INSTITUTE OF MICROBIOLOGY OF THE CZECH ACADEMY OF SCIENCES

Laboratory of Microbial Genetics and Gene Expression

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Selected Publications

Muchová K, Pospíšil J, Kalocsaiová E, Chromiková Z, Žarnovičanová S, Šanderová H, Krásný L, Barák I. (2024) σE of Streptomyces coelicolor can function both as a direct activator or repressor of transcription. J Biol Chem. 107339. doi: 10.1016/j.jbc.2024.107339. PubMed

Vaňková Hausnerová V, Shoman M, Kumar D, Schwarz M, Modrák M, Jirát Matějčková J, Mikesková E, Neva S, Herrmannová A, Šiková M, Halada P, Novotná I, Pajer P, Valášek LS, Převorovský M, Krásný L, Hnilicová J. (2024) RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria. Nucleic Acids Res. 52(8):4604-4626. doi: 10.1093/nar/gkae081. PubMed

 Pospíšil J, Schwarz M, Ziková A, Vítovská D, Hradilová M, Kolář M, Křenková A, Hubálek M, Krásný L, Vohradský J. (2024) σE of Streptomyces coelicolor can function both as a direct activator or repressor of transcription. Commun Biol. 7(1):46. doi: 10.1038/s42003-023-05716-y. PubMed 

Burton AT, Pospíšilová D, Sudzinova P, Snider EV, Burrage AM, Krásný L, Kearns DB. (2023) The alternative sigma factor SigN of Bacillus subtilis is intrinsically toxic. J Bacteriol. 205(10):e0011223. doi: 10.1128/jb.00112-23. PubMed 

Tužinčin D, Padrta P, Šanderová H, Rabatinová A, Bendová K, Krásný L, Žídek L, Kadeřávek P. (2023) Characterization of a transitionally occupied state and thermal unfolding of domain 1.1 of SiA factor of RNA polymerase from Bacillus subtilis. Proteins. 91(9):1276-1287. doi: 10.1002/prot.26531. PubMed 

Sudzinová P, Šanderová H, Kovaľ T, Skálová T, Borah N, Hnilicová J, Kouba T, Dohnálek J, Krásný L (2023) What the Hel: Recent advances in rifampicin resistance in bacteria. FEMS Microbiol Rev. 47(6):fuac051. doi: 10.1093/femsre/fuac051. PubMed 

Do Pham DD, Mojr V, Helusová M, Mikušová G, Pohl R, Dávidová E, Šanderová H, Vítovská D, Bogdanová K, Večeřová R, Sedláková MH, Fišer R, Sudzinová P, Pospíšil J, Benada O, Křížek T, Galandáková A, Kolář M, Krásný L, Rejman D. (2022) LEGO-Lipophosphonoxins: A Novel Approach in Designing Membrane Targeting Antimicrobials. J Med Chem. 65(14):10045-10078. doi: 10.1021/acs.jmedchem.2c00684. PubMed

 Gracias F, Ruiz-Larrabeiti O, Vaňková Hausnerová V, Pohl R, Klepetářová B, Sýkorová V, Krásný L, Hocek M. (2022) Homologues of epigenetic pyrimidines: 5-alkyl-, 5-hydroxyalkyl and 5-acyluracil and -cytosine nucleotides: synthesis, enzymatic incorporation into DNA and effect on transcription with bacterial RNA polymerase. RSC Chem Biol. 3(8):1069-1075. doi: 10.1039/d2cb00133k. eCollection 2022 Aug 3. PubMed

Pospíšil Š, Panattoni A, Gracias F, Sýkorová V, Hausnerová VV, Vítovská D, Šanderová H, Krásný L, Hocek M. (2022) Epigenetic Pyrimidine Nucleotides in Competition with Natural dNTPs as Substrates for Diverse DNA Polymerases. ACS Chem Biol.  doi: 10.1021/acschembio.2c00342. PubMed

Vaňková Hausnerová V, Marvalová O, Šiková M, Shoman M, Havelková J, Kambová M, Janoušková M, Kumar D, Halada P, Schwarz M, Krásný L, Hnilicová J, Pánek J. (2022) Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search. Front Microbiol. 13:848536. doi: 10.3389/fmicb.2022.848536. PubMed

Chakrapani A, Ruiz-Larrabeiti O, Pohl R, Svoboda M, Krásný L, Hocek M. (2022) Glucosylated 5-Hydroxymethylpyrimidines as Epigenetic DNA Bases Regulating Transcription and Restriction Cleavage.Chemistry, 28(31):e202200911. PubMed

Wiedermannová J, Krásný L (2021) β-CASP proteins removing RNA polymerase from DNA: when a torpedo is needed to shoot a sitting duck. Nucleic Acids Res 49(18):10221-10234. doi: 10.1093/nar/gkab803.PubMed
Do Pham DD, Jenčová V, Kaňuchová M, Bayram J, Grossová I, Šuca H, Urban L, Havlíčková K, Novotný V, Mikeš P, Mojr V, Asatiani N, Košťáková EK, Maixnerová M, Vlková A, Vítovská D, Šanderová H, Nemec A, Krásný L, Zajíček R, Lukáš D, Rejman D, Gál P. (2021) Novel lipophosphonoxin-loaded polycaprolactone electrospun nanofiber dressing reduces Staphylococcus aureus induced wound infection in mice. Sci Rep. 11(1):17688. PubMed
Benda M, Woelfel S, Faßhauer P, Gunka K, Klumpp S, Poehlein A, Kálalová D, Šanderová H, Daniel R, Krásný L, Stülke J. (2021) Quasi-essentiality of RNase Y in Bacillus subtilis is caused by its critical role in the control of mRNA homeostasis. Nucleic Acids Res. 2021 49(12):7088-7102. PubMed
Vohradsky J, Schwarz M, Ramaniuk O, Ruiz-Larrabeiti O, Vaňková Hausnerová V, Šanderová H, Krásný L. (2021) Kinetic Modeling and Meta-Analysis of the Bacillus subtilis SigB Regulon during Spore Germination and Outgrowth. Microorganisms 9(1):112. PubMed
Sudzinová P, Kambová M, Ramaniuk O, Benda M, Šanderová H, Krásný L. (2021) Effects of DNA Topology on Transcription from rRNA Promoters in Bacillus subtilis. Microorganisms 9(1):87. PubMed
Kouba T, Koval' T, Sudzinová P, Pospíšil J, Brezovská B, Hnilicová J, Šanderová H, Janoušková M, Šiková M, Halada P, Sýkora M, Barvík I, Nováček J, Trundová M, Dušková J, Skálová T, Chon U, Murakami KS, Dohnálek J, Krásný L. (2020) Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase. Nat Commun. 11(1):6419. doi: 10.1038/s41467-020-20158-4. PubMed
Chakrapani A, Vaňková Hausnerová V, Ruiz-Larrabeiti O, Pohl R, Krásný L, Hocek M. (2020) Photocaged 5-(Hydroxymethyl)pyrimidine Nucleoside Phosphoramidites for Specific Photoactivatable Epigenetic Labeling of DNA. Org Lett. 2020 22(22):9081-9085. PubMed

Pospíšil J, Vítovská D, Kofroňová O, Muchová K, Šanderová H, Hubálek M, Šiková M, Modrák M, Benada O, Barák I, Krásný L. (2020)  Bacterial nanotubes as a manifestation of cell death. Nat Commun. (2020) 11(1):4963. doi: 10.1038/s41467-020-18800-2. PubMed 

Schäfer H, Beckert B, Frese CK, Steinchen W, Nuss AM, Beckstette M, Hantke I, Driller K, Sudzinová P, Krásný L, Kaever V, Dersch P, Bange G, Wilson DN, Turgay K. (2020) The alarmones (p)ppGpp are part of the heat shoc response in Bacillus subtilis. PLoS Genet. 16(3):e1008275. PubMed 

Hudeček, O., Benoni, R., Reyes-Gutierrez, P. E., Culka, M., Šanderová, H., Hubálek, M., Rulíšek, L., Cvačka, J., Krásný, L., Cahová, H. (2020) Dinucleoside polyphosphates act as 5’-RNA caps in bacteria. Nat. Comm. 26;11(1):1052. PubMed 

Zborníková, E.,Gallo, J., Večeřová, R.,; Bogdanova, K., Kolář, M., Vítovská, D., Do Pham, D. D., Paces, O., Mojr, V., Šanderová, H., Ulrichová, J., Galandáková, A., Čadek, D., Hrdlička, Z., Krásný, L., Rejman, D. (2020) Evaluation of 2nd generation lipophosphonoxins as antimicrobial additives in bone cement. ACS Omega 12;5(7):3165-3171. PubMed 

Šiková, M., Wiedermannová, J., Převorovský, M., Barvík, I., Sudzinová, P., Kofroňová, O., Benada, O., Šanderová, H., Condon, C., Krásný, L. (2020) The Torpedo Effect in Bacillus subtilis: RNase J1 Resolves Stalled Transcription Complexes. EMBO J  39(3):e102500. doi: 10.15252/embj.2019102500. PubMed

Kubáň V, Srb P, Štégnerová H, Padrta P, Zachrdla M, Jaseňáková Z, Šanderová H, Vítovská D, Krásný L, Koval' T, Dohnálek J, Ziemska-Legiecka J, Grynberg M, Jarnot P, Gruca A, Jensen MR, Blackledge M, Žídek L. (2019) Quantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase. J Am Chem Soc. 141(42):16817-16828. PubMed

Zborníková E, Knejzlík Z, Hauryliuk V, Krásný L, Rejman D. (2019) Analysis of nucleotide pools in bacteria using HPLC-MS in HILIC mode. Talanta. 205:120161. PubMed

Kovaľ, T., Sudzinová, P., Perháčová, T., Trundová, M., Skálová, T., Fejfarová, K., Šanderová, H., Krásný, L., Dušková, J., Dohnálek, J. (2019) Domain structure of HelD – an RNAP interacting partner from Bacillus subtilis. FEBS Letters 593(9):996-1005. doi: 10.1002/1873-3468.13385. PubMed

Vaníková, Z, Martina Janoušková, M., Kambová, M., Krásný and Hocek, M. (2019) Switching transcription with bacterial RNA polymerase through photocaging, photorelease and phosphorylation reactions in the major groove of DNA. Chemical Science, 10(14):3937-3942. PubMed

Šiková M, Janoušková M, Ramaniuk O, Páleníková P, Pospíšil J, Bartl P, Suder A, Pajer P, Kubičková P, Pavliš O, Hradilová M, Vítovská D, Šanderová H, Převorovský M, Hnilicová J, Krásný L. (2019) Ms1 increases the amount of RNA polymerase in Mycobacterium smegmatis. Mol Microbiol. 111(2):354-372. PubMed

Schäfer H, Heinz A, Sudzinová P, Voß M, Hantke I, Krásný L, Turgay K. (2019) Spx, the central regulator of the heat and oxidative stress response in B. subtilis can repress transcription of translation-related genes. Mol Microbiol. 111(2):514-533. PubMed

Kouba T, Pospíšil J, Hnilicová J, Šanderová H, Barvík I, Krásný L. (2019) The core and holoenzyme forms of RNA polymerase from Mycobacterium smegmatis. J. Bacteriol 201(4). pii: e00583-18. doi: 10.1128/JB.00583-18. PubMed

Sykora, M., Pospisek, M., Novak, J., Mrvova, S., Krásný, L., Vopalensky, V. (2018) Transcription apparatus of the yeast virus-like elements: Architecture, function, and evolutonary origin. PLoS Pathog. 14(10):e1007377. PubMed

Ramaniuk O, Převorovský M, Pospíšil J, Vítovská D, Kofroňová O, Benada O, Schwarz M, Šanderová H, Hnilicová J, Krásný L. (2018) sI from Bacillus subtilis: Impact on gene expression and characterization of sI-dependent transcription that requires new types of promoters with extended -35 and -10 elements. J. Bacteriol pii: e00251-18. doi: 10.1128/JB.00251-18. PubMed

Vvedenskaya, I. O., Bird, J. G., Zhang, Y, Zhang, Y, Jiao, X., Barvík, I., Krásný, L., Kiledjian, M., Taylor, D. M., Ebright, R. H., Nickels, B. E. (2018) "CapZyme-Seq" comprehensively defines promoter-sequence determinants for RNA 5' capping with NAD+. Mol Cell 3;70(3):553-564. PubMed

Slavíčková, M., Janoušková, M., Šimonová, A., Cahová, H., Kambová, M., Šanderová, H., Krásný, L., Hocek, M. (2018) Turning off transcription with bacterial RNA polymerase through CuAAC clisk reactions of DNA containing 5-ethylenuracil. Chemistry - A European Journal 24(33):8311-8314. PubMed

Janoušková, M., Vaníková, Z., Nici, F., Boháčová, S., Vítovská, D., Šanderová, H., Hocek, M., and Krásný, L. (2017) 5-(Hydroxymethyl)uracil and -cytosine as potential epigenetic marks enhancing or inhibiting transcription with bacterial RNA polymerase. Chem Comm 53(99):13253-13255. PubMed

Srb, P., Nováček, J., Kadeřávek, P., Rabatinová, A., Krásný, L., Žídková, J., Bobálová, J., Sklenář, V., Žídek, L. (2017) Triple resonance 15N NMR relaxation experiments for studies of intrinsically disordered proteins. J. Biomol. NMR. 69(3):133-146. PubMed

Seydlová G, Pohl R, Zborníková E, Ehn M, Simak O, Panova N, Kolar M, Bogdanova K, Vecerova R, Fiser R, Šanderová H, Vítovská D, Sudzinová P, Pospíšil J, Benada O, Křížek T, Sedlak D, Bartunek P, Krasny L, Rejman D. (2017)Lipophosphonoxins II: Design, Synthesis and Properties of Novel Broad Spectrum Antibacterial Agents. J Med Chem. 60(14):6098-6118. PubMed

Ramaniuk O, Černý M, Krásný L, Vohradský J (2017) Kinetic modelling and meta-analysis of the B. subtilis SigA regulatory network during spore germination and outgrowth. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms1860(8):894-904. PubMed

Zachrdla M, Padrta P, Rabatinová A, Šanderová H, Barvík I, Krásný L, Žídek L (2017)Solution Structure of Domain 1.1 of the σA Factor from Bacillus subtilis is Preformed for Binding to the RNA Polymerase Core. J Biol Chem 292(28): 11640-17. PubMed

Barvík, I., Rejman, D., Panova, N., Šanderová, H., Krásný, L. (2017) Non-canonical transcription initiation: The expanding universe of transcription initiating substrates FEMS Microbiol Rev 41(2): 131-8. PubMed

Bird, J. G., Zhang, Y, Tian, Y, Panova, N, Barvík, I, Greene, L, Liu, M, Buckley, B, Krásný, L, Lee, J. K, Kaplan, C.D., Ebright, R.E., Nickels, B. E. (2016) The mechanism of RNA 5' capping with NAD+, NADH, and desphospho-CoA. Nature, 535(7612):444-447.  PubMed

Raindlová, V., Janoušková, M., Slavíčková, M., Perlíková, P., Boháčová, S.,  Milisavljevič, N., Šanderová, H., Benda, M., Barvík, I., Krásný, L. and Hocek, M. (2016) Influence of major-groove chemical modifications of DNA on transcription by bacterial RNA polymerases. Nucleic Acids Res, 44(7):3000-12. PubMed

Panova, N., Zborníková,E., Šimák, O., Pohl, R., Kolář, M., Bogdanová, K., Večeřová, R., Seydlová,G., Fišer, R., Hadravová, R., Šanderová, H., Vítovská, D., Šiková, M., Látal, T., Lovecká, P., Barvík, I., Krásný, L., Rejman, R. (2015) Insights into the mechanism of action of bactericidal lipophosphonoxins. PLOS ONE, 10(12)e0145918. PubMed

Hnilicová, J., Jirát Matějčková, J., Šiková, M., Pospíšil, J., Halada, P., Pánek, J., Krásný, L. (2014) Ms1, a novel sRNA interacting with the RNA polymerase core in mycobacteria. Nucleic Acids Res 42(18):11763-76. PubMed

Keller, A., Yang, X., Wiedermannová, J., Delumeau, O., Krásný, L., Lewis, P. J. (2014)Epsilon: A new subunit of RNA polymerase found in Gram positive bacteria. J Bacteriol 196(20): 3622-32. PubMed

Demo, G., Papoušková, V., Komárek, J., Kadeřávek, P., Otrusinová, O., Srb, P., Rabatinová, A., Krásný, L., Žídek, L., Sklenář, V., and Wimmerová, M. (2014) X-ray vs. NMR structure of N-terminal domain of delta subunit of RNA polymerase. J Struct Biol 187(2): 174-86. PubMed

Wiedermannová, J., Sudzinová, P., Kovaľ, T., Rabatinová, A., Šanderová, H., Ramaniuk, O., Rittich, Š., Dohnálek, J., Zhihui, F., Halada, P., Lewis, P., Krásný, L. (2014)Characterization of HelD, an interacting partner of RNA polymerase from Bacillus subtilis. Nucleic Acids Res 42(8): 5151-63. PubMed

 Kadeřávek, P., Zapletal, V., Rabatinová, A., Krásný, L., Sklenář, V., Žídek, L. (2014)Spectral density mapping protocols for analysis of molecular motions in disordered proteins. J Biomol NMR 58(3): 193-207. PubMed

Papoušková, V., Kadeřávek, P., Otrusinová, O., Rabatinová., A., Šanderová, H., Nováček, J., Krásný, L., Sklenář, V., Žídek, L. (2013) Structural study of the partially disordered full length delta subunit of RNA polymerase from Bacillus subtilis. Chembiochem 14(14): 1772-9. PubMed

Rabatinová, A., Šanderová, H., Jirát Matějčková, Korelusová, J., Sojka, L., Barvík, I., Papoušková, V., Sklenář, V., Žídek, L., and Krásný, L. (2013) The delta subunit of RNA polymerase is required for rapid changes in gene expression and competitive fitness of the cell. J Bacteriol 195(11): 2603-11. PubMed

Rochat T, Nicolas P, Delumeau O, Rabatinová A, Korelusová J, Leduc A, Bessières P, Dervyn E, Krásný L, and Noirot P. (2012) Genome-wide identification of genes directly regulated by the pleiotropic transcription factor Spx in Bacillus subtilis.Nucleic Acids Res 40 (19): 9571-9573. PubMed

Holátko, J., Šilar, R., Rabatinová, A., Šanderová, H., Halada, P., Nešvera, J., Krásný, L., Pátek, M. (2012) Construction of in vitro transcription system for Corynebacterium glutamicum and its use in the recognition of promoters of different classes. Appl Microbiol Biotechnol 96(2): 521-9. PubMed

Zawadska-Kazimierczuk, A., Kozminski, W., Sanderova, H., and Krasny, L. (2012) High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins. J Biomol NMR 52: 329-37. PubMed

Rejman, D., Rabatinová, A., Pombinho, A., .Kovačková, S. ,Pohl, R, Zborníková, E.,Kolář, M., Bogdanová, K., Nyč, O., Šanderová, H., Látal, T., Bartůněk, P.,Krásný, L. (2011) Lipophosphonoxins – new modular molecular structures with significant antibacterial properties. J Med Chem 54(22): 7884-7898. PubMed

Sojka L, Kouba T, Barvík I, Sanderová H, Maderová Z, Jonák J, Krásny L. (2011) Rapid changes in gene expression: DNA determinants of promoter regulation by the concentration of the transcription initiating NTP in Bacillus subtilis. Nucleic Acids Res  39(11): 4598-611. PubMed

Nováček J, Zawadzka-Kazimierczuk A, Papoušková V, Zídek L, Sanderová H, Krásný L, Koźmiński W, Sklenář V. (2011) 5D (13)C-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion. J Biomolecular NMR  50(1): 1-11. PubMed 

Pánek, J., Krásný, L., Bobek, J., Ježková, E., Korelusová, J., Vohradský, J.(2011) The suboptimal structures find the optimal RNAs: homology search for bacterial non-coding RNAs using suboptimal RNA structures. Nucleic Acids Res. 39(8):3418-26.PubMed

Motáčková V., Nováček, J., Zawadska-Kazimierczuk, A., Kazimierczuk, K., Žídek, L., Šanderová, H., Krásný, L., Koźmiński, W., and Sklenář, V. (2010) Strategy for complete NMR assignement of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments. J Biomolecular NMR , 48(3):169-77. PubMed

Motáčková V., Šanderová H., Zídek L., Nováček J., Padrta P., Švenková A., Korelusová J., Jonák J., Krásný L., Sklenář V. (2010) Solution structure of the N-terminal domain of Bacillus subtilis delta subunit of RNA polymerase and its classification based on structural homologs. Proteins, 78(7):1807-10. PubMed

Novák, P., Žídek, L., Motáčková, V., Padrta, P., Švenková, A., Nuzillard, J. M., Krásný, L., Sklenář, V. (2010) S3EPY: a Sparky extension for determination of small scalar couplings from spin-state-selective excitation NMR experiments. J Biomolecular NMR 46:191-7. PubMed

Šanderová H, Tišerová H, Barvík I, Sojka L, Jonák J, Krásný L. (2010) The N-terminal region is crucial for the thermostability of the G-domain of Bacillus stearothermophilus EF-Tu.BBA Proteins & Proteomics 1804: 147-155. PubMed

Rejman D, Pohl R, Kovacková S, Kocalka P, Svenková A, Sanderová H, Krásný L, Rosenberg I. (2008) Pyrrolidine analogues of nucleosides and nucleotides. Nucleic Acids Symp Ser (Oxf). 52:577-8. PubMed

Krásný, L., Tišerová, H., Jonák, J., Rejman, D., and Šanderová, H. (2008) The identity of the transcription +1 position is crucial for changes in gene expression  in response to amino acid starvation in Bacillus subtilis. Mol Microbiol 69: 42-54. PubMed

Sojka, L., Fučík, V., Krásný, L, Barvík, I., and Jonák, J. (2007) YbxF – a protein associated with exponential phase ribosomes in Bacillus subtilis. J. Bacteriol 189: 4809-14. PubMed

Krásný, L. and Gourse R. L. (2004) An alternative strategy for bacterial ribosome synthesis: Bacillus subtilis rRNA transcription regulation. EMBO J.  23:4473-4483. PubMed

Tomincová, H., Krásný, L., and Jonák, J. (2002) Isolation of chimaeric forms of elongation factor EF-Tu by affinity chromatography. J Chromatogr B Analyt Technol Biomed Life Sci.,770: 129-135. PubMed

Krásný, L., Vacík, T., Fučík, V. and Jonák, J. (2000) Cloning and characterization of the str operon and elongation factor Tu expression in Bacillus stearothermophilus. J. Bacteriol., 182, 6114-6122. PubMed

Fučík, V., Beran, J., Krásný, L. and Jonák, J. (2000) Effect of host bacteria genotype on spontaneous reversions of Bacillus subtilis bacteriophage Phi29 sus17 nonsense codon. FEMS Microbiol. Lett. 183, 143-146. PubMed

Krásný, L., Mesters, J. R., Tieleman, L. N., Kraal, B., Fučík, V., Hilgenfeld, R. and Jonák, J. (1998) Structure and expression of elongation factor Tu from Bacillus stearothermophilus. J. Mol. Biol., 283, 371-381. PubMed

Vlášková, H., Krásný, L., Fučík, V., and Jonák, J. (1998) The pyrAb gene coding for the large subunit of carbamoylphosphate synthetase from Bacillus stearothermophilus: molecular cloning and functional characterization. Folia Biol (Prague), 44(5):163-72. PubMed