Veronika Papoušková1,2, Pavel Kadeřávek1,2, Jiří Nováček1,2, Petr Padrta1,2, Hana Šanderová3, Alžběta Švenková3, Anna Zawadzka-Kazimierczuk4, Krzysztof Kazimierczuk4, Lukáš Žídek1,2, Wiktor Koźmiński4, Libor Krásný3, Vladimír Sklenář1,2


1National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic

2Central European Institute of Technology, Masaryk University, Žerotínovo nám. 9, 60177 Brno,

Czech Republic

3Institute of Microbiology, Academy of Sciences of the Czech Rep., Vídeňská 1083, 142 20, Prague, Czech Republic

4Faculty of Chemistry, University of Warsaw, Pasteura 1, 02 093 Warsaw, Poland


RNA polymerase (RNAP) from gram-positive bacteria such as Bacillus subtilis differs from well-studied RNA polymerase from gram-negative bacteria in the presence of two additional subunits interacting with the core enzyme, delta and omega1. Recent results indicated that the presence of delta subunit increases the transcription specificity and the efficiency of RNA synthesis. Moreover, the absence of delta subunit is proposed to decrease a virulence of some pathogens. As crystallization at structure genomics centers failed, we focused on NMR studies of  the delta subunit to reveal its structure and related dynamics. As the previous study showed (López de Saro et al., JMB, 1995), the C-terminal domain of the delta subunit is unstructured and its sequence is highly repetitive. Therefore, we started a systematic investigation of the protein with a shorten construct, corresponding to the well-structured N-terminal part. The construct constitution was confirmed using mass spectrometry and the secondary structure content as well as the protein thermostability were determined from circular dichroism spectra. So far, we have published its high-quality structure and the work on the analysis of  internal motions is almost finished.

The more challenging part of the protein, the C-terminal domain, was not initially studied because the NMR methodology for disordered, flexible proteins was not sufficiently developed at the beginning of the project. Fortunately, during last few years many new approaches for study of biologically interesting intrinsically disordered proteins appeared. In contrast to X-ray crystallography, NMR can provide valuable information on residual secondary structure, possible long-range contacts, and internal dynamics of the disordered polypeptide chain.

The full-length delta protein was prepared using a standard protocol of overexpression in the E.coli system to produce a 15N,13C-uniformly labeled sample. The basic spectra, including a standard set of triple resonance NMR experiments, 3D TOCSY, and 3D NOESY, were measured on a 600MHz spectrometer. However, the analysis of the spectra was almost impossible due to a very small differences in chemical shifts. Therefore, a new methodology coming from Wiktor Koźmiński lab was used to improve the spectra resolution and the full-size protein was then completely assigned. It was a major step for further analysis including secondary structure prediction, study of internal motions or measurement of dipolar couplings.  

The interactions between the delta subunit and the RNAP was studied by NMR titration and gel-shift assay to indicate which subunits are essential for binding of the protein to the core enzyme. The experience retrieved in the presented study will be used for the innovation of the seminar C9531 taught at Masaryk University.


This work was supported by the Grants MSM0021622413, LC06030, and 2B06065 from the Ministry of Education, Youth and Physical Culture of the Czech Republic, by the FRVŠ grant 2066/2011, by the Grants 204/09/0583 and 301/09/H004 from Czech Science Foundation, and 7FP of the EC (Contract 228461, EAST-NMR).