Detailed Information on Publication Record
2011
Study of RNA polymerase delta subunit unique for gram-positive bacteria
PAPOUŠKOVÁ, Veronika, Pavel KADEŘÁVEK, Jiří NOVÁČEK, Petr PADRTA, Šanderová HANA et. al.Basic information
Original name
Study of RNA polymerase delta subunit unique for gram-positive bacteria
Name in Czech
Studie delta podjednotky RNA polymerazi jedinečné pro gram-poziotivní bakterie
Name (in English)
Study of RNA polymerase delta subunit unique for gram-positive bacteria
Authors
PAPOUŠKOVÁ, Veronika, Pavel KADEŘÁVEK, Jiří NOVÁČEK, Petr PADRTA, Šanderová HANA, Rabatinová ALŽBĚTA, Zawadzka-Kazimierczuk ANNA, Kazimierczuk KRZYSZTOF, Lukáš ŽÍDEK, Kozminski WIKTOR, Krásný LIBOR and Vladimír SKLENÁŘ
Edition
9th Discussions in Structural Molecular Biology Nove Hrady, 2011
Other information
Type of outcome
Konferenční abstrakt
Confidentiality degree
není předmětem státního či obchodního tajemství
References:
Organization unit
Faculty of Science
ISSN
Keywords (in Czech)
nmr, delta podjednotka, RNA polymeraza, struktura, dynamika, interakce
Keywords in English
nmr, delta subunit, RNA polymerase, structure, dynamics, interactions
Změněno: 29/3/2011 11:24, Mgr. Veronika Papoušková, Ph.D.
V originále
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 Ko¿mi¿ski 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.
In English
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 Ko¿mi¿ski 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.
Links
| FRVS/2066/2011, interní kód MU |
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| GA204/09/0583, research and development project |
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| GD301/09/H004, research and development project |
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| LC06030, research and development project |
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| MSM0021622413, plan (intention) |
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