News


2nd of Feb, 2024 

This ending week marks a visit of our colleagues and friends, Lynne-Maria Postovit from Queen’s University of Ontario and Ivan Topisirovic from McGill, Montreal. They spent 4 days with us, both gave talks at our institute, discussed our projects with everyone, enjoyed Czech meals and beers, a bit of sightseeing and bought a Bohemias 1905 football jersey for Lynne’s son (in fact that’s why they came :)) It was fun! “Thank you both for your openness and common sense attitude in every aspect of life”. It is very rare these days! 

 

24th of Jan, 2024

Guess what? The new lab web – including our new logo! - is up and running. It still requires a bit of fine-tuning, but the hard work is done! Many thanks to everybody, especially to Filip (the 1 st ) and Terka and her husband Alex! Other than that, Anicka’s eLife is in, Zuzka’s NSMB and Anya’s Cell Rep under re-revision, Kristina’s RNA submission being finalized, 5 more collaborative papers at various stages of the process ... looks like 2024 is going to be a Good Year, Continentally, woo-hoo! We will soon be welcoming our new post-doc, Filip (the 2 nd ) Trcka, and will soon open a new PhD position for the 2024/25 academic year. And finally, the real thrill! British The Vaccines are performing at the Roxy tonight! Cannot wait! C U there 😉 

 

10th of Dec, 2023

We are happy to announce that we have just hit the road with this brand new website – still a bit under construction but we R getting there! It has been a collaborative creative effort with everyone contributing his/her artistic bit to the mill. Filip, our new post-doc from Slovakia, then put it altogether in this 0 and 1 format. Hope you like it as much as we do (at least some of us :)). Other than that, after clinching our first Nature earlier this year, we have 5 more papers in the pipeline, with Zuzka’s NSMB, which is awaiting our resubmission, likely to cross the finish line first. We also have a new PhD student Adriana Šubrtová from Slovakia, who has joined Adriana Sr. on her T-cell project to create a fail-safe “Adrianas duet” that warrants its 100% success. When both Filip and Adriana Jr. travel home, they always bring back something very tasteful from their country’s finest delicacies! We want more people from countries like this! Finally, this year we’ve also won decent funding for the next five years … OP JAK, a CSF-DFG collaborative grant and a standard CSF grant. So, we are all set to perform our finest tunes. Btw, we got over 30 cm of new snow today. Marvelous, skiing is nearing!!!

Who R we?


We are a medium-sized group (~15 people) of enthusiastic, passionate and hard-working “musicians” from post-docs to undergraduate students with one skillful lab assistant, who are eager to learn more and more every day while having fun at the same time. Our recording studio is based at the Institute of Microbiology (IMIC) of the Czech Academy of Sciences (CAS) in Prague, Czech Republic.

Our band nicknamed Laboratory of Regulation of Gene Expression  (LRGE) was established in June 2006 and investigates fundamentals of one of the key, life-giving molecular processes in the cell and its regulation at both general as well as gene-specific levels. We R talking about protein synthesis! Simply speaking, our mostly basic research is focused on figuring out how the cell deciphers the genetic code of DNA using relatively simple decoding keys and uses this gene-encoded information to produce proteins, i.e., cellular effectors, through a very complex process also called translation.

Recently, we have become very much interested in various alternatives to these decoding keys, so-called alternative genetic codes, the detailed knowledge of which could be exploited in the treatment of various genetic diseases. In addition, we are interested in understanding how translation is regulated in response to constantly changing environmental conditions that the cell faces and to which it must immediately respond in order to adapt its repertoire of proteins that it is currently producing.

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As for the importance of our research from the socio-economic and medical perspectives, we want to broaden and deepen the general understanding of how these basic cellular processes properly operate in the cell, so that our collaborators who are primarily interested in applied research; i.e., research directly aimed at developing the most appropriate treatment for a particular disease, can feed from it while investigating various pathologies. 

Overall, paying the utmost tribute to our distinguished ancient predecessors, our major goal is to help to transmute lead ( basic research discoveries) into gold (useful therapeutics) with the simplest and finest tones.

Our compositions combine the use of mammalian cells lines and partly also the budding yeast Saccharomyces cerevisiae model organism and employ tools of molecular and structural biology, biochemistry and genetics. 

We also very much enjoy participating in numerous popularization gigs (like Open Science, Researcher’s Night, etc.), giving interviews to news and radio, contributing to popularization magazines, etc. 

Our band won “The best original research publication carried out at the Institute of Microbiology CAS Award” (our home institute) in years 2008, 2011, 2013, 2015, 2016, 2017, 2018, 2019, 2020, 2021, and 2022. In February 2016, the international evaluation committee selected our band as one of the 13 most prestigious ones in the entire CAS.

Our recording is (or until recently was) supported by the national and world renowned funding bodies such as the the Wellcome Trust, Howard Hughes Medical Institute, NIH FIC, German Science Foundation, Czech Science Foundation and Czech Academy of Sciences (Praemium Academiae). Altogether, we have produced >75 records with record labels like Nature (see our winning cover page),  Molecular Cell, Nature Protocols, Nucleic Acids Research, Genes & Development, EMBO J., eLife, etc. Music is always composed by LRGE, lyrics usually by LSV.

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The Group


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Leoš Shivaya Valášek

Group leader

e-mail: valasekl@biomed.cas.cz

5 bullets CV 

  • I have always wanted to be a hockey player or a rock-star, but never a scientist. 
  • So why did I end up becoming a scientist then? Serendipity involving music, indeed, but at the end of the day I'm not complaining 😊 
  • What do I like about science? Freedom of choice (slowly dying these days but still worth fighting for), the quest for truth (very relative, indeed 😊), meeting and interacting with smart and entertaining people (ignoring exceptions 😉), solving puzzles (often unsolvable!), and the eternal discovery of new causal relationships. 
  • I'm not religious in that sense, but I recognize myself in many Buddhist ideas, such as letting things flow and trusting the natural course of our lives, no matter how near or far the sun is shining, if it is shining at all at any given moment. 
  • Personal motto: “Believe nothing, but admit everything”.
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Anna Herrmannová

post-doctoral fellow

e-mail: herrmannova@biomed.cas.cz

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Petra Beznosková

post-doctoral fellow

e-mail: beznoskova@biomed.cas.cz

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Mahabub Pasha Mohammad

post-doctoral fellow

e-mail: mpasha@biomed.cas.cz

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Jana Chumová

post-doctoral fellow

e-mail: jana.chumova@biomed.cas.cz

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Jana Vojtová

post-doctoral fellow

e-mail: jana.vojtova@biomed.cas.cz

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Adriana Roithová 

post-doctoral fellow

e-mail:adriana.roithova@biomed.cas.cz

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Vladislava Hronová

post-doctoral fellow

e-mail: vladislava.hronova@biomed.cas.cz

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Filip Brázdovič

post-doctoral fellow

e-mail: filip.brazdovic@biomed.cas.cz

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Filip Trčka

post-doctoral fellow

e-mail: to_be_announced@biomed.cas.cz

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Zuzana Pavlíková

Ph.D. student

e-mail: zuzana.pavlikova@biomed.cas.cz

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Terezie Prilepskaja

Ph.D. student

e-mail: terezie.svobodova@biomed.cas.cz

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Anna Michajlovna Smirnova

Ph.D. student

e-mail: anna.smirnova@biomed.cas.cz

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Kristína Jendruchová

Ph.D. student

e-mail: kristina.jendruchova@biomed.cas.cz

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Klára Pospíšilová

Ph.D. student

e-mail: klara.pospisilova@biomed.cas.cz

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Adriana Šubrtová

Ph.D. student

e-mail: adriana.subrtova@biomed.cas.cz

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Petra Miletínová

Master's student

e-mail: petra.miletinova@biomed.cas.cz

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Olga Staňková

Lab assistant

e-mail: olga.krydova@biomed.cas.cz

  • Betty Bavorová, high school student CZE
  • Lucie Cuchalová, PhD student & post-doc, CZE
  • István Dányi, PhD student, HUN
  • Anna Delijannisová, lab tech, CZE
  • Stanislava Gunišová, post-doc, SVK
  • Adam Hlaváček, bachelor student, CZE
  • Zuzana Hovorková, bachelor student, CZE
  • Martina Janošková, PhD student, CZE
  • Olga Janoušková, post-doc, CZE
  • Myrte Jansen, PhD student, NLD
  • Farkas Kerenyi, post-doc, HUN
  • Jan Kosla, PhD student, CZE
  • Tomáš Kouba, PhD student & post-doc, CZE
  • Kristína Koudelová, lab tech, CZE
  • Veronika Kovaničová, lab tech, SVK
  • Michaela Kučerová, master student, CZE
  • Abhijith Makki, PhD student, IND
  • Vanda Munzarová, PhD student & post-doc, CZE
  • Lucie Peclínovská, bachelor student, CZE
  • Kristýna Poncová, PhD student & post-doc, CZE
  • Edit Rutkai, post-doc, HUN
  • Béla Szamecz, post-doc, HUN
  • Petr Šimandl, bachelor student, CZE
  • Darina Širková, master student, SVK
  • Susan Wagner, PhD student & post-doc, GER
  • Monica Yun Liu, Erasmus student, USA
  • Jakub Zeman, PhD student & post-doc, CZE

Records


Top records since we first took the stage.

#co-first authors; *co-corresponding authors; $ lead contact, members of the LRGE lab are underlined
For our complete setlist, please see:
Pubmed Linkedin

 

  1. Kachale, A.#, Pavlíková, Z.#, Nenarokova, A.#, Roithová, A., Durante, I.M., Miletínová, P., Záhonová, K., Nenarokov, S., Votýpka, J., Horáková, E., Ross, L.R., Yurchenko, V., Beznosková, P., Paris, Z*, Valášek, L.S.*$, and Lukeš, J.* (2023) Short tRNA anticodon stem with mutant eRF1 allow stop codon reassignment.  Nature, 613, 751-758. https://pubmed.ncbi.nlm.nih.gov/36631608/
  2.  

  3. Wagner, S.#, Bohlen, J.#, Herrmannová, A.#, Jelínek, J., Preiss, T.*, Valášek, L.S.*, and Teleman, A.* (2022) Selective footprinting of 40S and 80S ribosome subpopulations (Sel-TCP-seq) to study translation and its control. Nat Prot., 17,(10), 2139-2187. https://doi.org/10.1038/s41596-022-00708-4
  4.  

  5. Beznosková, P.*, Bidou, L., Namy, O., and Valášek, L.S.* (2021) Increased expression of tryptophan and tyrosine tRNAs elevates stop codon readthrough of reporter systems in human cell lines. Nucleic Acids Res., 49, (9), 5202-5215. https://doi.org/10.1093/nar/gkab315
  6.  

  7. Wagner, S.*, Herrmannová, A., Hronová, V., Gunišová, S., Sen, N., Hannan, R.D., Hinnebusch, A.G., Shirokikh, N.E., Preiss, T.*, and Valášek, L.S.*$ (2020) Selective translation complex profiling reveals staged initiation and co-translational assembly of initiation factor complexes. Mol. Cell, 79, (4), 546-560.e7. https://doi.org/10.1016/j.molcel.2020.06.004
  8.  

  9.  Herrmannová, A.*, Prilepskaja, T., Wagner, S., Šikrová, D., Zeman, J., Poncová, K., and Valášek, L.S.* (2020) Adapted formaldehyde gradient cross-linking protocol implicates human eIF3d and eIF3c, k and l subunits in the 43S and 48S pre-initiation complex assembly, respectively. Nucleic Acids Res., 48, (4), 1969-1984. https://doi.org/10.1093/nar/gkz1185
  10.  

  11. Beznosková, P.*, Pavlíková, Z., Zeman, J., Aitken, C.E., and Valášek, L.S.* (2019) Yeast applied readthrough inducing system (YARIS): An in vivo assay for the comprehensive study of translational readthrough. Nucleic Acids Res., 47(12), 6339-6350. https://doi.org/10.1093/nar/gkz346
  12.  

  13. Guan, B-J., van Hoef, V., Jobava, R., Elroy-Stein, O., Valášek, L.S., Cargnello, M., Gao, X-H., Krokowski, D., Merrick, W.C., Kimball, S.R., Komar, A.A., Koromilas, A.E., Wynshaw-Boris, A., Topisirovic, I.*, Larsson, O.*, and Hatzoglou, M.* (2017) A unique ISR program determines cellular responses to chronic stress. Mol Cell, 68 (5), 885-900. https://doi.org/10.1016/j.molcel.2017.11.007
  14.  

  15. Valášek, L.S.*, Zeman, J., Wagner, S., Beznosková, P., Pavlíková, Z., Mohammad, M.P., Hronová, V., Herrmannová, A., Hashem, Y., and Gunišová, S. (2017) Embraced by eIF3: structural and functional insights into the roles of eIF3 across the translation cycle. Nucleic Acids Res., 45 (19), 10948-10968, Epub 2017 Sep 14. https://doi.org/10.1093/nar/gkx805
  16.  

  17. Mohammad, M.P., Munzarová Pondělíčková, V., Zeman, J., Gunišová, S., and Valášek, L.S.* (2017) In vivo evidence that eIF3 stays bound to ribosomes elongating and terminating on short upstream ORFs to promote reinitiation. Nucleic Acids Res., 45 (5), 2658-2674, Epub 2017 Jan 24. https://doi.org/10.1093/nar/gkx049
  18.  

  19. Wagner, S., Herrmannová, A., Šikrová, D., and Valášek, L.S.* (2016) Human eIF3b and eIF3a serve as the nucleation core to assemble the remaining eIF3 subunits into two interconnected modules – the yeast-like core and the octamer. Nucleic Acids Res., 44 (22), 10772-10788, Epub 2016 Oct 19. https://doi.org/10.1093/nar/gkw972
  20.  

  21. Beznosková, P., Wagner, S., Jansen, M.E., von der Haar, T. and Valášek, L.S.* (2015) Translation initiation factors eIF3 promotes programmed stop codon readthrough. Nucleic Acid Res., 43(10), 5099-111. Epub 2015 April 29. https://doi.org/10.1093/nar/gkv421
  22.  

  23. Beznosková, P.#, Cuchalová, L. #, Wagner, S., Shoemaker, C.J., Gunišová, S., von der Haar, T. and Valášek, L.S.* (2013) Translation initiation factors eIF3 and HCR1 control translation termination and stop codon read-through in yeast cells. PLoS Genet., 9, e1003962. https://doi.org/10.1371/journal.pgen.1003962
  24.  

  25. Valášek, L.S.* (2012) ’Ribozoomin’ – Translation Initiation from the Perspective of the ribosome-bound Eukaryotic Initiation Factors (eIFs). Curr Protein Pept Sci., 13, 305-330. https://doi.org/10.2174/138920312801619385
  26.  

  27. Kouba, T., Rutkai, E., Karasková, M., and Valášek, L.S.* (2012) The eIF3c/NIP1 PCI Domain Interacts with RNA and RACK1/ASC1 and Promotes Assembly of Translation Pre-initiation Complexes. Nucleic Acids Res., 40(6), 2683-99. Epub 2011 Nov 28. https://doi.org/10.1093/nar/gkr1083
  28.  

  29. Herrmannová, A.#, Daujotytė, D.#, Yang, J-C., Cuchalová, L., Gorrec, F., Wagner, S., Dányi, I., Lukavsky, P.J.*, and Valášek, L.S.* (2012) Structural Analysis of an eIF3 Subcomplex Reveals Conserved Interactions Required for a Stable and Proper Translation Pre-Initiation Complex Assembly. Nucleic Acids Res., 40(5), 2294-311. Epub 2011 Nov 15. https://pubmed.ncbi.nlm.nih.gov/22090426/
  30.  

  31. Munzarová, V., Pánek, J., Gunišová, S., Danyi, I., Szamecz, B. and Valášek, L.S.* (2011) Translation Reinitiation Relies on the Interaction Between eIF3a/TIF32 and Progressively Folded cis-acting mRNA Elements Preceding Short uORFs. PLoS Genet., 7, e1002137. https://doi.org/10.1371/journal.pgen.1002137
  32.  

  33. Cuchalová, L., Kouba, T., Herrmannová, A., Danyi, I., Chiu, W.-l. and Valášek, L.* (2010) The RNA Recognition Motif of Eukaryotic Translation Initiation Factor 3g (eIF3g) Is Required for Resumption of Scanning of Posttermination Ribosomes for Reinitiation on GCN4 and Together with eIF3i Stimulates Linear Scanning. Mol Cell Biol., 30, 4671-4686. https://doi.org/10.1128/mcb.00430-10
  34.  

  35. Szamecz, B., Rutkai, E., Cuchalová, L., Munzarová, V., Herrmannová, A., Nielsen, K.H., Burela, L., Hinnebusch, A.G., and Valášek, L.* (2008) eIF3a cooperates with sequences 5' of uORF1 to promote resumption of scanning by post-termination ribosomes for reinitiation on GCN4 mRNA. Genes & Dev., 22, 2414-2425. https://doi.org/10.1101/gad.480508

 

Contact


Laboratory of Regulation of Gene Expression

Institute of Microbiology, AS CR, v.v.i.
Vídeňská 1083, Prague 4, 142 20
Czech Republic
Phone: +420 241 062 288 (2483)
Cell: +420 724 731 661
e-mail: valasekl@biomed.cas.cz


How to reach us

Take C-line metro to the station „Kačerov“.
Get on the bus 138 to the final station "Ustavy akademie ved".
We are in the Bldg. L, second floor, lab #128.

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