1. Biochemistry and Chemical Biology
  2. Plant Biology
Download icon

Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts

  1. Anika Küken
  2. Frederik Sommer
  3. Liliya Yaneva-Roder
  4. Luke C M Mackinder
  5. Melanie Höhne
  6. Stefan Geimer
  7. Martin C Jonikas
  8. Michael Schroda
  9. Mark Stitt
  10. Zoran Nikoloski
  11. Tabea Mettler-Altmann  Is a corresponding author
  1. Max Planck Institute of Molecular Plant Physiology, Germany
  2. Carnegie Institution for Science, United States
  3. Universität Bayreuth, Germany
Research Article
  • Cited 11
  • Views 2,150
  • Annotations
Cite this article as: eLife 2018;7:e37960 doi: 10.7554/eLife.37960

Abstract

Cells and organelles are not homogeneous but include microcompartments that alter the spatiotemporal characteristics of cellular processes. The effects of microcompartmentation on metabolic pathways are however difficult to study experimentally. The pyrenoid is a microcompartment that is essential for a carbon concentrating mechanism (CCM) that improves the photosynthetic performance of eukaryotic algae. Using Chlamydomonas reinhardtii, we obtained experimental data on photosynthesis, metabolites, and proteins in CCM-induced and CCM-suppressed cells. We then employed a computational strategy to estimate how fluxes through the Calvin-Benson cycle are compartmented between the pyrenoid and the stroma. Our model predicts that ribulose-1,5-bisphosphate (RuBP), the substrate of Rubisco, and 3-phosphoglycerate (3PGA), its product, diffuse in and out of the pyrenoid, respectively, with higher fluxes in CCM-induced cells. It also indicates that there is no major diffusional barrier to metabolic flux between the pyrenoid and stroma. Our computational approach represents a stepping stone to understanding microcompartmentalized CCM in other organisms.

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, 5 and 6.

Article and author information

Author details

  1. Anika Küken

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1367-0719
  2. Frederik Sommer

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Liliya Yaneva-Roder

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Luke C M Mackinder

    Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1440-3233
  5. Melanie Höhne

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Stefan Geimer

    Institute of Cell Biology, Universität Bayreuth, Bayreuth, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Martin C Jonikas

    Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Michael Schroda

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    The authors declare that no competing interests exist.
  9. Mark Stitt

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    The authors declare that no competing interests exist.
  10. Zoran Nikoloski

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2671-6763
  11. Tabea Mettler-Altmann

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    For correspondence
    tabea.mettler@hhu.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9161-4889

Funding

Deutsche Forschungsgemeinschaft (EXC 1028)

  • Tabea Mettler-Altmann

Bundesministerium für Bildung und Forschung (FKZ0313924)

  • Frederik Sommer
  • Liliya Yaneva-Roder
  • Michael Schroda
  • Mark Stitt
  • Tabea Mettler-Altmann

Max-Planck-Gesellschaft (Open-access funding)

  • Anika Küken

National Science Foundation (EF-1105617)

  • Martin C Jonikas

National Institutes of Health (DP2-GM-119137)

  • Martin C Jonikas

Simons Foundation (55108535)

  • Martin C Jonikas

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

Reviewing Editor

  1. Daniel J Kliebenstein, University of California, Davis, United States

Publication history

  1. Received: April 30, 2018
  2. Accepted: September 27, 2018
  3. Accepted Manuscript published: October 11, 2018 (version 1)
  4. Version of Record published: November 14, 2018 (version 2)
  5. Version of Record updated: May 15, 2020 (version 3)

Copyright

© 2018, Küken 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

  • 2,150
    Page views
  • 418
    Downloads
  • 11
    Citations

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

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

  1. Further reading

Further reading

    1. Biochemistry and Chemical Biology
    Maria Carmela Filomena et al.
    Research Article

    Myopalladin (MYPN) is a striated muscle-specific immunoglobulin domain-containing protein located in the sarcomeric Z-line and I-band. MYPN gene mutations are causative for dilated (DCM), hypertrophic and restrictive cardiomyopathy. In a yeast two-hybrid screening, MYPN was found to bind to titin in the Z-line, which was confirmed by microscale thermophoresis. Cardiac analyses of MYPN knockout (MKO) mice showed the development of mild cardiac dilation and systolic dysfunction, associated with decreased myofibrillar isometric tension generation and increased resting tension at longer sarcomere lengths. MKO mice exhibited a normal hypertrophic response to transaortic constriction (TAC), but rapidly developed severe cardiac dilation and systolic dysfunction, associated with fibrosis, increased fetal gene expression, higher intercalated disc fold amplitude, decreased calsequestrin-2 protein levels, and increased desmoplakin and SORBS2 protein levels. Cardiomyocyte analyses showed delayed Ca2+ release and reuptake in unstressed MKO mice as well as reduced Ca2+ spark amplitude post-TAC, suggesting that altered Ca2+ handling may contribute to the development of DCM in MKO mice.

    1. Biochemistry and Chemical Biology
    Xavier Portillo et al.
    Research Article Updated

    An RNA polymerase ribozyme that has been the subject of extensive directed evolution efforts has attained the ability to synthesize complex functional RNAs, including a full-length copy of its own evolutionary ancestor. During the course of evolution, the catalytic core of the ribozyme has undergone a major structural rearrangement, resulting in a novel tertiary structural element that lies in close proximity to the active site. Through a combination of site-directed mutagenesis, structural probing, and deep sequencing analysis, the trajectory of evolution was seen to involve the progressive stabilization of the new structure, which provides the basis for improved catalytic activity of the ribozyme. Multiple paths to the new structure were explored by the evolving population, converging upon a common solution. Tertiary structural remodeling of RNA is known to occur in nature, as evidenced by the phylogenetic analysis of extant organisms, but this type of structural innovation had not previously been observed in an experimental setting. Despite prior speculation that the catalytic core of the ribozyme had become trapped in a narrow local fitness optimum, the evolving population has broken through to a new fitness locale, raising the possibility that further improvement of polymerase activity may be achievable.