Molecular switching of a DNA-sliding clamp to a repressor mediates long-range gene silencing

McLean, T. C.; Balaguer-Perez, F.; Chandanani, J.; Thomas, C. M.; Aicart-Ramos, C.; Burick, S.; Olinares, P. D. B.; Gobbato, G.; Mundy, J. E. A.; Chait, B. T.; Lawson, D. M.; Darst, S. A.; Campbell, E. A.; Moreno-Herrero, F.; Le, T. B. K.

doi:10.1101/2024.02.16.579611

bioRxiv · 10.1101/2024.02.16.579611

Molecular switching of a DNA-sliding clamp to a repressor mediates long-range gene silencing

McLean, T. C.·Balaguer-Perez, F.·Chandanani, J.·Thomas, C. M.·Aicart-Ramos, C.·Burick, S.·Olinares, P. D. B.·Gobbato, G.·Mundy, J. E. A.·Chait, B. T.·Lawson, D. M.·Darst, S. A.·Campbell, E. A.·Moreno-Herrero, F.·Le, T. B. K.

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Abstract

Long-range gene regulation is rare in bacteria and is confined to the classical DNA looping model. Here, we use a combination of biophysical approaches, including X-ray crystallography and single-molecule analysis, to show that long-range gene silencing on the plasmid RK2, a source of multidrug resistance across diverse Gram-negative bacteria, is achieved cooperatively by a DNA-sliding clamp, KorB, and a clamp-locking protein, KorA. We find that KorB is a CTPase clamp that can entrap and slide along DNA to reach distal target promoters. We resolved the tripartite crystal structure of a KorB-KorA-DNA co-complex, revealing that KorA latches KorB into a closed-clamp state. KorA thus stimulates repression by stalling KorB sliding at target promoters to occlude RNA polymerase holoenzymes. Altogether, our findings explain the mechanistic basis for KorB role-switching from a DNA-sliding clamp to a co-repressor, and provide a new paradigm for the long-range regulation of gene expression.

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McLean, T. C., Balaguer-Perez, F., Chandanani, J., Thomas, C. M., Aicart-Ramos, C., Burick, S., Olinares, P. D. B., Gobbato, G., Mundy, J. E. A., Chait, B. T., Lawson, D. M., Darst, S. A., Campbell, E. A., Moreno-Herrero, F., Le, T. B. K.. 2024-02-16. Molecular switching of a DNA-sliding clamp to a repressor mediates long-range gene silencing. https://doi.org/10.1101/2024.02.16.579611

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