Regulatory perturbations of ribosome allocation in bacteria reshape the growth proteome with a trade-off in adaptation capacity

David Hidalgo; César A Martínez-Ortiz; Bernhard O Palsson; José I Jiménez; José Utrilla

doi:10.1016/j.isci.2022.103879

Regulatory perturbations of ribosome allocation in bacteria reshape the growth proteome with a trade-off in adaptation capacity

iScience. 2022 Feb 7;25(3):103879. doi: 10.1016/j.isci.2022.103879. eCollection 2022 Mar 18.

Authors

David Hidalgo¹, César A Martínez-Ortiz¹, Bernhard O Palsson^{2

3}, José I Jiménez⁴, José Utrilla¹

Affiliations

¹ Systems and Synthetic Biology Program, Centre for Genomic Sciences, Universidad Nacional Autónoma de México, Campus Morelos, Cuernavaca, México.
² Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
³ Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
⁴ Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.

Abstract

Bacteria regulate their cellular resource allocation to enable fast growth-adaptation to a variety of environmental niches. We studied the ribosomal allocation, growth, and expression profiles of two sets of fast-growing mutants of Escherichia coli K-12 MG1655. Mutants with only three of the seven copies of ribosomal RNA operons grew faster than the wild-type strain in minimal media and show similar phenotype to previously studied fast-growing rpoB mutants. Comparing these two different regulatory perturbations (rRNA promoters or rpoB mutations), we show how they reshape the proteome for growth with a concomitant fitness cost. The fast-growing mutants shared downregulation of hedging functions and upregulated growth functions. They showed longer diauxic shifts and reduced activity of gluconeogenic promoters during glucose-acetate shifts, suggesting reduced availability of the RNA polymerase for expressing hedging proteome. These results show that the regulation of ribosomal allocation underlies the growth/hedging phenotypes obtained from laboratory evolution experiments.

Keywords: Bacteriology; Bacterium; Cell biology.