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Nouhin J, Tzou PL, Rhee SY, Sahoo MK, Pinsky BA, Krupkin M, Puglisi JD, Puglisi EV, Shafer RW. Human immunodeficiency virus 1 5'-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations. J Gen Virol 2023; 104:001898. [PMID: 37801004 PMCID: PMC10721937 DOI: 10.1099/jgv.0.001898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/29/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) reverse transcriptase (RT) initiation depends on interaction between viral 5'-leader RNA, RT and host tRNA3Lys. Therefore, we sought to identify co-evolutionary changes between the 5'-leader and RT in viruses developing RT-inhibitor resistance mutations. We sequenced 5'-leader positions 37-356 of paired plasma virus samples from 29 individuals developing the nucleoside RT inhibitor (NRTI)-resistance mutation M184V, 19 developing a non-nucleoside RT inhibitor (NNRTI)-resistance mutation and 32 untreated controls. 5'-Leader variants were defined as positions where ≥20 % of next-generation sequencing (NGS) reads differed from the HXB2 sequence. Emergent mutations were defined as nucleotides undergoing a ≥4-fold change in proportion between baseline and follow-up. Mixtures were defined as positions containing ≥2 nucleotides each present in ≥20 % of NGS reads. Among 80 baseline sequences, 87 positions (27.2 %) contained a variant; 52 contained a mixture. Position 201 was the only position more likely to develop a mutation in the M184V (9/29 vs 0/32; P=0.0006) or NNRTI-resistance (4/19 vs 0/32; P=0.02; Fisher's exact test) groups than the control group. Mixtures at positions 200 and 201 occurred in 45.0 and 28.8 %, respectively, of baseline samples. Because of the high proportion of mixtures at these positions, we analysed 5'-leader mixture frequencies in two additional datasets: five publications reporting 294 dideoxyterminator clonal GenBank sequences from 42 individuals and six National Center for Biotechnology Information (NCBI) BioProjects reporting NGS datasets from 295 individuals. These analyses demonstrated position 200 and 201 mixtures at proportions similar to those in our samples and at frequencies several times higher than at all other 5'-leader positions. Although we did not convincingly document co-evolutionary changes between RT and 5'-leader sequences, we identified a novel phenomenon, wherein positions 200 and 201 immediately downstream of the HIV-1 primer binding site exhibited an extraordinarily high likelihood of containing a nucleotide mixture. Possible explanations for the high mixture rates are that these positions are particularly error-prone or provide a viral fitness advantage.
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Affiliation(s)
- Janin Nouhin
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh, Cambodia
| | - Philip Lei Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Malaya K. Sahoo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Benjamin A. Pinsky
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Miri Krupkin
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Joseph D. Puglisi
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Elisabetta V. Puglisi
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
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2
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Nouhin J, Tzou PL, Rhee SY, Sahoo MK, Pinsky BA, Krupkin M, Puglisi JD, Puglisi EV, Shafer RW. HIV-1 5'-Leader Mutations in Plasma Viruses Before and After the Development of Reverse Transcriptase Inhibitor-Resistance Mutations. medRxiv 2023:2023.06.04.23290942. [PMID: 37333388 PMCID: PMC10274971 DOI: 10.1101/2023.06.04.23290942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Background HIV-1 RT initiation depends on interaction between viral 5'-leader RNA, RT, and host tRNA3Lys. We therefore sought to identify co-evolutionary changes between the 5'-leader and RT in viruses developing RT-inhibitor resistance mutations. Methods We sequenced 5'-leader positions 37-356 of paired plasma virus samples from 29 individuals developing the NRTI-resistance mutation M184V, 19 developing an NNRTI-resistance mutation, and 32 untreated controls. 5'-leader variants were defined as positions where ≥20% of NGS reads differed from the HXB2 sequence. Emergent mutations were defined as nucleotides undergoing ≥4-fold change in proportion between baseline and follow-up. Mixtures were defined as positions containing ≥2 nucleotides each present in ≥20% of NGS reads. Results Among 80 baseline sequences, 87 positions (27.2%) contained a variant; 52 contained a mixture. Position 201 was the only position more likely to develop a mutation in the M184V (9/29 vs. 0/32; p=0.0006) or NNRTI-resistance (4/19 vs. 0/32; p=0.02; Fisher's Exact Test) groups than the control group. Mixtures at positions 200 and 201 occurred in 45.0% and 28.8%, respectively, of baseline samples. Because of the high proportion of mixtures at these positions, we analyzed 5'-leader mixture frequencies in two additional datasets: five publications reporting 294 dideoxyterminator clonal GenBank sequences from 42 individuals and six NCBI BioProjects reporting NGS datasets from 295 individuals. These analyses demonstrated position 200 and 201 mixtures at proportions similar to those in our samples and at frequencies several times higher than at all other 5'-leader positions. Conclusions Although we did not convincingly document co-evolutionary changes between RT and 5'-leader sequences, we identified a novel phenomenon, wherein positions 200 and 201, immediately downstream of the HIV-1 primer binding site exhibited an extraordinarily high likelihood of containing a nucleotide mixture. Possible explanations for the high mixture rates are that these positions are particularly error-prone or provide a viral fitness advantage.
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Affiliation(s)
- Janin Nouhin
- Division of Infectious Diseases, Stanford University, Stanford, CA, USA and Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh, Cambodia
| | - Philip L Tzou
- Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Benjamin A Pinsky
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA
| | - Miri Krupkin
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elisabetta V Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert W Shafer
- Division of Infectious Diseases, Stanford University, Stanford, CA, USA
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Wagner CE, Krupkin M, Smith-Dupont KB, Wu CM, Bustos NA, Witten J, Ribbeck K. Comparison of Physicochemical Properties of Native Mucus and Reconstituted Mucin Gels. Biomacromolecules 2023; 24:628-639. [PMID: 36727870 DOI: 10.1021/acs.biomac.2c01016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Simulating native mucus with model systems such as gels made from reconstituted mucin or commercially available polymers presents experimental advantages including greater sample availability and reduced inter- and intradonor heterogeneity. Understanding whether these gels reproduce the complex physical and biochemical properties of native mucus at multiple length scales is critical to building relevant experimental models, but few systematic comparisons have been reported. Here, we compared bulk mechanical properties, microstructure, and biochemical responses of mucus from different niches, reconstituted mucin gels (with similar pH and polymer concentrations as native tissues), and commonly used commercially available polymers. To evaluate gel properties across these length scales, we used small-amplitude oscillatory shear, single-particle tracking, and microaffinity chromatography with small analytes. With the exception of human saliva, the mechanical response of mucin gels was qualitatively similar to that of native mucus. The transport behavior of charged peptides through native mucus gels was qualitatively reproduced in gels composed of corresponding isolated mucins. Compared to native mucus, we observed substantial differences in the physicochemical properties of gels reconstituted from commercially available mucins and the substitute carboxymethylcellulose, which is currently used in artificial tear and saliva treatments. Our study highlights the importance of selecting a mucus model system guided by the length scale relevant to the scientific investigation or disease application.
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Affiliation(s)
- Caroline E Wagner
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Miri Krupkin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Kathryn B Smith-Dupont
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Chloe M Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Nicole A Bustos
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Jacob Witten
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States.,Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Katharina Ribbeck
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
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Prabhakar A, Krahn N, Zhang J, Vargas-Rodriguez O, Krupkin M, Fu Z, Acosta-Reyes FJ, Ge X, Choi J, Crnković A, Ehrenberg M, Puglisi EV, Söll D, Puglisi J. Uncovering translation roadblocks during the development of a synthetic tRNA. Nucleic Acids Res 2022; 50:10201-10211. [PMID: 35882385 PMCID: PMC9561287 DOI: 10.1093/nar/gkac576] [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: 05/13/2022] [Revised: 06/14/2022] [Accepted: 07/22/2022] [Indexed: 11/24/2022] Open
Abstract
Ribosomes are remarkable in their malleability to accept diverse aminoacyl-tRNA substrates from both the same organism and other organisms or domains of life. This is a critical feature of the ribosome that allows the use of orthogonal translation systems for genetic code expansion. Optimization of these orthogonal translation systems generally involves focusing on the compatibility of the tRNA, aminoacyl-tRNA synthetase, and a non-canonical amino acid with each other. As we expand the diversity of tRNAs used to include non-canonical structures, the question arises as to the tRNA suitability on the ribosome. Specifically, we investigated the ribosomal translation of allo-tRNAUTu1, a uniquely shaped (9/3) tRNA exploited for site-specific selenocysteine insertion, using single-molecule fluorescence. With this technique we identified ribosomal disassembly occurring from translocation of allo-tRNAUTu1 from the A to the P site. Using cryo-EM to capture the tRNA on the ribosome, we pinpointed a distinct tertiary interaction preventing fluid translocation. Through a single nucleotide mutation, we disrupted this tertiary interaction and relieved the translation roadblock. With the continued diversification of genetic code expansion, our work highlights a targeted approach to optimize translation by distinct tRNAs as they move through the ribosome.
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Affiliation(s)
| | | | | | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Miri Krupkin
- Department of Structural Biology, Stanford University, Stanford, CA 94305-5126, USA
| | - Ziao Fu
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Francisco J Acosta-Reyes
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Xueliang Ge
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 751 24, Sweden
| | - Junhong Choi
- Department of Structural Biology, Stanford University, Stanford, CA 94305-5126, USA
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 751 24, Sweden
| | | | - Dieter Söll
- Correspondence may also be addressed to Dieter Söll.
| | - Joseph Puglisi
- To whom correspondence should be addressed. Tel: +1 650 498 4397;
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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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6
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Krupkin M, Jackson LN, Ha B, Puglisi EV. Advances in understanding the initiation of HIV-1 reverse transcription. Curr Opin Struct Biol 2020; 65:175-183. [PMID: 32916568 PMCID: PMC9973426 DOI: 10.1016/j.sbi.2020.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/12/2020] [Accepted: 07/21/2020] [Indexed: 01/18/2023]
Abstract
Many viruses, including Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Human Immunodeficiency Virus (HIV), use RNA as their genetic material. How viruses harness RNA structure and RNA-protein interactions to control their replication remains obscure. Recent advances in the characterization of HIV-1 reverse transcriptase, the enzyme that converts its single-stranded RNA genome into a double-stranded DNA copy, reveal how the reverse transcription complex evolves during initiation. Here we highlight these advances in HIV-1 structural biology and discuss how they are furthering our understanding of HIV and related ribonucleoprotein complexes implicated in viral disease.
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Affiliation(s)
- Miri Krupkin
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lynnette Nthenya Jackson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Betty Ha
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elisabetta Viani Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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7
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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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8
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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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9
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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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10
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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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11
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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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12
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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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13
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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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 04/30/2015] [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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14
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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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15
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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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16
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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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17
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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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