Research Plan
Research plan includes activities and synergies between the research Groups in the fields of cell cycle regulation, an area where the Perrakis, Lygerou and Taraviras lab have excellent track record applying well-established protocols and to specifically develop methodology on the border between cell biology imaging and biophysics, e.g. single molecule biophysics by TIRF or confocal microscopy, will be considered.
Τhe use of existing equipment and methods (NMR and biophysics) to establish fragment based lead drug discovery and support hit to lead campaigns is also among the foreseen research activities. The Spyroulias group and the Perrakis group have complementary expertise in this subject and can establish robust pipelines both for academic discovery but also crucially for industrial application. Targets will include enzymes in ADP-ribosylation pathway implicated in viral infection and host-cell defense, such as non-structural polyproteins (nsP3, and especially the so-called “macro” domains) or proteolytic enzymes from SARS1, MERS, SARS-CoV-2 and human enzymes, like Poly(ADP-ribose) polymerases proteins, from the Spyroulias lab and mitotic kinases or their regulatory domains from the Perrakis lab.
Additionally, collaborative research in the area of cell cycle regulation, bridging structural biology and functional imaging is planned. These projects will focus on the maintainance of genome integrity through accurate spatio-temporal regulation of genome replication and chromosome segregation and will build on ongoing research in UPAT and the ERA-Chair teams. Functional live cell imaging and high-content microscopy will be combined to studies of protein-protein interactions in cells and to biophysical/structural analyses to study key factors ensuring timely DNA replication, centrosome duplication and chromosome biattachment at the mitotic spindle. Prior collaborative efforts of the Lygerou, Taraviras and Perrakis teams have paved the way for planned research activities, which will build on existing and recently acquired state-of-the-art equipment, and on the transfer of know-how from the ERA-Chair Team.
Infrastructure
UPAT is a science and technology (S&T) hub and hosts a National RI, providing access to institutional and external users (from academia or industry), collaborating with regional/national pharma and food industry, exhibiting a significant network and a unique research Infrastructure at the national/Greek level.
Publications of the Collaborating groups
A. Perrakis’ Group
Posttranslational modification of microtubules by the MATCAP detyrosinase
Posttranslational modification of microtubules by the MATCAP detyrosinase.
Landskron L, Bak J, Adamopoulos A, et al, Taraviras S, Perrakis A, Brummelkamp TR.
Science. 2022
A type IV Autotaxin inhibitor ameliorates acute liver injury and nonalcoholic steatohepatitis.
A type IV Autotaxin inhibitor ameliorates acute liver injury and nonalcoholic steatohepatitis.
Booijink R, Salgado-Polo F, Jamieson C, Perrakis A, Bansal R.
EMBO Molecular Medicine. 2022
AlphaFill: enriching AlphaFold models with ligands and cofactors
AlphaFill: enriching AlphaFold models with ligands and cofactors.
Hekkelman ML, de Vries I, Joosten RP, Perrakis A.
Nature Methods. 2022
Z. Lygerou’s Group (UPAT, Medicine Dept)
Fanconi anemia proteins and genome fragility: unraveling replication defects for cancer therapy
Fanconi anemia proteins and genome fragility: unraveling replication defects for cancer therapy.
Badra Fajardo N, Taraviras S, Lygerou Z. Trends Cancer. 2022 Jun;8(6):467-481. doi: 10.1016/j.trecan.2022.01.015.
Ribosomal DNA and the nucleolus at the heart of aging
Ribosomal DNA and the nucleolus at the heart of aging.
Kasselimi E, Pefani DE, Taraviras S, Lygerou Z. Trends Biochem Sci. 2022 Apr;47(4):328-341. doi: 10.1016/j.tibs.2021.12.007.
In silico analysis of DNA re-replication across a complete genome reveals cell-to-cell heterogeneity and genome plasticity
Rapsomaniki MA, Maxouri S, Nathanailidou P, Garrastacho MR, Giakoumakis NN, Taraviras S, Lygeros J, Lygerou Z. NAR Genom Bioinform. 2021 Jan 28;3(1):lqaa112. doi: 10.1093/nargab/lqaa112.
DNA Replication Control: Liquid-liquid Phase Separation Comes Into Play
DNA Replication Control: Liquid-liquid Phase Separation Comes Into Play.
Nathanailidou P, Taraviras S, Lygerou Z. J Mol Biochem. 2020 Dec 30;9(1):54-56.
Chromatin and Nuclear Architecture: Shaping DNA Replication in 3D
Chromatin and Nuclear Architecture: Shaping DNA Replication in 3D.
Nathanailidou P, Taraviras S, Lygerou Z. Trends Genet. 2020 Dec;36(12):967-980. doi: 10.1016/j.tig.2020.07.003.
S. Taraviras (UPAT, Medicine Dept)
Small Molecule Inhibitor Targeting CDT1/Geminin Protein Complex Promotes DNA Damage and Cell Death in Cancer Cells.
Karantzelis N, Petropoulos M, De Marco V, Egan DA, Fish A, Christodoulou E, Will DW, Lewis JD, Perrakis A, Lygerou Z, Taraviras S. Front Pharmacol. 2022 Apr 25;13:860682. doi: 10.3389/fphar.2022.860682.
Cdt1 overexpression drives colorectal carcinogenesis through origin overlicensing and DNA damage.
Cdt1 overexpression drives colorectal carcinogenesis through origin overlicensing and DNA damage.
Petropoulos M, Champeris Tsaniras S, Nikou S, Maxouri S, Dionellis VS, Kalogeropoulou A, Karamichali A, Ioannidis K, Danalatos IR, Obst M, Naumann R, Delinasios GJ, Gorgoulis VG, Roukos V, Anastassiadis K, Halazonetis TD, Bravou V, Lygerou Z, Taraviras S. J Pathol. 2023 Jan;259(1):10-20. doi: 10.1002/path.6017.
Intrinsic neural stem cell properties define brain hypersensitivity to genotoxic stress
Intrinsic neural stem cell properties define brain hypersensitivity to genotoxic stress.
Kalogeropoulou A, Mougkogianni M, Iliadou M, Nikolopoulou E, Flordelis S, Kanellou A, Arbi M, Nikou S, Nieminuszczy J, Niedzwiedz W, Kardamakis D, Bravou V, Lygerou Z, Taraviras S. Stem Cell Reports. 2022 Jun 14;17(6):1395-1410. doi: 10.1016/j.stemcr.2022.04.018.
3D Reconstitution of the Neural Stem Cell Niche: Connecting the Dots
3D Reconstitution of the Neural Stem Cell Niche: Connecting the Dots.
Ioannidis K, Angelopoulos I, Gakis G, Karantzelis N, Spyroulias GA, Lygerou Z, Taraviras S. Front Bioeng Biotechnol. 2021 Oct 28;9:705470. doi: 10.3389/fbioe.2021.705470.
A Custom Ultra-Low-Cost 3D Bioprinter Supports Cell Growth and Differentiation
A Custom Ultra-Low-Cost 3D Bioprinter Supports Cell Growth and Differentiation.
Ioannidis K, Danalatos RI, Champeris Tsaniras S, Kaplani K, Lokka G, Kanellou A, Papachristou DJ, Bokias G, Lygerou Z, Taraviras S. Front Bioeng Biotechnol. 2020 Nov 4;8:580889. doi: 10.3389/fbioe.2020.580889.
G.A. Spyroulias’ Group (UPAT, Pharmacy Dept)
Comprehensive Fragment Screening of the SARS-CoV-2 Proteome Explores Novel Chemical Space for Drug Development
COVID19-NMR Consortium. Angew Chem Int Ed Engl. 2022 Nov 14;61(46):e202205858. doi: 10.1002/anie.202205858.
Binding Adaptation of GS-441524 Diversifies Macro Domains and Downregulates SARS-CoV-2 de-MARylation Capacity.
Tsika AC, Gallo A, Fourkiotis NK, Argyriou AI, Sreeramulu S, Löhr F, Rogov VV, Richter C, Linhard V, Gande SL, Altincekic N, Krishnathas R, Elamri I, Schwalbe H, Wollenhaupt J, Weiss MS, Spyroulias GA. J Mol Biol. 2022 Aug 30;434(16):167720. doi: 10.1016/j.jmb.2022.167720.
Unveiling the Essential Role of Arkadia’s Non-RING Elements in the Ubiquitination Process.
Unveiling the Essential Role of Arkadia’s Non-RING Elements in the Ubiquitination Process.
Birkou M, Delegkou GN, Marousis KD, Fragkaki N, Toro T, Episkopou V, Spyroulias GA. Int J Mol Sci. 2022 Sep 13;23(18):10585. doi: 10.3390/ijms231810585.
Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications
COVID19-NMR Consortium. Front Mol Biosci. 2021 May 10;8:653148. doi: 10.3389/fmolb.2021.653148.
Deciphering the Nucleotide and RNA Binding Selectivity of the Mayaro Virus Macro Domain
Deciphering the Nucleotide and RNA Binding Selectivity of the Mayaro Virus Macro Domain.
Tsika AC, Melekis E, Tsatsouli SA, Papageorgiou N, Maté MJ, Canard B, Coutard B, Bentrop D, Spyroulias GA. J Mol Biol. 2019 May 31;431(12):2283-2297. doi: 10.1016/j.jmb.2019.04.013.