Compartmentalization of the replication fork by single-stranded DNA-binding protein regulates translesion synthesis

• Published in: Nature structural & molecular biology Vol. 29; no. 9; pp. 932 - 941
• Main Authors: Chang, Seungwoo, Thrall, Elizabeth S., Laureti, Luisa, Piatt, Sadie C., Pagès, Vincent, Loparo, Joseph J.
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.09.2022; Nature Publishing Group
• Subjects: 14; 14/35; 631/337/151; 631/337/151/2356; 631/45/147; 692/699; 82; Addition polymerization; Biochemistry; Biological Microscopy; Biomedical and Life Sciences; Chemical synthesis; Clamps; Clips; Deoxyribonucleic acid; DNA; DNA - metabolism; DNA biosynthesis; DNA polymerase; DNA Replication; DNA-binding protein; DNA-Binding Proteins - metabolism; DNA-directed DNA polymerase; DNA-Directed DNA Polymerase - metabolism; E coli; Enrichment; Escherichia coli - genetics; Escherichia coli - metabolism; Genomes; Life Sciences; Membrane Biology; Protein biosynthesis; Protein Structure; Proteins; Replication; Replication forks; Single-stranded DNA; Single-stranded DNA-binding protein; Stalling
• ISSN: 1545-9993; 1545-9985; 1545-9985
• DOI: 10.1038/s41594-022-00827-2

Processivity clamps tether DNA polymerases to DNA, allowing their access to the primer–template junction. In addition to DNA replication, DNA polymerases also participate in various genome maintenance activities, including translesion synthesis (TLS). However, owing to the error-prone nature of TLS polymerases, their association with clamps must be tightly regulated. Here we show that fork-associated ssDNA-binding protein (SSB) selectively enriches the bacterial TLS polymerase Pol IV at stalled replication forks. This enrichment enables Pol IV to associate with the processivity clamp and is required for TLS on both the leading and lagging strands. In contrast, clamp-interacting proteins (CLIPs) lacking SSB binding are spatially segregated from the replication fork, minimally interfering with Pol IV-mediated TLS. We propose that stalling-dependent structural changes within clusters of fork-associated SSB establish hierarchical access to the processivity clamp. This mechanism prioritizes a subset of CLIPs with SSB-binding activity and facilitates their exchange at the replication fork. Escherichia coli SSB enriches Pol IV polymerase at lesion-stalled replication forks, promoting translesion synthesis. Loss of this enrichment increases repriming of DNA synthesis, revealing a pivotal role of SSB in the pathway choice of stalled replication forks.