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

• Published in: Cell reports (Cambridge) Vol. 32; no. 3; p. 107928
• Main Authors: Jalal, Adam S.B., Tran, Ngat T., Stevenson, Clare E., Chan, Elliot W., Lo, Rebecca, Tan, Xiao, Noy, Agnes, Lawson, David M., Le, Tung B.K.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 21.07.2020; Cell Press
• Subjects: Amino Acid Sequence; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Base Sequence; chromosome organization; chromosome segregation; Conserved Sequence; Crystallography, X-Ray; DNA, Bacterial - metabolism; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; DNA-binding specificity; Escherichia coli - metabolism; gene duplication; Models, Biological; molecular evolution; Mutation - genetics; Noc-NBS; nucleoid occlusion; ParB-parS; Protein Binding; Protein Domains; protein-DNA interaction; chromosome organization; DNA-binding specificity; chromosome segregation; nucleoid occlusion; gene duplication; ParB-parS; protein-DNA interaction; Noc-NBS; molecular evolution
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2020.107928

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. [Display omitted] •DNA-binding specificity for parS and NBS is conserved within ParB and Noc family•Specificity is encoded by a set of four residues at the protein-DNA interface•Mutations must be introduced in a defined order to reprogram specificity Jalal et al. elucidate the molecular basis for how specific protein-DNA interactions can evolve, using ParB and Noc as models. Using X-ray crystallography and deep mutational scanning, they define protein-DNA interfaces and suggest that permissive mutations must be introduced before specificity-switching mutations to reprogram specificity.