Multiscale dissection of bacterial proteome optimization
Name
1241733373-MIT.pdf
Size
46.39 MB
Format
Adobe PDF
Checksum (MD5)
a7a62c7c2680fc09b3774810d612531a
Author(s)
Lalanne, Jean-Benoît.
Advisor(s)
Gene-Wei Li and Jeff Gore.
Date Issued
2020
Publisher
Massachusetts Institute of Technology
Abstract
The quantitative composition of proteomes results from biophysical and biochemical selective pressures acting under system-level resource allocation constraints. The nature and strength of these evolutionary driving forces remain obscure. Through the development of analytical tools and precision measurement platforms spanning biological scales, we found evidence of optimization in bacterial gene expression programs. We compared protein synthesis rates across distant lineages and found tight conservation of in-pathway enzyme expression stoichiometry, suggesting generic selective pressures on expression setpoints. Beyond conservation, we used high-resolution transcriptomics to identify numerous examples of stoichiometry preserving cis-elements compensation in pathway operons. Genome-wide mapping of transcription termination sites also led to the discovery of a phylogenetically widespread mode of bacterial gene expression, 'runaway transcription', whereby RNA polymerases are functionally uncoupled from pioneering ribosomes on mRNAs. To delineate biophysical rationales underlying these pressures, we formulated a parsimonious ribosome allocation model capturing the trade-off between reaction flux and protein production cost. The model correctly predicts the expression hierarchy of key translation factors. We then directly measured the quantitative relationship between expression and fitness for specific translation factors in the Gram-positive species Bacillus subtilis. These precision measurements confirmed that endogenous expression maximizes growth rate. Idiosyncratic transcriptional changes in regulons were however observed away from endogenous expression. The resulting physiological burdens sharpened the fitness landscapes. Spurious system-level responses to targeted expression perturbations, called 'regulatory entrenchment', thus exacerbate the requirement for precisely set expression stoichiometry.
Description
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Physics, May, 2020
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 315-348).
Subjects
Physics.
MIT Department
Massachusetts Institute of Technology. Department of Physics
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MIT theses may be protected by copyright. Please reuse MIT thesis content according to the MIT Libraries Permissions Policy, which is available through the URL provided.
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