• Dpt. of Chemistry and Biochemistry

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Recent Publications

• Oxidative Damage of RNA: Structure, Function, and... Mammalian In Vitro Translation... The human vault RNA enhances tumorigenesis and...rRNA expansion segment 27Lb modulates the factor recruitment ....Loss of the ribosomal RNA methyltransferase NSUN5 ....mRNA-specific translation regulation by a ribosome ....Atomic mutagenesis of stop codon nucleotides ...

Projects

• Atomic mutagenesis of the ribosome
• The regulatory non-coding RNA interactome of translating ribosomesThe elusive molecular biology of the vault RNA

RNA Gallery

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Publications

 

2024

• Robert Rauscher, Cristian Eggers, Lyudmila Dimitrova-Paternoga, Vaishnavi Shankar, Alessia Rosina, Marina Cristodero, Helge Paternoga, Daniel N Wilson, Sebastian A Leidel and Norbert Polacek (2024). Evolving precision: rRNA expansion segment 7S modulates translation velocity and accuracy in eukaryal ribosomes. Nucleic Acids Res 2024 Feb 7:gkae067. doi: 10.1093/nar/gkae067.

2023

• Rebecca Brogli; Marina Cristodero; André Schneider and Norbert Polacek (2023).
  A ribosome-bound tRNA half stimulates mitochondrial translation during stress recovery in Trypanosoma brucei. Cell reports, 42(9), S. 113112. Cell Press 10.1016/j.celrep.2023.113112
• Andrew D Holmes, Patricia P Chan, Qi Chen, Pavel Ivanov, Laurence Drouard, Norbert Polacek, Mark A Kay, Todd M Lowe (2023). A standardized ontology for naming tRNA-derived RNAs based on molecular origin. Nat Methods 2023 Mar 3. doi: 10.1038/s41592-023-01813-2.

2022

• Nicole Raad, Disha Tandon, Siegfried Hapfelmeier and Norbert Polacek (2022).

  The stationary phase-specific sRNA FimR2 is a multifunctional regulator of bacterial motility, biofilm formation and virulence. Nucleic Acids Res 2022 Nov 10;gkac1025. doi: 10.1093/nar/gkac1025

• Stefano Gallo, EunBin Kong, Iolanda Ferro and Norbert Polacek (2022). Small but Powerful: The Human Vault RNAs as Multifaceted Modulators of Pro-Survival Characteristics and Tumorigenesis. Cancers 2022, 14, 2787. https://doi.org/10.3390/cancers14112787.
• Valentina Pecoraro, Alessia Rosina and Norbert Polacek (2022). Ribosome-Associated ncRNAs (rancRNAs) Adjust Translation and Shape Proteomes. Non-Coding RNA 2022, 8(2), 22; https://doi.org/10.3390/ncrna8020022.
• Lynn Htet Htet Aung, Peifeng Li, Claudia Perez-Cruz, Norbert Polacek and
  Marino J. E. Resendiz (2022). Oxidative Damage of RNA: Structure, Function, and Biological
  Implications - From Nucleotides to Short and Long RNAs in Chemistry and Biology. Front. Mol. Biosci., 25 February 2022 | https://doi.org/10.3389/fmolb.2022.853725.
• Gonskikh Y., Pecoraro V. and Polacek N. (2022). Mammalian In Vitro Translation Systems. Methods Mol Biol 2022;2428:101-111. doi: 10.1007/978-1-0716-1975-9_7.
• Ferro I., Gavini J., Gallo S., Bracher L., Landolfo M., Candinas D., Stroka D. M. and Polacek N. (2022). The human vault RNA enhances tumorigenesis and chemoresistance through the lysosome in hepatocellular carcinoma. Autophagy 2022 Jan;18(1):191-203. doi: 10.1080/15548627.2021.1922983.
• Fasnacht M., Gallo S., Sharma P., Himmelstoss M., Limbach P. A., Willi J. and Polacek N. (2022). Dynamic 23S rRNA modification ho5C2501 benefits Escherichia coli under oxidative stress. Nucleic Acids Res.
  

2021

• Krauer N., Rauscher R. and Polacek N. (2021). tRNA synthetases are recruited to yeast ribosomes by rRNA expansion segment 7L but do notrequire association for functionality. Non-coding RNA, 7:73, https://doi.org/10.3390/ncrna7040073.
• Reuther J., Schneider L., Iacovache I., Pircher A., Gharib W. H., Zuber B., Polacek N. (2021). A small ribosome-associated ncRNA globally inhibits translation by restricting ribosome dynamics. RNA Biology, S. 1-16. 10.1080/15476286.2021.1935573
• Svetlov M. S., Koller T. O., Meydan S., Shankar V., Klepacki D., Polacek N., Guydosh N. R., Vázquez-Laslop N., Wilson D. N. & Mankin A. S. (2021). Context-specific action of macrolide antibiotics on the eukaryotic ribosome. Nat Commun 2021 May 14;12(1):2803. doi: 10.1038/s41467-021-23068-1.
• Fasnacht M. and Polacek N. (2021). Oxidative Stress in Bacteria and the Central Dogma of Molecular Biology. Front. Mol. Biosci. doi: 10.3389/fmolb.2021.671037.
• Raad N., Luidalepp H., Fasnacht M. and Polacek N. (2021). Transcriptome-Wide Analysis of Stationary Phase Small ncRNAs in E. coli. Int. J. Mol. Sci. 2021, 22(4), 1703; https://doi.org/10.3390/ijms22041703
• Cristodero M., Brogli R., Joss O., Schimanski B., Schneider A. and Polacek N. (2021). tRNA 3' shortening by LCCR4 as a response to stress in Trypanosoma brucei. Nucleic Acids Res. 2021 Jan 6;gkaa1261. doi: 10.1093/nar/gkaa1261.
• Pinel-Marie M.-L., Brielle R., Riffaud C., Germain-Amiot N., Polacek N. and Felden B. (2021). RNA antitoxin SprF1 binds ribosomes to attenuate translation and promote persister cell formation in Staphylococcus aureus. Nat Microbiol 2021 Jan 4. doi: 10.1038/s41564-020-00819-2.

2020

• Polacek, N. and Ivanov, P. (2020).
  The regulatory world of tRNA fragments beyond canonical tRNA biology. RNA Biol Aug 2020; 17(8):1057-1059; doi: 10.1080/15476286.2020.1785196.
• Bracher, L.; Ferro, I.; Pulido-Quetglas, C.; Ruepp, M.-D.; Johnson, R. and Polacek, N. (2020). Human vtRNA1-1 Levels Modulate Signaling Pathways and Regulate Apoptosis in Human Cancer Cells. Biomolecules 2020, 10, 614.
•  Gonskikh Y., Gerstl M., Kos M., Borth N., Schosserer M., Grillari J. & Polacek N. (2020). Modulation of mammalian translation by a ribosome-associated tRNA half. RNA Biol., doi.org/10.1080/15476286.2020.1744296
• Shankar V., Rauscher R., Reuther J., Gharib W.H., Koch M. and Polacek N. (2020). rRNA expansion segment 27Lb modulates the factor recruitment capacity of the yeast ribosome and shapes the proteome. Nucleic Acids Research, 2020, in press; doi:10.1093/nar/gkaa003

2019

• Heissenberger C., Liendl L., Nagelreiter F., Gonskikh Y., Yang G., Stelzer EM., Krammer TL., Micutkova L., Vogt S., Kreil DP., Sekot G., Siena E., Poser I., Harreither E., Linder A., Ehret V., Helbich TH., Grillari-Voglauer R., Jansen-Dürr P., Koš M., Polacek N., Grillari J. and Schosserer M. (2019). Loss of the ribosomal RNA methyltransferase NSUN5 impairs global protein synthesis and normal growth. Nucleic Acids Research, 2019, doi: 10.1093/nar/gkz1043.
• Shikha S., Brogli R., Schneider A. and Polacek N. (2019). tRNA Biology in Trypanosomes. Chimia (Aarau). 2019 May 29;73(6):395-405. doi: 10.2533/chimia.2019.395.
• Fricker R., Brogli R., Luidalepp H., Wyss L., Fasnacht M., Joss O., Zywicki M., Helm M., Schneider A., Cristodero M. and Polacek N. (2019). A tRNA half modulates translation as stress response in Trypanosoma brucei. Nat Commun. 2019 Jan 10;10(1):118. doi: 10.1038/s41467-018-07949-6.
  • Press release from the University of Bern in German
• Press release from the University of Bern in English

2018

• Wyss L., Waser M., Gebetsberger J., Zywicki M. and Polacek N. (2018). mRNA-specific translation regulation by a ribosome-associated ncRNA in Haloferax volcanii. Sci Rep. 2018 Aug 21;8(1):12502. doi: 10.1038/s41598-018-30332-w.
• Hoernes TP., Clementi N., Juen MA., Shi X., Faserl K., Willi J., Gasser C., Kreutz C., Joseph S., Lindner H., Hüttenhofer A. and Erlacher MD. (2018). Atomic mutagenesis of stop codon nucleotides reveals the chemical prerequisites for release factor-mediated peptide release. Proc Natl Acad Sci U S A, doi: 10.1073/pnas.1714554115.
• Willi J., Küpfer P., Evéquoz D., Fernandez G., Katz A., Leumann Ch. and Polacek N. (2018). Oxidative stress damages rRNA inside the ribosome and differentially affects the catalytic center. Nucleic Acids Research, doi:10.1093/nar/gkx1308
  2017
• Cristodero M. and Polacek N. (2017). The multifaceted regulatory potential of tRNA-derived fragments. Non-coding RNA Investig 2017;1:7. doi: 10.21037/ncri.2017.08.07
• Gonskikh Y. and Polacek N. (2017). Alterations of the translation apparatus during aging and stress response. Mech Ageing Dev. 2017 Apr 13. pii: S0047-6374(16)30221-4. doi: 10.1016/j.mad.2017.04.003.
• Koch, M., Willi, J., Pradère, U., Hall, J. and Polacek, N. (2017). Critical 23S rRNA interactions for
  macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain. Nucleic Acids Res.: doi:10.1093/nar/gkx195

  - Press release from the University of Bern in German

- Press release from the University of Bern in English

2016

• Gebetsberger,  J., Wyss, L., Mleczko,  A.M., Reuther,  J., and Polacek,  N. (2016). A tRNA-derived fragment competes with mRNA for ribosome binding and regulates translation during stress. RNA Biol., doi.org/10.1080/15476286.2016.1257470
• Luidalepp H., Berger S., Joss O., Tenson T. and Polacek N. (2016). Ribosome Shut-Down by 16S rRNA Fragmentation in Stationary-Phase Escherichia coli. J Mol Biol. 2016 Apr 8. pii: S0022-2836(16)30048-1.

2015

• Amort M., Nachbauer B., Tuzlak S., Kieser A., Schepers A., Villunger A. and Polacek N. (2015). Expression of the vault RNA protects cells from undergoing apoptosis. Nat Commun. May 8; 6:7030. doi: 10.1038/ncomms8030.
• Koch, M., Flür, S., Kreutz, C., Ennifar, E., Micura, R. and Polacek, N. (2015). Role of a ribosomal RNA phosphate oxygen during the EF-G–triggered GTP hydrolysis. PNAS; May 4, doi:10.1073/pnas.1505231112
• Koch, M., Clementi, N., Rusca, N., Vögele, P., Erlacher, M., and  Polacek, N. (2015). The integrity of the G2421-C2395 base pair in the ribosomal E-site is crucial for protein synthesis. RNA Biol. 12:70-81.
• Gebetsberger, J., Fricker, R., and Polacek, N. (2015). cDNA library generation for the analysis of small RNAs by high-throughput sequencing. Methods Mol. Biol. 1296:139-149.
• Schosserer M. et al. (2015). Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan. Nature Comm. 6: 6158.

2014

• Pircher A., Gebetsberger J. and Polacek N. (2014). Ribosome-associated ncRNAs: An emerging class of translation regulators. RNA Biology 11:11, 1335-1339.
• Pircher, A., Bakowska-Zywicka, K., Schneider, L., Zywicki, M., and Polacek, N. (2014).
  An mRNA-derived noncoding RNA targets and regulates the ribosome. Mol. Cell 54: 147-155.

2013

• Polacek N., Gebetsberger J. (2013). Slicing tRNAs to boost functional ncRNA diversity.RNA Biol., 10:1798-1806
• Polacek, N. (2013). Atomic Mutagenesis of the Ribosome: Towards a Molecular Understanding of
  Translation. CHIMIA 2013, 67, Nr. 5
  

2012

• Gebetsberger, J., Zywicki, M., Künzi, A. and Polacek N. (2012). tRNA-Derived Fragments Target the Ribosome and Function as Regulatory Non-Coding RNA in Haloferax volcanii. Archea doi:10.1155/2012/260909
• Erlacher, M. and Polacek, N. (2012). Probing functions of the ribosomal peptidyl transferase center by nucleotide analog interference. Methods Mol. Biol. 848:215-226
• Graber, D., Trappl, K., Steger, J., Geiermann A.S., Rigger, L., Moroder H., Polacek, N. and Micura, R.(2012). Deoxyribozyme-based, semisynthetic access to stable peptidyl-tRNAs exemplified by tRNA(Val) carrying a macrolide antibiotic resistance peptide. Methods Mol. Biol. 848:201-213.

• Zywicki, M., Bakowska-Zywicka, K. and  Polacek, N. (2012). Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis. Nucleic Acids Res.: doi:10.1093/nar/gks020

2011

• Geiermann, A.-S., Polacek, N. and Micura R. (2011). Native chemical ligation of hydrolysis-resistant 3’-peptidyl-tRNA mimics. J. Am. Chem. Soc. 133:19068-19071.
• Erlacher, M., Chirkova, A., Voegele, P. and Polacek, N. (2011). Generation of chemically engineered ribosomes for atomic mutagenesis studies on protein biosynthesis. Nature Prot., 6:580-592.
• Polacek, N. (2011). The ribosome meets synthetic biology. ChemBioChem 19: 2122-2124.
• Trappl, K., and Polacek, N. (2011). The ribosome: A molecular machine powered by RNA. In: Metal Ions Life Sci. 9 (Structural and Catalytic Roles of Metal Ions in RNA):253-275.

2010

• Graber, D., Moroder, H., Steger, J., Trappl, K., Polacek, N. and Micura, R. (2010). Reliable semi-synthesis of hydrolysis-resistant 3’-peptidyl-tRNA conjugates containing genuine tRNA modifications. Nucleic Acids Res., 38:6796-6802.
• Clementi, N., Chirkova, A., Puffer, B., Micura, R. and Polacek, N. (2010). Atomic mutagenesis reveals A2660 of 23S ribosomal RNA as key to EF-G GTPase activation. Nature Chem. Biol., 6:344-351.
• Chirkova, A., Erlacher, M., Clementi, N., Zywicki, M., Aigner, M., and Polacek, N. (2010). The role of the universally conserved A2450-C2063 base pair in the ribosomal peptidyl transferase center. Nucleic Acids Res., 38:4844-4855.
• Clementi, N., and Polacek, N. (2010). Ribosome-associated GTPases: The role of RNA for GTPase activation. RNA Biol., 7:521-527.
• Chirkova, A., Erlacher, M., Micura, R, and Polacek, N. (2010). Chemically engineered ribosomes: a new frontier in synthetic biology. Curr. Org. Chem., 14:148-161.

2009

1. Hutzinger, R., Feederle, R., Mrazek, J., Schiefermeier, N., Balwierz, P.J., Zavolan, M., Polacek, N., Delecluse H.-J., and Hüttenhofer, A. (2009). Expression and processing of a small nucleolar RNA from the Epstein-Barr virus genome. PLoS Pathogens, 5:e1000547.
2. Nandy, C., Mrazek, J., Stoiber, H., Grässer, F.A., Hüttenhofer, A., and Polacek, N. (2009). Epstein-Barr virus-induced expression of a novel human vault RNA. J. Mol. Biol., 388:776-784.
3. Moroder, H., Steger, J., Graber, D., Fauster, K., Trappl, K., Marquez, V., Polacek, N., Wilson, D. W., and Micura, R. (2009). Non-hydrolyzable RNA-peptide conjugates: a powerful advance in the synthesis of mimics for 3'-peptidyl tRNA termini. Angew. Chem., 48:4056-4060.
4. Rieder, U., Lang, K., Kreutz, C., Polacek, N., and Micura, R. (2009). Evidence for pseudoknot formation of class I preQ1 riboswitch aptamers. ChemBioChem., 10:1141-1144.
5. Erlacher, M. D., and Polacek, N. (2009). Role of RNA backbone groups for ribosomal catalysis. Biotechnologia, 1 (84):65-80.

2008

• Lang, K., Erlacher, M. D., Wilson, D. N., Micura, R., and Polacek, N. (2008). The role of 23S ribosomal RNA residue A2451 in peptide bond formation revealed by atomic mutagenesis. Chem Biol, 15:485-492.
• Erlacher, M. D., and Polacek, N. (2008). Ribosomal catalysis: The evolution of mechanistic concepts for peptide bond formation and peptidyl-tRNA hydrolysis. RNA Biol., 5:5-12.
• Mankin, A.S., and Polacek, N. (2008). SPARK – A new peptidyl transferase activity assay. In: Champney S. eds. New Antibiotic Targets. Totowa, NJ: Humana Press Inc., Methods in Molecular Medicine 142:107-116.

2007

• Amort, M., Wotzel, B., Bakowska-Zywicka, K., Erlacher, M. D., Micura, R., and Polacek, N. (2007). An intact ribose moiety at A2602 of 23S rRNA is key to trigger peptidyl-tRNA hydrolysis during translation termination. Nucleic Acids Res., 35:5130-5140.
• Mrazek, J., Kreutmayer, S. B., Grässer, F. A., Polacek, N., and Hüttenhofer, A. (2007). Subtractive hybridization identifies novel differentially expressed ncRNA species in EBV infected human B cells. Nucleic Acids Res., 35:e73.
  2006
• Qin, Y., Polacek, N., Vesper, O., Staub, E., Einfeldt, E., Wilson, D., and Nierhaus, K.H. (2006). The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome. Cell 127:721-733.
• Erlacher, M.D., Lang, K., Wotzel, B., Rieder, R., Micura, R., and Polacek, N. (2006). Efficient ribosomal peptidyl transfer critically relies on the presence of the ribose 2'-OH at A2451 of 23S rRNA. J. Am. Chem. Soc. 128:4453-4459.

2005

• Erlacher, M.D., Lang, K., Shankaran, N., Wotzel, B., Hüttenhofer, A., Micura, R., Mankin, AS. and Polacek, N. (2005). Chemical engineering of the peptidyl transferase center reveals an important role of the 2’-hydroxyl group of A2451. Nucleic Acids Res. 33:1618-1627.
• Thang, TH., Polacek, N., Zywicki, M., Huber, H., Brügger, K., Garrett, R., Bachellerie, JP., and Hüttenhofer, A. (2005). Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus. Mol. Micro. 55:469-481.
• Hüttenhofer, A., Schattner, P., and Polacek, N. (2005). Non-coding RNAs: hope or hype? Trends Genet. 21:289-297.
• Polacek, N., and Mankin, A.S. (2005). The Ribosomal Peptidyl Transferase Center: Structure, Function, Evolution, Inhibition. Crit. Rev. Biochem. Mol. 40:285-311.

2003

• Polacek, N., Gomez, MJ., Ito, K., Xiong, L., Nakamura, Y., and Mankin, AS. (2003). The critical role of the universally conserved A2602 of 23S ribosomal RNA in the release of the nascent peptide during translation termination. Mol. Cell 11:103-112.

2002

• Polacek, N., Swaney, S., Shinarbarger, D., and Mankin, AS. (2002). SPARK-A novel method to monitor ribosomal peptidyl transferase activity. Biochem. 41:11602-11610.
• Dorner, S., Polacek, N., Schulmeister, U., Panuschka, C., and Barta, A. (2002). Molecular aspects of ribosomal peptidyl transferase. Biochem. Soc. Trans. 30:1131-1137.

2001

• Xiong, L., Polacek, N., Sander, P., Böttger, EC., and Mankin AS. (2001). pKa of adenine 2451 in the ribosomal peptidyl transferase center remains elusive. RNA 7:1365-1369.
• Polacek, N., Gaynor, M., Yassin, A. and Mankin, AS. (2001). Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide. Nature 441:498-501.
• Barta, A., Dorner, S., Polacek, N. (2001). Mechanism of ribosomal peptide bond formation. Science 291:203a.
• Polacek, N. (2001). Peptidyl transferase directed drugs: Inhibitors of an RNA-enzyme? In: Schroeder R., Wallis M.G., eds. RNA-binding Antibiotics. Georgetown, Texas: Landes Bioscience, 1-11.

2000

• Polacek, N., Patzke, S., Nierhaus, K.H. and Barta, A. (2000). Periodic conformational changes in rRNA: Monitoring the dynamics of translating ribosomes. Mol. Cell 6:159-171.

1998

• Polacek, N. and Barta, A. (1998). Metal ion probing of rRNAs: Evidence for evolutionarily conserved divalent cation binding pockets. RNA 4:1282-1294.

1997

• Winter, D., Polacek, N., Halama, I., Streicher, B. and Barta, A. (1997). Lead-catalysed specific cleavage of ribosomal RNAs. Nucleic Acids Res. 25:1817-1824.
• Oehler, R., Polacek, N., Steiner, G. and Barta, A. (1997). Interaction of tetracycline with RNA: photoincorporation into ribosomal RNA of Escherichia coli. Nucleic Acids Res. 25:1219-1224.

Copyright © Norbert Polacek 2011 | Designed by Christina Schüpbach | Department of Chemistry and Biochemistry DCB | Bern