Inter-membrane association of the Sec and BAM translocons for bacterial outer-membrane biogenesis

  1. Sara Alvira
  2. Daniel W Watkins
  3. Luca A Troman
  4. William J Allen
  5. James Stuart Lorriman
  6. Gianluca Degliesposti
  7. Eli J Cohen
  8. Morgan Beeby
  9. Bertram Daum
  10. Vicki AM Gold
  11. J Mark Skehel
  12. Ian Collinson  Is a corresponding author
  1. University of Bristol, United Kingdom
  2. Francis Crick Institute, United Kingdom
  3. Imperial College London, United Kingdom
  4. University of Exeter, United Kingdom

Abstract

The outer-membrane of Gram-negative bacteria is critical for surface adhesion, pathogenicity, antibiotic resistance and survival. The major constituent – hydrophobic b-barrel Outer-Membrane Proteins (OMPs) – are first secreted across the inner-membrane through the Sec-translocon for delivery to periplasmic chaperones e.g. SurA, which prevent aggregation. OMPs are then offloaded to the b-Barrel Assembly Machinery (BAM) in the outer-membrane for insertion and folding. We show the Holo-TransLocon (HTL) – an assembly of the protein-channel core-complex SecYEG, the ancillary sub-complex SecDF, and the membrane 'insertase' YidC – contacts BAM through periplasmic domains of SecDF and YidC, ensuring efficient OMP maturation. Furthermore, the proton-motive-force (PMF) across the inner-membrane acts at distinct stages of protein secretion: (1) SecA-driven translocation through SecYEG; and (2) communication of conformational changes via SecDF across the periplasm to BAM. The latter presumably drives efficient passage of OMPs. These interactions provide insights of inter-membrane organisation and communication, the importance of which is becoming increasingly apparent.

Data availability

All data generated or analysed during this study are included in the manuscript and supplementary information. Information regarding statistical testing is located in materials and methods and corresponding figure legends.

Article and author information

Author details

  1. Sara Alvira

    School of Biochemistry, University of Bristol, Bristol, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  2. Daniel W Watkins

    School of Biochemistry, University of Bristol, Bristol, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3825-5036
  3. Luca A Troman

    School of Biochemistry, University of Bristol, Bristol, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. William J Allen

    School of Biochemistry, University of Bristol, Bristol, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9513-4786
  5. James Stuart Lorriman

    School of Biochemistry, University of Bristol, Bristol, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1755-0805
  6. Gianluca Degliesposti

    Mass Spectrometry science technology platform, Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  7. Eli J Cohen

    Department of Life Sciences, Imperial College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  8. Morgan Beeby

    Department of Life Sciencesa, Imperial College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6413-9835
  9. Bertram Daum

    Living Systems Institute, University of Exeter, Frankfurt, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3767-264X
  10. Vicki AM Gold

    Living Systems Institute, University of Exeter, Exeter, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6908-0745
  11. J Mark Skehel

    Mass Spectrometry science technology platform, Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  12. Ian Collinson

    School of Biochemistry, University of Bristol, Bristol, United Kingdom
    For correspondence
    ian.collinson@bristol.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3931-0503

Funding

Biotechnology and Biological Sciences Research Council (BB/S008349/1)

  • Sara Alvira

EMBO (LTFCOFUND2013)

  • Sara Alvira

EMBO (GA-2013-609409)

  • Sara Alvira

Biotechnology and Biological Sciences Research Council (BB/S008349/1)

  • Daniel W Watkins

Biotechnology and Biological Sciences Research Council (BB/S008349/1)

  • Ian Collinson

Biotechnology and Biological Sciences Research Council (BB/N015126/1)

  • Ian Collinson

Biotechnology and Biological Sciences Research Council (BB/N015126/1)

  • Daniel W Watkins

Biotechnology and Biological Sciences Research Council (BB/M003604/1)

  • Ian Collinson

Biotechnology and Biological Sciences Research Council (BB/M003604/1)

  • Sara Alvira

Biotechnology and Biological Sciences Research Council (BB/J014400/1)

  • Luca A Troman

EMBO (ALTF 710-2015)

  • Sara Alvira

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

Copyright

© 2020, Alvira 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

  • 3,689
    views
  • 600
    downloads
  • 40
    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. Sara Alvira
  2. Daniel W Watkins
  3. Luca A Troman
  4. William J Allen
  5. James Stuart Lorriman
  6. Gianluca Degliesposti
  7. Eli J Cohen
  8. Morgan Beeby
  9. Bertram Daum
  10. Vicki AM Gold
  11. J Mark Skehel
  12. Ian Collinson
(2020)
Inter-membrane association of the Sec and BAM translocons for bacterial outer-membrane biogenesis
eLife 9:e60669.
https://doi.org/10.7554/eLife.60669

Share this article

https://doi.org/10.7554/eLife.60669

Further reading

    1. Biochemistry and Chemical Biology
    2. Cell Biology
    Santi Mestre-Fos, Lucas Ferguson ... Jamie HD Cate
    Research Article

    Stem cell differentiation involves a global increase in protein synthesis to meet the demands of specialized cell types. However, the molecular mechanisms underlying this translational burst and the involvement of initiation factors remains largely unknown. Here, we investigate the role of eukaryotic initiation factor 3 (eIF3) in early differentiation of human pluripotent stem cell (hPSC)-derived neural progenitor cells (NPCs). Using Quick-irCLIP and alternative polyadenylation (APA) Seq, we show eIF3 crosslinks predominantly with 3’ untranslated region (3’-UTR) termini of multiple mRNA isoforms, adjacent to the poly(A) tail. Furthermore, we find that eIF3 engagement at 3’-UTR ends is dependent on polyadenylation. High eIF3 crosslinking at 3’-UTR termini of mRNAs correlates with high translational activity, as determined by ribosome profiling, but not with translational efficiency. The results presented here show that eIF3 engages with 3’-UTR termini of highly translated mRNAs, likely reflecting a general rather than specific regulatory function of eIF3, and supporting a role of mRNA circularization in the mechanisms governing mRNA translation.

    1. Biochemistry and Chemical Biology
    2. Genetics and Genomics
    Federico A Vignale, Andrea Hernandez Garcia ... Adrian G Turjanski
    Research Article

    Yerba mate (YM, Ilex paraguariensis) is an economically important crop marketed for the elaboration of mate, the third-most widely consumed caffeine-containing infusion worldwide. Here, we report the first genome assembly of this species, which has a total length of 1.06 Gb and contains 53,390 protein-coding genes. Comparative analyses revealed that the large YM genome size is partly due to a whole-genome duplication (Ip-α) during the early evolutionary history of Ilex, in addition to the hexaploidization event (γ) shared by core eudicots. Characterization of the genome allowed us to clone the genes encoding methyltransferase enzymes that catalyse multiple reactions required for caffeine production. To our surprise, this species has converged upon a different biochemical pathway compared to that of coffee and tea. In order to gain insight into the structural basis for the convergent enzyme activities, we obtained a crystal structure for the terminal enzyme in the pathway that forms caffeine. The structure reveals that convergent solutions have evolved for substrate positioning because different amino acid residues facilitate a different substrate orientation such that efficient methylation occurs in the independently evolved enzymes in YM and coffee. While our results show phylogenomic constraint limits the genes coopted for convergence of caffeine biosynthesis, the X-ray diffraction data suggest structural constraints are minimal for the convergent evolution of individual reactions.