New Nucleic Acids Research paper: The RecBCD complex interacts directly with the DNA sliding clamp in Escherichia coli
Summary from the authors:
A tiny protein ring helps bacteria survive DNA damage
When the DNA inside a bacterium breaks, the cell has only a narrow window to find the break, repair it, and resume copying its genome before the damage becomes lethal. New research from our lab shows that a small ring-shaped protein at the heart of DNA copying, the β-clamp, plays a more direct role in this emergency repair than previously recognized. When we disrupt a single point of contact between the β-clamp and the cell's main break-repair machine, Escherichia coli becomes worse at surviving DNA damage.
Molecular docking stations
In all living cells, DNA must be copied accurately and repaired constantly. In bacteria, the β-clamp is a ring-shaped protein that encircles DNA and acts as a central "dock," holding DNA-copying enzymes in place and coordinating many steps of replication and repair. Its counterpart in human and other eukaryotic cells, PCNA, plays a similarly central role and is of growing interest as a target in cancer research.
Although β-clamp and PCNA share almost none of their amino acid sequence, they fold into near-identical 3D shapes: closed rings that encircle DNA and present small "docking pockets" on their surface. Many different proteins plug into these pockets using short sequence motifs, allowing the clamp to organize complex DNA-processing machines. This resemblance has long suggested that the bacterial β-clamp, like PCNA in eukaryotes, might help coordinate recombination-based repair, but a direct link had been missing.
A direct line to the repair machinery
In bacteria, broken DNA ends are processed by a different set of proteins, led by the RecBCD complex and the DNA strand-exchange protein RecA. Until now, β-clamp had not been tied directly to this pathway. Our study closes that gap. Using bacterial two-hybrid assays, co-immunoprecipitation, fluorescence microscopy, and NMR spectroscopy we show that β-clamp binds directly to RecB, one of the core subunits of RecBCD, through a specific clamp-binding motif in RecB's nuclease domain.
Notably, this contact does not appear to be permanent. It seems to form at a particular moment: when RecBCD reaches a "Chi site" on the DNA and switches into its recombination-promoting mode. In other words, the clamp engages the repair machine right when the cell commits to mending a break.
When we mutate the motif to break the interaction, RecBCD still assembles and retains its DNA-cutting activity, yet cells carrying the mutation are less able to survive after DNA damage. The contact is therefore not required for the machine to function, but it matters for the cell's ability to weather genotoxic stress.
A new layer of coordination
By revealing a direct physical link between β-clamp and RecBCD, our work points to an additional layer of coordination between DNA replication and DNA-break repair in bacteria — connecting the machinery that copies the genome with the machinery that mends it. The finding strengthens the parallel between bacterial and eukaryotic DNA-maintenance systems and raises new questions about how cells integrate copying and repair to protect their genomes.
The study was led by joint first authors Ida Mathilde Marstein Riisnæs and Synnøve Brandt Ræder, with collaborators at the University of Oslo, the Norwegian University of Science and Technology (NTNU), and the University of Copenhagen.
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Read the paper:
The RecBCD complex interacts directly with the DNA sliding clamp in Escherichia coli
Nucleic Acids Res, 54 (11)
DOI 10.1093/nar/gkag570, PubMed 42273914
OUS - Bacterial Defense Systems and Antimicrobial Resistance Group
Division of Laboratory Medicine