Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post-transfer refinement

  1. Joshua K Michener
  2. Aline A Camargo Neves
  3. Stéphane Vuileumier
  4. Françoise Bringel
  5. Christopher J Marx  Is a corresponding author
  1. Harvard University, United States
  2. Harvard University, Cambridge, United States
  3. Université de Strasbourg, France

Abstract

When microbes acquire new abilities through horizontal gene transfer, the genes and pathways must function under conditions with which they did not coevolve. If newly-acquired genes burden the host, effective use will depend on further evolutionary refinement of the recombinant strain. We used laboratory evolution to recapitulate this process of transfer and refinement, demonstrating that effective use of an introduced dichloromethane degradation pathway required one of several mutations to the bacterial host that are predicted to increase chloride efflux. We then used this knowledge to identify parallel, beneficial mutations that independently evolved in two natural dichloromethane-degrading strains. Finally, we constructed a synthetic mobile genetic element carrying both the degradation pathway and a chloride exporter, which preempted the adaptive process and directly enabled effective dichloromethane degradation across diverse Methylobacterium environmental isolates. Our results demonstrate the importance of post-transfer refinement in horizontal gene transfer, with potential applications in bioremediation and synthetic biology.

Article and author information

Author details

  1. Joshua K Michener

    Harvard University, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Aline A Camargo Neves

    Harvard University, Cambridge, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Stéphane Vuileumier

    Université de Strasbourg, Strasbourg, France
    Competing interests
    The authors declare that no competing interests exist.
  4. Françoise Bringel

    Université de Strasbourg, Strasbourg, France
    Competing interests
    The authors declare that no competing interests exist.
  5. Christopher J Marx

    Harvard University, Cambridge, United States
    For correspondence
    cmarx@uidaho.edu
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Michael Laub, Massachusetts Institute of Technology, United States

Publication history

  1. Received: August 7, 2014
  2. Accepted: November 22, 2014
  3. Accepted Manuscript published: November 24, 2014 (version 1)
  4. Version of Record published: December 22, 2014 (version 2)

Copyright

© 2014, Michener 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

  • 1,205
    Page views
  • 146
    Downloads
  • 27
    Citations

Article citation count generated by polling the highest count across the following sources: Scopus, Crossref, 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)

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. Joshua K Michener
  2. Aline A Camargo Neves
  3. Stéphane Vuileumier
  4. Françoise Bringel
  5. Christopher J Marx
(2014)
Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post-transfer refinement
eLife 3:e04279.
https://doi.org/10.7554/eLife.04279

Further reading

    1. Microbiology and Infectious Disease
    Heiner Atze et al.
    Research Article Updated

    Antibiotics of the β-lactam (penicillin) family inactivate target enzymes called D,D-transpeptidases or penicillin-binding proteins (PBPs) that catalyze the last cross-linking step of peptidoglycan synthesis. The resulting net-like macromolecule is the essential component of bacterial cell walls that sustains the osmotic pressure of the cytoplasm. In Escherichia coli, bypass of PBPs by the YcbB L,D-transpeptidase leads to resistance to these drugs. We developed a new method based on heavy isotope labeling and mass spectrometry to elucidate PBP- and YcbB-mediated peptidoglycan polymerization. PBPs and YcbB similarly participated in single-strand insertion of glycan chains into the expanding bacterial side wall. This absence of any transpeptidase-specific signature suggests that the peptidoglycan expansion mode is determined by other components of polymerization complexes. YcbB did mediate β-lactam resistance by insertion of multiple strands that were exclusively cross-linked to existing tripeptide-containing acceptors. We propose that this undocumented mode of polymerization depends upon accumulation of linear glycan chains due to PBP inactivation, formation of tripeptides due to cleavage of existing cross-links by a β-lactam-insensitive endopeptidase, and concerted cross-linking by YcbB.

    1. Microbiology and Infectious Disease
    Pengge Qian et al.
    Research Article

    Malaria is caused by infection of the erythrocytes by the parasites Plasmodium. Inside the erythrocytes, the parasites multiply via schizogony, an unconventional cell division mode. The Inner Membrane Complex (IMC), an organelle located beneath the parasite plasma membrane, serving as the platform for protein anchorage, is essential for schizogony. So far, complete repertoire of IMC proteins and their localization determinants remain unclear. Here we used biotin ligase (TurboID)-based proximity labelling to compile the proteome of the schizont IMC of rodent malaria parasite Plasmodium yoelii. In total, 300 TurboID-interacting proteins were identified. 18 of 21 selected candidates were confirmed to localize in the IMC, indicating good reliability. In light of the existing palmitome of Plasmodium falciparum, 83 proteins of the P. yoelii IMC proteome are potentially palmitoylated. We further identified DHHC2 as the major resident palmitoyl-acyl-transferase of the IMC. Depletion of DHHC2 led to defective schizont segmentation and growth arrest both in vitro and in vivo. DHHC2 was found to palmitoylate two critical IMC proteins CDPK1 and GAP45 for their IMC localization. In summary, this study reports an inventory of new IMC proteins and demonstrates a central role of DHHC2 in governing IMC localization of proteins during the schizont development.