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Garaeva N, Fatkhullin B, Murzakhanov F, Gafurov M, Golubev A, Bikmullin A, Glazyrin M, Kieffer B, Jenner L, Klochkov V, Aganov A, Rogachev A, Ivankov O, Validov S, Yusupov M, Usachev K. Structural aspects of RimP binding on small ribosomal subunit from Staphylococcus aureus. Structure 2024; 32:74-82.e5. [PMID: 38000368 DOI: 10.1016/j.str.2023.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/18/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023]
Abstract
Ribosome biogenesis is an energy-intense multistep process where even minimal defects can cause severe phenotypes up to cell death. Ribosome assembly is facilitated by biogenesis factors such as ribosome assembly factors. These proteins facilitate the interaction of ribosomal proteins with rRNA and correct rRNA folding. One of these maturation factors is RimP which is required for efficient 16S rRNA processing and 30S ribosomal subunit assembly. Here, we describe the binding mode of Staphylococcus aureus RimP to the small ribosomal subunit and present a 4.2 Å resolution cryo-EM reconstruction of the 30S-RimP complex. Together with the solution structure of RimP solved by NMR spectroscopy and RimP-uS12 complex analysis by EPR, DEER, and SAXS approaches, we show the specificity of RimP binding to the 30S subunit from S. aureus. We believe the results presented in this work will contribute to the understanding of the RimP role in the ribosome assembly mechanism.
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Affiliation(s)
- Nataliia Garaeva
- Laboratory for Structural Analysis of Biomacromolecules, Federal Research Center «Kazan Scientific Center of Russian Academy of Sciences», Kazan 420111, Russian Federation; Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russian Federation
| | - Bulat Fatkhullin
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, 67400 Illkirch, France; Institute of Protein Research RAS, 4 Institutskaya, Pushchino 142290, Russian Federation
| | - Fadis Murzakhanov
- Institute of Physics, Kazan Federal University, Kazan 420008, Russian Federation
| | - Marat Gafurov
- Institute of Physics, Kazan Federal University, Kazan 420008, Russian Federation
| | - Alexander Golubev
- Laboratory for Structural Analysis of Biomacromolecules, Federal Research Center «Kazan Scientific Center of Russian Academy of Sciences», Kazan 420111, Russian Federation
| | - Aydar Bikmullin
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russian Federation
| | - Maxim Glazyrin
- Laboratory for Structural Analysis of Biomacromolecules, Federal Research Center «Kazan Scientific Center of Russian Academy of Sciences», Kazan 420111, Russian Federation
| | - Bruno Kieffer
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, 67400 Illkirch, France
| | - Lasse Jenner
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, 67400 Illkirch, France
| | - Vladimir Klochkov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kazan 420008, Russian Federation
| | - Albert Aganov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kazan 420008, Russian Federation
| | - Andrey Rogachev
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russian Federation; Joint Institute for Nuclear Research, Dubna 141980, Russian Federation
| | - Oleksandr Ivankov
- Joint Institute for Nuclear Research, Dubna 141980, Russian Federation
| | - Shamil Validov
- Laboratory for Structural Analysis of Biomacromolecules, Federal Research Center «Kazan Scientific Center of Russian Academy of Sciences», Kazan 420111, Russian Federation; Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russian Federation
| | - Marat Yusupov
- Laboratory for Structural Analysis of Biomacromolecules, Federal Research Center «Kazan Scientific Center of Russian Academy of Sciences», Kazan 420111, Russian Federation; Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, 67400 Illkirch, France.
| | - Konstantin Usachev
- Laboratory for Structural Analysis of Biomacromolecules, Federal Research Center «Kazan Scientific Center of Russian Academy of Sciences», Kazan 420111, Russian Federation; Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russian Federation.
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Bikmullin A, Klochkova E, Krasnovid F, Blokhin D. The data of heterologous expression protocol for synthesis of 15N, 13C-labeled SEM1(68-107) peptide fragment of homo sapiens semenogelin 1. MethodsX 2021; 8:101512. [PMID: 34754783 PMCID: PMC8563649 DOI: 10.1016/j.mex.2021.101512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/06/2021] [Indexed: 10/31/2022] Open
Abstract
The semenogelin 1 protein is secreted in the seminal vesicles. After ejaculation it is split into small peptide fragments using internal proteases. It was shown that the fragments SEM1(45-107), SEM1(49-107), SEM1(68-107) (SEM1(86-107) form amyloid fibrils, which increase the possibility of HIV infection. The article presents a protocol for the synthesis and purification of a 15N, 13C-labeled SEM1(68-107) peptide for further structural studies by high-resolution NMR spectroscopy. The work describes cloning, expression of fusion protein GB1-SEM1(68-107) in E.coli, its purification, removal of GB1 and purification of SEM1(68-107). The purity of SEM1(68-107) samples on each purification steps was evaluated by polyacrylamide gel electrophoresis under denaturing conditions (SDS-PAGE) and tricine-SDS-PAGE. The developed protocol allows to obtain SEM1(68-107) peptide for NMR studies (using 3D experiments), instead of costly solid-phase synthesis.
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Affiliation(s)
- Aydar Bikmullin
- Kazan Federal University, 18 Kremlevskaya, Kazan 420008, Russia
| | | | | | - Dmitriy Blokhin
- Kazan Federal University, 18 Kremlevskaya, Kazan 420008, Russia
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Golubev A, Fatkhullin B, Gabdulkhakov A, Bikmullin A, Nurullina L, Garaeva N, Islamov D, Klochkova E, Klochkov V, Aganov A, Khusainov I, Validov S, Yusupova G, Yusupov M, Usachev K. NMR and crystallographic structural studies of the Elongation factor P from Staphylococcus aureus. Eur Biophys J 2020; 49:223-230. [PMID: 32152681 DOI: 10.1007/s00249-020-01428-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/20/2020] [Accepted: 02/25/2020] [Indexed: 01/24/2023]
Abstract
Elongation factor P (EF-P) is a translation protein factor that plays an important role in specialized translation of consecutive proline amino acid motifs. EF-P is an essential protein for cell fitness in native environmental conditions. It regulates synthesis of proteins involved in bacterial motility, environmental adaptation and bacterial virulence, thus making EF-P a potential drug target. In the present study, we determined the solution and crystal structure of EF-P from the pathogenic bacteria Staphylococcus aureus at 1.48 Å resolution. The structure can serve as a platform for structure-based drug design of novel antibiotics to combat the growing antibiotic resistance of S. aureus.
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Affiliation(s)
- Alexander Golubev
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya, Kazan, 420008, Russian Federation.,Département de Biologie Et de Génomique Structurales, Institut de Génétique Et de Biologie Moléculaire Et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, 1 rue Laurent Fries, 67400, Illkirch, France
| | - Bulat Fatkhullin
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya, Kazan, 420008, Russian Federation.,Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290, Puschino, Moscow Region, Russian Federation
| | - Azat Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290, Puschino, Moscow Region, Russian Federation
| | - Aydar Bikmullin
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya, Kazan, 420008, Russian Federation
| | - Liliya Nurullina
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya, Kazan, 420008, Russian Federation
| | - Natalia Garaeva
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya, Kazan, 420008, Russian Federation
| | - Daut Islamov
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya, Kazan, 420008, Russian Federation
| | - Evelina Klochkova
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya, Kazan, 420008, Russian Federation
| | - Vladimir Klochkov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, 18 Kremlyovskaya, Kazan, 420008, Russian Federation
| | - Albert Aganov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, 18 Kremlyovskaya, Kazan, 420008, Russian Federation
| | - Iskander Khusainov
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya, Kazan, 420008, Russian Federation.,Département de Biologie Et de Génomique Structurales, Institut de Génétique Et de Biologie Moléculaire Et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, 1 rue Laurent Fries, 67400, Illkirch, France.,Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany
| | - Shamil Validov
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya, Kazan, 420008, Russian Federation
| | - Gulnara Yusupova
- Département de Biologie Et de Génomique Structurales, Institut de Génétique Et de Biologie Moléculaire Et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, 1 rue Laurent Fries, 67400, Illkirch, France
| | - Marat Yusupov
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya, Kazan, 420008, Russian Federation.,Département de Biologie Et de Génomique Structurales, Institut de Génétique Et de Biologie Moléculaire Et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, 1 rue Laurent Fries, 67400, Illkirch, France
| | - Konstantin Usachev
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya, Kazan, 420008, Russian Federation. .,NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, 18 Kremlyovskaya, Kazan, 420008, Russian Federation.
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