Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors sigmaD and sigmaH deciphered using computer modeling and point mutagenesis

Blumenstein, J.; Dostálová, H.; Rucká, L.; Stepánek, V.; Busche, Tobias; Kalinowski, Jörn; Pátek, M.; Barvík, I.

Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors sigmaD and sigmaH deciphered using computer modeling and point mutagenesis

Blumenstein J, Dostálová H, Rucká L, Stepánek V, Busche T, Kalinowski J, Pátek M, Barvík I (2024)
Journal of Computer-Aided Molecular Design 39(1): 1.

Zeitschriftenaufsatz | Veröffentlicht | Englisch

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DOI

https://doi.org/10.1007/s10822-024-00577-x

Autor*in

Blumenstein, J.; Dostálová, H.; Rucká, L.; Stepánek, V.; Busche, Tobias^UniBi; Kalinowski, Jörn^UniBi; Pátek, M.; Barvík, I.

Einrichtung

Centrum für Biotechnologie - CeBiTec > Omics Core Facility - Leitung Next-Generation Sequencing
Centrum für Biotechnologie > Technologieplattformen > Technologieplattform Genomik
Centrum für Biotechnologie > Arbeitsgruppe J. Kalinowski

Abstract / Bemerkung

This study aimed to reveal interactions of the stress response sigma subunits (factors) sigmaD and sigmaH of RNA polymerase and promoters in Gram-positive bacterium Corynebacterium glutamicum by combining wet-lab obtained data and in silico modeling. Computer modeling-guided point mutagenesis of C. glutamicum sigmaH subunit led to the creation of a panel of sigmaH variants. Their ability to initiate transcription from naturally occurring hybrid sigmaD/sigmaH-dependent promoter Pcg0441 and two control canonical promoters (sigmaD-dependent PrsdA and sigmaH-dependent PuvrD3) was measured and interpreted using molecular dynamics simulations of homology models of all complexes. The results led us to design the artificial hybrid promoter PD35H10 combining the-10 element of the PuvrD3 promoter and the-35 element of the PrsdA promoter. This artificial hybrid promoter PD35-rsdAH10-uvrD3 showed almost optimal properties needed for the bio-orthogonal transcription (not interfering with the native biological processes). © 2024. The Author(s).

Erscheinungsjahr

2024

Zeitschriftentitel

Journal of Computer-Aided Molecular Design

Band

Ausgabe

Art.-Nr.

eISSN

1573-4951

Page URI

https://pub.uni-bielefeld.de/record/2999351

Zitieren

Blumenstein J, Dostálová H, Rucká L, et al. Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors sigmaD and sigmaH deciphered using computer modeling and point mutagenesis. Journal of Computer-Aided Molecular Design . 2024;39(1): 1.

Blumenstein, J., Dostálová, H., Rucká, L., Stepánek, V., Busche, T., Kalinowski, J., Pátek, M., et al. (2024). Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors sigmaD and sigmaH deciphered using computer modeling and point mutagenesis. Journal of Computer-Aided Molecular Design , 39(1), 1. https://doi.org/10.1007/s10822-024-00577-x

Blumenstein, J., Dostálová, H., Rucká, L., Stepánek, V., Busche, Tobias, Kalinowski, Jörn, Pátek, M., and Barvík, I. 2024. “Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors sigmaD and sigmaH deciphered using computer modeling and point mutagenesis”. Journal of Computer-Aided Molecular Design 39 (1): 1.

Blumenstein, J., Dostálová, H., Rucká, L., Stepánek, V., Busche, T., Kalinowski, J., Pátek, M., and Barvík, I. (2024). Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors sigmaD and sigmaH deciphered using computer modeling and point mutagenesis. Journal of Computer-Aided Molecular Design 39:1.

Blumenstein, J., et al., 2024. Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors sigmaD and sigmaH deciphered using computer modeling and point mutagenesis. Journal of Computer-Aided Molecular Design , 39(1): 1.

J. Blumenstein, et al., “Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors sigmaD and sigmaH deciphered using computer modeling and point mutagenesis”, Journal of Computer-Aided Molecular Design , vol. 39, 2024, : 1.

Blumenstein, J., Dostálová, H., Rucká, L., Stepánek, V., Busche, T., Kalinowski, J., Pátek, M., Barvík, I.: Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors sigmaD and sigmaH deciphered using computer modeling and point mutagenesis. Journal of Computer-Aided Molecular Design . 39, : 1 (2024).

Blumenstein, J., Dostálová, H., Rucká, L., Stepánek, V., Busche, Tobias, Kalinowski, Jörn, Pátek, M., and Barvík, I. “Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors sigmaD and sigmaH deciphered using computer modeling and point mutagenesis”. Journal of Computer-Aided Molecular Design 39.1 (2024): 1.

Daten bereitgestellt von European Bioinformatics Institute (EBI)