1
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Rajan KS, Madmoni H, Bashan A, Taoka M, Aryal S, Nobe Y, Doniger T, Galili Kostin B, Blumberg A, Cohen-Chalamish S, Schwartz S, Rivalta A, Zimmerman E, Unger R, Isobe T, Yonath A, Michaeli S. A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei. Nat Commun 2023; 14:7462. [PMID: 37985661 PMCID: PMC10662448 DOI: 10.1038/s41467-023-43263-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/05/2023] [Indexed: 11/22/2023] Open
Abstract
Trypanosomes are protozoan parasites that cycle between insect and mammalian hosts and are the causative agent of sleeping sickness. Here, we describe the changes of pseudouridine (Ψ) modification on rRNA in the two life stages of the parasite using four different genome-wide approaches. CRISPR-Cas9 knock-outs of all four snoRNAs guiding Ψ on helix 69 (H69) of the large rRNA subunit were lethal. A single knock-out of a snoRNA guiding Ψ530 on H69 altered the composition of the 80S monosome. These changes specifically affected the translation of only a subset of proteins. This study correlates a single site Ψ modification with changes in ribosomal protein stoichiometry, supported by a high-resolution cryo-EM structure. We propose that alteration in rRNA modifications could generate ribosomes preferentially translating state-beneficial proteins.
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Affiliation(s)
- K Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Hava Madmoni
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Anat Bashan
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Saurav Aryal
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Beathrice Galili Kostin
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Amit Blumberg
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Smadar Cohen-Chalamish
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Andre Rivalta
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ella Zimmerman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Ada Yonath
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
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Nguyen AMT, Shalev-Benami M, Rosa-Teijeiro C, Ibarra-Meneses AV, Yonath A, Bashan A, Jaffe CL, Olivier M, Fernandez-Prada C, Lubell WD. Systematic Exploration of Functional Group Relevance for Anti-Leishmanial Activity of Anisomycin. Biomedicines 2023; 11:2541. [PMID: 37760981 PMCID: PMC10526209 DOI: 10.3390/biomedicines11092541] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Assessment of structure-activity relationships for anti-protozoan activity revealed a strategy for preparing potent anisomycin derivatives with reduced host toxicity. Thirteen anisomycin analogs were synthesized by modifying the alcohol, amine, and aromatic functional groups. Examination of anti-protozoal activity against various strains of Leishmania and cytotoxicity against leucocytes with comparison against the parent natural product demonstrated typical losses of activity with modifications of the alcohol, amine, and aromatic meta-positions. On the other hand, the para-phenol moiety of anisomycin proved an effective location for introducing substituents without significant loss of anti-protozoan potency. An entry point for differentiating activity against Leishmania versus host has been uncovered by this systematic study.
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Affiliation(s)
| | - Moran Shalev-Benami
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (M.S.-B.); (A.Y.); (A.B.)
| | - Chloé Rosa-Teijeiro
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (C.R.-T.); (A.V.I.-M.); (C.F.-P.)
- The Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, Université de Montréal, Montreal, QC J2S 2M2, Canada
| | - Ana Victoria Ibarra-Meneses
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (C.R.-T.); (A.V.I.-M.); (C.F.-P.)
- The Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, Université de Montréal, Montreal, QC J2S 2M2, Canada
| | - Ada Yonath
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (M.S.-B.); (A.Y.); (A.B.)
| | - Anat Bashan
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (M.S.-B.); (A.Y.); (A.B.)
| | - Charles L. Jaffe
- Department of Microbiology & Molecular Genetics, Kuvin Center for the Study of Tropical & Infectious Diseases, Institute for Medical Research (IMRIC), Hadassah Hebrew University Medical Center, Jerusalem 9112102, Israel;
| | - Martin Olivier
- Departments of Medicine, and of Microbiology and Immunology, Faculty of Medicine, McGill University, Montreal, QC H3A 2B4, Canada;
- The Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, QC H4A 3J1, Canada
| | - Christopher Fernandez-Prada
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (C.R.-T.); (A.V.I.-M.); (C.F.-P.)
- The Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, Université de Montréal, Montreal, QC J2S 2M2, Canada
| | - William D. Lubell
- Department of Chemistry, Université de Montréal, Montreal, QC H3T 1J4, Canada
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Hiregange DG, Rivalta A, Yonath A, Zimmerman E, Bashan A, Yonath H. Mutations in RPS19 may affect ribosome function and biogenesis in Diamond Blackfan Anemia. FEBS Open Bio 2022; 12:1419-1434. [PMID: 35583751 PMCID: PMC9249338 DOI: 10.1002/2211-5463.13444] [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: 03/29/2022] [Revised: 05/04/2022] [Accepted: 05/17/2022] [Indexed: 11/12/2022] Open
Abstract
Ribosomes, the cellular organelles translating the genetic code to proteins, are assemblies of RNA chains and many proteins (RPs) arranged in precise fine-tuned interwoven structures. Mutated ribosomal genes cause ribosomopathies, including Diamond Blackfan Anemia (DBA, a rare heterogeneous red-cell aplasia connected to ribosome malfunction) or failed biogenesis. Combined bioinformatical, structural, and predictive analyses of potential consequences of possibly expressed mutations in eS19, the protein product of the highly mutated RPS19, suggests that mutations in its exposed surface could alter its positioning during assembly and consequently prevent biogenesis, implying a natural selective strategy to avoid malfunctions in ribosome assembly. A search for RPS19 pseudogenes indicated >90% sequence identity with the wild type, hinting at its expression in cases of absent or truncated gene products.
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Affiliation(s)
| | - Andre Rivalta
- The Department of Chemical and Structural Biology, Weizmann Institute of Science, Israel
| | - Ada Yonath
- The Department of Chemical and Structural Biology, Weizmann Institute of Science, Israel
| | - Ella Zimmerman
- The Department of Chemical and Structural Biology, Weizmann Institute of Science, Israel
| | - Anat Bashan
- The Department of Chemical and Structural Biology, Weizmann Institute of Science, Israel
| | - Hagith Yonath
- Internal Medicine A and Genetics Institute Sheba Medical Center, and Sackler School of Medicine, Tel Aviv University, Israel
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Cimicata G, Fridkin G, Bose T, Eyal Z, Halfon Y, Breiner-Goldstein E, Fox T, Zimmerman E, Bashan A, de Val N, Wlodawer A, Yonath A. Structural Studies Reveal the Role of Helix 68 in the Elongation Step of Protein Biosynthesis. mBio 2022; 13:e0030622. [PMID: 35348349 PMCID: PMC9040758 DOI: 10.1128/mbio.00306-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023] Open
Abstract
The ribosome, a multicomponent assembly consisting of RNA and proteins, is a pivotal macromolecular machine that translates the genetic code into proteins. The large ribosomal subunit rRNA helix 68 (H68) is a key element in the protein synthesis process, as it coordinates the coupled movements of the actors involved in translocation, including the tRNAs and L1 stalk. Examination of cryo-electron microscopy (cryo-EM) structures of ribosomes incubated for various time durations at physiological temperatures led to the identification of functionally relevant H68 movements. These movements assist the transition of the L1 stalk between its open and closed states. H68 spatial flexibility and its significance to the protein synthesis process were confirmed through its effective targeting with antisense PNA oligomers. Our results suggest that H68 is actively involved in ribosome movements that are central to the elongation process. IMPORTANCE The mechanism that regulates the translocation step in ribosomes during protein synthesis is not fully understood. In this work, cryo-EM techniques used to image ribosomes from Staphylococcus aureus after incubation at physiological temperature allowed the identification of a conformation of the helix 68 that has never been observed so far. We then propose a mechanism in which such helix, switching between two different conformations, actively coordinates the translocation step, shedding light on the dynamics of ribosomal components. In addition, the relevance of helix 68 to ribosome function and its potential as an antibiotic target was proved by inhibiting Staphylococcus aureus ribosomes activity in vitro using oligomers with sequence complementarity.
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Affiliation(s)
- Giuseppe Cimicata
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Gil Fridkin
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Tanaya Bose
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Zohar Eyal
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Yehuda Halfon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Elinor Breiner-Goldstein
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Tara Fox
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Ella Zimmerman
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Anat Bashan
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Alexander Wlodawer
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Ada Yonath
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
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5
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Bose T, Fridkin G, Bashan A, Yonath A. Origin of Life: Chiral Short RNA Chains Capable of Non‐Enzymatic Peptide Bond Formation. Isr J Chem 2022. [DOI: 10.1002/ijch.202100054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tanaya Bose
- Department of Structural Biology Weizmann Institute of Science 76100 Rehovot Israel
| | - Gil Fridkin
- Department of Structural Biology Weizmann Institute of Science 76100 Rehovot Israel
- Department of Organic Chemistry Israel Institute for Biological Research P.O. Box 19 Ness Ziona 7410001 Israel
| | - Anat Bashan
- Department of Structural Biology Weizmann Institute of Science 76100 Rehovot Israel
| | - Ada Yonath
- Department of Structural Biology Weizmann Institute of Science 76100 Rehovot Israel
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Bose T, Fridkin G, Davidovich C, Krupkin M, Dinger N, Falkovich A, Peleg Y, Agmon I, Bashan A, Yonath A. Origin of life: protoribosome forms peptide bonds and links RNA and protein dominated worlds. Nucleic Acids Res 2022; 50:1815-1828. [PMID: 35137169 PMCID: PMC8886871 DOI: 10.1093/nar/gkac052] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 12/13/2021] [Accepted: 01/25/2022] [Indexed: 12/15/2022] Open
Abstract
Although the mode of action of the ribosomes, the multi-component universal effective protein-synthesis organelles, has been thoroughly explored, their mere appearance remained elusive. Our earlier comparative structural studies suggested that a universal internal small RNA pocket-like segment called by us the protoribosome, which is still embedded in the contemporary ribosome, is a vestige of the primordial ribosome. Herein, after constructing such pockets, we show using the "fragment reaction" and its analyses by MALDI-TOF and LC-MS mass spectrometry techniques, that several protoribosome constructs are indeed capable of mediating peptide-bond formation. These findings present strong evidence supporting our hypothesis on origin of life and on ribosome's construction, thus suggesting that the protoribosome may be the missing link between the RNA dominated world and the contemporary nucleic acids/proteins life.
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Affiliation(s)
- Tanaya Bose
- Department of Chemical and Structural Biology, Weizmann Institute of Science 7610001 Rehovot, Israel
| | - Gil Fridkin
- Department of Chemical and Structural Biology, Weizmann Institute of Science 7610001 Rehovot, Israel,Department of Organic Chemistry, Israel Institute for Biological Research, P.O. Box 19, Ness Ziona 7410001, Israel
| | - Chen Davidovich
- Department of Chemical and Structural Biology, Weizmann Institute of Science 7610001 Rehovot, Israel
| | - Miri Krupkin
- Department of Chemical and Structural Biology, Weizmann Institute of Science 7610001 Rehovot, Israel
| | - Nikita Dinger
- Department of Chemical and Structural Biology, Weizmann Institute of Science 7610001 Rehovot, Israel
| | - Alla H Falkovich
- Department of Chemical and Structural Biology, Weizmann Institute of Science 7610001 Rehovot, Israel
| | - Yoav Peleg
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Agmon
- Institute for Advanced Studies in Theoretical Chemistry, Schulich Faculty of Chemistry-Technion-Israel Institute of Technology, Haifa 3200003, Israel,Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem 9190401, Israel
| | - Anat Bashan
- Department of Chemical and Structural Biology, Weizmann Institute of Science 7610001 Rehovot, Israel
| | - Ada Yonath
- To whom correspondence should be addressed. Tel : +972 89343028;
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7
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Hiregange DG, Rivalta A, Bose T, Breiner-Goldstein E, Samiya S, Cimicata G, Kulakova L, Zimmerman E, Bashan A, Herzberg O, Yonath A. Cryo-EM structure of the ancient eukaryotic ribosome from the human parasite Giardia lamblia. Nucleic Acids Res 2022; 50:1770-1782. [PMID: 35100413 PMCID: PMC8860606 DOI: 10.1093/nar/gkac046] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/12/2022] [Accepted: 01/25/2022] [Indexed: 12/13/2022] Open
Abstract
Giardiasis is a disease caused by the protist Giardia lamblia. As no human vaccines have been approved so far against it, and resistance to current drugs is spreading, new strategies for combating giardiasis need to be developed. The G. lamblia ribosome may provide a promising therapeutic target due to its distinct sequence differences from ribosomes of most eukaryotes and prokaryotes. Here, we report the cryo-electron microscopy structure of the G. lamblia (WB strain) ribosome determined at 2.75 Å resolution. The ribosomal RNA is the shortest known among eukaryotes, and lacks nearly all the eukaryote-specific ribosomal RNA expansion segments. In contrast, the ribosomal proteins are typically eukaryotic with some species-specific insertions/extensions. Most typical inter-subunit bridges are maintained except for one missing contact site. Unique structural features are located mainly at the ribosome’s periphery. These may be exploited as target sites for the design of new compounds that inhibit selectively the parasite’s ribosomal activity.
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Affiliation(s)
- Disha-Gajanan Hiregange
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Andre Rivalta
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tanaya Bose
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elinor Breiner-Goldstein
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarit Samiya
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Giuseppe Cimicata
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Liudmila Kulakova
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20742-4454, USA
| | - Ella Zimmerman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Bashan
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Osnat Herzberg
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20742-4454, USA
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-4454, USA
| | - Ada Yonath
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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8
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Breiner-Goldstein E, Eyal Z, Matzov D, Halfon Y, Cimicata G, Baum M, Rokney A, Ezernitchi A, Lowell A, Schmidt J, Rozenberg H, Zimmerman E, Bashan A, Valinsky L, Anzai Y, Sherman D, Yonath A. Ribosome-binding and anti-microbial studies of the mycinamicins, 16-membered macrolide antibiotics from Micromonospora griseorubida. Nucleic Acids Res 2021; 49:9560-9573. [PMID: 34417608 PMCID: PMC8450085 DOI: 10.1093/nar/gkab684] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/25/2021] [Accepted: 07/28/2021] [Indexed: 02/02/2023] Open
Abstract
Macrolides have been effective clinical antibiotics for over 70 years. They inhibit protein biosynthesis in bacterial pathogens by narrowing the nascent protein exit tunnel in the ribosome. The macrolide class of natural products consist of a macrolactone ring linked to one or more sugar molecules. Most of the macrolides used currently are semi-synthetic erythromycin derivatives, composed of a 14- or 15-membered macrolactone ring. Rapidly emerging resistance in bacterial pathogens is among the most urgent global health challenges, which render many antibiotics ineffective, including next-generation macrolides. To address this threat and advance a longer-term plan for developing new antibiotics, we demonstrate how 16-membered macrolides overcome erythromycin resistance in clinically isolated Staphylococcus aureus strains. By determining the structures of complexes of the large ribosomal subunit of Deinococcus radiodurans (D50S) with these 16-membered selected macrolides, and performing anti-microbial studies, we identified resistance mechanisms they may overcome. This new information provides important insights toward the rational design of therapeutics that are effective against drug resistant human pathogens.
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Affiliation(s)
- Elinor Breiner-Goldstein
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Zohar Eyal
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Donna Matzov
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Yehuda Halfon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Giuseppe Cimicata
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Moti Baum
- Government Central Laboratories, Ministry of Health, Jerusalem 91342, Israel
| | - Assaf Rokney
- Government Central Laboratories, Ministry of Health, Jerusalem 91342, Israel
| | - Analia V Ezernitchi
- Government Central Laboratories, Ministry of Health, Jerusalem 91342, Israel
| | - Andrew N Lowell
- Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Jennifer J Schmidt
- Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Haim Rozenberg
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Ella Zimmerman
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Anat Bashan
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Lea Valinsky
- Government Central Laboratories, Ministry of Health, Jerusalem 91342, Israel
| | - Yojiro Anzai
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-0072, Japan
| | - David H Sherman
- Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Ada Yonath
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
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9
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Matzov D, Taoka M, Nobe Y, Yamauchi Y, Halfon Y, Asis N, Zimermann E, Rozenberg H, Bashan A, Bhushan S, Isobe T, Gray MW, Yonath A, Shalev-Benami M. Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis. Nucleic Acids Res 2020; 48:11750-11761. [PMID: 33091122 PMCID: PMC7672448 DOI: 10.1093/nar/gkaa893] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/21/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022] Open
Abstract
Ribosomal RNA is the central component of the ribosome, mediating its functional and architectural properties. Here, we report the cryo-EM structure of a highly divergent cytoplasmic ribosome from the single-celled eukaryotic alga Euglena gracilis. The Euglena large ribosomal subunit is distinct in that it contains 14 discrete rRNA fragments that are assembled non-covalently into the canonical ribosome structure. The rRNA is substantially enriched in post-transcriptional modifications that are spread far beyond the catalytic RNA core, contributing to the stabilization of this highly fragmented ribosome species. A unique cluster of five adenosine base methylations is found in an expansion segment adjacent to the protein exit tunnel, such that it is positioned for interaction with the nascent peptide. As well as featuring distinctive rRNA expansion segments, the Euglena ribosome contains four novel ribosomal proteins, localized to the ribosome surface, three of which do not have orthologs in other eukaryotes.
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Affiliation(s)
- Donna Matzov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yehuda Halfon
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nofar Asis
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ella Zimermann
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Haim Rozenberg
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shashi Bhushan
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Moran Shalev-Benami
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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10
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Halfon Y, Jimenez-Fernandez A, La Rosa R, Espinosa Portero R, Krogh Johansen H, Matzov D, Eyal Z, Bashan A, Zimmerman E, Belousoff M, Molin S, Yonath A. Structure of Pseudomonas aeruginosa ribosomes from an aminoglycoside-resistant clinical isolate. Proc Natl Acad Sci U S A 2019; 116:22275-22281. [PMID: 31611393 PMCID: PMC6825255 DOI: 10.1073/pnas.1909831116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Resistance to antibiotics has become a major threat to modern medicine. The ribosome plays a fundamental role in cell vitality by the translation of the genetic code into proteins; hence, it is a major target for clinically useful antibiotics. We report here the cryo-electron microscopy structures of the ribosome of a pathogenic aminoglycoside (AG)-resistant Pseudomonas aeruginosa strain, as well as of a nonresistance strain isolated from a cystic fibrosis patient. The structural studies disclosed defective ribosome complex formation due to a conformational change of rRNA helix H69, an essential intersubunit bridge, and a secondary binding site of the AGs. In addition, a stable conformation of nucleotides A1486 and A1487, pointing into helix h44, is created compared to a non-AG-bound ribosome. We suggest that altering the conformations of ribosomal protein uL6 and rRNA helix H69, which interact with initiation-factor IF2, interferes with proper protein synthesis initiation.
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Affiliation(s)
- Yehuda Halfon
- Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Alicia Jimenez-Fernandez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ruggero La Rosa
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Rocio Espinosa Portero
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 1165 Copenhagen, Denmark
| | - Donna Matzov
- Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Zohar Eyal
- Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Anat Bashan
- Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ella Zimmerman
- Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Matthew Belousoff
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, 3800 Clayton, VIC, Australia
| | - Søren Molin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark;
| | - Ada Yonath
- Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel;
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11
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Halfon Y, Matzov D, Eyal Z, Bashan A, Zimmerman E, Kjeldgaard J, Ingmer H, Yonath A. Exit tunnel modulation as resistance mechanism of S. aureus erythromycin resistant mutant. Sci Rep 2019; 9:11460. [PMID: 31391518 PMCID: PMC6685948 DOI: 10.1038/s41598-019-48019-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/25/2019] [Indexed: 12/16/2022] Open
Abstract
The clinical use of the antibiotic erythromycin (ery) is hampered owing to the spread of resistance genes that are mostly mutating rRNA around the ery binding site at the entrance to the protein exit tunnel. Additional effective resistance mechanisms include deletion or insertion mutations in ribosomal protein uL22, which lead to alterations of the exit tunnel shape, located 16 Å away from the drug's binding site. We determined the cryo-EM structures of the Staphylococcus aureus 70S ribosome, and its ery bound complex with a two amino acid deletion mutation in its ß hairpin loop, which grants the bacteria resistance to ery. The structures reveal that, although the binding of ery is stable, the movement of the flexible shorter uL22 loop towards the tunnel wall creates a wider path for nascent proteins, thus enabling bypass of the barrier formed by the drug. Moreover, upon drug binding, the tunnel widens further.
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Affiliation(s)
- Yehuda Halfon
- The Weizmann Institute of Science, The Department of structural biology, Rehovot, 7610001, Israel
| | - Donna Matzov
- The Weizmann Institute of Science, The Department of structural biology, Rehovot, 7610001, Israel
| | - Zohar Eyal
- The Weizmann Institute of Science, The Department of structural biology, Rehovot, 7610001, Israel
| | - Anat Bashan
- The Weizmann Institute of Science, The Department of structural biology, Rehovot, 7610001, Israel
| | - Ella Zimmerman
- The Weizmann Institute of Science, The Department of structural biology, Rehovot, 7610001, Israel
| | - Jette Kjeldgaard
- National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800, Kgs, Lyngby, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark
| | - Ada Yonath
- The Weizmann Institute of Science, The Department of structural biology, Rehovot, 7610001, Israel.
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12
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Matzov D, Bashan A, Yap MNF, Yonath A. Stress response as implemented by hibernating ribosomes: a structural overview. FEBS J 2019; 286:3558-3565. [PMID: 31230411 PMCID: PMC6746590 DOI: 10.1111/febs.14968] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 03/05/2019] [Revised: 05/14/2019] [Accepted: 06/20/2019] [Indexed: 02/07/2023]
Abstract
Protein synthesis is one of the most energy demanding cellular processes. The ability to regulate protein synthesis is essential for cells under normal as well as stress conditions, such as nutrient deficiencies. One mechanism for protein synthesis suppression is the dimerization of ribosomes into hibernation complexes. In most cells, this process is promoted by the hibernating promoting factor (HPF) and in a small group of Gram-negative bacteria (γ-proteobacteria), the dimer formation is induced by a shorter version of HPF (HPFshort ) and by an additional protein, the ribosome modulation factor. In most bacteria, the product of this process is the 100S ribosome complex. Recent advances in cryogenic electron microscopy methods resulted in an abundance of detailed structures of near atomic resolutions 100S complexes that allow for a better understanding of the dimerization process and the way it inhibits protein synthesis. As ribosomal dimerization is vital for cell survival, this process is an attractive target for the development of novel antimicrobial substances that might inhibit or stabilize the complex formation. As different dimerization processes exist among bacteria, including pathogens, this process may provide the basis for species-specific design of antimicrobial agents. Here, we review in detail the various dimerization mechanisms and discuss how they affect the overall dimer structures of the bacterial ribosomes.
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Affiliation(s)
- Donna Matzov
- Structural Biology, Weizmann Institute. Rehovot, Israel
| | - Anat Bashan
- Structural Biology, Weizmann Institute. Rehovot, Israel
| | - Mee-Ngan F Yap
- Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA.,Microbiology and Immunology, Northwestern University, Chicago, IL, USA
| | - Ada Yonath
- Structural Biology, Weizmann Institute. Rehovot, Israel
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13
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Matzov D, Eyal Z, Benhamou RI, Shalev-Benami M, Halfon Y, Krupkin M, Zimmerman E, Rozenberg H, Bashan A, Fridman M, Yonath A. Structural insights of lincosamides targeting the ribosome of Staphylococcus aureus. Nucleic Acids Res 2017; 45:10284-10292. [PMID: 28973455 PMCID: PMC5622323 DOI: 10.1093/nar/gkx658] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/18/2017] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance within a wide range of pathogenic bacteria is an increasingly serious threat to global public health. Among these pathogenic bacteria are the highly resistant, versatile and possibly aggressive bacteria, Staphylococcus aureus. Lincosamide antibiotics were proved to be effective against this pathogen. This small, albeit important group of antibiotics is mostly active against Gram-positive bacteria, but also used against selected Gram-negative anaerobes and protozoa. S. aureus resistance to lincosamides can be acquired by modifications and/or mutations in the rRNA and rProteins. Here, we present the crystal structures of the large ribosomal subunit of S. aureus in complex with the lincosamides lincomycin and RB02, a novel semisynthetic derivative and discuss the biochemical aspects of the in vitro potency of various lincosamides. These results allow better understanding of the drugs selectivity as well as the importance of the various chemical moieties of the drug for binding and inhibition.
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Affiliation(s)
- Donna Matzov
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Zohar Eyal
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Raphael I Benhamou
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Moran Shalev-Benami
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yehuda Halfon
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Miri Krupkin
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ella Zimmerman
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Haim Rozenberg
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Bashan
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Micha Fridman
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ada Yonath
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
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14
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Matzov D, Aibara S, Basu A, Zimmerman E, Bashan A, Yap MNF, Amunts A, Yonath AE. The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus. Nat Commun 2017; 8:723. [PMID: 28959035 PMCID: PMC5620080 DOI: 10.1038/s41467-017-00753-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 07/25/2017] [Indexed: 02/02/2023] Open
Abstract
Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Trans-acting factors ribosome modulation factor (RMF) and hibernating promoting factor (HPF) were shown to directly mediate this process in E. coli. Gram-positive S. aureus lacks an RMF homolog and the structural basis for its 100S formation was not known. Here we report the cryo-electron microscopy structure of the native 100S ribosome from S. aureus, revealing the molecular mechanism of its formation. The structure is distinct from previously reported analogs and relies on the HPF C-terminal extension forming the binding platform for the interactions between both of the small ribosomal subunits. The 100S dimer is formed through interactions between rRNA h26, h40, and protein uS2, involving conformational changes of the head as well as surface regions that could potentially prevent RNA polymerase from docking to the ribosome.Under conditions of nutrient limitation, bacterial ribosomes undergo dimerization, forming a 100S complex that is translationally inactive. Here the authors present the structural basis for formation of the 100S complexes in Gram-positive bacteria, shedding light on the mechanism of translation suppression by the ribosome-silencing factors.
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Affiliation(s)
- Donna Matzov
- Faculty of Chemistry, Department of Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shintaro Aibara
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden
| | - Arnab Basu
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Ella Zimmerman
- Faculty of Chemistry, Department of Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Anat Bashan
- Faculty of Chemistry, Department of Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Mee-Ngan F Yap
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA.
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden.
| | - Ada E Yonath
- Faculty of Chemistry, Department of Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel.
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15
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Wekselman I, Zimmerman E, Davidovich C, Belousoff M, Matzov D, Krupkin M, Rozenberg H, Bashan A, Friedlander G, Kjeldgaard J, Ingmer H, Lindahl L, Zengel JM, Yonath A. The Ribosomal Protein uL22 Modulates the Shape of the Protein Exit Tunnel. Structure 2017; 25:1233-1241.e3. [PMID: 28689968 DOI: 10.1016/j.str.2017.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 05/08/2017] [Accepted: 06/02/2017] [Indexed: 10/19/2022]
Abstract
Erythromycin is a clinically useful antibiotic that binds to an rRNA pocket in the ribosomal exit tunnel. Commonly, resistance to erythromycin is acquired by alterations of rRNA nucleotides that interact with the drug. Mutations in the β hairpin of ribosomal protein uL22, which is rather distal to the erythromycin binding site, also generate resistance to the antibiotic. We have determined the crystal structure of the large ribosomal subunit from Deinococcus radiodurans with a three amino acid insertion within the β hairpin of uL22 that renders resistance to erythromycin. The structure reveals a shift of the β hairpin of the mutated uL22 toward the interior of the exit tunnel, triggering a cascade of structural alterations of rRNA nucleotides that propagate to the erythromycin binding pocket. Our findings support recent studies showing that the interactions between uL22 and specific sequences within nascent chains trigger conformational rearrangements in the exit tunnel.
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Affiliation(s)
- Itai Wekselman
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ella Zimmerman
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Chen Davidovich
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Matthew Belousoff
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Donna Matzov
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Miri Krupkin
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Haim Rozenberg
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Bashan
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gilgi Friedlander
- The Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jette Kjeldgaard
- Department of Veterinary Disease Biology, University of Copenhagen, 1870 Frederiksbergc, Denmark
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, University of Copenhagen, 1870 Frederiksbergc, Denmark
| | - Lasse Lindahl
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Janice M Zengel
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Ada Yonath
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel.
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16
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Affiliation(s)
- Donna Matzov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel;, ,
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel;, ,
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel;, ,
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17
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Eyal Z, Matzov D, Krupkin M, Paukner S, Riedl R, Rozenberg H, Zimmerman E, Bashan A, Yonath A. A novel pleuromutilin antibacterial compound, its binding mode and selectivity mechanism. Sci Rep 2016; 6:39004. [PMID: 27958389 PMCID: PMC5154188 DOI: 10.1038/srep39004] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/16/2016] [Indexed: 01/07/2023] Open
Abstract
The increasing appearance of pathogenic bacteria with antibiotic resistance is a global threat. Consequently, clinically available potent antibiotics that are active against multidrug resistant pathogens are becoming exceedingly scarce. Ribosomes are a main target for antibiotics, and hence are an objective for novel drug development. Lefamulin, a semi-synthetic pleuromutilin compound highly active against multi-resistant pathogens, is a promising antibiotic currently in phase III trials for the treatment of community-acquired bacterial pneumonia in adults. The crystal structure of the Staphylococcus aureus large ribosomal subunit in complex with lefamulin reveals its protein synthesis inhibition mechanism and the rationale for its potency. In addition, analysis of the bacterial and eukaryotes ribosome structures around the pleuromutilin binding pocket has elucidated the key for the drug's selectivity.
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Affiliation(s)
- Zohar Eyal
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Donna Matzov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Miri Krupkin
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | | | - Haim Rozenberg
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ella Zimmerman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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18
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Zaccai G, Natali F, Peters J, Řihová M, Zimmerman E, Ollivier J, Combet J, Maurel MC, Bashan A, Yonath A. The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering. Sci Rep 2016; 6:37138. [PMID: 27849042 PMCID: PMC5111069 DOI: 10.1038/srep37138] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/25/2016] [Indexed: 01/08/2023] Open
Abstract
Conformational changes associated with ribosome function have been identified by X-ray crystallography and cryo-electron microscopy. These methods, however, inform poorly on timescales. Neutron scattering is well adapted for direct measurements of thermal molecular dynamics, the ‘lubricant’ for the conformational fluctuations required for biological activity. The method was applied to compare water dynamics and conformational fluctuations in the 30 S and 50 S ribosomal subunits from Haloarcula marismortui, under high salt, stable conditions. Similar free and hydration water diffusion parameters are found for both subunits. With respect to the 50 S subunit, the 30 S is characterized by a softer force constant and larger mean square displacements (MSD), which would facilitate conformational adjustments required for messenger and transfer RNA binding. It has been shown previously that systems from mesophiles and extremophiles are adapted to have similar MSD under their respective physiological conditions. This suggests that the results presented are not specific to halophiles in high salt but a general property of ribosome dynamics under corresponding, active conditions. The current study opens new perspectives for neutron scattering characterization of component functional molecular dynamics within the ribosome.
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Affiliation(s)
- Giuseppe Zaccai
- Institut Laue Langevin, F-38042 Grenoble, France.,Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Francesca Natali
- Institut Laue Langevin, F-38042 Grenoble, France.,CNR-IOM, OGG, F-38042 Grenoble, France
| | - Judith Peters
- Institut Laue Langevin, F-38042 Grenoble, France.,Univ. Grenoble Alpes, LiPhy, F-38044 Grenoble, France
| | - Martina Řihová
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205- CNRS, MNHN, UPMC, EPHE UPMC, Sorbonne Universités, 57 rue Cuvier, CP 50, 75005 Paris, France.,Institute of Physics, Charles University, Faculty of Mathematics and Physics, CZ-121 16 Prague, Czech Republic
| | - Ella Zimmerman
- Weizmann Institute, Department of Structural Biology, 76100 Rehovot, Israel
| | - J Ollivier
- Institut Laue Langevin, F-38042 Grenoble, France
| | - J Combet
- Institut Laue Langevin, F-38042 Grenoble, France.,Institut Charles Sadron, CNRS-UdS, 67034 Strasbourg Cedex 2, France
| | - Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205- CNRS, MNHN, UPMC, EPHE UPMC, Sorbonne Universités, 57 rue Cuvier, CP 50, 75005 Paris, France
| | - Anat Bashan
- Weizmann Institute, Department of Structural Biology, 76100 Rehovot, Israel
| | - Ada Yonath
- Weizmann Institute, Department of Structural Biology, 76100 Rehovot, Israel
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19
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Shalev-Benami M, Zhang Y, Matzov D, Halfon Y, Zackay A, Rozenberg H, Zimmerman E, Bashan A, Jaffe CL, Yonath A, Skiniotis G. 2.8-Å Cryo-EM Structure of the Large Ribosomal Subunit from the Eukaryotic Parasite Leishmania. Cell Rep 2016; 16:288-294. [PMID: 27373148 DOI: 10.1016/j.celrep.2016.06.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 04/19/2016] [Accepted: 05/25/2016] [Indexed: 12/21/2022] Open
Abstract
Leishmania is a single-cell eukaryotic parasite of the Trypanosomatidae family, whose members cause an array of tropical diseases. The often fatal outcome of infections, lack of effective vaccines, limited selection of therapeutic drugs, and emerging resistant strains, underline the need to develop strategies to combat these pathogens. The Trypanosomatid ribosome has recently been highlighted as a promising therapeutic target due to structural features that are distinct from other eukaryotes. Here, we present the 2.8-Å resolution structure of the Leishmania donovani large ribosomal subunit (LSU) derived from a cryo-EM map, further enabling the structural observation of eukaryotic rRNA modifications that play a significant role in ribosome assembly and function. The structure illustrates the unique fragmented nature of leishmanial LSU rRNA and highlights the irregular distribution of rRNA modifications in Leishmania, a characteristic with implications for anti-parasitic drug development.
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Affiliation(s)
- Moran Shalev-Benami
- Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yan Zhang
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Donna Matzov
- Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yehuda Halfon
- Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Arie Zackay
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel
| | - Haim Rozenberg
- Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ella Zimmerman
- Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Bashan
- Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Charles L Jaffe
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel
| | - Ada Yonath
- Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Georgios Skiniotis
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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20
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Auerbach-Nevo T, Baram D, Bashan A, Belousoff M, Breiner E, Davidovich C, Cimicata G, Eyal Z, Halfon Y, Krupkin M, Matzov D, Metz M, Rufayda M, Peretz M, Pick O, Pyetan E, Rozenberg H, Shalev-Benami M, Wekselman I, Zarivach R, Zimmerman E, Assis N, Bloch J, Israeli H, Kalaora R, Lim L, Sade-Falk O, Shapira T, Taha-Salaime L, Tang H, Yonath A. Ribosomal Antibiotics: Contemporary Challenges. Antibiotics (Basel) 2016; 5:antibiotics5030024. [PMID: 27367739 PMCID: PMC5039520 DOI: 10.3390/antibiotics5030024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/07/2016] [Accepted: 06/20/2016] [Indexed: 11/30/2022] Open
Abstract
Most ribosomal antibiotics obstruct distinct ribosomal functions. In selected cases, in addition to paralyzing vital ribosomal tasks, some ribosomal antibiotics are involved in cellular regulation. Owing to the global rapid increase in the appearance of multi-drug resistance in pathogenic bacterial strains, and to the extremely slow progress in developing new antibiotics worldwide, it seems that, in addition to the traditional attempts at improving current antibiotics and the intensive screening for additional natural compounds, this field should undergo substantial conceptual revision. Here, we highlight several contemporary issues, including challenging the common preference of broad-range antibiotics; the marginal attention to alterations in the microbiome population resulting from antibiotics usage, and the insufficient awareness of ecological and environmental aspects of antibiotics usage. We also highlight recent advances in the identification of species-specific structural motifs that may be exploited for the design and the creation of novel, environmental friendly, degradable, antibiotic types, with a better distinction between pathogens and useful bacterial species in the microbiome. Thus, these studies are leading towards the design of “pathogen-specific antibiotics,” in contrast to the current preference of broad range antibiotics, partially because it requires significant efforts in speeding up the discovery of the unique species motifs as well as the clinical pathogen identification.
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Affiliation(s)
- Tamar Auerbach-Nevo
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - David Baram
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Matthew Belousoff
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Elinor Breiner
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Chen Davidovich
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Giuseppe Cimicata
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Zohar Eyal
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Yehuda Halfon
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Miri Krupkin
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Donna Matzov
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Markus Metz
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Mruwat Rufayda
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Moshe Peretz
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Ophir Pick
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Erez Pyetan
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Haim Rozenberg
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Moran Shalev-Benami
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Itai Wekselman
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Raz Zarivach
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Ella Zimmerman
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Nofar Assis
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Joel Bloch
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Hadar Israeli
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Rinat Kalaora
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Lisha Lim
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Ofir Sade-Falk
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Tal Shapira
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Leena Taha-Salaime
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Hua Tang
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
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Eyal Z, Matzov D, Krupkin M, Wekselman I, Paukner S, Zimmerman E, Rozenberg H, Bashan A, Yonath A. Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus. Proc Natl Acad Sci U S A 2015; 112:E5805-14. [PMID: 26464510 PMCID: PMC4629319 DOI: 10.1073/pnas.1517952112] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [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] [Indexed: 11/18/2022] Open
Abstract
The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus.
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Affiliation(s)
- Zohar Eyal
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Donna Matzov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Miri Krupkin
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Itai Wekselman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Ella Zimmerman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Haim Rozenberg
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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22
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Sun L, Xiong Y, Bashan A, Zimmerman E, Shulman Daube S, Peleg Y, Albeck S, Unger T, Yonath H, Krupkin M, Matzov D, Yonath A. Cover Picture: A Recombinant Collagen-mRNA Platform for Controllable Protein Synthesis (ChemBioChem 10/2015). Chembiochem 2015. [DOI: 10.1002/cbic.201590024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Sun L, Xiong Y, Bashan A, Zimmerman E, Shulman Daube S, Peleg Y, Albeck S, Unger T, Yonath H, Krupkin M, Matzov D, Yonath A. A Recombinant Collagen-mRNA Platform for Controllable Protein Synthesis. Chembiochem 2015; 16:1415-9. [PMID: 25930950 PMCID: PMC4517095 DOI: 10.1002/cbic.201500205] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Indexed: 12/19/2022]
Abstract
We have developed a collagen–mRNA platform for controllable protein production that is intended to be less prone to the problems associated with commonly used mRNA therapy as well as with collagen skin-healing procedures. A collagen mimic was constructed according to a recombinant method and was used as scaffold for translating mRNA chains into proteins. Cysteines were genetically inserted into the collagen chain at positions allowing efficient ribosome translation activity while minimizing mRNA misfolding and degradation. Enhanced green fluorescence protein (eGFP) mRNA bound to collagen was successfully translated by cell-free Escherichia coli ribosomes. This system enabled an accurate control of specific protein synthesis by monitoring expression time and level. Luciferase–mRNA was also translated on collagen scaffold by eukaryotic cell extracts. Thus we have demonstrated the feasibility of controllable protein synthesis on collagen scaffolds by ribosomal machinery.
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Affiliation(s)
- Liping Sun
- Department of Biomaterials, College of Materials, Xiamen University, 422, Siming South Road, Xiamen 361005 (China)
| | - Yunjing Xiong
- Department of Biomaterials, College of Materials, Xiamen University, 422, Siming South Road, Xiamen 361005 (China)
| | - Anat Bashan
- Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001 (Israel)
| | - Ella Zimmerman
- Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001 (Israel)
| | | | - Yoav Peleg
- Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001 (Israel)
| | - Shira Albeck
- Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001 (Israel)
| | - Tamar Unger
- Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001 (Israel)
| | - Hagith Yonath
- Sheba Medical Center, 1 Sheba Street, Tel Hashomer 52621 (Israel).,Sackler School of Medicine, Tel Aviv University, 10 Levanon Street, Tel Aviv 69978 (Israel)
| | - Miri Krupkin
- Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001 (Israel)
| | - Donna Matzov
- Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001 (Israel)
| | - Ada Yonath
- Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001 (Israel).
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Berezin Y, Bashan A, Havlin S. Comment on "Percolation transitions are not always sharpened by making networks interdependent". Phys Rev Lett 2013; 111:189601. [PMID: 24237574 DOI: 10.1103/physrevlett.111.189601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 07/14/2013] [Indexed: 06/02/2023]
Abstract
A Comment on the Letter by S. W. Son, P. Grassberger, and M. Paczuski, Phys. Rev. Lett. 107, 195702 (2011). The authors of the Letter offer a Reply.
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Affiliation(s)
- Y Berezin
- Department of Physics, Bar Ilan University, Ramat Gan 5290002, Israel
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25
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Zimmerman E, Bashan A, Yonath A. Antibiotics at the Ribosomal Exit Tunnel-Selected Structural Aspects. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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26
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Krupkin M, Zimmerman E, Bashan A, Yonath A. 2 A prebiotic RNA apparatus functions within the contemporary ribosome. J Biomol Struct Dyn 2013. [DOI: 10.1080/07391102.2013.786328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Krupkin M, Matzov D, Tang H, Metz M, Kalaora R, Belousoff MJ, Zimmerman E, Bashan A, Yonath A. A vestige of a prebiotic bonding machine is functioning within the contemporary ribosome. Philos Trans R Soc Lond B Biol Sci 2012; 366:2972-8. [PMID: 21930590 PMCID: PMC3158926 DOI: 10.1098/rstb.2011.0146] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Based on the presumed capability of a prebiotic pocket-like entity to accommodate substrates whose stereochemistry enables the creation of chemical bonds, it is suggested that a universal symmetrical region identified within all contemporary ribosomes originated from an entity that we term the ‘proto-ribosome’. This ‘proto-ribosome’ could have evolved from an earlier machine that was capable of performing essential tasks in the RNA world, called here the ‘pre-proto-ribosome’, which was adapted for producing proteins.
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Affiliation(s)
- Miri Krupkin
- Weizmann Institute of Science, Rehovot 76100, Israel
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28
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Davidovich C, Belousoff M, Wekselman I, Shapira T, Krupkin M, Zimmerman E, Bashan A, Yonath A. Cover Picture: The Proto-Ribosome: An Ancient Nano-machine for Peptide Bond Formation (Isr. J. Chem. 1/2010). Isr J Chem 2010. [DOI: 10.1002/ijch.201090003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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29
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Davidovich C, Belousoff M, Wekselman I, Shapira T, Krupkin M, Zimmerman E, Bashan A, Yonath A. The Proto-Ribosome: an ancient nano-machine for peptide bond formation. Isr J Chem 2010. [PMID: 26207070 DOI: 10.1002/ijch.201000012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The ribosome is a ribozyme whose active site, the peptidyl transferase center (PTC) is situated within a highly conserved universal symmetrical region that connects all ribosomal functional centers involved in amino-acid polymerization. The linkage between this elaborate architecture and A-site tRNA position revealed that the A to P-site passage of the tRNA 3' terminus during protein synthesis is performed by a rotary motion, synchronized with the overall tRNA/mRNA sideways movement and Guided by the PTC. This rotary motion leads to suitable stereochemistry for peptide bond formation as well as for substrate mediated catalysis. Analysis of the substrate binding modes to ribosomes led to the hypothesis that the ancient ribosome produced single peptide bonds and non-coded chains, potentially in a similar manner to the modern PTC. Later in evolution, a mechanism, enabling some type of decoding genetic control triggered the emergence of the small ribosomal subunit or part of it. This seems to be the result of the appearance of reaction products that could have evolved after polypeptides capable of enzymatic function were generated sporadically, while an ancient stable RNA fold was converted into an old version of a tRNA molecule. As in the contemporary ribosome the symmetry relates only the backbone fold and nucleotides orientations but not nucleotide sequences, it emphasizes the superiority of functional requirement over sequence conservation, and indicates that the PTC may have evolved by gene fusion or gene duplication.
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Affiliation(s)
- Chen Davidovich
- Department of Structural Biology, Weizmann Inst., 76100 Rehovot, Israel
| | - Matthew Belousoff
- Department of Structural Biology, Weizmann Inst., 76100 Rehovot, Israel
| | - Itai Wekselman
- Department of Structural Biology, Weizmann Inst., 76100 Rehovot, Israel
| | - Tal Shapira
- Department of Structural Biology, Weizmann Inst., 76100 Rehovot, Israel
| | - Miri Krupkin
- Department of Structural Biology, Weizmann Inst., 76100 Rehovot, Israel
| | - Ella Zimmerman
- Department of Structural Biology, Weizmann Inst., 76100 Rehovot, Israel
| | - Anat Bashan
- Department of Structural Biology, Weizmann Inst., 76100 Rehovot, Israel
| | - Ada Yonath
- Department of Structural Biology, Weizmann Inst., 76100 Rehovot, Israel
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Davidovich C, Belousoff M, Bashan A, Yonath A. The evolving ribosome: from non-coded peptide bond formation to sophisticated translation machinery. Res Microbiol 2009; 160:487-92. [PMID: 19619641 DOI: 10.1016/j.resmic.2009.07.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 07/02/2009] [Accepted: 07/04/2009] [Indexed: 11/25/2022]
Abstract
Structural analysis supported by biochemical, mutagenesis and computational evidence, revealed that the contemporary ribosome's active site is a universal symmetrical pocket made of ribosomal RNA. This pocket seems to be the remnant of the proto-ribosome, a dimeric RNA assembly evolved by gene duplication, capable of autonomously catalyzing peptide bond formation and non-coded amino acid polymerization.
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Affiliation(s)
- Chen Davidovich
- The Department of Structural Biology, Weizmann Institute, Rehovot, Israel
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31
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Wekselman I, Davidovich C, Agmon I, Zimmerman E, Rozenberg H, Bashan A, Berisio R, Yonath A. Ribosome's mode of function: myths, facts and recent results. J Pept Sci 2009; 15:122-30. [DOI: 10.1002/psc.1077] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
Crystallography of ribosomes, the universal cell nucleoprotein assemblies facilitating the translation of the genetic-code into proteins, met with severe problems owing to their large size, complex structure, inherent flexibility and high conformational variability. For the case of the small ribosomal subunit, which caused extreme difficulties, post crystallization treatment by minute amounts of a heteropolytungstate cluster allowed structure determination at atomic resolution. This cluster played a dual role in ribosomal crystallography: providing anomalous phasing power and dramatically increased the resolution, by stabilization of a selected functional conformation. Thus, four out of the fourteen clusters that bind to each of the crystallized small subunits are attached to a specific ribosomal protein in a fashion that may control a significant component of the subunit internal flexibility, by "gluing" symmetrical related subunits. Here we highlight basic issues in the relationship between metal ions and macromolecules and present common traits controlling in the interactions between polymetalates and various macromolecules, which may be extended towards the exploitation of polymetalates for therapeutical treatment.
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Affiliation(s)
- Anat Bashan
- Department of Structural Biology, Weizmann Inst., 76100 Rehovot, Israel
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Bashan A, Yonath A. Correlating ribosome function with high-resolution structures. Trends Microbiol 2008; 16:326-35. [PMID: 18547810 DOI: 10.1016/j.tim.2008.05.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Revised: 05/03/2008] [Accepted: 05/07/2008] [Indexed: 10/22/2022]
Abstract
Ribosome research has undergone astonishing progress in recent years. Crystal structures have shed light on the functional properties of the translation machinery and revealed how the striking architecture of the ribosome is ingeniously designed as the framework for its unique capabilities: precise decoding, substrate-mediated peptide-bond formation and efficient polymerase activity. New findings include the two concerted elements of tRNA translocation: sideways shift and a ribosomal-navigated rotatory motion; the dynamics of the nascent-chain exit tunnel and the shelter formed by the ribosome-bound trigger-factor, which acts as a chaperone to prevent nascent-chain aggregation and misfolding. The availability of these structures has also illuminated the action, selectivity, resistance and synergism of antibiotics that target ribosomes.
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Affiliation(s)
- Anat Bashan
- Department of Structural Biology, Weizmann Institute, Rehovot, 76100, Israel
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34
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Davidovich C, Bashan A, Auerbach-Nevo T, Yaggie RD, Gontarek RR, Yonath A. Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity. Proc Natl Acad Sci U S A 2007; 104:4291-6. [PMID: 17360517 PMCID: PMC1817833 DOI: 10.1073/pnas.0700041104] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Indexed: 11/18/2022] Open
Abstract
New insights into functional flexibility at the peptidyl transferase center (PTC) and its vicinity were obtained by analysis of pleuromutilins binding modes to the ribosome. The crystal structures of Deinococcus radiodurans large ribosomal subunit complexed with each of three pleuromutilin derivatives: retapamulin (SB-275833), SB-280080, and SB-571519, show that all bind to the PTC with their core oriented similarly at the A-site and their C14 extensions pointing toward the P-site. Except for an H-bond network with a single nucleotide, G2061, which involves the essential keto group of all three compounds, only minor hydrophobic contacts are formed between the pleuromutilin C14 extensions and any ribosomal component, consistent with the PTC tolerance to amino acid diversity. Efficient drug binding mode is attained by a mechanism based on induced-fit motions exploiting the ribosomal intrinsic functional flexibility and resulting in conformational rearrangements that seal the pleuromutilin-binding pocket and tightens it up. Comparative studies identified a network of remote interactions around the PTC, indicating that pleuromutilins selectivity is acquired by nonconserved nucleotides residing in the PTC vicinity, in a fashion resembling allosterism. Likewise, pleuromutilin resistant mechanisms involve nucleotides residing in the environs of the binding pocket, consistent with their slow resistance-development rates.
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Affiliation(s)
- Chen Davidovich
- *Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel; and
| | - Anat Bashan
- *Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel; and
| | - Tamar Auerbach-Nevo
- *Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel; and
| | - Rachel D. Yaggie
- Department of Enzymology and Mechanistic Pharmacology, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426
| | - Richard R. Gontarek
- Department of Enzymology and Mechanistic Pharmacology, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426
| | - Ada Yonath
- *Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel; and
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35
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Abstract
Using quantum mechanics and exploiting known crystallographic coordinates of tRNA substrate located in the ribosome peptidyl transferase center around the 2-fold axis, we have investigated the mechanism for peptide-bond formation. The calculation is based on a choice of 50 atoms assumed to be important in the mechanism. We used density functional theory to optimize the geometry and energy of the transition state (TS) for peptide-bond formation. The TS is formed simultaneously with the rotatory motion enabling the translocation of the A-site tRNA 3' end into the P site, and we estimated the magnitude of rotation angle between the A-site starting position and the place at which the TS occurs. The calculated TS activation energy, E(a), is 35.5 kcal (1 kcal = 4.18 kJ)/mol, and the increase in hydrogen bonding between the rotating A-site tRNA and ribosome nucleotides as the TS forms appears to stabilize it to a value qualitatively estimated to be approximately 18 kcal/mol. The optimized geometry corresponds to a structure in which the peptide bond is being formed as other bonds are being broken, in such a manner as to release the P-site tRNA so that it may exit as a free molecule and be replaced by the translocating A-site tRNA. At TS formation the 2' OH group of the P-site tRNA A76 forms a hydrogen bond with the oxygen atom of the carboxyl group of the amino acid attached to the A-site tRNA, which may be indicative of its catalytic role, consistent with recent biochemical experiments.
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Affiliation(s)
- Asta Gindulyte
- *Hunter College and the Graduate School, City University of New York, New York, NY 10021
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel; and
| | - Ilana Agmon
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel; and
| | - Lou Massa
- *Hunter College and the Graduate School, City University of New York, New York, NY 10021
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel; and
- To whom correspondence should be addressed. E-mail:
| | - Jerome Karle
- Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, DC 20375-5341
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Abstract
The ribosome is a ribozyme whose active site, the peptidyl transferase center (PTC), is situated within a highly conserved universal symmetrical region that connects all ribosomal functional centers involved in amino acid polymerization. The linkage between this elaborate architecture and A-site tRNA position revealed that the A-> P-site passage of the tRNA terminus in the peptidyl transferase center is performed by a rotatory motion, synchronized with the overall tRNA/mRNA sideways movement. Guided by the PTC, the rotatory motion leads to stereochemistry suitable for peptide bond formation, as well as for substrate-mediated catalysis, consistent with quantum mechanical calculations elucidating the transition state mechanism for peptide bond formation and indicating that the peptide bond is being formed during the rotatory motion.
Analysis of substrate binding modes to inactive and active ribosomes illuminated the significant PTC mobility and supported the hypothesis that the ancient ribosome produced single peptide bonds and non-coded chains, utilizing free amino acids. Genetic control of the reaction evolved after poly-peptides capable of enzymatic function were created, and an ancient stable RNA fold was converted into tRNA molecules. As the symmetry relates only the backbone fold and nucleotide orientations, but not nucleotide sequence, it emphasizes the superiority of functional requirement over sequence conservation, and indicates that the PTC has evolved by gene fusion, presumably by taking advantage of similar RNA fold structures.
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Affiliation(s)
- Ilana Agmon
- Department of Structural Biology, Weizmann Institute of Science
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute of Science
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute of Science
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37
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Abstract
The sizable symmetrical region, comprising 180 ribosomal RNA nucleotides, which has been identified in and around the peptidyl transferase center (PTC) in crystal structures of eubacterial and archaeal large ribosomal subunits, indicates its universality, confirms that the ribosome is a ribozyme and evokes the suggestion that the PTC evolved by gene fusion. The symmetrical region can act as a center that coordinates amino acid polymerization by transferring intra-ribosomal signals between remote functional locations, as it connects, directly or through its extensions, the PTC, the three tRNA sites, the tunnel entrance, and the regions hosting elongation factors. Significant deviations from the overall symmetry stabilize the entire region and can be correlated with the shaping and guiding of the motion of the tRNA 3'-end from the A- into the P-site. The linkage between the elaborate PTC architecture and the spatial arrangements of the tRNA 3'-ends revealed the rotatory mechanism that integrates peptide bond formation, translocation within the PTC and nascent protein entrance into the exit tunnel. The positional catalysis exerted by the ribosome places the reactants in stereochemistry close to the intermediate state and facilitates the catalytic contribution of the P-site tRNA 2'-hydroxyl.
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Affiliation(s)
- Ilana Agmon
- Department of Structural Biology, The Weizmann Institute, 76100 Rehovot, Israel
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Pyetan E, Baram D, Sittner A, Auerbach-Nevo T, Bashan A, Greenberg I, Rozenberg H, Zarivach R, Yonath A. Structural parameters influencing the affinities and effectiveness of ribosomal antibiotics. Acta Crystallogr A 2005. [DOI: 10.1107/s010876730508952x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Baram D, Pyetan E, Sittner A, Auerbach-Nevo T, Bashan A, Yonath A. Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome reveals its chaperone action. Proc Natl Acad Sci U S A 2005; 102:12017-22. [PMID: 16091460 PMCID: PMC1183488 DOI: 10.1073/pnas.0505581102] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Trigger factor (TF), the first chaperone in eubacteria to encounter the emerging nascent chain, binds to the large ribosomal subunit in the vicinity of the protein exit tunnel opening and forms a sheltered folding space. Here, we present the 3.5-A crystal structure of the physiological complex of the large ribosomal subunit from the eubacterium Deinococcus radiodurans with the N-terminal domain of TF (TFa) from the same organism. For anchoring, TFa exploits a small ribosomal surface area in the vicinity of proteins L23 and L29, by using its "signature motif" as well as additional structural elements. The molecular details of TFa interactions reveal that L23 is essential for the association of TF with the ribosome and may serve as a channel of communication with the nascent chain progressing in the tunnel. L29 appears to induce a conformational change in TFa, which results in the exposure of TFa hydrophobic patches to the opening of the ribosomal exit tunnel, thus increasing its affinity for hydrophobic segments of the emerging nascent polypeptide. This observation implies that, in addition to creating a protected folding space for the emerging nascent chain, TF association with the ribosome prevents aggregation by providing a competing hydrophobic environment and may be critical for attaining the functional conformation necessary for chaperone activity.
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Affiliation(s)
- David Baram
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
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Berisio R, Amit M, Baram D, Harms J, Bashan A, Hansen H, Schluenzen F, Yonath A. Productive and non-productive binding of polyketides to the ribosome large subunit. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305090306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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41
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Bashan A, Yonath A. Ribosome crystallography: catalysis and evolution of peptide-bond formation, nascent chain elongation and its co-translational folding. Biochem Soc Trans 2005; 33:488-92. [PMID: 15916549 DOI: 10.1042/bst0330488] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A ribosome is a ribozyme polymerizing amino acids, exploiting positional- and substrate-mediated chemical catalysis. We showed that peptide-bond formation is facilitated by the ribosomal architectural frame, provided by a sizable symmetry-related region in and around the peptidyl transferase centre, suggesting that the ribosomal active site was evolved by gene fusion. Mobility in tunnel components is exploited for elongation arrest as well as for trafficking nascent proteins into the folding space bordered by the bacterial chaperone, namely the trigger factor.
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Affiliation(s)
- A Bashan
- Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel
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42
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Abstract
RNA protection experiments and the crystal structure of a complex of the large ribosomal subunit from the eubacterium Deinococcus radiodurans with rapamycin, a polyketide compound resembling macrolides and ketolides, showed that rapamycin binds to a crevice located at the boundaries of the nascent protein exit tunnel, near its entrance. At this location rapamycin cannot occlude the ribosome exit tunnel, consistent with its failure to act as a ribosomal antibiotic drug. In accord with recent biochemical data, this crevice may play a role in facilitating local cotranslational folding of nascent chains, in particular for transmembrane proteins.
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Affiliation(s)
- Maya Amit
- Department of Structural Biology, The Weizmann Institute, 76100 Rehovot, Israel
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43
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Abstract
High-resolution structures of ribosomal complexes revealed that minute amounts of clinically relevant antibiotics hamper protein biosynthesis by limiting ribosomal mobility or perturbing its elaborate architecture, designed for navigating and controlling peptide bond formation and continuous amino acid polymerization. To accomplish this, the ribosome contributes positional rather than chemical catalysis, provides remote interactions governing accurate substrate alignment within the flexible peptidyl-transferase center (PTC) pocket, and ensures nascent-protein chirality through spatial limitations. Peptide bond formation is concurrent with aminoacylated-tRNA 3' end translocation and is performed by a rotatory motion around the axis of a sizable ribosomal symmetry-related region, which is located around the PTC in all known crystal structures. Guided by ribosomal-RNA scaffold along an exact pattern, the rotatory motion results in stereochemistry that is optimal for peptide bond formation and for nascent protein entrance into the exit tunnel, the main target of antibiotics targeting ribosomes. By connecting the PTC, the decoding center, and the tRNA entrance and exit regions, the symmetry-related region can transfer intraribosomal signals, guaranteeing smooth processivity of amino acid polymerization.
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Affiliation(s)
- Ada Yonath
- Department of Structural Biology, The Weizmann Institute, 76100 Rehovot, Israel.
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44
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Abstract
Various antibiotics bind to ribosomes at functionally relevant locations such as the peptidyl-transferase center (PTC) and the exit tunnel for nascent proteins. High-resolution structures of antibiotics bound to ribosomal particles from a eubacterium that is similar to pathogens and an archaeon that shares properties with eukaryotes are deciphering subtle differences in these highly conserved locations that lead to drug selectivity and thereby facilitate clinical usage. These structures also show that members of antibiotic families with structural differences might bind to specific ribosomal pockets in different modes dominated by their chemical properties. Similarly, the chemical properties of drugs might govern variations in the nature of seemingly identical mechanisms of drug resistance. The observed variability in binding modes justifies expectations for structural design of improved antibiotic properties.
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Affiliation(s)
- Tamar Auerbach
- Department of Structural Biology, The Weizmann Institute, 76100 Rehovot, Israel
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45
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Zarivach R, Bashan A, Berisio R, Harms J, Auerbach T, Schluenzen F, Bartels H, Baram D, Pyetan E, Sittner A, Amit M, Hansen HAS, Kessler M, Liebe C, Wolff A, Agmon I, Yonath A. Functional aspects of ribosomal architecture: symmetry, chirality and regulation. J PHYS ORG CHEM 2004. [DOI: 10.1002/poc.831] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Raz Zarivach
- Department of Structural Biology, The Weizmann Institute, 76100 Rehovot, Israel
| | - Anat Bashan
- Department of Structural Biology, The Weizmann Institute, 76100 Rehovot, Israel
| | - Rita Berisio
- Max‐Planck‐Research Unit for Ribosomal Structure, 22603 Hamburg, Germany
| | - Joerg Harms
- Department of Structural Biology, The Weizmann Institute, 76100 Rehovot, Israel
| | - Tamar Auerbach
- Department of Structural Biology, The Weizmann Institute, 76100 Rehovot, Israel
- Max‐Planck‐Research Unit for Ribosomal Structure, 22603 Hamburg, Germany
| | - Frank Schluenzen
- Max‐Planck‐Research Unit for Ribosomal Structure, 22603 Hamburg, Germany
| | - Heike Bartels
- Max‐Planck‐Research Unit for Ribosomal Structure, 22603 Hamburg, Germany
| | - David Baram
- Department of Structural Biology, The Weizmann Institute, 76100 Rehovot, Israel
- Max‐Planck‐Research Unit for Ribosomal Structure, 22603 Hamburg, Germany
| | - Erez Pyetan
- Department of Structural Biology, The Weizmann Institute, 76100 Rehovot, Israel
- Max‐Planck‐Research Unit for Ribosomal Structure, 22603 Hamburg, Germany
| | - Assa Sittner
- Department of Structural Biology, The Weizmann Institute, 76100 Rehovot, Israel
| | - Maya Amit
- Department of Structural Biology, The Weizmann Institute, 76100 Rehovot, Israel
| | - Harly A. S. Hansen
- Max‐Planck‐Research Unit for Ribosomal Structure, 22603 Hamburg, Germany
| | - Maggie Kessler
- Department of Structural Biology, The Weizmann Institute, 76100 Rehovot, Israel
| | - Christa Liebe
- Max‐Planck‐Research Unit for Ribosomal Structure, 22603 Hamburg, Germany
| | - Anja Wolff
- Max‐Planck‐Research Unit for Ribosomal Structure, 22603 Hamburg, Germany
| | - Ilana Agmon
- Department of Structural Biology, The Weizmann Institute, 76100 Rehovot, Israel
| | - Ada Yonath
- Department of Structural Biology, The Weizmann Institute, 76100 Rehovot, Israel
- Max‐Planck‐Research Unit for Ribosomal Structure, 22603 Hamburg, Germany
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46
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Agmon I, Amit M, Auerbach T, Bashan A, Baram D, Bartels H, Berisio R, Greenberg I, Harms J, Hansen HAS, Kessler M, Pyetan E, Schluenzen F, Sittner A, Yonath A, Zarivach R. Ribosomal crystallography: a flexible nucleotide anchoring tRNA translocation, facilitates peptide-bond formation, chirality discrimination and antibiotics synergism. FEBS Lett 2004; 567:20-6. [PMID: 15165888 DOI: 10.1016/j.febslet.2004.03.065] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2004] [Accepted: 03/14/2004] [Indexed: 11/23/2022]
Abstract
The linkage between internal ribosomal symmetry and transfer RNA (tRNA) positioning confirmed positional catalysis of amino-acid polymerization. Peptide bonds are formed concurrently with tRNA-3' end rotatory motion, in conjunction with the overall messenger RNA (mRNA)/tRNA translocation. Accurate substrate alignment, mandatory for the processivity of protein biosynthesis, is governed by remote interactions. Inherent flexibility of a conserved nucleotide, anchoring the rotatory motion, facilitates chirality discrimination and antibiotics synergism. Potential tRNA interactions explain the universality of the tRNA CCA-end and P-site preference of initial tRNA. The interactions of protein L2 tail with the symmetry-related region periphery explain its conservation and its contributions to nascent chain elongation.
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Affiliation(s)
- Ilana Agmon
- Department of Structural Biology, The Weizmann Institute, 76100 Rehovot, Israel
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47
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Bashan A, Zarivach R, Schluenzen F, Agmon I, Harms J, Auerbach T, Baram D, Berisio R, Bartels H, Hansen HAS, Fucini P, Wilson D, Peretz M, Kessler M, Yonath A. Ribosomal crystallography: peptide bond formation and its inhibition. Biopolymers 2003; 70:19-41. [PMID: 12925991 DOI: 10.1002/bip.10412] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Ribosomes, the universal cellular organelles catalyzing the translation of genetic code into proteins, are protein/RNA assemblies, of a molecular weight 2.5 mega Daltons or higher. They are built of two subunits that associate for performing protein biosynthesis. The large subunit creates the peptide bond and provides the path for emerging proteins. The small has key roles in initiating the process and controlling its fidelity. Crystallographic studies on complexes of the small and the large eubacterial ribosomal subunits with substrate analogs, antibiotics, and inhibitors confirmed that the ribosomal RNA governs most of its activities, and indicated that the main catalytic contribution of the ribosome is the precise positioning and alignment of its substrates, the tRNA molecules. A symmetry-related region of a significant size, containing about two hundred nucleotides, was revealed in all known structures of the large ribosomal subunit, despite the asymmetric nature of the ribosome. The symmetry rotation axis, identified in the middle of the peptide-bond formation site, coincides with the bond connecting the tRNA double-helical features with its single-stranded 3' end, which is the moiety carrying the amino acids. This thus implies sovereign movements of tRNA features and suggests that tRNA translocation involves a rotatory motion within the ribosomal active site. This motion is guided and anchored by ribosomal nucleotides belonging to the active site walls, and results in geometry suitable for peptide-bond formation with no significant rearrangements. The sole geometrical requirement for this proposed mechanism is that the initial P-site tRNA adopts the flipped orientation. The rotatory motion is the major component of unified machinery for peptide-bond formation, translocation, and nascent protein progression, since its spiral nature ensures the entrance of the nascent peptide into the ribosomal exit tunnel. This tunnel, assumed to be a passive path for the growing chains, was found to be involved dynamically in gating and discrimination.
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Affiliation(s)
- Anat Bashan
- Department of Structural Biology, The Weizmann Institute, 76100 Rehovot, Israel
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48
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Bashan A, Agmon I, Zarivach R, Schluenzen F, Harms J, Pioletti M, Bartels H, Gluehmann M, Hansen H, Auerbach T, Franceschi F, Yonath A. High-resolution structures of ribosomal subunits: initiation, inhibition, and conformational variability. Cold Spring Harb Symp Quant Biol 2003; 66:43-56. [PMID: 12762007 DOI: 10.1101/sqb.2001.66.43] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- A Bashan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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49
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Agmon I, Auerbach T, Baram D, Bartels H, Bashan A, Berisio R, Fucini P, Hansen HAS, Harms J, Kessler M, Peretz M, Schluenzen F, Yonath A, Zarivach R. On peptide bond formation, translocation, nascent protein progression and the regulatory properties of ribosomes. Derived on 20 October 2002 at the 28th FEBS Meeting in Istanbul. Eur J Biochem 2003; 270:2543-56. [PMID: 12787020 DOI: 10.1046/j.1432-1033.2003.03634.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
High-resolution crystal structures of large ribosomal subunits from Deinococcus radiodurans complexed with tRNA-mimics indicate that precise substrate positioning, mandatory for efficient protein biosynthesis with no further conformational rearrangements, is governed by remote interactions of the tRNA helical features. Based on the peptidyl transferase center (PTC) architecture, on the placement of tRNA mimics, and on the existence of a two-fold related region consisting of about 180 nucleotides of the 23S RNA, we proposed a unified mechanism integrating peptide bond formation, A-to-P site translocation, and the entrance of the nascent protein into its exit tunnel. This mechanism implies sovereign, albeit correlated, motions of the tRNA termini and includes a spiral rotation of the A-site tRNA-3' end around a local two-fold rotation axis, identified within the PTC. PTC features, ensuring the precise orientation required for the A-site nucleophilic attack on the P-site carbonyl-carbon, guide these motions. Solvent mediated hydrogen transfer appears to facilitate peptide bond formation in conjunction with the spiral rotation. The detection of similar two-fold symmetry-related regions in all known structures of the large ribosomal subunit, indicate the universality of this mechanism, and emphasizes the significance of the ribosomal template for the precise alignment of the substrates as well as for accurate and efficient translocation. The symmetry-related region may also be involved in regulatory tasks, such as signal transmission between the ribosomal features facilitating the entrance and the release of the tRNA molecules. The protein exit tunnel is an additional feature that has a role in cellular regulation. We showed by crystallographic methods that this tunnel is capable of undergoing conformational oscillations and correlated the tunnel mobility with sequence discrimination, gating and intracellular regulation.
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Affiliation(s)
- Ilana Agmon
- Department of Structural Biology, The Weizmann Institute, Rehovot, Israel
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50
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Berisio R, Schluenzen F, Harms J, Bashan A, Auerbach T, Baram D, Yonath A. Structural insight into the role of the ribosomal tunnel in cellular regulation. Nat Struct Mol Biol 2003; 10:366-70. [PMID: 12665853 DOI: 10.1038/nsb915] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2002] [Accepted: 03/06/2003] [Indexed: 11/09/2022]
Abstract
Nascent proteins emerge out of ribosomes through an exit tunnel, which was assumed to be a firmly built passive path. Recent biochemical results, however, indicate that the tunnel plays an active role in sequence-specific gating of nascent chains and in responding to cellular signals. Consistently, modulation of the tunnel shape, caused by the binding of the semi-synthetic macrolide troleandomycin to the large ribosomal subunit from Deinococcus radiodurans, was revealed crystallographically. The results provide insights into the tunnel dynamics at high resolution. Here we show that, in addition to the typical steric blockage of the ribosomal tunnel by macrolides, troleandomycin induces a conformational rearrangement in a wall constituent, protein L22, flipping the tip of its highly conserved beta-hairpin across the tunnel. On the basis of mutations that alleviate elongation arrest, the tunnel motion could be correlated with sequence discrimination and gating, suggesting that specific arrest motifs within nascent chain sequences may induce a similar gating mechanism.
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Affiliation(s)
- Rita Berisio
- Max-Planck-Research Unit for Ribosomal Structure, Hamburg, Germany
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