Lipoate-binding proteins and specific lipoate-protein ligases in microbial sulfur oxidation reveal an atypcial role for an old cofactor

  1. Xinyun Cao
  2. Tobias Koch
  3. Lydia Steffens
  4. Julia Finkensieper
  5. Renate Zigann
  6. John E Cronan
  7. Christiane Dahl  Is a corresponding author
  1. University of Illinois, United States
  2. Rheinische Friedrich-Wilhelms-Universität Bonn, Germany

Abstract

Many Bacteria and Archaea employ the heterodisulfide reductase (Hdr)-like sulfur oxidation pathway. The relevant genes are inevitably associated with genes encoding lipoate-binding proteins (LbpA). Here, deletion of the gene identified LbpA as an essential component of the Hdr-like sulfur-oxidizing system in the Alphaproteobacterium Hyphomicrobium denitrificans. Thus, a biological function was established for the universally conserved cofactor lipoate that is markedly different from its canonical roles in central metabolism. LbpAs likely function as sulfur-binding entities presenting substrate to different catalytic sites of the Hdr-like complex, similar to the substrate-channeling function of lipoate in carbon-metabolizing multienzyme complexes, e.g. pyruvate dehydrogenase. LbpAs serve a specific function in sulfur oxidation, cannot functionally replace the related GcvH protein in Bacillus subtilis and are not modified by the canonical E. coli and B. subtilis lipoyl attachment machineries. Instead, LplA-like lipoate-protein ligases encoded in or in immediate vicinity of hdr-lpbA gene clusters act specifically on these proteins.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 2 and 3.

Article and author information

Author details

  1. Xinyun Cao

    Department of Biochemistry, University of Illinois, Urbana, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7346-3909
  2. Tobias Koch

    Institut für Mikrobiologie and Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Lydia Steffens

    Institut für Mikrobiologie and Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Julia Finkensieper

    Institut für Mikrobiologie and Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Renate Zigann

    Institut für Mikrobiologie and Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. John E Cronan

    Department of Biochemistry, University of Illinois, Urbana, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Christiane Dahl

    Institut für Mikrobiologie and Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
    For correspondence
    ChDahl@uni-bonn.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8288-7546

Funding

Deutsche Forschungsgemeinschaft (Da 351/8-1)

  • Christiane Dahl

National Institutes of Health (AI15650)

  • John E Cronan

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

Copyright

© 2018, Cao 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

  • 2,187
    views
  • 269
    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. Xinyun Cao
  2. Tobias Koch
  3. Lydia Steffens
  4. Julia Finkensieper
  5. Renate Zigann
  6. John E Cronan
  7. Christiane Dahl
(2018)
Lipoate-binding proteins and specific lipoate-protein ligases in microbial sulfur oxidation reveal an atypcial role for an old cofactor
eLife 7:e37439.
https://doi.org/10.7554/eLife.37439

Share this article

https://doi.org/10.7554/eLife.37439

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Angel D'Oliviera, Xuhang Dai ... Jeffrey S Mugridge
    Research Article

    The SARS-CoV-2 main protease (Mpro or Nsp5) is critical for production of viral proteins during infection and, like many viral proteases, also targets host proteins to subvert their cellular functions. Here, we show that the human tRNA methyltransferase TRMT1 is recognized and cleaved by SARS-CoV-2 Mpro. TRMT1 installs the N2,N2-dimethylguanosine (m2,2G) modification on mammalian tRNAs, which promotes cellular protein synthesis and redox homeostasis. We find that Mpro can cleave endogenous TRMT1 in human cell lysate, resulting in removal of the TRMT1 zinc finger domain. Evolutionary analysis shows the TRMT1 cleavage site is highly conserved in mammals, except in Muroidea, where TRMT1 is likely resistant to cleavage. TRMT1 proteolysis results in reduced tRNA binding and elimination of tRNA methyltransferase activity. We also determined the structure of an Mpro-TRMT1 peptide complex that shows how TRMT1 engages the Mpro active site in an uncommon substrate binding conformation. Finally, enzymology and molecular dynamics simulations indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis following substrate binding. Together, these data provide new insights into substrate recognition by SARS-CoV-2 Mpro that could help guide future antiviral therapeutic development and show how proteolysis of TRMT1 during SARS-CoV-2 infection impairs both TRMT1 tRNA binding and tRNA modification activity to disrupt host translation and potentially impact COVID-19 pathogenesis or phenotypes.

    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease
    Qian Wang, Jinxin Liu ... Qian Liu
    Research Article

    Paramyxovirus membrane fusion requires an attachment protein for receptor binding and a fusion protein for membrane fusion triggering. Nipah virus (NiV) attachment protein (G) binds to ephrinB2 or -B3 receptors, and fusion protein (F) mediates membrane fusion. NiV-F is a class I fusion protein and is activated by endosomal cleavage. The crystal structure of a soluble GCN4-decorated NiV-F shows a hexamer-of-trimer assembly. Here, we used single-molecule localization microscopy to quantify the NiV-F distribution and organization on cell and virus-like particle membranes at a nanometer precision. We found that NiV-F on biological membranes forms distinctive clusters that are independent of endosomal cleavage or expression levels. The sequestration of NiV-F into dense clusters favors membrane fusion triggering. The nano-distribution and organization of NiV-F are susceptible to mutations at the hexamer-of-trimer interface, and the putative oligomerization motif on the transmembrane domain. We also show that NiV-F nanoclusters are maintained by NiV-F–AP-2 interactions and the clathrin coat assembly. We propose that the organization of NiV-F into nanoclusters facilitates membrane fusion triggering by a mixed population of NiV-F molecules with varied degrees of cleavage and opportunities for interacting with the NiV-G/receptor complex. These observations provide insights into the in situ organization and activation mechanisms of the NiV fusion machinery.