Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors

Anthony T Meger; Matthew A Spence; Mahakaran Sandhu; Dana Matthews; Jackie Chen; Colin J Jackson; Srivatsan Raman

doi:10.1016/j.cels.2024.03.002

Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors

Cell Syst. 2024 Apr 17;15(4):374-387.e6. doi: 10.1016/j.cels.2024.03.002. Epub 2024 Mar 26.

Authors

Anthony T Meger¹, Matthew A Spence², Mahakaran Sandhu², Dana Matthews³, Jackie Chen¹, Colin J Jackson⁴, Srivatsan Raman⁵

Affiliations

¹ Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
² Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
³ Research School of Biology, Australian National University, Canberra, ACT 2601, Australia.
⁴ Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia; ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia; ARC Centre of Excellence for Innovations in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia. Electronic address: colin.jackson@anu.edu.au.
⁵ Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address: sraman4@wisc.edu.

PMID: 38537640
DOI: 10.1016/j.cels.2024.03.002

Abstract

How a protein's function influences the shape of its fitness landscape, smooth or rugged, is a fundamental question in evolutionary biochemistry. Smooth landscapes arise when incremental mutational steps lead to a progressive change in function, as commonly seen in enzymes and binding proteins. On the other hand, rugged landscapes are poorly understood because of the inherent unpredictability of how sequence changes affect function. Here, we experimentally characterize the entire sequence phylogeny, comprising 1,158 extant and ancestral sequences, of the DNA-binding domain (DBD) of the LacI/GalR transcriptional repressor family. Our analysis revealed an extremely rugged landscape with rapid switching of specificity, even between adjacent nodes. Further, the ruggedness arises due to the necessity of the repressor to simultaneously evolve specificity for asymmetric operators and disfavors potentially adverse regulatory crosstalk. Our study provides fundamental insight into evolutionary, molecular, and biophysical rules of genetic regulation through the lens of fitness landscapes.

Keywords: ASR; DMS; ancestral sequence reconstruction; deep mutational scanning; epistasis; fitness landscape; protein evolution; sequence-function relationships; transcription regulators.

MeSH terms

Phylogeny*