Deciphering the mechanism of processive ssDNA digestion by the Dna2-RPA ensemble

• Published in: Nature communications Vol. 13; no. 1; p. 359
• Main Authors: Shen, Jiangchuan, Zhao, Yiling, Pham, Nhung Tuyet, Li, Yuxi, Zhang, Yixiang, Trinidad, Jonathan, Ira, Grzegorz, Qi, Zhi, Niu, Hengyao
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 18.01.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 631/337/1427/2190; 631/45/147; Biocatalysis; Cell Survival - drug effects; Cell viability; Deoxyribonucleic acid; Digestion; DNA; DNA biosynthesis; DNA Breaks, Double-Stranded; DNA Helicases - metabolism; DNA Repair; DNA, Fungal - metabolism; DNA, Single-Stranded - metabolism; Double-strand break repair; Endonuclease; Humanities and Social Sciences; Integrity; Intermediates; Metabolic pathways; Models, Biological; multidisciplinary; Mutation - genetics; Nuclease; Peptides - metabolism; Phleomycins - pharmacology; Protein Binding; Protein Domains; Repair; Replication Protein A - metabolism; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - metabolism; Science; Science (multidisciplinary); Single-stranded DNA; Tyrosine - metabolism; Yeast; Yeasts
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-27940-y

Single-stranded DNA (ssDNA) commonly occurs as intermediates in DNA metabolic pathways. The ssDNA binding protein, RPA, not only protects the integrity of ssDNA, but also directs the downstream factor that signals or repairs the ssDNA intermediate. However, it remains unclear how these enzymes/factors outcompete RPA to access ssDNA. Using the budding yeast Saccharomyces cerevisiae as a model system, we find that Dna2 — a key nuclease in DNA replication and repair — employs a bimodal interface to act with RPA both in cis and in trans. The cis-activity makes RPA a processive unit for Dna2-catalyzed ssDNA digestion, where RPA delivers its bound ssDNA to Dna2. On the other hand, activity in trans is mediated by an acidic patch on Dna2, which enables it to function with a sub-optimal amount of RPA, or to overcome DNA secondary structures. The trans-activity mode is not required for cell viability, but is necessary for effective double strand break (DSB) repair. RPA protects the integrity of single stranded DNA during DNA repair processes. Here the authors show how RPA actively participates in DNA transactions through its interactions with the endonuclease Dna2.