Swedish experiments show bacterial DNA repair completed in 15 minutes

DNA, the famous double-strand helix that holds the genetic code, can break either one or both strands. Double-stranded breaks can kill a cell or create an opportunity for cancerous growth if not repaired properly.

Fortunately, cells possess elaborate mechanisms for DNA repair, which work most of the time. The best studied of the double-strand repair systems is an enzyme complex called RecBCD that is found in Escherichia coli (E. coli) bacteria. 

Recently, a team of scientists at two universities in Sweden directly visualized how this enzyme complex searches and finds the broken strand, and then carries out the repair all within an average time of 15 minutes. 

The work was done by Jakub Wiktor, Arvid Gynnå, Prune Leroy, and Jimmy Larsson of Uppsala University, Sweden, and by Giovanna Coceano, Ilaria Testa, and Johan Elf of the KTH Royal Institute of Technology in Stockholm.

Their results appear Nov. 12 in the journal Nature.

How repair works

The process by which the enzyme complex finds and repairs the DNA break is called homologous recombination. 

To better study the mechanism, the researchers created a laboratory system utilizing a three-stage process to induce the double-strand break, visualize the location of the break with fluorescent tagging, and identify the cells undergoing repair.

First, the break is created by exposing the E. coli bacteria cells to an enzyme known as Cas9 nuclease that creates double strand breaks at a specific location on the chromosome called the “cut site.” The E. coli cells are grown in a “mother machine” which is a microfluidic device that allows for visualization of two different strains and switching of conditions.

Next the RecBCD enzyme complex binds to the ends of the DNA at the cut site of the double-strand break. The RecBCD enzyme causes the ParB proteins bound to nearby DNA to be thrown off and generates a single-stranded tail to which another important enzyme, RecA, binds. The binding induces the DNA repair response known as SOS.

The single-strand DNA filament bound up with the RecA enzyme now initiates the search process, looking for a homologous (similarly configured) structure on the genome. Once the match is made, the repair process can move to the next step.

Remarkable speed

The repair time in individual cells proved to be remarkably fast. The authors report the average repair time for a double-strand break of 15.2 ± 5.0 minutes. “These results were consistent between replicates, and notably, when I-SceI was used instead of Cas9 to induce breaks . . .” they note. I-Scel is another enzyme (nuclease) that can cause cleavage of the DNA strand.

Such a speed could not be explained if the repair depended upon the slow diffusion rates throughout the chromosome of the large complex molecule formed by the binding of RecA and single-strand DNA (RecA-ssDNA).

To explain the speed, the authors propose that the search is reduced from three to two dimensions by what they call a “reduced dimensional mechanism” that accelerates the process in two ways. 

“First, ATP hydrolysis enables mechanical extension of the RecA–ssDNA filament across the cell in less than a minute, rapidly covering most of the distance between the broken ends and the search target. . .” they wrote. 

“Second, the extended filament interacts with many different sequences in parallel," the team said. "Such simultaneous probing has previously been suggested on the basis of single-molecule experiments and cryo-electron microscopy structures.” 

“Our addition to the model,” they write, “is the realization that at any z coordinate [that is, along the long axis of the cell] there is always at least one segment of the stretched RecA–ssDNA filament that is homologous to a double-stranded DNA (dsDNA) segment at the same z position. This makes the search problem independent of the z coordinate and reduces the complexity from three to two dimensions." 

The team added, "The time of homology pairing is equal to the time it takes for a segment of chromosomal dsDNA to diffuse radially to the RecA–ssDNA filament, and not the time it takes for two segments to find each other by 3D diffusion in the whole cell. In this case, 2D search is approximately 100 times faster than 3D search. . .” 

The authors also suggest that this reduced dimensionality mechanism may be a “conserved property,” that is one that will be found in a variety of other organisms. This is partly what makes the paper so significant. In support of this hypothesis they note, “RecA is a prototypic member of the strand-exchange protein family, which is found in all forms of life and shares a common mechanism.” They add that long RecA structures have already been observed in two other bacterial species, Caulobacter crescentus and Bacillus subtilis.

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Jakub Wiktor et al. RecA finds homologous DNA by reduced dimensionality search. Nature (Nov. 12, 2021). DOI: https://doi.org/10.1038/s41586-021-03877-6