reveals metabolic reprogramming during the Integrated Stress Response

  1. Xing-Huang Gao
  2. Dawid Krokowski
  3. Bo-Jhih Guan
  4. Ilya Bederman
  5. Mithu Majumder
  6. Marc Parisien
  7. Luda Diatchenko
  8. Omer Kabil
  9. Belinda Willard
  10. Ruma Banerjee
  11. Benlian Wang
  12. Gurkan Bebek
  13. Charles R Evans
  14. Paul L Fox
  15. Stanton L Gerson
  16. Charles Hoppel
  17. Ming Liu
  18. Peter Arvan
  19. Maria Hatzoglou  Is a corresponding author
  1. Case Western Reserve University, United States
  2. McGill University, Canada
  3. University of Michigan Medical School, United States
  4. Cleveland Clinic Lerner Research Institute, United States

Abstract

The sulfhydration of cysteine residues in proteins is an important mechanism involved in diverse biological processes. We have developed a proteomics approach to quantitatively profile the changes of sulfhydrated cysteines in biological systems. Bioinformatics analysis revealed that sulfhydrated cysteines are part of a wide range of biological functions. In pancreatic β cells exposed to endoplasmic reticulum (ER) stress, elevated H2S promotes the sulfhydration of enzymes in energy metabolism and stimulates glycolytic flux. We propose that transcriptional and translational reprogramming by the Integrated Stress Response (ISR) in pancreatic β cells is coupled to metabolic alternations triggered by sulfhydration of key enzymes in intermediary metabolism.

Article and author information

Author details

  1. Xing-Huang Gao

    Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Dawid Krokowski

    Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Bo-Jhih Guan

    Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Ilya Bederman

    Department of Pediatrics, Case Western Reserve University, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Mithu Majumder

    Department of Pharmacology, Case Western Reserve University, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Marc Parisien

    Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  7. Luda Diatchenko

    Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  8. Omer Kabil

    Biological Chemistry, University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Belinda Willard

    Mass Spectrometry Laboratory for Protein Sequencing, Cleveland Clinic Lerner Research Institute, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Ruma Banerjee

    Biological Chemistry, University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Benlian Wang

    Center for Proteomics and Bioinformatics,Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Gurkan Bebek

    Center for Proteomics and Bioinformatics, Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Charles R Evans

    Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. Paul L Fox

    Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  15. Stanton L Gerson

    Department of Medicine, Division of Hematology/Oncology, School of Medicine, Case Western Reserve University, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  16. Charles Hoppel

    Department of Pharmacology, Case Western Reserve University, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  17. Ming Liu

    Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  18. Peter Arvan

    Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
  19. Maria Hatzoglou

    Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
    For correspondence
    mxh8@case.edu
    Competing interests
    The authors declare that no competing interests exist.

Ethics

Animal experimentation: Experimental protocols were approved by the Case Western Reserve University Institutional Animal Care and Use Committee.

Human subjects: Human Islet Study-Institutional review board approval for research use of isolated human islets was obtained from the University of Michigan (IRB number 2014-0069). Human islets were isolated from previously healthy, nondiabetic organ donors by the University of Chicago Transplant Center. Three independent human islet batches from two male donors aged 20 and 58 and one female donor aged 48 were used in this study.

Copyright

© 2015, Gao 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

  • 4,785
    views
  • 1,152
    downloads
  • 161
    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. Xing-Huang Gao
  2. Dawid Krokowski
  3. Bo-Jhih Guan
  4. Ilya Bederman
  5. Mithu Majumder
  6. Marc Parisien
  7. Luda Diatchenko
  8. Omer Kabil
  9. Belinda Willard
  10. Ruma Banerjee
  11. Benlian Wang
  12. Gurkan Bebek
  13. Charles R Evans
  14. Paul L Fox
  15. Stanton L Gerson
  16. Charles Hoppel
  17. Ming Liu
  18. Peter Arvan
  19. Maria Hatzoglou
(2015)
Quantitative H2S-mediated protein sulfhydration reveals metabolic reprogramming during the Integrated Stress Response
eLife 4:e10067.
https://doi.org/10.7554/eLife.10067

Share this article

https://doi.org/10.7554/eLife.10067

Further reading

    1. Biochemistry and Chemical Biology
    Daljit Sangar, Elizabeth Hill ... Jan Bieschke
    Research Article

    Prions replicate via the autocatalytic conversion of cellular prion protein (PrPC) into fibrillar assemblies of misfolded PrP. While this process has been extensively studied in vivo and in vitro, non-physiological reaction conditions of fibril formation in vitro have precluded the identification and mechanistic analysis of cellular proteins, which may alter PrP self-assembly and prion replication. Here, we have developed a fibril formation assay for recombinant murine and human PrP (23-231) under near-native conditions (NAA) to study the effect of cellular proteins, which may be risk factors or potential therapeutic targets in prion disease. Genetic screening suggests that variants that increase syntaxin-6 expression in the brain (gene: STX6) are risk factors for sporadic Creutzfeldt-Jakob disease (CJD). Analysis of the protein in NAA revealed, counterintuitively, that syntaxin-6 is a potent inhibitor of PrP fibril formation. It significantly delayed the lag phase of fibril formation at highly sub-stoichiometric molar ratios. However, when assessing toxicity of different aggregation time points to primary neurons, syntaxin-6 prolonged the presence of neurotoxic PrP species. Electron microscopy and super-resolution fluorescence microscopy revealed that, instead of highly ordered fibrils, in the presence of syntaxin-6 PrP formed less-ordered aggregates containing syntaxin-6. These data strongly suggest that the protein can directly alter the initial phase of PrP self-assembly and, uniquely, can act as an 'anti-chaperone', which promotes toxic aggregation intermediates by inhibiting fibril formation.

    1. Biochemistry and Chemical Biology
    2. Cell Biology
    Birol Cabukusta, Shalom Borst Pauwels ... Jacques Neefjes
    Research Article

    Numerous lipids are heterogeneously distributed among organelles. Most lipid trafficking between organelles is achieved by a group of lipid transfer proteins (LTPs) that carry lipids using their hydrophobic cavities. The human genome encodes many intracellular LTPs responsible for lipid trafficking and the function of many LTPs in defining cellular lipid levels and distributions is unclear. Here, we created a gene knockout library targeting 90 intracellular LTPs and performed whole-cell lipidomics analysis. This analysis confirmed known lipid disturbances and identified new ones caused by the loss of LTPs. Among these, we found major sphingolipid imbalances in ORP9 and ORP11 knockout cells, two proteins of previously unknown function in sphingolipid metabolism. ORP9 and ORP11 form a heterodimer to localize at the ER-trans-Golgi membrane contact sites, where the dimer exchanges phosphatidylserine (PS) for phosphatidylinositol-4-phosphate (PI(4)P) between the two organelles. Consequently, loss of either protein causes phospholipid imbalances in the Golgi apparatus that result in lowered sphingomyelin synthesis at this organelle. Overall, our LTP knockout library toolbox identifies various proteins in control of cellular lipid levels, including the ORP9-ORP11 heterodimer, which exchanges PS and PI(4)P at the ER-Golgi membrane contact site as a critical step in sphingomyelin synthesis in the Golgi apparatus.