Homologous recombination (HR) is an essential biological process that is involved in DNA repair and in the maintenance of genome integrity. In Escherichia coli, HR proceeds via two main pathways, RecBCD and RecFOR, which use different enzymes for DNA end resection and loading of RecA recombinase. In radioresistant bacterium Deinococcus radiodurans, the majority of double-strand DNA break (DSB) repair proceeds via two homology-driven processes, extended synthesis-dependent strand annealing and classical HR by crossovers, both of which require the RecA recombinase. We have recently identified two alternative recombination pathways: (i) the RecBCD- RecFOR-independent (RecBFI) recombination pathway that operates in sbcB15 sbcCD mutants of E. coli, in which the mutant SbcB15 protein act as a mediator of RecA filament assembly, and (ii) the alternative end-joining (A-EJ) that enables substantial but inaccurate RecA-independent DSB repair in D. radiodurans leading to gross genome rearrangements. In this project we aim to identify novel functions and conditions that facilitate RecBFI recombination pathway in E. coli and A-EJ pathway (and accompanying genome rearrangements) in D. radiodurans. The research will engage next-generation sequencing and advanced bioinformatic tools for (i) identification of suppressor mutations that facilitate RecBFI pathway in E. coli and (ii) identification of various types of genome rearrangements in D. radiodurans. In addition, genetic, molecular biology and cell biology (microscopy) approaches will be used to study the effect of different mutations of interest on bacterial growth, viability and DNA repair capacity as well as on chromosome morphology and segregation. Given that homologous recombination is a highly conserved process, our research on bacteria could be instructive for research on cancer and other human diseases associated with DNA recombination defects and genome rearrangements.

Publications

Zahradka K, Zahradka D, Repar J. Structural Differences between the Genomes of Deinococcus radiodurans Strains from Different Laboratories // Genes, 15 (2024) 847. https://doi.org/10.3390/genes15070847

Conference organization

EEMGS 2024 - 52nd European Environmental Mutagenesis and Genomics Society Meeting and 15th International Comet Assay Workshop, Rovinj, Croatia, 23-27 Sept 2024 // Zahradka K - Organizing and Scientific Committee member 

Conference participation

Repar J, Zahradka D, Zahradka K. DNA double-strand break repair and genome stability in the bacterium Deinococcus radiodurans // 52nd EEMGS and 15th ICAW Meeting, Rovinj, Croatia, 23-27 Sept 2024 - invited lecture by J. Repar

Repar J, Zahradka D, Zahradka K. New evidence for alternative end-joining mechanism of DNA double-strand break repair in Deinococcus radiodurans // 52nd EEMGS and 15th ICAW Meeting, Rovinj, Croatia, 23-27 Sept 2024 - poster

Other activities

Repar J. Accuracy of DNA repair and genome stability in Deinococcus radiodurans // Ruđer Bošković Institute, Zagreb, Croatia, 15 Oct 2024 - lecture

Kumek L, Božić F – participation in the HDIR workshop “Introduction to molecular modeling”, Ruđer Bošković Institute, Zagreb, December 2024.

Research group:

Davor Zahradka, PhD, Head of the Laboratory

Jelena Repar, PhD

Damir Đermić, PhD

Lucija Kumek, univ.mag.biol.mol.

Filip Božić, univ.mag.biol.mol.

Project duration: 28 Dec 2023 – 27 Dec 2027

Project funded by: Croatian Science Foundation