Study of RNA polymerase delta subunit unique for gram-positive bacteria

PAPOUŠKOVÁ, Veronika, Pavel KADEŘÁVEK, Jiří NOVÁČEK, Petr PADRTA, Šanderová HANA, Rabatinová ALŽBĚTA, Zawadzka-Kazimierczuk ANNA, Kazimierczuk KRZYSZTOF, Lukáš ŽÍDEK, Kozminski WIKTOR, Krásný LIBOR a Vladimír SKLENÁŘ. Study of RNA polymerase delta subunit unique for gram-positive bacteria. In 9th Discussions in Structural Molecular Biology Nove Hrady. 2011. ISSN 1211-5894.

Základní údaje

• Originální název: Study of RNA polymerase delta subunit unique for gram-positive bacteria
• Název česky: Studie delta podjednotky RNA polymerazi jedinečné pro gram-poziotivní bakterie
• Název anglicky: Study of RNA polymerase delta subunit unique for gram-positive bacteria
• Autoři: PAPOUŠKOVÁ, Veronika, Pavel KADEŘÁVEK, Jiří NOVÁČEK, Petr PADRTA, Šanderová HANA, Rabatinová ALŽBĚTA, Zawadzka-Kazimierczuk ANNA, Kazimierczuk KRZYSZTOF, Lukáš ŽÍDEK, Kozminski WIKTOR, Krásný LIBOR a Vladimír SKLENÁŘ.
• Vydání: 9th Discussions in Structural Molecular Biology Nove Hrady, 2011.

Další údaje

• Typ výsledku: Konferenční abstrakt
• Utajení: není předmětem státního či obchodního tajemství
• WWW: URL
• Organizační jednotka: Přírodovědecká fakulta
• ISSN: 1211-5894
• Klíčová slova česky: nmr, delta podjednotka, RNA polymeraza, struktura, dynamika, interakce
• Klíčová slova anglicky: nmr, delta subunit, RNA polymerase, structure, dynamics, interactions

Anotace

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.

Anotace anglicky

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.

Návaznosti

• FRVS/2066/2011, interní kód MU: Název: Inovace předmětu "Strukturní biochemie - seminář" formou virtuální laboratoře a e-learningových odpovědníků

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Inovace předmětu "Strukturní biochemie - seminář" formou virtuální laboratoře a e-learningových odpovědníků, G - Tvůrčí činnost studentů

• GA204/09/0583, projekt VaV: Název: Delta podjednotka RNA polymerázy z Gram pozitivních bakterií (Akronym: DELTA)

Investor: Grantová agentura ČR, Delta podjednotka RNA polymerázy z Gram pozitivních bakterií

• GD301/09/H004, projekt VaV: Název: Molekulární a strukturní biologie vybraných cytostatik. Od mechanistických studií k chemoterapii rakoviny

Investor: Grantová agentura ČR, Molekulární a strukturní biologie vybraných cytostatik. Od mechanických studií k chemoterapii rakoviny

• LC06030, projekt VaV: Název: Biomolekulární centrum

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum

• MSM0021622413, záměr: Název: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Proteiny v metabolismu a při interakci organismů s prostředím