2025 as a significant year for the DNA Repair and Replication Research Center
The year 2025 will be a breakthrough for us – says dr Karol Kramarz, head of the Incubator of Scientific Excellence – Research Centre for DNA Repair and Replication at the Faculty of Biological Sciences of University of Wrocław, with whom we talk about the research successes of the Incubator and future plans.
Ewelina Kośmider: The Incubator of Scientific Excellence – DNA Repair and Replication Research Center, started operating over 3 years ago, can you tell what it does?
Dr Karol Kramarz: The incubator was established on October 1, 2021. The team of the Incubator of Scientific Excellence – Research Center for DNA Repair and Replication is implementing a project entitled Decoding SUMO-interactions at replication stress sites: mechanisms and consequences for genome maintenance. Overall, this project aims to describe the mechanisms of specific modification of proteins, called SUMOilation, at sites of replication stress, i.e. the directly disturbed process of duplication of genetic material. In addition, during the functioning of the team, we undertook a number of new research axes, ultimately to enable us to obtain external funds for financing future projects.
E.K.: What research goals have you achieved so far?
Dr Karol Kramarz: The most important task set for me, as the head of the Incubator, after I was awarded funding, was to create a new research unit at the Faculty of Biological Sciences – a well-coordinated team composed of young scientists in the early stages of their scientific careers. Together with dr Ireneusz Litwin and dr Katarzyna Markowska, who were part of the incubator. We began the tedious process of introducing and optimizing techniques related to the use of our favorite model organism, the cleft yeast Schizosaccharomyces pombe. After completing the necessary equipment and implementing research methods, we began to achieve the goals set in the incubator project. Currently, the team also includes mgr Aleksandra Broczkowska, an independent biologist, PhD student Dorota Misiorna, MA student Julia Kończak and MA student Mika Haenen. Who is a student from the Belgian Katholieke Universiteit Leuvem, contributing to this research project in my team as part of the Erasmus+ educational program.
E.K.: First, could you please explain what SUMO is? Since it is the subject of your research.
Dr Karol Kramarz: SUMO, or “small ubiquitin like modifier” is a small signaling protein, similar to ubiquitin, present in both single-celled yeast and human cells.
E.K.: Is that signal protein acting as an information carrier?
Dr Karol Kramarz: Yes, signaling proteins carry information about intracellular or intercellular signaling. SUMO molecules, when attached to target proteins involved in DNA metabolism, can modify the functions of these proteins, affect their location or possibly direct them towards degradation. In this context, it can be assumed that SUMO molecules carry information about the fate of target proteins. SUMO can be attached as single molecules, but it can also form polymeric chains. SUMOylation is crucial for cell survival, modulating a variety of cellular processes, including DNA metabolism – duplication and repair. In humans, it has been shown that disorders in the SUMOilation may come from cancer. Despite the fact that more than 30 years have passed since the discovery of SUMOilation in baker’s yeast cells. The SUMO mechanisms are the subject of research by numerous teams around the world, many aspects of this modification still remain poorly understood. Our research aims, among other things, to describe the impact of the formation of SUMO polymeric chains – until now, it was thought that these chains were only a signal for the degradation of modified proteins. However, the analyses carried out by our team suggest that the role of SUMO chains is much broader and affects, among other things, maintaining the genetic stability of difficult-to-replicate genome sites, such as centromeres, through the appropriate recruitment of repair enzymes, including homologous recombination proteins. The manuscript in which we present the results of this research is currently in the review process, we are at the stage of preparing a comprehensive response to the reviewers’ comments and soon we will send a modified work to the editors, supplemented with a number of new analyses. By “soon” I mean about 3-4 months, due to the introduction of further techniques and the preparation of an adequate response to the reviewers’ comments.
In addition, as I have already mentioned, we have started the implementation of several new research axes. In 2023, dr Ireneusz Litwin received an OPUS24 research grant entitled Map of DNA damage and repair processes induced by arsenic in the amount of PLN 2,199,660. Dr Katarzyna Markowska has started a new project using catalytically inactive Cas9 nuclease (dCas9) as a tool for producing a specific replication blockade under IDUB internal grants. I also submitted the OPUS28 grant myself, the results will be announced in the upcoming months.
E.K.: How is the long-planned cooperation with the Institute Curie in France going? What has it achieved; what contribution has the Institute Curie made to your achievements?
Dr Karol Kramarz: Cooperation with the Institute Curie, where I did my postdoctoral internship, has been very fruitful after my return to the University of Wrocław. Back in 2021, together with dr Sara Lambert, we published a review paper in which we summarized the current state of knowledge about the movement of various DNA damages inside cell nuclei, in particular emphasizing the regulatory role of SUMOylation for the above processes. In mid 2024, an article was published, in the prestigious journal Nucleic Acids Research, about my scientific research while I was still employed at the Institute Curie, work which was continued by Sara Lambert’s team. I did some of my research at the University of Wrocław as part of the Incubator of Scientific Excellence. The publication of this article was possible thanks to the joint coordination of research between Sara Lambert’s team, the Incubator of Scientific Excellence and the group of prof. Antoni Carr from University of Sussex in England. This work shows the role of removal of SUMOylated proteins by enzymes located on the nuclear envelope (the cell membrane separating the nucleus from the cytoplasm) for the resumption of DNA synthesis during replication disorders. In this way, we were able to answer, at least to some extent, the open questions posed in the 2021 review article.
These are the most visible benefits of our cooperation so far, and a very important aspect in the exchange of information and discussion on various research axes. Undertaken both in dr Lambert’s group and in the Incubator run by me. We try to maintain regular contact, not only via international conferences, but also in the form of direct visits. In September 2023, Sarah Lambert visited Wrocław and our University. In addition to the opportunity to listen to her lecture by the staff, it was a chance for us to establish the main research strategy for the project, which eventually ended with the publication in Nucleic Acids Research. Sara Lambert’s visit in Wrocław was also her first trip to Poland, which fills us with hope to build a positive image of our country among foreigners. On the other hand, I visited the Institute Curie three times (2022-2024), while participating in doctoral defenses of students whom I had the pleasure of training and supervising during my postdoctoral internship. As for the contribution of the Institute Curie to the research objectives of the Incubator of Scientific Excellence – Research Centre for DNA Repair and Replication, we take advantage of the opportunity to consult and discuss problematic results together with internationally recognized experts. We have plans to meet dr Lambert again in the future, both on the occasion of participation in international scientific conferences and direct visits, which allows us to carry out future projects together.
E.K.: When you created the incubator, you tried to create such cooperation within the University of Wrocław. With whom did you work? To what extent? What were the fruits of this cooperation?
Dr Karol Kramarz: At the University, we are actively cooperating with the Department of Genetics and Cell Physiology of prof. Robert Wysocki at the Faculty of Biological Sciences, which enabled us to publish our research in the journal Nucleic Acids Research in 2023 on the effect of the Isw1 chromatin remodeler on the organization of cohesion in baking yeast centromeres. On the other hand, I have been working for many years with dr Dorota Dziadkowiec from the Faculty of Biotechnology. In 2022, we wrote a review paper together on collaborative research on DNA translocases – enzymes that remodel chromatin in response to replication stress. In early 2024, we published a study on the modulation of replication stress responses in cleft yeast. In addition, I am the assistant supervisor of PhD student Dorota Misiorna together with dr Dziadkowiec, which strengthens our cooperation in the long run. We are currently preparing a manuscript about our research; I think it will be reviewed by this summer.
E.K.: What research methods did you use?
Dr Karol Kramarz: First, due to incomplete information on modified substrates at sites where DNA replication stops or is damaged, we have introduced a molecular technique (called SUMO-ID) that enables the analysis of SUMOylation at the sites of DNA repair. This allows the identification of SUMO-regulated proteins on a mass spectrometer. This is a method that allows the analysis of the composition of the so-called ‘clouds’ of SUMOilation – the group attachment of SUMO molecules at DNA repair sites.
Second, we have introduced chromatin immunoprecipitation techniques combined with next-generation sequencing for regular use. This gives the opportunity to visualize the interaction of the studied proteins with DNA in the context of the entire genome, which significantly expands our initial analyses using the classic quantitative PCR (polymerase chain reaction) method.
We were able to introduce and optimize the technique of bidirectional DNA electrophoresis. It is a method that allows imaging of DNA replication occurring at selected sites in the genome. Importantly, it is an advanced molecular biology technique used by only a few laboratories in the world, mainly due to its complexity. During my postdoctoral internship, I learned how to make 2D gels, which made it possible to introduce this technique to regular use in the Incubator of Scientific Excellence at the University of Wrocław.
E.K.: The aim of the Incubators of Scientific Excellence is to “measurably increase scientific achievements in research areas that have less international recognition in the scale of the University of Wrocław”, have you already achieved this goal?
Dr Karol Kramarz: As the project is still ongoing, the goal of increasing scientific achievement is still in the making. So far, we have completed several projects that have resulted in publications in prestigious international journals, we have also participated in a number of top scientific conferences where we directly represented the University of Wrocław, including in Lisbon, Portugal in 2023 at the 23rd Recombination Mechanisms Conference, as well as in Leiden, the Netherlands at the EMBO Workshop Chromatin dynamics and nuclear organization in genome maintenance in 2024.
As I mentioned earlier, the manuscript that is the result of the work of the Incubator team is currently under review, after the first round of reviewers’ comments. In addition, one of the projects we are carrying out in cooperation with the laboratory of ERC Starting 2022 grant winner, Dr. Marcin Suskiewicz from Orléans, France, is the analysis of Ctp1 endonuclease SUMOilation in the regulation of replication stress responses. It is worth mentioning that in 2023, dr Litwin went on a two-month internship to Orléans, where he successfully performed biochemical analyses on purified Ctp1, which allowed him to show the SUMOylation of Ctp1 in vitro. This also increases the international recognition of the University of Wrocław.
E.K.: What are your plans for this year?
Dr Karol Kramarz: The year 2025 will be a breakthrough for us – not only are we finalizing one of the main research axes – successfully I hope, but we are also on the verge of completing the Incubator of Scientific Excellence project. The coming months will be decisive for the further fate of the Research Center I have built. Much will depend on me obtaining new funding for research projects resulting directly from the implementation of the Incubator’s tasks. I also hope to be active in contacts with foreign colleagues and participate in international conferences.
E.K.: Thank you very much for the interview and good luck.
Strona internetowa Inkubatora Doskonałości Naukowej – Centrum Badawczego Naprawy DNA i Replikacji
Date of publication: 29.01.2025
Added by E.K.
Translated by Szymon Pachurka (student of English Studies at the University of Wrocław) as part of the translation practice.
