Diversification of DNA-Binding Specificity by Permissive and Specificity-Switching Mutations in the ParB/Noc Protein Family.

Cell Reports
Adam S. B. JalalTung B.K Le

Abstract

Specific interactions between proteins and DNA are essential to many biological processes. Yet, it remains unclear how the diversification in DNA-binding specificity was brought about, and the mutational paths that led to changes in specificity are unknown. Using a pair of evolutionarily related DNA-binding proteins, each with a different DNA preference (ParB [Partitioning Protein B] and Noc [Nucleoid Occlusion Factor], which both play roles in bacterial chromosome maintenance), we show that specificity is encoded by a set of four residues at the protein-DNA interface. Combining X-ray crystallography and deep mutational scanning of the interface, we suggest that permissive mutations must be introduced before specificity-switching mutations to reprogram specificity and that mutational paths to new specificity do not necessarily involve dual-specificity intermediates. Overall, our results provide insight into the possible evolutionary history of ParB and Noc and, in a broader context, might be useful for understanding the evolution of other classes of DNA-binding proteins.

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Datasets Mentioned

BETA
GSE129285

Methods Mentioned

BETA
X-ray
immunoprecipitation
bio-layer interferometry
Dissection
One-Hybrid
biosensors
PCR
gel-filtration
gel filtration
biosensor

Software Mentioned

ForteBio
REFMAC5
seqtype
STAR
BLItz
PyMOL
PHASER
BEDTools
XIA2
- Toolkit

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