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Self-Organization Controls Expression More than Abundance of Molecular Components of Transcription and Translation in Confined Cell-Free Gene Expression

17 Pages Posted: 2 Oct 2018 Publication Status: Review Complete

See all articles by Patrick M. Caveney

Patrick M. Caveney

Oak Ridge National Laboratory - Center for Nanophase Materials Sciences

Rosemary M. Dabbs

University of Tennessee, Knoxville - Bredesen Center for Interdisciplinary Research and Graduate Education

Gaurav Chauhan

University of Tennessee, Knoxville - Department of Chemical and Biomolecular Engineering

S. Elizabeth Norred

Oak Ridge National Laboratory - Center for Nanophase Materials Sciences

C. Patrick Collier

Oak Ridge National Laboratory - Center for Nanophase Materials Sciences

Steven M. Abel

University of Tennessee, Knoxville - Department of Chemical and Biomolecular Engineering

Michael L. Simpson

Oak Ridge National Laboratory - Center for Nanophase Materials Sciences

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Abstract

At cell-relevant reactor volumes, cell-free expression suffers from excessive variability (noise) such that protein concentrations may vary by more than an order of magnitude across a population of identically constructed reaction chambers. Consensus opinion holds that variability in expression is due to the stochastic distribution of expression resources (DNA, RNAP, ribosomes, etc.) across the population of reaction chambers. In contrast, here we find that chamber-to-chamber variation in the expression efficiency generates the large variability in protein production. We show that chambers self-organize into expression centers that control expression efficiency. Chambers that organize into many centers, each having relatively few expression resources, exhibit high expression efficiency. Conversely, chambers that organize into few centers where each has an abundance of resources, exhibit low expression efficiency. A surprising finding is that diluting expression resources reduces chamber-to-chamber variation in protein production, which provides the means to tune expression noise. These results demonstrate that in cell-free systems, self-organization exerts more influence over expression than the abundance of the molecular components of transcription and translation. These observations may elucidate how self-organized, membrane-less structures emerge and function in cells.

Suggested Citation

Caveney, Patrick M. and Dabbs, Rosemary M. and Chauhan, Gaurav and Norred, S. Elizabeth and Collier, C. Patrick and Abel, Steven M. and Simpson, Michael L., Self-Organization Controls Expression More than Abundance of Molecular Components of Transcription and Translation in Confined Cell-Free Gene Expression (October 2, 2018). Available at SSRN: https://ssrn.com/abstract=3259136 or http://dx.doi.org/10.2139/ssrn.3259136
This version of the paper has not been formally peer reviewed.

Patrick M. Caveney (Contact Author)

Oak Ridge National Laboratory - Center for Nanophase Materials Sciences

1 Bethel Valley Road, P.O. Box 2008, Mail Stop 608
Room B-106, Building 5700
Oak Ridge, TN 37831
United States

Rosemary M. Dabbs

University of Tennessee, Knoxville - Bredesen Center for Interdisciplinary Research and Graduate Education

Knoxville, TN 37996
United States

Gaurav Chauhan

University of Tennessee, Knoxville - Department of Chemical and Biomolecular Engineering

Knoxville, TN 37996
United States

S. Elizabeth Norred

Oak Ridge National Laboratory - Center for Nanophase Materials Sciences

1 Bethel Valley Road, P.O. Box 2008, Mail Stop 608
Room B-106, Building 5700
Oak Ridge, TN 37831
United States

C. Patrick Collier

Oak Ridge National Laboratory - Center for Nanophase Materials Sciences

1 Bethel Valley Road, P.O. Box 2008, Mail Stop 608
Room B-106, Building 5700
Oak Ridge, TN 37831
United States

Steven M. Abel

University of Tennessee, Knoxville - Department of Chemical and Biomolecular Engineering

Knoxville, TN 37996
United States

Michael L. Simpson

Oak Ridge National Laboratory - Center for Nanophase Materials Sciences ( email )

1 Bethel Valley Road, P.O. Box 2008, Mail Stop 608
Room B-106, Building 5700
Oak Ridge, TN 37831
United States