Bacterial helicase-like transcription-associated factor HelD

T. Kovaľ¹, T. Kouba², P. Sudzinová³, H. Šanderová³, M. Trundová¹, J. Dušková¹, T. Skálová¹, L. Krásný³, J. Dohnálek¹

¹Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic

²EMBL Grenoble, 71 Avenue des Martyrs, Grenoble, France

³Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic

tomas.koval@ibt.cas.cz

Regulation of bacterial transcription performed by RNA polymerase (RNAP) is facilitated by various transcription factors (e.g. σ factors), which interact with RNAP. One of these factors is HelD, a transcription-associated protein unique for many Gram-positive bacteria (e.g. Bacillus subtilis or Mycobacterium smegmatis) [1]. This study focuses on the structure-function analysis of the complexes between RNAP and HelD. As there was no structure of HelD homologue known and full-length HelD itself resisted all attempts for crystallization, we used a combination of X-ray crystallography (one HelD domain), cryo-EM, small-angle X-ray scattering and homologous modelling [2, 3].

HelD interacts with RNAP in different stages of transcription. It penetrates deep into the RNAP primary channel, interacts with the critical active site residues and also binds tightly in the RNAP secondary channel. These channels are responsible for nucleic acids binding and substrate delivery. As these interactions are incompatible with the binding of DNA to the RNAP core, HelD effectively hinders the elongation process of transcription and can effectively clear RNAP of nucleic acids by dismantling RNAP-DNA complexes [3]. HelD itself is a multi-domain protein capable of structural changes both in solution [2] and in complex with RNAP [3]. These changes are linked to its function. The structural basis for the DNA-clearing function of HelD was explained but the recycling of RNAP inhibited by the HelD binding remains to be elucidated.

1. Wiedermannová, J., Sudzinová, P., Kovaľ, T., Rabatinová, A., Šanderova, H., Ramaniuk, O., Rittich, Š. & Dohnálek, J. (2014). Nucleic Acids Res. 42, 5151-5163.

2. Kovaľ, T., Sudzinová, P., Perháčová, T., Trundová, M., Skálová, T., Fejfarová, K., Šanderová, H., Krásný, L., Dušková, J. & Dohnálek, J. (2019). FEBS Lett. 593, 996-1005.

3. 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, K.S., Dohnálek, J. & Krásný, L. (2020). Nat Commun.11, 6419.

This work was supported by MEYS (LM2015043 and CZ.1.05/1.1.00/02.0109), CSF (20-12109S and 20-07473S), NIH (grant R35GM131860), AS CR (86652036), ERDF (CZ.02.1.01/0.0/0.0/16_013/0001776 and CZ.02.1.01/0.0/0.0/15_003/0000447), EMBL (EI3POD) and Marie Skłodowska-Curie grant (664726) and by support of Biocev CMS – core facilities Crystallization of Proteins and Nucleic Acids, and Diffraction Techniques of CIISB, part of Instruct-ERIC).