Recombination-dependent DNA replication



Silvia Ayora Hirsch

Group Leader



Research summary

We are analyzing how a replication fork is reassembled, and how replication can restart by a recombination-dependent mechanism, using Bacillus subtilis and its bacteriophage SPP1. In these two models, the outcome of the recombination-dependent replication is different, as in the bacteria the product is replication restart by a theta mechanism, whereas in SPP1, replication restart leads to concatemeric DNA synthesis which is the substrate for viral DNA packaging.



Neamah MM, Mir-Sanchis I, López-Sanz M, Acosta S, Baquedano I, Haag AF, Marina A, Ayora S, Penadés JR. Sak and Sak4 recombinases are required for bacteriophage replication in Staphylococcus aureus. Nucleic Acids Res. 2017 May 5. doi: 10.1093/nar/gkx308.

Condezo GN, Marabini R, Ayora S, Carazo JM, Alba R, Chillón M, San Martín C. Structures of Adenovirus Incomplete Particles Clarify Capsid Architecture and Show Maturation Changes of Packaging Protein L1 52/55k. J Virol 2015; 89: 9653-9664

Lioy VS, Volante A, Soberón NE, Lurz R, Ayora S, Alonso JC. ParAB Partition Dynamics in Firmicutes: Nucleoid Bound ParA Captures and Tethers ParB-Plasmid Complexes. PLoS One 2015; 10: e0131943

Vlasic I, Mertens R, Seco EM, Carrasco B, Ayora S, Reitz G, Commichau FM, Alonso JC, Moeller R. Bacillus subtilis RecA and its accessory factors, RecF, RecO, RecR and RecX, are required for spore resistance to DNA double-strand break. Nucl Acids Res 2014; 42:2295-230

Cañas C, Suzuki Y, Marchisone C, Carrasco B, Freire-Benéitez V, Takeyasu K, Alonso JC, Ayora S. Interaction of branch migration translocases with the Holliday junction-resolving enzyme and their implications in Holliday junction resolution. J Biol Chem 2014; 289:17634-1764


FigAyora1Our research focuses on the mechanisms that cells use to continue DNA replication when this process encounters impediments that can collapse the fork, producing a broken DNA end. Replication restart is then mediated by proteins that were initially identified by their roles in homologous recombination and repair of DNA double-strand breaks (DSB). We use a simple model system, Bacillus subtilis and its bacteriophage SPP1, and several biophysical, structural and molecular biology techniques to study the recombination mechanisms that lead to replication restart.

A central step in the recombination reaction is the resolution of the recombination intermediate. Using single molecule analysis, we analysed the cleavage preference of the RecU Holliday junction-resolving enzyme, and how it is modulated by other proteins such as the branch migration helicases RecG and RuvAB. Our results can be extended to other systems and the method developed should be applicable for the study of mechanisms used by other junction-binding enzymes involved in branch migration and junction resolution of the recombination intermediate.

We have reconstituted the replisomes of phage SPP1 and its host B. subtilis in vitro, and analysed the effect of recombination proteins in DNA replication in vitro. RecA slightly affects DNA replication in vitro, and RecO addition facilitates RecA-mediated inhibition of DNA synthesis. These results will be further analysed in the next few years. They suggest that RecA might prevent potentially dangerous forms of DNA repair that occur during replication.






Silvia Ayora Hirsch Principal investigator
Elena M. Seco Senior scientist
María López Sanz Technician

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