Tomas Kouba (0000-0001-8173-6930)

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IOCB Prague: Prague, CZ

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Tomas Kouba

Mycobacterial HelD connects RNA polymerase recycling with transcription initiation

Nature Communications

2024-10-09 | Journal article | Author

DOI: 10.1038/s41467-024-52891-5

Part of ISSN: 2041-1723

Contributors: Tomáš Kovaľ; Nabajyoti Borah; Petra Sudzinová; Barbora Brezovská; Hana Šanderová; Viola Vaňková Hausnerová; Alena Křenková; Martin Hubálek; Mária Trundová; Kristýna Adámková et al.

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Tomas Kouba

Deciphering the allosteric regulation of mycobacterial inosine-5′-monophosphate dehydrogenase

Nature Communications

2024-08-06 | Journal article

DOI: 10.1038/s41467-024-50933-6

Contributors: Ondřej Bulvas; Zdeněk Knejzlík; Jakub Sýs; Anatolij Filimoněnko; Monika Čížková; Kamila Clarová; Dominik Rejman; Tomáš Kouba; Iva Pichová

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Multivalency of nucleosome recognition by LEDGF

Nucleic Acids Research

2023-10-13 | Journal article

DOI: 10.1093/nar/gkad674

Contributors: Eliška Koutná; Vanda Lux; Tomáš Kouba; Jana Škerlová; Jiří Nováček; Pavel Srb; Rozálie Hexnerová; Hana Šváchová; Zdeněk Kukačka; Petr Novák et al.

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Direct observation of backtracking by influenza A and B polymerases upon consecutive incorporation of the nucleoside analog T1106

Cell Reports

2023-01 | Journal article

DOI: 10.1016/j.celrep.2022.111901

Part of ISSN: 2211-1247

Contributors: Tomas Kouba; Anna Dubankova; Petra Drncova; Elisa Donati; Pietro Vidossich; Valentina Speranzini; Alex Pflug; Johanna Huchting; Chris Meier; Marco De Vivo et al.

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Tomas Kouba

Conformational changes in Lassa virus L protein associated with promoter binding and RNA synthesis activity

Nature Communications

2021-12-02 | Journal article

DOI: 10.1038/s41467-021-27305-5

Contributors: Tomas Kouba; Dominik Vogel; Sigurdur R. Thorkelsson; Emmanuelle R. J. Quemin; Harry M. Williams; Morlin Milewski; Carola Busch; Stephan Günther; Kay Grünewald; Maria Rosenthal et al.

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Structure and Function of Influenza Polymerase

Cold Spring Harbor Perspectives in Medicine

2021-09-27 | Journal article

DOI: 10.1101/cshperspect.a038372

Contributors: Joanna M. Wandzik; Tomas Kouba; Stephen Cusack

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Conformational changes in Lassa virus L protein associated with promoter binding and RNA synthesis activity

2021-06-24 | Other

DOI: 10.1101/2021.06.24.449696

Contributors: Tomas Kouba; Dominik Vogel; Sigurdur R. Thorkelsson; Emmanuelle R. J. Quemin; Harry M. Williams; Morlin Milewski; Carola Busch; Stephan Günther; Kay Grünewald; Maria Rosenthal et al.

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Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase

Nature Communications

2020-12-18 | Journal article

DOI: 10.1038/s41467-020-20158-4

Contributors: Tomáš Kouba; Tomáš Koval’; Petra Sudzinová; Jiří Pospíšil; Barbora Brezovská; Jarmila Hnilicová; Hana Šanderová; Martina Janoušková; Michaela Šiková; Petr Halada et al.

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Structural and functional characterization of the severe fever with thrombocytopenia syndrome virus L protein.

Nucleic acids research

2020-06 | Journal article

DOI: 10.1093/nar/gkaa253

PMID: 32313945

PMC: PMC7261188

Contributors: Vogel D; Thorkelsson SR; Quemin ERJ; Meier K; Kouba T; Gogrefe N; Busch C; Reindl S; Günther S; Cusack S et al.

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Tomas Kouba via Europe PubMed Central

A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase.

Cell

2020-04 | Journal article

DOI: 10.1016/j.cell.2020.03.061

PMID: 32304664

Contributors: Wandzik JM; Kouba T; Karuppasamy M; Pflug A; Drncova P; Provaznik J; Azevedo N; Cusack S

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Tomas Kouba via Europe PubMed Central

Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changes.

Nucleic acids research

2019-09 | Journal article

DOI: 10.1093/nar/gkz570

PMID: 31291455

PMC: PMC6735954

Contributors: Zeman J; Itoh Y; Kukačka Z; Rosůlek M; Kavan D; Kouba T; Jansen ME; Mohammad MP; Novák P; Valášek LS

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Tomas Kouba via Europe PubMed Central

Structural snapshots of actively transcribing influenza polymerase.

Nature structural & molecular biology

2019-06 | Journal article

DOI: 10.1038/s41594-019-0232-z

PMID: 31160782

Contributors: Kouba T; Drncová P; Cusack S

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Tomas Kouba via Europe PubMed Central

The Core and Holoenzyme Forms of RNA Polymerase from Mycobacterium smegmatis.

Journal of bacteriology

2019-01 | Journal article

DOI: 10.1128/JB.00583-18

PMID: 30478083

PMC: PMC6351736

Contributors: Kouba T; Pospíšil J; Hnilicová J; Šanderová H; Barvík I; Krásný L

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Tomas Kouba via Europe PubMed Central

Structures of closed and open conformations of dimeric human ATM.

Science advances

2017-05 | Journal article

DOI: 10.1126/sciadv.1700933

PMID: 28508083

PMC: PMC5425235

Contributors: Baretić D; Pollard HK; Fisher DI; Johnson CM; Santhanam B; Truman CM; Kouba T; Fersht AR; Phillips C; Williams RL

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Tomas Kouba via Europe PubMed Central

Structural integrity of the PCI domain of eIF3a/TIF32 is required for mRNA recruitment to the 43S pre-initiation complexes.

Nucleic acids research

2014-01 | Journal article

DOI: 10.1093/nar/gkt1369

PMID: 24423867

PMC: PMC3973348

Contributors: Khoshnevis S; Gunišová S; Vlčková V; Kouba T; Neumann P; Beznosková P; Ficner R; Valášek LS

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Tomas Kouba via Europe PubMed Central

Small ribosomal protein RPS0 stimulates translation initiation by mediating 40S-binding of eIF3 via its direct contact with the eIF3a/TIF32 subunit.

PloS one

2012-07 | Journal article

DOI: 10.1371/journal.pone.0040464

PMID: 22792338

PMC: PMC3390373

Contributors: Kouba T; Dányi I; Gunišová S; Munzarová V; Vlčková V; Cuchalová L; Neueder A; Milkereit P; Valášek LS

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Tomas Kouba via Europe PubMed Central

The eIF3c/NIP1 PCI domain interacts with RNA and RACK1/ASC1 and promotes assembly of translation preinitiation complexes.

Nucleic acids research

2011-11 | Journal article

DOI: 10.1093/nar/gkr1083

PMID: 22123745

PMC: PMC3315329

Contributors: Kouba T; Rutkai E; Karásková M; Valášek L

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Tomas Kouba via Europe PubMed Central

Rapid changes in gene expression: DNA determinants of promoter regulation by the concentration of the transcription initiating NTP in Bacillus subtilis.

Nucleic acids research

2011-02 | Journal article

DOI: 10.1093/nar/gkr032

PMID: 21303765

PMC: PMC3113569

Contributors: Sojka L; Kouba T; Barvík I; Sanderová H; Maderová Z; Jonák J; Krásny L

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Tomas Kouba via Europe PubMed Central

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.

Molecular and cellular biology

2010-08 | Journal article

DOI: 10.1128/MCB.00430-10

PMID: 20679478

PMC: PMC2950517

Contributors: Cuchalová L; Kouba T; Herrmannová A; Dányi I; Chiu WL; Valásek L

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Tomas Kouba via Europe PubMed Central

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Tomas Kouba

https://orcid.org/0000-0001-8173-6930

Personal information

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Employment (1)

IOCB Prague: Prague, CZ

Works (19)

Mycobacterial HelD connects RNA polymerase recycling with transcription initiation

Deciphering the allosteric regulation of mycobacterial inosine-5′-monophosphate dehydrogenase

Multivalency of nucleosome recognition by LEDGF

Direct observation of backtracking by influenza A and B polymerases upon consecutive incorporation of the nucleoside analog T1106

Conformational changes in Lassa virus L protein associated with promoter binding and RNA synthesis activity

Structure and Function of Influenza Polymerase

Conformational changes in Lassa virus L protein associated with promoter binding and RNA synthesis activity

Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase

Structural and functional characterization of the severe fever with thrombocytopenia syndrome virus L protein.

A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase.

Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changes.

Structural snapshots of actively transcribing influenza polymerase.

The Core and Holoenzyme Forms of RNA Polymerase from Mycobacterium smegmatis.

Structures of closed and open conformations of dimeric human ATM.

Structural integrity of the PCI domain of eIF3a/TIF32 is required for mRNA recruitment to the 43S pre-initiation complexes.

Small ribosomal protein RPS0 stimulates translation initiation by mediating 40S-binding of eIF3 via its direct contact with the eIF3a/TIF32 subunit.

The eIF3c/NIP1 PCI domain interacts with RNA and RACK1/ASC1 and promotes assembly of translation preinitiation complexes.

Rapid changes in gene expression: DNA determinants of promoter regulation by the concentration of the transcription initiating NTP in Bacillus subtilis.

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.

Peer review (1 review for 1 publication/grant)