Restoration of fitness lost due to dysregulation of the pyruvate dehydrogenase complex is triggered by ribosomal binding site modifications
Amitesh Anand,
Connor A. Olson,
Anand V. Sastry,
Arjun Patel,
Richard Szubin,
Laurence Yang,
Adam M. Feist,
Bernhard O. Palsson
Affiliations
Amitesh Anand
Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
Connor A. Olson
Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
Anand V. Sastry
Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
Arjun Patel
Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
Richard Szubin
Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
Laurence Yang
Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemical Engineering, Queen’s University, Kingston, ON, Canada
Adam M. Feist
Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
Bernhard O. Palsson
Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark; Corresponding author
Summary: Pyruvate dehydrogenase complex (PDC) functions as the main determinant of the respiro-fermentative balance because it converts pyruvate to acetyl-coenzyme A (CoA), which then enters the TCA (tricarboxylic acid cycle). PDC is repressed by the pyruvate dehydrogenase complex regulator (PdhR) in Escherichia coli. The deletion of the pdhR gene compromises fitness in aerobic environments. We evolve the E. coli pdhR deletion strain to examine its achievable growth rate and the underlying adaptive strategies. We find that (1) optimal proteome allocation to PDC is critical in achieving optimal growth rate; (2) expression of PDC in evolved strains is reduced through mutations in the Shine-Dalgarno sequence; (3) rewiring of the TCA flux and increased reactive oxygen species (ROS) defense occur in the evolved strains; and (4) the evolved strains adapt to an efficient biomass yield. Together, these results show how adaptation can find alternative regulatory mechanisms for a key cellular process if the primary regulatory mode fails.
