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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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Valdez N, Hughes C, Palmer SO, Sepulveda A, Dean FB, Escamilla Y, Bullard JM, Zhang Y. Rational Design of an Antimicrobial Peptide Based on Structural Insight into the Interaction of Pseudomonas aeruginosa Initiation Factor 1 with Its Cognate 30S Ribosomal Subunit. ACS Infect Dis 2021; 7:3161-3167. [PMID: 34709785 DOI: 10.1021/acsinfecdis.1c00256] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial infections continue to represent a major worldwide health hazard following the emergence of drug-resistant pathogenic strains. Pseudomonas aeruginosa is an opportunistic pathogen causing nosocomial infections with increased morbidity and mortality. The increasing antibiotic resistance in P. aeruginosa has led to an unmet need for discovery of new antibiotic candidates. Bacterial protein synthesis is an essential metabolic process and a validated target for antibiotic development; however, the precise structural mechanism in P. aeruginosa remains unknown. In this work, the interaction of P. aeruginosa initiation factor 1 (IF1) with the 30S ribosomal subunit was studied by NMR, which enabled us to construct a structure of IF1-bound 30S complex. A short α-helix in IF1 was found to be critical for IF1 ribosomal binding and function. A peptide derived from this α-helix was tested and displayed a high ability to inhibit bacterial growth. These results provide a clue for rational design of new antimicrobials.
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Affiliation(s)
- Nicolette Valdez
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Casey Hughes
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Stephanie O. Palmer
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Alyssa Sepulveda
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Frank B. Dean
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Yaritza Escamilla
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - James M. Bullard
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Yonghong Zhang
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
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Giuliodori AM, Spurio R, Milón P, Fabbretti A. Antibiotics Targeting the 30S Ribosomal Subunit: A Lesson from Nature to Find and Develop New Drugs. Curr Top Med Chem 2019; 18:2080-2096. [PMID: 30360712 DOI: 10.2174/1568026618666181025092546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 11/22/2022]
Abstract
The use of antibiotics has revolutionized medicine, greatly improving our capacity to save millions of lives from otherwise deadly bacterial infections. Unfortunately, the health-associated benefits provided by antibiotics have been counteracted by bacteria developing or acquiring resistance mechanisms. The negative impact to public health is now considered of high risk due to the rapid spreading of multi-resistant strains. More than 60 % of clinically relevant antibiotics of natural origin target the ribosome, the supramolecular enzyme which translates the genetic information into proteins. Although many of these antibiotics bind the small ribosomal subunit, only a few are reported to inhibit the initiation of protein synthesis, with none reaching commercial availability. Counterintuitively, translation initiation is the most divergent phase of protein synthesis between prokaryotes and eukaryotes, a fact which is a solid premise for the successful identification of drugs with reduced probability of undesired effects to the host. Such a paradox is one of its kind and deserves special attention. In this review, we explore the inhibitors that bind the 30S ribosomal subunit focusing on both the compounds with proved effects on the translation initiation step and the underreported translation initiation inhibitors. In addition, we explore recent screening tests and approaches to discover new drugs targeting translation.
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Affiliation(s)
- Anna Maria Giuliodori
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Roberto Spurio
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Pohl Milón
- Centre for Research and Innovation, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru, Italy
| | - Attilio Fabbretti
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
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Ji X. Structural insights into cell cycle control by essential GTPase Era. Postepy Biochem 2016; 62:335-342. [PMID: 28132488 PMCID: PMC6622462] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 06/06/2016] [Indexed: 06/06/2023]
Abstract
Era (Escherichia coli Ras-like protein), essential for bacterial cell viability, is composed of an N-terminal GTPase domain and a C-terminal KH domain. In bacteria, it is required for the processing of 16S ribosomal RNA (rRNA) and maturation of 30S (small) ribosomal subunit. Era recognizes 10 nucleotides (1530GAUCACCUCC1539) near the 3' end of 16S rRNA and interacts with helix 45 (h45, nucleotides 1506-1529). GTP binding enables Era to bind RNA, RNA binding stimulates Era's GTP-hydrolyzing activity, and GTP hydrolysis releases Era from matured 30S ribosomal subunit. As such, Era controls cell growth rate via regulating the maturation of the 30S ribosomal subunit. Ribosomes manufacture proteins in all living organisms. The GAUCA sequence and h45 are highly conserved in all three kingdoms of life. Homologues of Era are present in eukaryotic cells. Hence, the mechanism of bacterial Era action also sheds light on the cell cycle control of eukaryotes.
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Affiliation(s)
- Xinhua Ji
- Biomolecular Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
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Demirci H, Sierra RG, Laksmono H, Shoeman RL, Botha S, Barends TRM, Nass K, Schlichting I, Doak RB, Gati C, Williams GJ, Boutet S, Messerschmidt M, Jogl G, Dahlberg AE, Gregory ST, Bogan MJ. Serial femtosecond X-ray diffraction of 30S ribosomal subunit microcrystals in liquid suspension at ambient temperature using an X-ray free-electron laser. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1066-9. [PMID: 23989164 PMCID: PMC3758164 DOI: 10.1107/s174430911302099x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/27/2013] [Indexed: 12/03/2022]
Abstract
High-resolution ribosome structures determined by X-ray crystallography have provided important insights into the mechanism of translation. Such studies have thus far relied on large ribosome crystals kept at cryogenic temperatures to reduce radiation damage. Here, the application of serial femtosecond X-ray crystallography (SFX) using an X-ray free-electron laser (XFEL) to obtain diffraction data from ribosome microcrystals in liquid suspension at ambient temperature is described. 30S ribosomal subunit microcrystals diffracted to beyond 6 Å resolution, demonstrating the feasibility of using SFX for ribosome structural studies. The ability to collect diffraction data at near-physiological temperatures promises to provide fundamental insights into the structural dynamics of the ribosome and its functional complexes.
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Affiliation(s)
- Hasan Demirci
- Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA.
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Blundell CD, Packer MJ, Almond A. Quantification of free ligand conformational preferences by NMR and their relationship to the bioactive conformation. Bioorg Med Chem 2013; 21:4976-87. [PMID: 23886813 PMCID: PMC3744816 DOI: 10.1016/j.bmc.2013.06.056] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 06/24/2013] [Indexed: 12/22/2022]
Abstract
Accurate unbound solution 3D-structures of ligands provide unique opportunities for medicinal chemistry and, in particular, a context to understand binding thermodynamics and kinetics. Previous methods of deriving these 3D-structures have had neither the accuracy nor resolution needed for drug design and have not yet realized their potential. Here, we describe and apply a NMR methodology to the aminoglycoside streptomycin that can accurately quantify accessible 3D-space and rank the occupancy of observed conformers to a resolution that enables medicinal chemistry understanding and design. Importantly, it is based upon conventional small molecule NMR techniques and can be performed in physiologically-relevant solvents. The methodology uses multiple datasets, an order of magnitude more experimental data than previous NMR approaches and a dynamic model during refinement, is independent of computational chemistry and avoids the problem of virtual conformations. The refined set of solution 3D-shapes for streptomycin can be grouped into two major families, of which the most populated is almost identical to the 30S ribosomal subunit bioactive shape. We therefore propose that accurate unbound ligand solution conformations may, in some cases, provide a subsidiary route to bioactive shape without crystallography. This experimental technique opens up new opportunities for drug design and more so when complemented with protein co-crystal structures, SAR data and pharmacophore modeling.
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Affiliation(s)
- Charles D Blundell
- C4X Discovery Ltd, Unit 310 Ducie House, Ducie Street, Manchester M1 2JW, UK
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