Piotr Gerlach, PhD
Laboratory of Structural Virology
ORCID: 0000-0001-9599-7322
- RESEARCH
- MEMBERS OF THE GROUP
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Research interests
Translation is one of the major sites of the virus-host battlefront. On one hand, infected cell shuts down most of the translation, activating at the same time innate immune and integrated stress response pathways. At the same time, RNA viruses, being unconditionally dependent on cellular protein synthesis machinery, use a range of strategies to reorganize and exploit cellular translation, forcing ribosomes to translate viral mRNA. We are particularly interested in bunyaviruses – a large and understudied group of segmented, negative-strand RNA viruses. Three of them – Lassa, Rift Valley, and Crimean-Congo viruses, causing high fatality rate haemorrhagic fevers, are listed by WHO among eight pathogens that may cause future pandemics. Given the lack of vaccines and specific antivirals against bunyaviruses, there is a need to explore their molecular repertoire in order to fully understand their infection mechanisms and thus to raise our preparedness against this threat.
Upon infecting the cell, bunyaviruses release into the cytoplasm their viral ribonucleoproteins (vRNPs). Each vRNP contains an RNA genomic segment coated with nucleoproteins (N proteins) and attached to a single, multifunctional, RNA-dependent RNA polymerase (L protein). Bunyaviral vRNPs initiate the transcription of the viral genomic segments into mRNAs by cap-snatching the cytoplasmic host 5′-capped mRNA and by subsequent coupling of the viral transcription with the ongoing translation. Our goal is to unravel molecular details of this unique viral translation strategy. We hypothesize that bunyaviral RNA polymerase hijacks entire translation initiation complex during the cap-snatching step. This in consequence would lead to formation of a direct contact between the transcribing viral polymerase and the leading ribosome, unprecedented in the eukaryotic system. Moreover, we are exploring how the structural elements within the bunyaviral mRNA 5′ and 3′ UTRs mediate translation.
We use a modified mini-replicon system, mimicking bunyaviral transcription and replication inside the cell, in order to identify host factors involved in the bunyaviral transcription and translation, and to monitor changes in the cellular translation landscape. In parallel, we use cryo-EM to visualize viral-host complexes formed at different steps of the bunyaviral mRNA lifetime. We believe that output of our research will open new avenues in the RNA virus field and set the basis for the design of innovative therapies and broad-spectrum antivirals.
Members of the group
| Name | Surname | Degree | |||||
| Eliana | Dukhno | e.dukhno@imol.institute | |||||
| Moh Egy Rahman | Firdaus | f.rahman@imol.institute | |||||
| Piotr | Gerlach | PhD | p.gerlach@imol.institute | ||||
| Rupali | Kapoor | r.kapoor@imol.institute |
Publications
- Zakrzewski, M., Sas, Z., Cocom-Chan, B., Firdaus, M. E. R., Kałek, M., Szczepanowska, K., Gerlach, P., Marusiak, A., & Serwa, R. A. (2025). Profiling polyamine-protein interactions in live cells through photoaffinity labeling. RSC chemical biology, 10.1039/d5cb00103j. Advance online publication. https://doi.org/10.1039/d5cb00103j
- Firdaus, M. E. R., Dukhno, E., Kapoor, R., & Gerlach, P. (2025). Two Birds With One Stone: RNA Virus Strategies to Manipulate G3BP1 and Other Stress Granule Components. Wiley interdisciplinary reviews. RNA, 16(2), e70005. https://doi.org/10.1002/wrna.70005
- Polák P, Garland W, Rathore O, Schmid M, Salerno-Kochan A, Jakobsen L, Gockert M, Gerlach P, Silla T, Andersen JS, Conti E, Jensen TH. Dual agonistic and antagonistic roles of ZC3H18 provide for co-activation of distinct nuclear RNA decay pathways. Cell Rep (2023) 42:113325, doi.org/10.1016/j.celrep.2023.113325
- Gerlach P, Garland P, Lingaraju M, Salerno-Kochan M, Bonneau F, Basquin J, Jensen TH & Conti E. Structure and regulation of the Nuclear Exosome Targeting Complex guides RNA substrates to the exosome. Mol Cell (2022) 82: 2505-2518, doi.org/10.1016/j.molcel.2022.04.011
- Arragain B, Effantin G, Gerlach P, Reguera J, Schoehn G, Cusack S & Malet H. Pre-initiation and elongation structures of full-length La Crosse virus polymerase reveal functionally important conformational changes. Nat Commun (2020) 11: 3590, doi.org/10.1038/s41467-020-17349-4
- Lingaraju M, Schuller JM, Falk S, Gerlach P, Bonneau F, Basquin J, Benda C & Conti E (2020) To Process or to Decay: A Mechanistic View of the Nuclear RNA Exosome. Cold Spring Harb Symp Quant Biol (2019) 84: 155-163, doi.org/10.1101/sqb.2019.84.040295
- Gerlach P, Schuller JM, Bonneau F, Basquin J, Reichelt P, Falk S & Conti E. Distinct and evolutionary conserved structural features of the human nuclear exosome complex. eLife (2018) 7: e38686, doi.org/10.7554/eLife.38686.001
- Reguera J, Gerlach P, Rosenthal M, Gaudon S, Coscia F, Günther S & Cusack S. Comparative structural and functional analysis of bunyavirus and arenavirus cap-snatching endonucleases. PLoS Pathog (2016) 12: e1005636, doi.org/10.1371/journal.ppat.1005636
- Reguera J, Gerlach P & Cusack S. Towards a structural understanding of RNA synthesis by negative strand RNA viral polymerases. Curr Opin Struct Biol (2016) 36: 75-84, doi.org/10.1016/j.sbi.2016.01.002
- Gerlach P, Malet H, Cusack S & Reguera J. Structural insights into bunyavirus replication and its regulation by the vRNA promoter. Cell (2015) 161: 1267–1279, doi.org/10.1016/j.cell.2015.05.006
About Group Leader
Dr. Piotr Gerlach joined IMol in summer 2021 within the frame of the FNP-founded ReMedy IRAP. Originally from Warsaw, during his PhD in Dr. Stephen Cusack’s group at EMBL in Grenoble, he succeeded in determining the first atomic structure of a bunyaviral polymerase. Securing an EMBO Long Term Fellowship, he joined Prof. Elena Conti’s lab at Max Planck Institute of Biochemistry in Munich, where he used cryo-EM to study multi-subunit complexes involved in RNA metabolism. At IMol, supported by EMBO IG and NCN SONATA BIS grants, Dr. Gerlach’s Laboratory of Structural Virology is studying how infectious RNA viruses reorganize and exploit cellular translation.
Funding
- Foundation for Polish Science, First Team FENG: 5′HOOK – a novel, small RNA-based technology against negative-strand RNA viruses, (FENG.02.02-IP.05-0081/25), (01.01.2026-31.12.2029), leader: Piotr Gerlach
- National Science Centre, SONATA BIS 12: Bunyaviral strategies to reorganize and exploit cellular translation, (2022/46/E/NZ1/00273), (15.03.2023-14.03.2028), leader: Piotr Gerlach
- EMBO Installation Grant: Mechanism of the bunyaviral transcription-translation coupling, (IG 4742), (01.01.2021-31.12.2025), leader: Piotr Gerlach

Międzynarodowy Instytut Mechanizmów i Maszyn Molekularnych PAN uzyskał dotację z Unii Europejskiej na projekt FENG.02.02-IP.05-0081/25 “5’HAK – nowa, oparta na małych RNA technologia przeciwko wirusom RNA o ujemnej polarności genomu”.
Celem nadrzędnym projektu jest opracowanie nowej klasy cząsteczek, będących kandydatami na leki przeciwko wirusom posiadającym segmentowany genom RNA o ujemnej polarności nici – tj. pandemicznym i sezonowym wirusom grypy, jak również patogennym bunyawirusom.
Pandemiczna i sezonowa grypa oraz coraz częstsze infekcje wywoływane tropikalnymi bunyawirusami, stanowią olbrzymie wyzwania
zdrowotne, społeczne i ekonomiczne. Sprawia to, że zapotrzebowanie na nowe leki przeciw grypie jest bardzo duże, a na leki przeciw bunyawirusom fundamentalne. Projekt FirstTeam 5’HAK opiera się na kluczowym i unikatowym dla tej grupy wirusów oddziaływaniu polimerazy z końcem 5′ genomowego RNA. Przyjmuje ono na powierzchni białka strukturę haka, regulującą i aktywującą centrum katalityczne polimerazy. Planujemy na podstawie tego oddziaływania opracować i zaproponować nową, opartą o krótkie RNA, klasę cząstek, która zrewolucjonizuje rynek leków przeciwko tym wirusom. Projekt zakłada kompleksowy i komplementarny przebieg prac. Pierwsze generacje 5’HAK-RNA zaprojektujemy w oparciu o analizę wirusowych sekwencji oraz modelowanie in silico. Stosując preparaty białkowewybranych polimeraz, przeprowadzimy testy przesiewowe, które zidentyfikują RNA wiążące się i inhibujące polimerazy najsilniej. Wyniki te, w powiązaniu ze strukturami cryo-EM, pozwolą na iteratywne i racjonalne ulepszanie projektowanych RNA. Ponadto, firma Lipid Systems przygotuje LNP i liposomy zawierające wybrane 5’HAK-RNA, co umożliwi przetestowanie ich inhibitorowych właściwości w hodowlach komórkowych. Rezultatem projektu FirstTeam 5’HAK będą nowej klasy cząsteczki inhibitorowe, będące kandydatami na leki przeciw grypie i patogennym bunyawirusom.
Projekt FirstTeam 5’HAK wychodzi na przeciw społeczno-ekonomicznym problemom związanym z infekcjami powodowanymi przez wirusy grypy i patogenne bunyawirusy. Niebezpośrednimi, przyszłymi odbiorcami projektu będą pacjenci, lekarze, szpitale i firmy farmaceutyczne. Uzyskane prototypy cząsteczek inhibitorowych będą materiałem wyjściowym do dalszych badań nad ulepszeniem formuły, aż po ewentualne badania przedkliniczne i kliniczne. W związku z tym bezpośrednimi odbiorcami wyników projektu będą polskie i zagraniczne firmy biomedyczne i podmioty typu CRO, które przeprowadziłyby badania farmakokinetyczne, toksykologiczne i potwierdzające aktywność biologiczną w akredytowanych laboratoriach, zgodnie z zasadami GLP.
Wartość projektu: 4.000.000 zł
Wysokość wkładu z Funduszy Europejskich: 4.000.000 zł
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The International Institute of Molecular Mechanisms and Machines of the Polish Academy of Sciences has received European Union funding for the project FENG.02.02-IP.05-0081/25 “5′HOOK – a novel, small RNA-based technology against negative-strand RNA viruses”.
The overarching goal of the project is to develop a new class of drug candidate molecules targeting viruses with a segmented, negative-sense RNA genome – i.e. pandemic and seasonal influenza viruses and pathogenic bunyaviruses.
Pandemic and seasonal influenza, as well as the increasingly frequent infections caused by tropical bunyaviruses, pose enormous health, social, and economic challenges. Therfore, the demand for new influenza drugs is extremely high, and for bunyavirus therapeutics fundamental. The FirstTeam 5′HOOK project is based on a key and unique feature of this group of viruses, namely the interaction of their polymerase with the 5′ end of the viral genomic RNA. This short and conserved RNA fragment adopts a hook-like conformation on the polymerase surface, regulating and activating its catalytic center. We aim to use this principle to develop and propose a new class of short RNA-based particles that will revolutionize the antiviral drug market against these pathogens. The project envisions a comprehensive and complementary workflow. The first generations of 5′HOOK-RNAs will be designed using viral sequence analyses and in silico modeling. Using purified protein preparations of selected polymerases, we will conduct screening assays to identify RNA molecules that bind to and inhibit the polymerases most effectively. These results, combined with cryo-EM structures, will lead to iterative and rational optimization of the designed RNAs. In addition, Lipid Systems company will prepare LNPs and liposomes containing selected 5′HOOK-RNAs, enabling evaluation of their inhibitory properties in cell-culture systems. The outcome of the FirstTeam 5′HOOK project will be a new class of inhibitory molecules that will constitute drug candidates against influenza viruses and pathogenic bunyaviruses.
The FirstTeam 5’HAK project addresses the socio-economic problems associated with infections caused by influenza viruses and pathogenic bunyaviruses. The indirect, future beneficiaries of the project will include patients, physicians, hospitals, and pharmaceutical companies. The resulting prototypes of inhibitory molecules will serve as a starting point for further research aimed at improving their formulation, up to and including potential preclinical and clinical studies. Consequently, the direct recipients of the project’s outcomes will be Polish and international biomedical companies and CROs, which would conduct pharmacokinetic, toxicological, and biological-activity confirmation studies in accredited laboratories in accordance with GLP guidelines.
Total project value: 4.000.000 zł
Amount of the contribution from European Funds: 4.000.000 zł