Distinguishing different modes of growth using single-cell data

  1. Prathitha Kar
  2. Sriram Tiruvadi-Krishnan
  3. Jaana Männik
  4. Jaan Männik  Is a corresponding author
  5. Ariel Amir  Is a corresponding author
  1. Harvard University, United States
  2. University of Tennessee, United States
  3. The University of Tennessee, United States

Abstract

Collection of high-throughput data has become prevalent in biology. Large datasets allow the use of statistical constructs such as binning and linear regression to quantify relationships between variables and hypothesize underlying biological mechanisms based on it. We discuss several such examples in relation to single-cell data and cellular growth. In particular, we show instances where what appears to be ordinary use of these statistical methods leads to incorrect conclusions such as growth being non-exponential as opposed to exponential and vice versa. We propose that the data analysis and its interpretation should be done in the context of a generative model, if possible. In this way, the statistical methods can be validated either analytically or against synthetic data generated via the use of the model, leading to a consistent method for inferring biological mechanisms from data. On applying the validated methods of data analysis to infer cellular growth on our experimental data, we find the growth of length in E. coli to be non-exponential. Our analysis shows that in the later stages of the cell cycle the growth rate is faster than exponential.

Data availability

All data generated during this study are deposited in Dataverse-:Kar, Prathitha; Tiruvadi-Krishnan, Sriram; Männik, Jaana; Männik, Jaan; Amir, Ariel, 2021, "Distinguishing different modes of growth using single-cell data", https://doi.org/10.7910/DVN/BNQUDW, Harvard Dataverse, V1

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Prathitha Kar

    Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4091-6860
  2. Sriram Tiruvadi-Krishnan

    Department of Chemistry and Chemical Biology, University of Tennessee, Knoxville, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Jaana Männik

    Department of Chemistry and Chemical Biology, University of Tennessee, Knoxville, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Jaan Männik

    Department of Chemistry and Chemical Biology, The University of Tennessee, Knoxville, United States
    For correspondence
    jmannik@utk.edu
    Competing interests
    The authors declare that no competing interests exist.
  5. Ariel Amir

    Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, United States
    For correspondence
    arielamir@seas.harvard.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2611-0139

Funding

US-Israel BSF Research Grant (2017004)

  • Jaan Männik

National Institutes of Health (R01GM127413)

  • Jaan Männik

National Science Foundation (NSF CAREER 1752024)

  • Ariel Amir

National Science Foundation (NSF award 1806818)

  • Prathitha Kar

National Institutes of Health (NIH grant 103346)

  • Prathitha Kar

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

Reviewing Editor

  1. Gordon J Berman, Emory University, United States

Publication history

  1. Received: July 28, 2021
  2. Accepted: November 21, 2021
  3. Accepted Manuscript published: December 2, 2021 (version 1)
  4. Accepted Manuscript updated: December 8, 2021 (version 2)
  5. Version of Record published: January 4, 2022 (version 3)
  6. Version of Record updated: January 7, 2022 (version 4)

Copyright

© 2021, Kar 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

  • 1,388
    Page views
  • 187
    Downloads
  • 0
    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. Prathitha Kar
  2. Sriram Tiruvadi-Krishnan
  3. Jaana Männik
  4. Jaan Männik
  5. Ariel Amir
(2021)
Distinguishing different modes of growth using single-cell data
eLife 10:e72565.
https://doi.org/10.7554/eLife.72565

Further reading

    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease
    Florian Bleffert et al.
    Research Article Updated

    Cells steadily adapt their membrane glycerophospholipid (GPL) composition to changing environmental and developmental conditions. While the regulation of membrane homeostasis via GPL synthesis in bacteria has been studied in detail, the mechanisms underlying the controlled degradation of endogenous GPLs remain unknown. Thus far, the function of intracellular phospholipases A (PLAs) in GPL remodeling (Lands cycle) in bacteria is not clearly established. Here, we identified the first cytoplasmic membrane-bound phospholipase A1 (PlaF) from Pseudomonas aeruginosa, which might be involved in the Lands cycle. PlaF is an important virulence factor, as the P. aeruginosa ΔplaF mutant showed strongly attenuated virulence in Galleria mellonella and macrophages. We present a 2.0-Å-resolution crystal structure of PlaF, the first structure that reveals homodimerization of a single-pass transmembrane (TM) full-length protein. PlaF dimerization, mediated solely through the intermolecular interactions of TM and juxtamembrane regions, inhibits its activity. The dimerization site and the catalytic sites are linked by an intricate ligand-mediated interaction network, which might explain the product (fatty acid) feedback inhibition observed with the purified PlaF protein. We used molecular dynamics simulations and configurational free energy computations to suggest a model of PlaF activation through a coupled monomerization and tilting of the monomer in the membrane, which constrains the active site cavity into contact with the GPL substrates. Thus, these data show the importance of the PlaF-mediated GPL remodeling pathway for virulence and could pave the way for the development of novel therapeutics targeting PlaF.

    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease
    Lauren C Radlinski, Andreas J Bäumler
    Insight

    Listeria monocytogenes uses respiration to sustain a risky fermentative lifestyle during infection.