Dbf4-dependent kinase promotes cell cycle controlled resection of DNA double-strand breaks and repair by homologous recombination

Lorenzo Galanti, Martina Peritore, Robert Gnügge, Elda Cannavo, Johannes Heipke, Maria Dilia Palumbieri, Barbara Steigenberger, Lorraine S. Symington, Petr Cejka and Boris Pfander ()
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Lorenzo Galanti: TU Dortmund University, Faculty of Chemistry and Chemical Biology
Martina Peritore: Max Planck Institute of Biochemistry
Robert Gnügge: Columbia University Irving Medical Center
Elda Cannavo: Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI)
Johannes Heipke: TU Dortmund University, Faculty of Chemistry and Chemical Biology
Maria Dilia Palumbieri: Institute of Aerospace Medicine, German Aerospace Center (DLR)
Barbara Steigenberger: Max Planck Institute of Biochemistry
Lorraine S. Symington: Columbia University Irving Medical Center
Petr Cejka: Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI)
Boris Pfander: TU Dortmund University, Faculty of Chemistry and Chemical Biology

Nature Communications, 2024, vol. 15, issue 1, 1-19

Abstract: Abstract DNA double-strand breaks (DSBs) can be repaired by several pathways. In eukaryotes, DSB repair pathway choice occurs at the level of DNA end resection and is controlled by the cell cycle. Upon cell cycle-dependent activation, cyclin-dependent kinases (CDKs) phosphorylate resection proteins and thereby stimulate end resection and repair by homologous recombination (HR). However, inability of CDK phospho-mimetic mutants to bypass this cell cycle regulation, suggests that additional cell cycle regulators may be important. Here, we identify Dbf4-dependent kinase (DDK) as a second major cell cycle regulator of DNA end resection. Using inducible genetic and chemical inhibition of DDK in budding yeast and human cells, we show that end resection and HR require activation by DDK. Mechanistically, DDK phosphorylates at least two resection nucleases in budding yeast: the Mre11 activator Sae2, which promotes resection initiation, as well as the Dna2 nuclease, which promotes resection elongation. Notably, synthetic activation of DDK allows limited resection and HR in G1 cells, suggesting that DDK is a key component of DSB repair pathway selection.

Date: 2024
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DOI: 10.1038/s41467-024-46951-z

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