Charge-driven condensation of RNA and proteins suggests broad role of phase separation in cytoplasmic environments

Abstract

Phase separation processes are increasingly being recognized as important organizing mechanisms of biological macromolecules in cellular environments. Well established drivers of phase separation are multi-valency and intrinsic disorder. Here, we show that globular macromolecules may condense simply based on electrostatic complementarity. More specifically, phase separation of mixtures between RNA and positively charged proteins is described from a combination of multiscale computer simulations with microscopy and spectroscopy experiments. Phase diagrams were mapped out as a function of molecular concentrations in experiment and as a function of molecular size and temperature via simulations. The resulting condensates were found to retain at least some degree of internal dynamics varying as a function of the molecular composition. The results suggest a more general principle for phase separation that is based primarily on electrostatic complementarity without invoking polymer properties as in most previous studies. Simulation results furthermore suggest that such phase separation may occur widely in heterogenous cellular environment between nucleic acid and protein components.

Data availability

All experimental data generated and analyzed during this study are included in the manuscript and supporting files.

Article and author information

Author details

  1. Bercem Dutagaci

    Biochemistry & Molecular Biology, Michigan State University, East Lansing, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0333-5757
  2. Grzegorz Nawrocki

    Biochemistry & Molecular Biology, Michigan State University, East Lansing, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Joyce Goodluck

    Physics, Michigan State University, East Lansing, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Ali Akbar Ashkarran

    Precision Health Program and Department of Radiology, Michigan State University, East Lansing, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Charles G Hoogstraten

    Biochemistry & Molecular Biology, Michigan State University, East Lansing, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Lisa J Lapidus

    Physics, Michigan State University, East Lansing, United States
    For correspondence
    lapidus@msu.edu
    Competing interests
    The authors declare that no competing interests exist.
  7. Michael Feig

    Biochemistry & Molecular Biology, Michigan State University, East Lansing, United States
    For correspondence
    mfeiglab@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9380-6422

Funding

National Institutes of Health (R35 GM126948)

  • Bercem Dutagaci
  • Grzegorz Nawrocki
  • Michael Feig

National Science Foundation (MCB 1817307)

  • Bercem Dutagaci
  • Grzegorz Nawrocki
  • Joyce Goodluck
  • Lisa J Lapidus
  • Michael Feig

National Science Foundation (MCB 2018296)

  • Charles G Hoogstraten

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

Copyright

© 2021, Dutagaci 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

  • 6,782
    views
  • 792
    downloads
  • 58
    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. Bercem Dutagaci
  2. Grzegorz Nawrocki
  3. Joyce Goodluck
  4. Ali Akbar Ashkarran
  5. Charles G Hoogstraten
  6. Lisa J Lapidus
  7. Michael Feig
(2021)
Charge-driven condensation of RNA and proteins suggests broad role of phase separation in cytoplasmic environments
eLife 10:e64004.
https://doi.org/10.7554/eLife.64004

Share this article

https://doi.org/10.7554/eLife.64004

Further reading

    1. Physics of Living Systems
    Xiaowen Chen, Maciej Winiarksi ... Aleksandra M Walczak
    Research Article

    In social behavior research, the focus often remains on animal dyads, limiting the understanding of complex interactions. Recent trends favor naturalistic setups, offering unique insights into intricate social behaviors. Social behavior stems from chance, individual preferences, and group dynamics, necessitating high-resolution quantitative measurements and statistical modeling. This study leverages the Eco-HAB system, an automated experimental setup that employs radiofrequency identification tracking to observe naturally formed mouse cohorts in a controlled yet naturalistic setting, and uses statistical inference models to decipher rules governing the collective dynamics of groups of 10–15 individuals. Applying maximum entropy models on the coarse-grained co-localization patterns of mice unveils social rules in mouse hordes, quantifying sociability through pairwise interactions within groups, the impact of individual versus social preferences, and the effects of considering interaction structures among three animals instead of two. Reproducing co-localization patterns of individual mice reveals stability over time, with the statistics of the inferred interaction strength capturing social structure. By separating interactions from individual preferences, the study demonstrates that altering neuronal plasticity in the prelimbic cortex – the brain structure crucial for sociability – does not eliminate signatures of social interactions, but makes the transmission of social information between mice more challenging. The study demonstrates how the joint probability distribution of the mice positions can be used to quantify sociability.

    1. Physics of Living Systems
    Ning Liu, Wenan Qiang ... Huanyu Qiao
    Research Article

    Chromosome structure is complex, and many aspects of chromosome organization are still not understood. Measuring the stiffness of chromosomes offers valuable insight into their structural properties. In this study, we analyzed the stiffness of chromosomes from metaphase I (MI) and metaphase II (MII) oocytes. Our results revealed a tenfold increase in stiffness (Young’s modulus) of MI chromosomes compared to somatic chromosomes. Furthermore, the stiffness of MII chromosomes was found to be lower than that of MI chromosomes. We examined the role of meiosis-specific cohesin complexes in regulating chromosome stiffness. Surprisingly, the stiffness of chromosomes from three meiosis-specific cohesin mutants did not significantly differ from that of wild-type chromosomes, indicating that these cohesins may not be primary determinants of chromosome stiffness. Additionally, our findings revealed an age-related increase of chromosome stiffness for MI oocytes. Since aging is associated with elevated levels of DNA damage, we investigated the impact of etoposide-induced DNA damage on chromosome stiffness and found that it led to a reduction in stiffness in MI oocytes. Overall, our study underscores the dynamic and cyclical nature of chromosome stiffness, modulated by both the cell cycle and age-related factors.