1. Biochemistry and Chemical Biology
  2. Stem Cells and Regenerative Medicine
Download icon

SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells

  1. Samuel A Myers
  2. Sailaja Peddada
  3. Nilanjana Chatterjee
  4. Tara Freidreich
  5. Kiichrio Tomoda
  6. Gregor Krings
  7. Sean Thomas
  8. Michael Broeker
  9. Jason Maynard
  10. Matthew Thomson
  11. Katherine Pollard
  12. Shinya Yamanaka
  13. Alma L Burlingame
  14. Barbara Panning  Is a corresponding author
  1. University of California, San Francisco, United States
  2. Gladstone Institute University of California, San Francisco, United States
Research Article
  • Cited 29
  • Views 3,121
  • Annotations
Cite this article as: eLife 2016;5:e10647 doi: 10.7554/eLife.10647

Abstract

The transcription factor SOX2 is central in establishing and maintaining pluripotency. The processes that modulate SOX2 activity to promote pluripotency are not well understood. Here, we show SOX2 is O-GlcNAc modified in its transactivation domain during reprogramming and in mouse embryonic stem cells (mESCs). Upon induction of differentiation SOX2 O-GlcNAcylation at serine 248 is decreased. Replacing wild type with an O-GlcNAc-deficient SOX2 (S248A) increases reprogramming efficiency. ESCs with O-GlcNAc-deficient SOX2 exhibit alterations in gene expression. This change correlates with altered protein-protein interactions and genomic occupancy of the O-GlcNAc-deficient SOX2 compared to wild type. In addition, SOX2 O-GlcNAcylation impairs the SOX2-PARP1 interaction, which has been shown to regulate ESC self-renewal. These findings show that SOX2 activity is modulated by O-GlcNAc modification, and provide a novel regulatory mechanism for this crucial pluripotency transcription factor.

Article and author information

Author details

  1. Samuel A Myers

    Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  2. Sailaja Peddada

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  3. Nilanjana Chatterjee

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  4. Tara Freidreich

    Gladstone Institute University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  5. Kiichrio Tomoda

    Gladstone Institute University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  6. Gregor Krings

    Department of Pathology, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  7. Sean Thomas

    Gladstone Institute University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  8. Michael Broeker

    Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  9. Jason Maynard

    Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  10. Matthew Thomson

    Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  11. Katherine Pollard

    Gladstone Institute University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  12. Shinya Yamanaka

    Gladstone Institute University of California, San Francisco, San Francisco, United States
    Competing interests
    Shinya Yamanaka, scientific advisor of iPS Academia Japan without salary.

  13. Alma L Burlingame

    Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  14. Barbara Panning

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    For correspondence
    barbara.panning@gmail.com
    Competing interests
    No competing interests declared.

Reviewing Editor

  1. Kathrin Plath, University of California, Los Angeles, United States

Publication history

  1. Received: August 8, 2015
  2. Accepted: March 5, 2016
  3. Accepted Manuscript published: March 7, 2016 (version 1)
  4. Accepted Manuscript updated: March 22, 2016 (version 2)
  5. Version of Record published: April 19, 2016 (version 3)

Copyright

© 2016, Myers 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

  • 3,121
    Page views
  • 860
    Downloads
  • 29
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, Scopus, PubMed Central.

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)

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

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

Categories and tags

Research organism

Further reading

    1. Biochemistry and Chemical Biology

    Myopalladin knockout mice develop cardiac dilation and show a maladaptive response to mechanical pressure overload

    Maria Carmela Filomena et al.
    Research Article

    Myopalladin (MYPN) is a striated muscle-specific immunoglobulin domain-containing protein located in the sarcomeric Z-line and I-band. MYPN gene mutations are causative for dilated (DCM), hypertrophic and restrictive cardiomyopathy. In a yeast two-hybrid screening, MYPN was found to bind to titin in the Z-line, which was confirmed by microscale thermophoresis. Cardiac analyses of MYPN knockout (MKO) mice showed the development of mild cardiac dilation and systolic dysfunction, associated with decreased myofibrillar isometric tension generation and increased resting tension at longer sarcomere lengths. MKO mice exhibited a normal hypertrophic response to transaortic constriction (TAC), but rapidly developed severe cardiac dilation and systolic dysfunction, associated with fibrosis, increased fetal gene expression, higher intercalated disc fold amplitude, decreased calsequestrin-2 protein levels, and increased desmoplakin and SORBS2 protein levels. Cardiomyocyte analyses showed delayed Ca2+ release and reuptake in unstressed MKO mice as well as reduced Ca2+ spark amplitude post-TAC, suggesting that altered Ca2+ handling may contribute to the development of DCM in MKO mice.

    1. Biochemistry and Chemical Biology

    Witnessing the structural evolution of an RNA enzyme

    Xavier Portillo et al.
    Research Article Updated

    An RNA polymerase ribozyme that has been the subject of extensive directed evolution efforts has attained the ability to synthesize complex functional RNAs, including a full-length copy of its own evolutionary ancestor. During the course of evolution, the catalytic core of the ribozyme has undergone a major structural rearrangement, resulting in a novel tertiary structural element that lies in close proximity to the active site. Through a combination of site-directed mutagenesis, structural probing, and deep sequencing analysis, the trajectory of evolution was seen to involve the progressive stabilization of the new structure, which provides the basis for improved catalytic activity of the ribozyme. Multiple paths to the new structure were explored by the evolving population, converging upon a common solution. Tertiary structural remodeling of RNA is known to occur in nature, as evidenced by the phylogenetic analysis of extant organisms, but this type of structural innovation had not previously been observed in an experimental setting. Despite prior speculation that the catalytic core of the ribozyme had become trapped in a narrow local fitness optimum, the evolving population has broken through to a new fitness locale, raising the possibility that further improvement of polymerase activity may be achievable.

    1. Biochemistry and Chemical Biology

    A universal pocket in fatty acyl-AMP ligases ensures redirection of fatty acid pool away from coenzyme A-based activation

    Gajanan S Patil et al.
    Research Article Updated

    Fatty acyl-AMP ligases (FAALs) channelize fatty acids towards biosynthesis of virulent lipids in mycobacteria and other pharmaceutically or ecologically important polyketides and lipopeptides in other microbes. They do so by bypassing the ubiquitous coenzyme A-dependent activation and rely on the acyl carrier protein-tethered 4′-phosphopantetheine (holo-ACP). The molecular basis of how FAALs strictly reject chemically identical and abundant acceptors like coenzyme A (CoA) and accept holo-ACP unlike other members of the ANL superfamily remains elusive. We show that FAALs have plugged the promiscuous canonical CoA-binding pockets and utilize highly selective alternative binding sites. These alternative pockets can distinguish adenosine 3′,5′-bisphosphate-containing CoA from holo-ACP and thus FAALs can distinguish between CoA and holo-ACP. These exclusive features helped identify the omnipresence of FAAL-like proteins and their emergence in plants, fungi, and animals with unconventional domain organizations. The universal distribution of FAALs suggests that they are parallelly evolved with FACLs for ensuring a CoA-independent activation and redirection of fatty acids towards lipidic metabolites.