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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Mol. Biosci. | doi: 10.3389/fmolb.2019.00130

Kinetic Modelling of the Genetic Information Processes in a Minimal Cell

  • 1University of Illinois at Urbana-Champaign, United States
  • 2University of Pennsylvania, United States
  • 3Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Netherlands
  • 4J. Craig Venter Institute, United States

JCVI-syn3A is a minimal bacterial cell with a 543 kbp genome consisting of 493 coding genes.
For this slow growing minimal cell with a 105 minute doubling time, we recently established the
essential metabolism including the transport of required nutrients from the environment, the
gene map, and genome-wide proteomics. Of the 452 protein-coding genes, 143 are assigned
to metabolism and 212 are assigned to genetic information processing. Using genome-wide
proteomics and experimentally measured kinetic parameters from the literature we present here
kinetic models for the genetic information processes of DNA replication, replication initiation, transcription,
and translation which are solved stochastically and averaged over 1000 replicates/cells.
The model predicts the time required for replication initiation and DNA replication to be 8 minutes
and 50 minutes on average respectively and the number of proteins and ribosomal components
to be approximately doubled in a cell cycle. The model of genetic information processing when
combined with the essential metabolic and cell growth networks will provide a powerful platform
for studying the fundamental principles of life.

Keywords: Minimal cells, Kinetic paramerters, DNA Replication, transcription, translation, protein production, mRNA production, stochastic simulations

Received: 27 Aug 2019; Accepted: 07 Nov 2019.

Copyright: © 2019 Thornburg, Melo, Bianchi, Brier, Crotty, Breuer, Smith, Hutchison III, Glass and Luthey-Schulten. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Zaida Luthey-Schulten, University of Illinois at Urbana-Champaign, Champaign, United States, zan@illinois.edu