From plasmodesma geometry to effective symplasmic permeability through biophysical modelling

  1. Eva E Deinum  Is a corresponding author
  2. Bela M Mulder
  3. Yoselin Benitez-Alfonso
  1. Wageningen University, Netherlands
  2. AMOLF, Netherlands
  3. University of Leeds, United Kingdom

Abstract

Regulation of molecular transport via intercellular channels called plasmodesmata (PDs) is important for both coordinating developmental and environmental responses among neighbouring cells, and isolating (groups of) cells to execute distinct programs. Cell-to-cell mobility of fluorescent molecules and PD dimensions (measured from electron micrographs) are both used as methods to predict PD transport capacity (i.e., effective symplasmic permeability), but often yield very different values. Here, we build a theoretical bridge between both experimental approaches by calculating the effective symplasmic permeability from a geometrical description of individual PDs and considering the flow towards them. We find that a dilated central region has the strongest impact in thick cell walls and that clustering of PDs into pit fields strongly reduces predicted permeabilities. Moreover, our open source multi-level model allows to predict PD dimensions matching measured permeabilities and add a functional interpretation to structural differences observed between PDs in different cell walls.

Data availability

PDinsight can be downloaded from GitHub: https://github.com/eedeinum/PDinsight. Documentation on the use of PDinsight.py is included as an appendix to the manuscript with additional information at the head of the example parameter file. More extensive documentation is included with PDinsight on GitHub. PDinsight also has a citable DOI through Zenodo: 10.5281/zenodo.3536704. The PDinsight parameter files used for this manuscript are included as Source Code 1.

Article and author information

Author details

  1. Eva E Deinum

    Mathematical and Statistical Methods, Wageningen University, Wageningen, Netherlands
    For correspondence
    eva.deinum@wur.nl
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8564-200X
  2. Bela M Mulder

    Living Matter Department, AMOLF, Amsterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  3. Yoselin Benitez-Alfonso

    Centre for Plant Science, University of Leeds, Leeds, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

Funding

European Molecular Biology Organization (ASTF 105 - 2012)

  • Eva E Deinum

Nederlandse Organisatie voor Wetenschappelijk Onderzoek

  • Bela M Mulder

Engineering and Physical Sciences Research Council (EF/M027740/1)

  • Yoselin Benitez-Alfonso

Leverhulme Trust (RPG-2016-13)

  • Yoselin Benitez-Alfonso

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

Reviewing Editor

  1. Dominique C Bergmann, Stanford University, United States

Version history

  1. Received: June 3, 2019
  2. Accepted: November 16, 2019
  3. Accepted Manuscript published: November 22, 2019 (version 1)
  4. Accepted Manuscript updated: November 25, 2019 (version 2)
  5. Version of Record published: January 31, 2020 (version 3)

Copyright

© 2019, Deinum 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

  • 1,985
    Page views
  • 322
    Downloads
  • 20
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

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. Eva E Deinum
  2. Bela M Mulder
  3. Yoselin Benitez-Alfonso
(2019)
From plasmodesma geometry to effective symplasmic permeability through biophysical modelling
eLife 8:e49000.
https://doi.org/10.7554/eLife.49000

Further reading

    1. Cell Biology
    2. Developmental Biology
    Simon Schneider, Andjela Kovacevic ... Hubert Schorle
    Research Article

    Cylicins are testis-specific proteins, which are exclusively expressed during spermiogenesis. In mice and humans, two Cylicins, the gonosomal X-linked Cylicin 1 (Cylc1/CYLC1) and the autosomal Cylicin 2 (Cylc2/CYLC2) genes, have been identified. Cylicins are cytoskeletal proteins with an overall positive charge due to lysine-rich repeats. While Cylicins have been localized in the acrosomal region of round spermatids, they resemble a major component of the calyx within the perinuclear theca at the posterior part of mature sperm nuclei. However, the role of Cylicins during spermiogenesis has not yet been investigated. Here, we applied CRISPR/Cas9-mediated gene editing in zygotes to establish Cylc1- and Cylc2-deficient mouse lines as a model to study the function of these proteins. Cylc1 deficiency resulted in male subfertility, whereas Cylc2-/-, Cylc1-/yCylc2+/-, and Cylc1-/yCylc2-/- males were infertile. Phenotypical characterization revealed that loss of Cylicins prevents proper calyx assembly during spermiogenesis. This results in decreased epididymal sperm counts, impaired shedding of excess cytoplasm, and severe structural malformations, ultimately resulting in impaired sperm motility. Furthermore, exome sequencing identified an infertile man with a hemizygous variant in CYLC1 and a heterozygous variant in CYLC2, displaying morphological abnormalities of the sperm including the absence of the acrosome. Thus, our study highlights the relevance and importance of Cylicins for spermiogenic remodeling and male fertility in human and mouse, and provides the basis for further studies on unraveling the complex molecular interactions between perinuclear theca proteins required during spermiogenesis.

    1. Cell Biology
    2. Structural Biology and Molecular Biophysics
    Bronwyn A Lucas, Benjamin A Himes, Nikolaus Grigorieff
    Research Advance

    Previously we showed that 2D template matching (2DTM) can be used to localize macromolecular complexes in images recorded by cryogenic electron microscopy (cryo-EM) with high precision, even in the presence of noise and cellular background (Lucas et al., 2021; Lucas et al., 2022). Here, we show that once localized, these particles may be averaged together to generate high-resolution 3D reconstructions. However, regions included in the template may suffer from template bias, leading to inflated resolution estimates and making the interpretation of high-resolution features unreliable. We evaluate conditions that minimize template bias while retaining the benefits of high-precision localization, and we show that molecular features not present in the template can be reconstructed at high resolution from targets found by 2DTM, extending prior work at low-resolution. Moreover, we present a quantitative metric for template bias to aid the interpretation of 3D reconstructions calculated with particles localized using high-resolution templates and fine angular sampling.