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Frontiers in Molecular Biosciences
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Frontiers in Molecular Biosciences
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Kinetic Modeling of the Genetic Information Processes in a Minimal Cell

Authors: Zane R. Thornburg; Marcelo C. R. Melo; Marcelo C. R. Melo; David Bianchi; Troy A. Brier; Cole Crotty; Marian Breuer; +5 Authors

Kinetic Modeling of the Genetic Information Processes in a Minimal Cell

Abstract

JCVI-syn3A is a minimal bacterial cell with a 543 kbp genome consisting of 493 genes. For this slow growing minimal cell with a 105 min 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 1,000 replicates/cells. The model predicts the time required for replication initiation and DNA replication to be 8 and 50 min 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

DYNAMICS, QH301-705.5, POLYMERASE, kinetic parameters, stochastic simulations, translation, DNAA PROTEIN, DNA replication, REPLICATION-ORIGIN, ESCHERICHIA-COLI, minimal cells, BALANCE, SIMULATION, BINDING, GROWTH, mRNA production, Molecular Biosciences, RIBOSOME BIOGENESIS, protein production, Biology (General), transcription

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    Top 10%
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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
19
Top 10%
Top 10%
Top 10%
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gold