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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: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [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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Abstract
Mixed-mode chromatography on cysteine-SulfoLink resin efficiently separates ribosomes from cell lysates and is particularly effective at rapidly removing endogenous proteases and nucleases, resulting in ribosomes of improved purity, integrity, and activity. Binding occurs partly by anion exchange of the RNA of the ribosomes, so that cells must be lysed in a buffer of moderate ionic strength (conductivity no more than 20 mS for chromatography of bacterial ribosomes) without any highly charged additives (e.g., heparin, which is used to inhibit RNases in yeast). A robust protocol for Escherichia coli is given here as an example.
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Affiliation(s)
- Bruce A Maguire
- Primary Pharmacology Group, Pfizer Global Research and Development, Groton, Connecticut 06340
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Ladror DT, Frey BL, Scalf M, Levenstein ME, Artymiuk JM, Smith LM. Methylation of yeast ribosomal protein S2 is elevated during stationary phase growth conditions. Biochem Biophys Res Commun 2014; 445:535-41. [PMID: 24486316 DOI: 10.1016/j.bbrc.2014.01.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 01/14/2014] [Indexed: 01/12/2023]
Abstract
Ribosomes, as the center of protein translation in the cell, require careful regulation via multiple pathways. While regulation of ribosomal synthesis and function has been widely studied on the transcriptional and translational "levels," the biological roles of ribosomal post-translational modifications (PTMs) are largely not understood. Here, we explore this matter by using quantitative mass spectrometry to compare the prevalence of ribosomal methylation and acetylation for yeast in the log phase and the stationary phase of growth. We find that of the 27 modified peptides identified, two peptides experience statistically significant changes in abundance: a 1.9-fold decrease in methylation for k(Me)VSGFKDEVLETV of ribosomal protein S1B (RPS1B), and a 10-fold increase in dimethylation for r(DiMe)GGFGGR of ribosomal protein S2 (RPS2). While the biological role of RPS1B methylation has largely been unexplored, RPS2 methylation is a modification known to have a role in processing and export of ribosomal RNA. This suggests that yeast in the stationary phase increase methylation of RPS2 in order to regulate ribosomal synthesis. These results demonstrate the utility of mass spectrometry for quantifying dynamic changes in ribosomal PTMs.
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Affiliation(s)
- Daniel T Ladror
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Brian L Frey
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Mark E Levenstein
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Jacklyn M Artymiuk
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
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Frey BL, Ladror DT, Sondalle SB, Krusemark CJ, Jue AL, Coon JJ, Smith LM. Chemical derivatization of peptide carboxyl groups for highly efficient electron transfer dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1710-21. [PMID: 23918461 PMCID: PMC3827969 DOI: 10.1007/s13361-013-0701-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 07/01/2013] [Accepted: 07/06/2013] [Indexed: 05/11/2023]
Abstract
The carboxyl groups of tryptic peptides were derivatized with a tertiary or quaternary amine labeling reagent to generate more highly charged peptide ions that fragment efficiently by electron transfer dissociation (ETD). All peptide carboxyl groups-aspartic and glutamic acid side-chains as well as C-termini-were derivatized with an average reaction efficiency of 99 %. This nearly complete labeling avoids making complex peptide mixtures even more complex because of partially-labeled products, and it allows the use of static modifications during database searching. Alkyl tertiary amines were found to be the optimal labeling reagent among the four types tested. Charge states are substantially higher for derivatized peptides: a modified tryptic digest of bovine serum albumin (BSA) generates ~90% of its precursor ions with z > 2, compared with less than 40 % for the unmodified sample. The increased charge density of modified peptide ions yields highly efficient ETD fragmentation, leading to many additional peptide identifications and higher sequence coverage (e.g., 70 % for modified versus only 43 % for unmodified BSA). The utility of this labeling strategy was demonstrated on a tryptic digest of ribosomal proteins isolated from yeast cells. Peptide derivatization of this sample produced an increase in the number of identified proteins, a >50 % increase in the sequence coverage of these proteins, and a doubling of the number of peptide spectral matches. This carboxyl derivatization strategy greatly improves proteome coverage obtained from ETD-MS/MS of tryptic digests, and we anticipate that it will also enhance identification and localization of post-translational modifications.
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Affiliation(s)
- Brian L. Frey
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, WI 53706
| | - Daniel T. Ladror
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, WI 53706
| | - Samuel B. Sondalle
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, WI 53706
| | - Casey J. Krusemark
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, WI 53706
| | - April L. Jue
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, WI 53706
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, WI 53706
- Department of Biomolecular Chemistry, University of Wisconsin—Madison, 420 Henry Mall, Madison, WI 53706
- Genome Center of Wisconsin, University of Wisconsin—Madison, 425G Henry Mall, Madison, WI 53706
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, WI 53706
- Genome Center of Wisconsin, University of Wisconsin—Madison, 425G Henry Mall, Madison, WI 53706
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Trauner A, Bennett MH, Williams HD. Isolation of bacterial ribosomes with monolith chromatography. PLoS One 2011; 6:e16273. [PMID: 21326610 PMCID: PMC3033897 DOI: 10.1371/journal.pone.0016273] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 12/07/2010] [Indexed: 11/18/2022] Open
Abstract
We report the development of a rapid chromatographic method for the isolation of bacterial ribosomes from crude cell lysates in less than ten minutes. Our separation is based on the use of strong anion exchange monolithic columns. Using a simple stepwise elution program we were able to purify ribosomes whose composition is comparable to those isolated by sucrose gradient ultracentrifugation, as confirmed by quantitative proteomic analysis (iTRAQ). The speed and simplicity of this approach could accelerate the study of many different aspects of ribosomal biology.
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Affiliation(s)
- Andrej Trauner
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Mark H. Bennett
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Huw D. Williams
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail:
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