Abstract

Molecule clustering is an important mechanism underlying cellular self-organization. In the cell membrane, a variety of fundamentally different mechanisms drive membrane protein clustering into nanometre-sized assemblies. To date, it is unknown whether this clustering process can be dissected into steps differentially regulated by independent mechanisms. Using clustered syntaxin molecules as an example, we study the influence of a cytoplasmic protein domain on the clustering behaviour. Analysing protein mobility, cluster size and accessibility to myc-epitopes we show that forces acting on the transmembrane segment produce loose-clusters, while cytoplasmic protein interactions mediate a tightly packed state. We conclude that the data identify a hierarchy in membrane protein clustering likely being a paradigm for many cellular self-organization processes.

Article and author information

Author details

  1. Elisa Merklinger

    Membrane Biochemistry, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
    Competing interests
    The authors declare that no competing interests exist.
  2. Jan-Gero Schloetel

    Membrane Biochemistry, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Pascal Weber

    Membrane Biochemistry, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Helena Batoulis

    Membrane Biochemistry, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Sarah Holz

    Membrane Biochemistry, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Nora Karnowski

    Chemical Biology, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Jérôme Finke

    Membrane Biochemistry, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
    Competing interests
    The authors declare that no competing interests exist.
  8. Thorsten Lang

    Membrane Biochemistry, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
    For correspondence
    thorsten.lang@uni-bonn.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9128-0137

Funding

Deutsche Forschungsgemeinschaft (TRR83 to T.L.)

  • Thorsten Lang

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

Reviewing Editor

  1. Reinhard Jahn, Max Planck Institute for Biophysical Chemistry, Germany

Version history

  1. Received: August 16, 2016
  2. Accepted: July 17, 2017
  3. Accepted Manuscript published: July 19, 2017 (version 1)
  4. Version of Record published: July 31, 2017 (version 2)

Copyright

© 2017, Merklinger 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

  • 3,254
    views
  • 440
    downloads
  • 19
    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. Elisa Merklinger
  2. Jan-Gero Schloetel
  3. Pascal Weber
  4. Helena Batoulis
  5. Sarah Holz
  6. Nora Karnowski
  7. Jérôme Finke
  8. Thorsten Lang
(2017)
The packing density of a supramolecular membrane protein cluster is controlled by cytoplasmic interactions
eLife 6:e20705.
https://doi.org/10.7554/eLife.20705

Share this article

https://doi.org/10.7554/eLife.20705

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Isabelle Petit-Hartlein, Annelise Vermot ... Franck Fieschi
    Research Article

    NADPH oxidases (NOX) are transmembrane proteins, widely spread in eukaryotes and prokaryotes, that produce reactive oxygen species (ROS). Eukaryotes use the ROS products for innate immune defense and signaling in critical (patho)physiological processes. Despite the recent structures of human NOX isoforms, the activation of electron transfer remains incompletely understood. SpNOX, a homolog from Streptococcus pneumoniae, can serves as a robust model for exploring electron transfers in the NOX family thanks to its constitutive activity. Crystal structures of SpNOX full-length and dehydrogenase (DH) domain constructs are revealed here. The isolated DH domain acts as a flavin reductase, and both constructs use either NADPH or NADH as substrate. Our findings suggest that hydride transfer from NAD(P)H to FAD is the rate-limiting step in electron transfer. We identify significance of F397 in nicotinamide access to flavin isoalloxazine and confirm flavin binding contributions from both DH and Transmembrane (TM) domains. Comparison with related enzymes suggests that distal access to heme may influence the final electron acceptor, while the relative position of DH and TM does not necessarily correlate with activity, contrary to previous suggestions. It rather suggests requirement of an internal rearrangement, within the DH domain, to switch from a resting to an active state. Thus, SpNOX appears to be a good model of active NOX2, which allows us to propose an explanation for NOX2’s requirement for activation.

    1. Biochemistry and Chemical Biology
    2. Plant Biology
    Dietmar Funck, Malte Sinn ... Jörg S Hartig
    Research Article

    Metabolism and biological functions of the nitrogen-rich compound guanidine have long been neglected. The discovery of four classes of guanidine-sensing riboswitches and two pathways for guanidine degradation in bacteria hint at widespread sources of unconjugated guanidine in nature. So far, only three enzymes from a narrow range of bacteria and fungi have been shown to produce guanidine, with the ethylene-forming enzyme (EFE) as the most prominent example. Here, we show that a related class of Fe2+- and 2-oxoglutarate-dependent dioxygenases (2-ODD-C23) highly conserved among plants and algae catalyze the hydroxylation of homoarginine at the C6-position. Spontaneous decay of 6-hydroxyhomoarginine yields guanidine and 2-aminoadipate-6-semialdehyde. The latter can be reduced to pipecolate by pyrroline-5-carboxylate reductase but more likely is oxidized to aminoadipate by aldehyde dehydrogenase ALDH7B in vivo. Arabidopsis has three 2-ODD-C23 isoforms, among which Din11 is unusual because it also accepted arginine as substrate, which was not the case for the other 2-ODD-C23 isoforms from Arabidopsis or other plants. In contrast to EFE, none of the three Arabidopsis enzymes produced ethylene. Guanidine contents were typically between 10 and 20 nmol*(g fresh weight)-1 in Arabidopsis but increased to 100 or 300 nmol*(g fresh weight)-1 after homoarginine feeding or treatment with Din11-inducing methyljasmonate, respectively. In 2-ODD-C23 triple mutants, the guanidine content was strongly reduced, whereas it increased in overexpression plants. We discuss the implications of the finding of widespread guanidine-producing enzymes in photosynthetic eukaryotes as a so far underestimated branch of the bio-geochemical nitrogen cycle and propose possible functions of natural guanidine production.