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

Jalal ASB, Tran NT, Stevenson CE, Chan EW, Lo R, Tan X, Noy A, Lawson DM, Le TBK
Cell Rep 32 107928 (2020)
Cited: 11 times
EuropePMC logo PMID: 32698006

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.

Articles - 6y93 mentioned but not cited (2)

  1. Diversification of DNA-Binding Specificity by Permissive and Specificity-Switching Mutations in the ParB/Noc Protein Family. Jalal ASB, Tran NT, Stevenson CE, Chan EW, Lo R, Tan X, Noy A, Lawson DM, Le TBK. Cell Rep 32 107928 (2020)
  2. The CTP-binding domain is disengaged from the DNA-binding domain in a cocrystal structure of Bacillus subtilis Noc-DNA complex. Sukhoverkov KV, Jalal ASB, Ault JR, Sobott F, Lawson DM, Le TBK. J Biol Chem 299 103063 (2023)


Reviews citing this publication (2)

  1. Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom. Amemiya HM, Schroeder J, Freddolino PL. Transcription 12 182-218 (2021)
  2. Connecting the dots: key insights on ParB for chromosome segregation from single-molecule studies. Tišma M, Kaljević J, Gruber S, Le TBK, Dekker C. FEMS Microbiol Rev 48 fuad067 (2024)

Articles citing this publication (7)

  1. A CTP-dependent gating mechanism enables ParB spreading on DNA. Jalal AS, Tran NT, Stevenson CE, Chimthanawala A, Badrinarayanan A, Lawson DM, Le TB. Elife 10 e69676 (2021)
  2. CTP regulates membrane-binding activity of the nucleoid occlusion protein Noc. Jalal ASB, Tran NT, Wu LJ, Ramakrishnan K, Rejzek M, Gobbato G, Stevenson CEM, Lawson DM, Errington J, Le TBK. Mol Cell 81 3623-3636.e6 (2021)
  3. Programmable synthetic biomolecular condensates for cellular control. Dai Y, Farag M, Lee D, Zeng X, Kim K, Son HI, Guo X, Su J, Peterson N, Mohammed J, Ney M, Shapiro DM, Pappu RV, Chilkoti A, You L. Nat Chem Biol 19 518-528 (2023)
  4. Membrane mediated phase separation of the bacterial nucleoid occlusion protein Noc. Babl L, Merino-Salomón A, Kanwa N, Schwille P. Sci Rep 12 17949 (2022)
  5. Evolving origin-of-transfer sequences on staphylococcal conjugative and mobilizable plasmids-who's mimicking whom? Yui Eto K, Kwong SM, LaBreck PT, Crow JE, Traore DAK, Parahitiyawa N, Fairhurst HM, Merrell DS, Firth N, Bond CS, Ramsay JP. Nucleic Acids Res 49 5177-5188 (2021)
  6. Characterization of a pathway-specific activator of edeine biosynthesis and improved edeine production by its overexpression in Brevibacillus brevis. Du J, Zhang C, Long Q, Zhang L, Chen W, Liu Q. Front Plant Sci 13 1022476 (2022)
  7. Atomistic Molecular Dynamics Simulations of DNA in Complex 3D Arrangements for Comparison with Lower Resolution Structural Experiments. Watson G, Velasco-Berrelleza V, Noy A. Methods Mol Biol 2476 95-109 (2022)


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