Dr. Ksenija Zahradka

Senior research associate

E-mail

Ksenija.Zahradka@irb.hr

Telephone

+385 1 456 0971

Internal phone number

1546

Department

Division of Molecular Biology

Laboratory

Laboratory for Molecular Microbiology

Address

Department of Molecular Biology
Ruđer Bošković Institute
Bijenička 54
10000 Zagreb
Croatia

Education

1991 B.Sc. in Molecular Biology, Faculty of Science, University of Zagreb, Croatia

1994 M.Sc. in Biology, Faculty of Science, University of Zagreb, Croatia

1999 Ph.D. in Biology, Faculty of Science, University of Zagreb, Croatia

2002 Postdoctoral training in the group of Prof. Miroslav Radman, Faculté de Médecine Necker, Université Paris-Descartes, Paris, France

Research Areas

Prirodne znanosti Biologija Mikrobiologija Biokemija i molekularna biologija Genetika, evolucija i filogenija

Specific research interests

DNA recombination and repair, genome stability and dynamics, molecular mechanisms of radiation resistance

Projects

2014-2018 "DNA recombination, repair and maintenance of genome integrity: new pathways", IP-11-2013-2978, Croatian Science Foundation ; associate

2011-2015 "Biology of Robustness", Mediterranean Institute for Life Sciences (MedILS), Split, Croatia; associate

2007-2013 "Molecular mechanisms of DNA recombination and repair" (098-0982913-2862), Croatian Ministry of Science, Education and Sports ; associate

2007-2010 "Life under extreme conditions", Mediterranean Institute for Life Sciences (MedILS), Split, Croatia; co-leader

Awards and Achievements

2007 National Annual Science Award, Croatian Parliament

2006 Excellence in Science Grant, Croatian Ministry of Science and Education

2002 Necker Institute Postdoctoral Fellowship, Paris, France

Classes

Course “Genetic recombination and DNA repair”, PhD studies in Biology, Faculty of Science, University of Zagreb

Course “Mechanisms of DNA damage and repair”, PhD studies in Molecular Biosciences, University of Osijek, University of Dubrovnik and Ruđer Bošković Institute, Zagreb

Featured Publications

Repar, J., Zahradka, D., Sović, I., Zahradka, K. (2021) Characterization of gross genome rearrangements in Deinococcus radiodurans recA mutants. Sci Rep. 11: 10939. doi: 10.1038/s41598-021-89173-9

Buljubašić, M., Hlevnjak, A., Repar, J., Đermić, D., Filić, V., Weber, I., Zahradka, K., Zahradka, D. (2019) RecBCD- RecFOR-independent pathway of homologous recombination in Escherichia coli. DNA Repair 83: 102670. doi: 10.1016/j.dnarep.2019.102670

Repar, J., Supek, F., Klanjscek, T., Warnecke, T., Zahradka, K., Zahradka, D. (2017) Elevated rate of genome rearrangements in radiation-resistant bacteria. Genetics 205: 1677-1689.

Buljubašić, M., Zahradka, D., Zahradka, K. (2013) RecQ helicase acts before RuvABC, RecG and XerC proteins during recombination in recBC sbcBC mutants of Escherichia coli. Res. Microbiol. 164: 987-997.

Buljubašić, M., Repar, J., Zahradka, K., Đermić, D., Zahradka, D. (2012) RecF recombination pathway in Escherichia coli cells lacking RecQ, UvrD and HelD helicases. DNA Repair 11: 419-430.

Repar, J., Cvjetan, S., Slade, D., Radman, M., Zahradka, D., Zahradka, K. (2010) RecA protein assures fidelity of DNA repair and genome stability in Deinococcus radiodurans. DNA Repair 9: 1151-1161.

Zahradka, K., Buljubašić, M., Petranović, M., Zahradka, D. (2009) Roles of ExoI and SbcCD nucleases in "reckless" DNA degradation in recA mutants of Escherichia coli. J. Bacteriol. 191: 1677-1687.

Petranovic, D., Michelsen, O., Zahradka, K., Silva, C., Petranovic, M., Jensen, P. R., Mijakovic, I. (2007) Bacillus subtilis strain deficient for the protein-tyrosine kinase PtkA exhibits impaired DNA replication. Mol. Microbiol. 63: 1797-1805.

Zahradka, K., Slade, D., Bailone, A., Sommer, S., Averbeck, D., Petranovic, M., Lindner, A. B., Radman, M. (2006) Reassembly of shattered chromosomes in Deinococcus radiodurans. Nature 443: 569-573.

Zahradka, K., Šimić, S., Buljubašić, M., Petranović, M., Đermić, D., Zahradka, D. (2006) sbcB15 and delsbcB mutations activate two types of RecF recombination pathway in Escherichia coli. J. Bacteriol. 188: 7562-7571.

Publications

Books and book chapters

Book chapters

Zahradka, K. & Zahradka, D. (2013) Reckless DNA Degradation. U: Maloy, S. & Hughes, K. (ur.) Brenner's Encyclopedia of Genetics (2nd ed.). San Diego (CA), Academic Press, str. 72-74 doi:10.1016/B978-0-12-374984-0.01272-9.
doi
Zahradka, K. (2007) Bacteriophage DNA extraction. U: Ambriović Ristov, A., Brozović, A., Bruvo Mađarić, B., Ćetković, H., Herak Bosnar, M., Hranilović, D., Katušić Hećimović, S., Meštrović Radan, N., Mihaljević, S., Slade, N. & Vujaklija, D. (ur.) Metode u molekularnoj biologiji. Zagreb, Institut Ruđer Bošković, str. 171-174.
Zahradka, D. & Zahradka, K. (2007) Gene transfer by P1 transduction. U: Ambriović Ristov, A., Brozović, A., Bruvo Mađarić, B., Ćetković, H., Herak Bosnar, M., Hranilović, D., Katušić Hećimović, S., Meštrović Radan, N., Mihaljević, S., Slade, N. & Vujaklija, D. (ur.) Metode u molekularnoj biologiji. Zagreb, Institut Ruđer Bošković, str. 919-922.
Zahradka, K. (2007) Pulsed-field gel electrophoresis (PFGE). U: Ambriović Ristov, A., Brozović, A., Bruvo Mađarić, B., Ćetković, H., Herak Bosnar, M., Hranilović, D., Katušić Hećimović, S., Meštrović Radan, N., Mihaljević, S., Slade, N. & Vujaklija, D. (ur.) Metode u molekularnoj biologiji. Zagreb, Institut Ruđer Bošković, str. 206-209.
Zahradka, K. (2007) Preparation of high-molecular weight genomic DNA for pulsed-field gel electrophoresis (PFGE). U: Ambriović Ristov, A., Brozović, A., Bruvo Mađarić, B., Ćetković, H., Herak Bosnar, M., Hranilović, D., Katušić Hećimović, S., Meštrović Radan, N., Mihaljević, S., Slade, N. & Vujaklija, D. (ur.) Metode u molekularnoj biologiji. Zagreb, Institut Ruđer Bošković, str. 189-191.
Zahradka, K. (2007) Genomic DNA extraction from bacterial cells. U: Ambriović Ristov, A., Brozović, A., Bruvo Mađarić, B., Ćetković, H., Herak Bosnar, M., Hranilović, D., Katušić Hećimović, S., Meštrović Radan, N., Mihaljević, S., Slade, N. & Vujaklija, D. (ur.) Metode u molekularnoj biologiji. Zagreb, Institut Ruđer Bošković, str. 141-143.

Journal articles

Scientific and review papers

Zahradka, K., Repar, J., Đermić, D. & Zahradka, D. (2023) Chromosome Segregation and Cell Division Defects in Escherichia coli Recombination Mutants Exposed to Different DNA-Damaging Treatments. Microorganisms, 11 (3), 11030701, 30 doi:10.3390/microorganisms11030701.
doiwww.mdpi.comfulir.irb.hr
Zahradka, K., Repar, J., Đermić, D. & Zahradka, D. (2022) Genetic analysis of transductional recombination in Escherichia coli reveals differences in the postsynaptic stages of RecBCD and RecFOR pathways. Periodicum biologorum, 124 (3-4), 97-106 doi:10.18054/pb.v124i3-4.23604.
doihrcak.srce.hrhrcak.srce.hrdoi.orgfulir.irb.hr
Repar, J., Zahradka, D., Sović, I. & Zahradka, K. (2021) Characterization of gross genome rearrangements in Deinococcus radiodurans recA mutants. Scientific reports, 11 (1), 10939, 11 doi:10.1038/s41598-021-89173-9.
doiwww.nature.comdoi.orgfulir.irb.hr
Buljubašić, M., Hlevnjak, A., Repar, J., Đermić, D., Filić, V., Weber, I., Zahradka, K. & Zahradka, D. (2019) RecBCD- RecFOR-independent pathway of homologous recombination in Escherichia coli. DNA repair, 83, 102670, 16 doi:10.1016/j.dnarep.2019.102670.
doi
Feliciello, I., Zahradka, D., Zahradka, K., Ivanković, S., Puc, N. & Đermić, D. (2018) RecF, UvrD, RecX and RecN proteins suppress DNA degradation at DNA double-strand breaks in Escherichia coli. Biochimie, 148, 116-126 doi:10.1016/j.biochi.2018.03.005.
doi
Repar, J., Supek, F., Klanjšček, T., Warnecke, T., Zahradka, K. & Zahradka, D. (2017) Elevated rate of genome rearrangements in radiation-resistant bacteria. Genetics, 205 (4), 1677-1689 doi:10.1534/genetics.116.196154.
doi
Repar, J., Šućurović, S., Zahradka, K., Zahradka, D. & Ćurković-Perica, M. (2013) Stress resistance of Escherichia coli and Bacillus subtilis is modulated by auxins. Canadian journal of microbiology, 59 (11), 766-770 doi:10.1139/cjm-2013-0266.
doi
Buljubašić, M., Zahradka, D. & Zahradka, K. (2013) RecQ helicase acts before RuvABC, RecG and XerC proteins during recombination in recBCD sbcBC mutants of Escherichia coli. Research in microbiology, 164 (10), 987-997 doi:10.1016/j.resmic.2013.08.008.
doi
Repar, J., Zahradka, D. & Zahradka, K. (2013) Accuracy of genome reassembly in gamma-irradiated Escherichia coli. Food technology and biotechnology, 51 (3), 327-337.
fulir.irb.hr
Repar, J., Briški, N., Buljubašić, M., Zahradka, K. & Zahradka, D. (2013) Exonuclease VII is involved in "reckless" DNA degradation in UV-irradiated Escherichia coli. Mutation research. Genetic toxicology and environmental mutagenesis, 750 (1/2), 96-104 doi:10.1016/j.mrgentox.2012.10.005.
doi
Buljubašić, M., Repar, J., Zahradka, K., Đermić, D. & Zahradka, D. (2012) RecF recombination pathway in Escherichia coli cells lacking RecQ, UvrD and HelD helicases. DNA repair, 11 (4), 419-430 doi:10.1016/j.dnarep.2012.01.011.
doi
Repar, J., Cvjetan, S., Slade, D., Radman, M., Zahradka, D. & Zahradka, K. (2010) RecA protein assures fidelity of DNA repair and genome stability in Deinococcus radiodurans. DNA repair, 9 (11), 1151-1161 doi:10.1016/j.dnarep.2010.08.003.
doi
Zahradka, K., Buljubašić, M., Petranović, M. & Zahradka, D. (2009) Roles of ExoI and SbcCD nucleases in "reckless" DNA degradation in recA mutants of Escherichia coli. Journal of bacteriology, 191 (5), 1677-1687 doi:10.1128/JB.01877-07.
doijb.asm.org
Petranović, D., Michelsen, O., Zahradka, K., Silva, C., Petranović, M., Jensen, P. & Mijaković, I. (2007) Bacillus subtilis strain deficient for the protein-tyrosine kinase PtkA exhibits impaired DNA replication. Molecular microbiology, 63 (6), 1797-1805 doi:10.1111/j.1365-2958.2007.05625.x.
doionlinelibrary.wiley.com
Zahradka, K., Slade, D., Bailone, A., Sommer, S., Averbeck, D., Petranović, M., Lindner, A. & Radman, M. (2006) Reassembly of shattered chromosomes in Deinococcus radiodurans. Nature, 443, 569-573 doi:10.1038/nature05160.
doiwww.nature.com
Zahradka, K., Šimić, S., Buljubašić, M., Petranović, M., Đermić, D. & Zahradka, D. (2006) sbcB15 and delsbcB mutations activate two types of RecF recombination pathway in Escherichia coli. Journal of bacteriology, 188 (21), 7562-7571 doi:10.1128/JB.00613-06.
doi
Zahradka, K., Zahradka, D., Đermić, D., Džidić, S. & Petranović, M. (2002) The inactivation of free phages in UV-irradiated Escherichia coli. Periodicum Biologorum, 104 (4), 399-403.
Zahradka, D., Zahradka, K., Džidić, S., Đermić, D. & Petranović, M. (2002) The rus-1 mutation suppresses cytological defects in recBC sbcBC ruv mutants of Escherichia coli. Periodicum Biologorum, 104 (4), 389-397.
Zahradka, D., Zahradka, K., Petranović, M., Đermić, D. & Brčić-Kostić, K. (2002) The RuvABC resolvase is indispensable for recombinational repair in sbcB15 mutants of Escherichia coli. Journal of bacteriology, 184 (15), 4141-4147 doi:10.1128/JB.184.15.4141-4147.2002.
doi
Petranović, M., Zahradka, K., Zahradka, D., Petranović, D., Nagy, B., Salaj-Šmic, E. & Petranović, D. (2001) Genetic evidence that the elevated levels of Escherichia coli helicase II antagonize recombinational DNA repair. Biochimie, 83 (11-12), 1041-1047 doi:10.1016/S0300-9084(01)01346-3.
doi
Paškvan, I., Salaj-Šmic, E., Ivančić-Baće, I., Zahradka, K., Trgovčević, Ž. & Brčić-Kostić, K. (2001) The genetic dependence of RecBCD-Gam mediated double strand end repair in Escherichia coli. FEMS microbiology letters, 205 (2), 299-303 doi:10.1111/j.1574-6968.2001.tb10964.x.
doiacademic.oup.com
Zahradka, K., Zahradka, D. & Petranović, M. (2001) Loss of lambda prophage recombinogenicity in UV-irradiated Escherichia coli : the role of host genes ruvA, ruvB, ruvC and recG. Research in microbiology, 152 (10), 873-881 doi:10.1016/S0923-2508(01)01270-0.
doi
Vlahović, K., Petranović, M., Zahradka, D. & Petranović, D. (2000) Progressive loss of lambda prophage recombinogenicity in UV-irradiated Escherichia coli : the role of RecBCD enzyme. Research in microbiology, 151 (9), 727-738 doi:10.1016/S0923-2508(00)01138-4.
doi
Petranović, M., Vlahović, K., Zahradka, D., Džidić, S. & Radman, M. (2000) Mismatch repair in Xenopus egg extracts is not strand-directed by DNA methylation. Neoplasma, 47 (6), 375-381.
Zahradka, D., Vlahović, K., Petranović, M. & Petranović, D. (1999) Chromosome segregation and cell division defects in recBC sbcBC ruvC mutants of Escherichia coli. Journal of bacteriology, 181 (19), 6179-6183 doi:10.1128/JB.181.19.6179-6183.1999.
doi
Vlahović, K., Petranović, M., Zahradka, D. & Petranović, D. (1998) Effects of ruv and recG mutations on lambda prophage thermoinducibility in UV-irradiated Escherichia coli. Periodicum biologorum, 100 (3), 383-388.

Theses

Doctoral dissertation

Vlahović, K. (1999) 'Genetic analysis of lambda prophage recombinogenicity in irradiated Escherichia coli', doktorska disertacija, Prirodoslovno-matematički fakultet, Zagreb.

Membership in professional associations / societies

European Environmental Mutagenesis and Genomics Society (EEMGS); 2015-2019 Croatian delegate

Croatian Genetic Society: 2019-2022 Secretary; since 2022 Vice-president

Croatian Microbiological Society

Croatian Society for Biochemistry and Molecular Biology

Chair of the Knowledge and Discovery Council, Adris Foundation, Croatia (since 2015)

Scientific Board member of the Mediterranean Institute for Life Sciences (MedILS), Split, Croatia

Vice-president of the Scientific Council of Biology, Ruđer Bošković Institute, Zagreb, Croatia (2016-2022)

Mentorships

Supervisor of PhD theses:

Jelena Repar: "Fidelity of DNA repair in Υ-irradiated cells of Deinococcus radiodurans", Faculty of Science, University of Zagreb, 2012.

Svjetlana Cvjetan: "Radiation-induced chromosomal rearrangements in Deinococcus radiodurans cells: the role of insertion sequences and RecA protein", Faculty of Science, University of Zagreb, 2013.

Supervisor of diploma theses:

Sanela Šimić: "Effects of sbcB15 and ΔsbcB mutations on recombinational repair in recBC mutants of Escherichia coli", Faculty of Pharmacy and Biochemistry, University of Zagreb, 2006.

Marijana Vukić: "Genetic instability in Deinococcus radiodurans recA mutants", Faculty of Pharmacy and Biochemistry, University of Zagreb, 2010.

Lidija Dobša: "DNA repair in stationary phase Deinococcus radiodurans cells", Faculty of Pharmacy and Biochemistry, University of Zagreb, 2010.

Ana Hleb: "Genome rearrangements in Deinococcus radiodurans: the role of RecG protein", Faculty of Agriculture, University of Zagreb, 2018.

Organisation of scientific meetings:

4th Congress of Croatian Geneticists with international participation, Krk, Croatia, 2018 – Scientific Committee member
3^rd Congress of Croatian Geneticists with international participation, Krk, Croatia, 2012 – Scientific Committee member
"Power of Microbes in Industry and Environment 2010" - Central European Symposium on Industrial Microbiology and Microbial Ecology, Malinska, Croatia, 2010 - Organizing Committee member
10^th International Summer School in Biophysics "Supramolecular Structure and Function", Rovinj, 2009 - Organizing Committee member and Editor of the Book of Abstracts
10^th Croatian Biological Congress with international participation, Osijek, Croatia, 2009 – Scientific Committee and Organizing Committee member
Scientific Symposium "50 Years of Molecular Biology in Croatia", Zagreb, 2008 - President of the Organizing Committee and Editor of the Book of Abstracts
9^th Croatian Biological Congress with international participation, Rovinj, Croatia, 2006 – Scientific Committee member
Scientific Symposium "45 Years of Molecular Biology in Croatia and 50 Years of Double Helix", Zagreb, Croatia, 2003 - Organizing Committee member

Invited lectures at international scientific meetings:

HDBMB2008 – Congress of the Croatian Society of Biochemistry and Molecular Biology with International Participation, Osijek, Croatia, 2008; title: "DNA repair in radiation resistant bacterium Deinococcus radiodurans"
MedILS Summer School 2008 "Life in Extreme Conditions", Split, Croatia, 2008; title: "Survival of Deinococcus radiodurans in extreme environments"
7^th Symposium of the Croatian Radiation Protection Association with International Participation, Opatija, Croatia, 2008; title: "Deinococcus radiodurans - a radiation resistant bacterium"
Power of Microbes in Industry and Environment 2007 - Central European Symposium on Industrial Microbiology and Microbial Ecology, Zadar, Croatia, 2007; title: "Survival of Deinococcus radiodurans in extreme conditions: genome restoration by recombination"
MedILS Summer School 2007 “Surviving death – an interdisciplinary approach workshop“, Split, Croatia, 2007; title: "DNA repair in Deinococcus radiodurans: surviving extreme life conditions"
9^th Croatian Biological Congress with International Participation, Rovinj, Croatia, 2006; title: "DNA repair in Deinococcus radiodurans: from hundreds of fragments to the functional chromosomes"
1^st Central European Forum for Microbiology (CEFORM), Keszthely, Hungary, 2005; title: "Deinococcus radiodurans: the most efficient DNA repair involves coupled replication and recombination processes"
3^rd Croatian Congress of Microbiology with International Participation, Poreč, Croatia, 2004; title: "Reconstitution of Deinococcus radiodurans genome after gamma irradiation"

Granted patent:

PCT/EP2006/005826 (10/05/2006) "Process for chromosomal engineering using a novel DNA repair system", M. Radman and K. Zahradka inventors.