Insights into the key determinants of membrane protein topology enable the identification of new monotopic folds

  1. Sonya Entova
  2. Jean-Marc Billod
  3. Jean-Marie Swiecicki
  4. Sonsoles Martin-Santamaria
  5. Barbara Imperiali  Is a corresponding author
  1. Massachusetts Institute of Technology, United States
  2. Centro de Investigaciones Biológicas - CIB-CSIC, Spain

Abstract

Monotopic membrane proteins integrate into the lipid bilayer via reentrant hydrophobic domains that enter and exit on a single face of the membrane. Whereas many membrane-spanning proteins have been structurally characterized and transmembrane topologies can be predicted computationally, relatively little is known about the determinants of membrane topology in monotopic proteins. Recently, we reported the X-ray structure determination of PglC, a full-length monotopic membrane protein with phosphoglycosyl transferase (PGT) activity. The definition of this unique structure has prompted in vivo, biochemical, and computational analyses to understand and define two key motifs that contribute to the membrane topology and to provide insight into the dynamics of the enzyme in a lipid bilayer environment. Using the new information gained from studies on the PGT superfamily we demonstrate that the two motifs exemplify principles of topology determination that can be applied to the identification of reentrant domains among diverse monotopic proteins of interest.

Data availability

All data generated or analyzed during this study are included in the manuscript and supporting files.

Article and author information

Author details

  1. Sonya Entova

    Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5270-3336
  2. Jean-Marc Billod

    Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas - CIB-CSIC, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
  3. Jean-Marie Swiecicki

    Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7139-8621
  4. Sonsoles Martin-Santamaria

    Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas - CIB-CSIC, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
  5. Barbara Imperiali

    Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
    For correspondence
    imper@mit.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5749-7869

Funding

NIH Office of the Director (NIH GM-039334)

  • Sonya Entova
  • Barbara Imperiali

Ministerio de Economía y Competitividad (CTQ2014-57141-R)

  • Jean-Marc Billod
  • Sonsoles Martin-Santamaria

Jane Coffin Childs Memorial Fund for Medical Research

  • Jean-Marie Swiecicki

NIH Office of the Director (T32-GM007287)

  • Sonya Entova

Ministerio de Economía y Competitividad (CTQ2017-88353-R)

  • Jean-Marc Billod
  • Sonsoles Martin-Santamaria

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

Copyright

© 2018, Entova 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

  • 3,412
    views
  • 466
    downloads
  • 28
    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. Sonya Entova
  2. Jean-Marc Billod
  3. Jean-Marie Swiecicki
  4. Sonsoles Martin-Santamaria
  5. Barbara Imperiali
(2018)
Insights into the key determinants of membrane protein topology enable the identification of new monotopic folds
eLife 7:e40889.
https://doi.org/10.7554/eLife.40889

Share this article

https://doi.org/10.7554/eLife.40889

Further reading

    1. Biochemistry and Chemical Biology
    Jianheng Fox Liu, Ben R Hawley ... Samie R Jaffrey
    Tools and Resources

    N 6,2’-O-dimethyladenosine (m6Am) is a modified nucleotide located at the first transcribed position in mRNA and snRNA that is essential for diverse physiological processes. m6Am mapping methods assume each gene uses a single start nucleotide. However, gene transcription usually involves multiple start sites, generating numerous 5’ isoforms. Thus, gene-level annotations cannot capture the diversity of m6Am modification in the transcriptome. Here, we describe CROWN-seq, which simultaneously identifies transcription-start nucleotides and quantifies m6Am stoichiometry for each 5’ isoform that initiates with adenosine. Using CROWN-seq, we map the m6Am landscape in nine human cell lines. Our findings reveal that m6Am is nearly always a high stoichiometry modification, with only a small subset of cellular mRNAs showing lower m6Am stoichiometry. We find that m6Am is associated with increased transcript expression and provide evidence that m6Am may be linked to transcription initiation associated with specific promoter sequences and initiation mechanisms. These data suggest a potential new function for m6Am in influencing transcription.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Joar Esteban Pinto Torres, Mathieu Claes ... Yann G-J Sterckx
    Research Article

    African trypanosomes are the causative agents of neglected tropical diseases affecting both humans and livestock. Disease control is highly challenging due to an increasing number of drug treatment failures. African trypanosomes are extracellular, blood-borne parasites that mainly rely on glycolysis for their energy metabolism within the mammalian host. Trypanosomal glycolytic enzymes are therefore of interest for the development of trypanocidal drugs. Here, we report the serendipitous discovery of a camelid single-domain antibody (sdAb aka Nanobody) that selectively inhibits the enzymatic activity of trypanosomatid (but not host) pyruvate kinases through an allosteric mechanism. By combining enzyme kinetics, biophysics, structural biology, and transgenic parasite survival assays, we provide a proof-of-principle that the sdAb-mediated enzyme inhibition negatively impacts parasite fitness and growth.