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Fundamental limits on the rate of bacterial growth

Belliveau, Nathan M. and Chure, Griffin and Hueschen, Christina L. and Garcia, Hernan G. and Kondev, Jane and Fisher, Daniel S. and Theriot, Julie A. and Phillips, Rob (2020) Fundamental limits on the rate of bacterial growth. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20201021-080615473

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Abstract

Recent years have seen an experimental deluge interrogating the relationship between bacterial growth rate, cell size, and protein content, quantifying the abundance of proteins across growth conditions with unprecedented resolution. However, we still lack a rigorous understanding of what sets the scale of these quantities and when protein abundances should (or should not) depend on growth rate. Here, we seek to quantitatively understand this relationship across a collection of Escherichia coli proteomic data covering ≈ 4000 proteins and 36 growth rates. We estimate the basic requirements for steady-state growth by considering key processes in nutrient transport, cell envelope biogenesis, energy generation, and the central dogma. From these estimates, ribosome biogenesis emerges as a primary determinant of growth rate. We expand on this assessment by exploring a model of proteomic regulation as a function of the nutrient supply, revealing a mechanism that ties cell size and growth rate to ribosomal content.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2020.10.18.344382DOIDiscussion Paper
https://github.com/rpgroup-pboc/growth_limitsRelated ItemData/Code
https://doi.org/10.5281/zenodo.4091457Related ItemData
ORCID:
AuthorORCID
Belliveau, Nathan M.0000-0002-1536-1963
Chure, Griffin0000-0002-2216-2057
Hueschen, Christina L.0000-0002-3437-2895
Kondev, Jane0000-0001-7522-7144
Theriot, Julie A.0000-0002-2334-2535
Phillips, Rob0000-0003-3082-2809
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. Posted October 18, 2020. We thank Matthias Heinemann, Alexander Schmidt, and Gene-Wei Li for additional input regarding their data. We also thank all members of the Phillips, Theriot, Kondev, Garcia labs, as well as RonMilo and Terry Hwa for useful discussions. We thank Suzannah M. Beeler, Jonas Cremer, Avi Flamholz, Soichi Hirokawa, and Manuel Razo-Mejia for reading and providing comments on drafts of this manuscript. R.P. is supported by La Fondation Pierre-Gilles de Gennes, the Rosen Center at Caltech, and the NIH 1R35 GM118043 (MIRA). J.A.T. is supported by the Howard Hughes Medical Institute, and NIH Grant R37-AI036929. N.M.B is a HHMI Fellow of The Jane Coffin Childs Memorial Fund. H.G.G. is supported by the Burroughs Wellcome Fund Career Award at the Scientific Interface, the Sloan Research Foundation, the Human Frontiers Science Program, the Searle Scholars Program, the Shurl & Kay Curci Foundation, the Hellman Foundation, the NIH Director’s New Innovator Award (DP2 OD024541-01), and an NSF CAREER Award (1652236). D.S.F. is supported by an NSF award (PHY-1607606) and the NIH (NIH R01-AI13699201). Data Analysis and Availability: All proteomic measurements come from the experimental work of Schmidt et al. (2016); Peebo et al. (2015); Valgepea et al. (2013) (mass spectrometry) and Li et al. (2014) (ribosomal profiling). Data curation and analysis was done programmatically in Python, and compiled data and analysis files are accessible through a GitHub repository (DOI:10.5281/zenodo.4091457) associated with this paper as well as on the associated paper website. Additionally, we provide two interactive figures that allow for rapid exploration of the compiled data sets as well as exploration of the parameter space of the minimal model. The authors declare no competing interests.
Group:Rosen Bioengineering Center
Funders:
Funding AgencyGrant Number
La Fondation Pierre Gilles de GennesUNSPECIFIED
Donna and Benjamin M. Rosen Bioengineering CenterUNSPECIFIED
NIH1R35 GM118043
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
NIHR37-AI036929
Jane Coffin Childs Memorial Fund for Medical ResearchUNSPECIFIED
Burroughs Wellcome FundUNSPECIFIED
Alfred P. Sloan FoundationUNSPECIFIED
Human Frontier Science ProgramUNSPECIFIED
Searle Scholars ProgramUNSPECIFIED
Shurl and Kay Curci FoundationUNSPECIFIED
Hellman FoundationUNSPECIFIED
NIHDP2 OD024541-01
NSFPHY-1652236
NIHR01-AI13699201
Record Number:CaltechAUTHORS:20201021-080615473
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20201021-080615473
Official Citation:Fundamental limits on the rate of bacterial growth. Nathan M Belliveau, Griffin D Chure, Christina L Hueschen, Hernan G. Garcia, Jane Kondev, Daniel S Fisher, Julie A. Theriot, Rob Phillips. bioRxiv 2020.10.18.344382; doi: https://doi.org/10.1101/2020.10.18.344382
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:106178
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:21 Oct 2020 16:46
Last Modified:21 Oct 2020 16:46

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