Frequent template switching in postreplication gaps: suppression of deleterious consequences by the Escherichia coli Uup and RadD proteins

• Published in: Nucleic acids research 2020-01, Vol.48 (1), p.212-230
• Main Authors: Romero, Zachary J, Armstrong, Thomas J, Henrikus, Sarah S, Chen, Stefanie H, Glass, David J, Ferrazzoli, Alexander E, Wood, Elizabeth A, Chitteni-Pattu, Sindhu, van Oijen, Antoine M, Lovett, Susan T, Robinson, Andrew, Cox, Michael M
• Format: Article
• Language: English
• Subjects: Adenosine Triphosphatases - deficiency; Adenosine Triphosphatases - genetics; Anti-Bacterial Agents - pharmacology; ATP-Binding Cassette Transporters - deficiency; ATP-Binding Cassette Transporters - genetics; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Ciprofloxacin - pharmacology; DNA Replication; DNA, Bacterial - genetics; DNA, Bacterial - metabolism; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Drug Resistance, Bacterial - genetics; Escherichia coli - drug effects; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins - genetics; Gene Expression Regulation, Bacterial; Genome Integrity, Repair and; Genome, Bacterial; Plasmids - chemistry; Plasmids - metabolism; Replication Origin; Sequence Deletion
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkz960

Abstract When replication forks encounter template DNA lesions, the lesion is simply skipped in some cases. The resulting lesion-containing gap must be converted to duplex DNA to permit repair. Some gap filling occurs via template switching, a process that generates recombination-like branched DNA intermediates. The Escherichia coli Uup and RadD proteins function in different pathways to process the branched intermediates. Uup is a UvrA-like ABC family ATPase. RadD is a RecQ-like SF2 family ATPase. Loss of both functions uncovers frequent and RecA-independent deletion events in a plasmid-based assay. Elevated levels of crossing over and repeat expansions accompany these deletion events, indicating that many, if not most, of these events are associated with template switching in postreplication gaps as opposed to simple replication slippage. The deletion data underpin simulations indicating that multiple postreplication gaps may be generated per replication cycle. Both Uup and RadD bind to branched DNAs in vitro. RadD protein suppresses crossovers and Uup prevents nucleoid mis-segregation. Loss of Uup and RadD function increases sensitivity to ciprofloxacin. We present Uup and RadD as genomic guardians. These proteins govern two pathways for resolution of branched DNA intermediates such that potentially deleterious genome rearrangements arising from frequent template switching are averted.