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Lund T, Kulkova MY, Jersie-Christensen R, Atlung T. Essentiality of the Escherichia coli YgfZ Protein for the In Vivo Thiomethylation of Ribosomal Protein S12 by the RimO Enzyme. Int J Mol Sci 2023; 24:ijms24054728. [PMID: 36902159 PMCID: PMC10002905 DOI: 10.3390/ijms24054728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 03/05/2023] Open
Abstract
Enzymes carrying Iron-Sulfur (Fe-S) clusters perform many important cellular functions and their biogenesis require complex protein machinery. In mitochondria, the IBA57 protein is essential and promotes assembly of [4Fe-4S] clusters and their insertion into acceptor proteins. YgfZ is the bacterial homologue of IBA57 but its precise role in Fe-S cluster metabolism is uncharacterized. YgfZ is needed for activity of the radical S-adenosyl methionine [4Fe-4S] cluster enzyme MiaB which thiomethylates some tRNAs. The growth of cells lacking YgfZ is compromised especially at low temperature. The RimO enzyme is homologous to MiaB and thiomethylates a conserved aspartic acid in ribosomal protein S12. To quantitate thiomethylation by RimO, we developed a bottom-up LC-MS2 analysis of total cell extracts. We show here that the in vivo activity of RimO is very low in the absence of YgfZ and independent of growth temperature. We discuss these results in relation to the hypotheses relating to the role of the auxiliary 4Fe-4S cluster in the Radical SAM enzymes that make Carbon-Sulfur bonds.
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2
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Kornspan D, Brendebach H, Hofreuter D, Mathur S, Blum SE, Fleker M, Bardenstein S, Al Dahouk S. Protein Biomarker Identification for the Discrimination of Brucella melitensis Field Isolates From the Brucella melitensis Rev.1 Vaccine Strain by MALDI-TOF MS. Front Microbiol 2021; 12:712601. [PMID: 34745025 PMCID: PMC8569450 DOI: 10.3389/fmicb.2021.712601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Brucella melitensis Rev.1 is a live attenuated vaccine strain that is widely used to control brucellosis in small ruminants. For successful surveillance and control programs, rapid identification and characterization of Brucella isolates and reliable differentiation of vaccinated and naturally infected animals are essential prerequisites. Although MALDI-TOF MS is increasingly applied in clinical microbiology laboratories for the diagnosis of brucellosis, species or even strain differentiation by this method remains a challenge. To detect biomarkers, which enable to distinguish the B. melitensis Rev.1 vaccine strain from B. melitensis field isolates, we initially searched for unique marker proteins by in silico comparison of the B. melitensis Rev.1 and 16M proteomes. We found 113 protein sequences of B. melitensis 16M that revealed a homologous sequence in the B. melitensis Rev.1 annotation and 17 of these sequences yielded potential biomarker pairs. MALDI-TOF MS spectra of 18 B. melitensis Rev.1 vaccine and 183 Israeli B. melitensis field isolates were subsequently analyzed to validate the identified marker candidates. This approach detected two genus-wide unique biomarkers with properties most similar to the ribosomal proteins L24 and S12. These two proteins clearly discriminated B. melitensis Rev.1 from the closely related B. melitensis 16M and the Israeli B. melitensis field isolates. In addition, we verified their discriminatory power using a set of B. melitensis strains from various origins and of different MLVA types. Based on our results, we propose MALDI-TOF MS profiling as a rapid, cost-effective alternative to the traditional, time-consuming approach to differentiate certain B. melitensis isolates on strain level.
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Affiliation(s)
- David Kornspan
- Department of Bacteriology, Kimron Veterinary Institute (KVI), Bet Dagan, Israel
| | - Holger Brendebach
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Dirk Hofreuter
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Shubham Mathur
- Department of Bacteriology, Kimron Veterinary Institute (KVI), Bet Dagan, Israel
| | - Shlomo Eduardo Blum
- Department of Bacteriology, Kimron Veterinary Institute (KVI), Bet Dagan, Israel
| | - Marcelo Fleker
- Department of Bacteriology, Kimron Veterinary Institute (KVI), Bet Dagan, Israel
| | | | - Sascha Al Dahouk
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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3
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Shrestha HK, Appidi MR, Villalobos Solis MI, Wang J, Carper DL, Burdick L, Pelletier DA, Doktycz MJ, Hettich RL, Abraham PE. Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance. BMC Microbiol 2021; 21:308. [PMID: 34749649 PMCID: PMC8574000 DOI: 10.1186/s12866-021-02370-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Background Microbe-microbe interactions between members of the plant rhizosphere are important but remain poorly understood. A more comprehensive understanding of the molecular mechanisms used by microbes to cooperate, compete, and persist has been challenging because of the complexity of natural ecosystems and the limited control over environmental factors. One strategy to address this challenge relies on studying complexity in a progressive manner, by first building a detailed understanding of relatively simple subsets of the community and then achieving high predictive power through combining different building blocks (e.g., hosts, community members) for different environments. Herein, we coupled this reductionist approach with high-resolution mass spectrometry-based metaproteomics to study molecular mechanisms driving community assembly, adaptation, and functionality for a defined community of ten taxonomically diverse bacterial members of Populus deltoides rhizosphere co-cultured either in a complex or defined medium. Results Metaproteomics showed this defined community assembled into distinct microbiomes based on growth media that eventually exhibit composition and functional stability over time. The community grown in two different media showed variation in composition, yet both were dominated by only a few microbial strains. Proteome-wide interrogation provided detailed insights into the functional behavior of each dominant member as they adjust to changing community compositions and environments. The emergence and persistence of select microbes in these communities were driven by specialization in strategies including motility, antibiotic production, altered metabolism, and dormancy. Protein-level interrogation identified post-translational modifications that provided additional insights into regulatory mechanisms influencing microbial adaptation in the changing environments. Conclusions This study provides high-resolution proteome-level insights into our understanding of microbe-microbe interactions and highlights specialized biological processes carried out by specific members of assembled microbiomes to compete and persist in changing environmental conditions. Emergent properties observed in these lower complexity communities can then be re-evaluated as more complex systems are studied and, when a particular property becomes less relevant, higher-order interactions can be identified. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02370-4.
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Affiliation(s)
- Him K Shrestha
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States.,Department of Genome Science and Technology, University of Tennessee-Knoxville, 37996, Knoxville, Tennessee, United States
| | - Manasa R Appidi
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States.,Department of Genome Science and Technology, University of Tennessee-Knoxville, 37996, Knoxville, Tennessee, United States
| | | | - Jia Wang
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Dana L Carper
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Leah Burdick
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, Tennessee, United States.
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4
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Chen S, Wang J, Xie LG. Transition metal-free formal hydro/deuteromethylthiolation of unactivated alkenes. Org Biomol Chem 2021; 19:4037-4042. [PMID: 33876174 DOI: 10.1039/d1ob00413a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Methylthioether is involved in the methylthiotransfer process in organisms, and therefore its functionality is of paramount importance to living organisms. Several methods for the installation of the methylthio group in small molecules have been reported previously; however, procedures starting from unactivated alkenes are rare. Herein, we report a formal hydro/deuteromethylthiolation of alkenes by using dimethyl(methylthio)sulfonium trifluoromethanesulfonate as the stimulator and sodium borohydride/deuteride as the hydrogen/deuterium source. The process represents a mild, transition metal-free and methanethiol-free route towards the synthesis of methylthioethers from unactivated alkenes.
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Affiliation(s)
- Shuangyang Chen
- School of Chemistry and Materials Science, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Nanjing Normal University, Nanjing 210023, P. R. China.
| | - Jia Wang
- School of Medicine, Jiangsu University, Zhenjiang 212013, P. R. China.
| | - Lan-Gui Xie
- School of Chemistry and Materials Science, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Nanjing Normal University, Nanjing 210023, P. R. China.
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5
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Watson ZL, Ward FR, Méheust R, Ad O, Schepartz A, Banfield JF, Cate JH. Structure of the bacterial ribosome at 2 Å resolution. eLife 2020; 9:60482. [PMID: 32924932 DOI: 10.1101/2020.06.26.174334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/11/2020] [Indexed: 05/24/2023] Open
Abstract
Using cryo-electron microscopy (cryo-EM), we determined the structure of the Escherichia coli 70S ribosome with a global resolution of 2.0 Å. The maps reveal unambiguous positioning of protein and RNA residues, their detailed chemical interactions, and chemical modifications. Notable features include the first examples of isopeptide and thioamide backbone substitutions in ribosomal proteins, the former likely conserved in all domains of life. The maps also reveal extensive solvation of the small (30S) ribosomal subunit, and interactions with A-site and P-site tRNAs, mRNA, and the antibiotic paromomycin. The maps and models of the bacterial ribosome presented here now allow a deeper phylogenetic analysis of ribosomal components including structural conservation to the level of solvation. The high quality of the maps should enable future structural analyses of the chemical basis for translation and aid the development of robust tools for cryo-EM structure modeling and refinement.
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Affiliation(s)
- Zoe L Watson
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Fred R Ward
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Raphaël Méheust
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
- Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Omer Ad
- Department of Chemistry, Yale University, New Haven, United States
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
- Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, United States
| | - Jamie Hd Cate
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
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6
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Watson ZL, Ward FR, Méheust R, Ad O, Schepartz A, Banfield JF, Cate JHD. Structure of the bacterial ribosome at 2 Å resolution. eLife 2020; 9:e60482. [PMID: 32924932 PMCID: PMC7550191 DOI: 10.7554/elife.60482] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/11/2020] [Indexed: 12/31/2022] Open
Abstract
Using cryo-electron microscopy (cryo-EM), we determined the structure of the Escherichia coli 70S ribosome with a global resolution of 2.0 Å. The maps reveal unambiguous positioning of protein and RNA residues, their detailed chemical interactions, and chemical modifications. Notable features include the first examples of isopeptide and thioamide backbone substitutions in ribosomal proteins, the former likely conserved in all domains of life. The maps also reveal extensive solvation of the small (30S) ribosomal subunit, and interactions with A-site and P-site tRNAs, mRNA, and the antibiotic paromomycin. The maps and models of the bacterial ribosome presented here now allow a deeper phylogenetic analysis of ribosomal components including structural conservation to the level of solvation. The high quality of the maps should enable future structural analyses of the chemical basis for translation and aid the development of robust tools for cryo-EM structure modeling and refinement.
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Affiliation(s)
- Zoe L Watson
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - Fred R Ward
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Raphaël Méheust
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
- Earth and Planetary Science, University of California, BerkeleyBerkeleyUnited States
| | - Omer Ad
- Department of Chemistry, Yale UniversityNew HavenUnited States
| | - Alanna Schepartz
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
- Earth and Planetary Science, University of California, BerkeleyBerkeleyUnited States
- Environmental Science, Policy and Management, University of California BerkeleyBerkeleyUnited States
| | - Jamie HD Cate
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
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7
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Zhang N, Shi S, Jia TZ, Ziegler A, Yoo B, Yuan X, Li W, Zhang S. A general LC-MS-based RNA sequencing method for direct analysis of multiple-base modifications in RNA mixtures. Nucleic Acids Res 2020; 47:e125. [PMID: 31504795 PMCID: PMC6847078 DOI: 10.1093/nar/gkz731] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/07/2019] [Accepted: 08/15/2019] [Indexed: 12/31/2022] Open
Abstract
A complete understanding of the structural and functional potential of RNA requires understanding of chemical modifications and non-canonical bases; this in turn requires advances in current sequencing methods to be able to sequence not only canonical ribonucleotides, but at the same time directly sequence these non-standard moieties. Here, we present the first direct and modification type-independent RNA sequencing method via introduction of a 2-dimensional hydrophobic end-labeling strategy into traditional mass spectrometry-based sequencing (2D HELS MS Seq) to allow de novo sequencing of RNA mixtures and enhance sample usage efficiency. Our method can directly read out the complete sequence, while identifying, locating, and quantifying base modifications accurately in both single and mixed RNA samples containing multiple different modifications at single-base resolution. Our method can also quantify stoichiometry/percentage of modified RNA versus its canonical counterpart RNA, simulating a real biological sample where modifications exist but may not be 100% at a particular site in the RNA. This method is a critical step towards fully sequencing real complex cellular RNA samples of any type and containing any modification type and can also be used in the quality control of modified therapeutic RNAs.
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Affiliation(s)
- Ning Zhang
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, NY 10023, USA.,Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Shundi Shi
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,Blue Marble Space Institute of Science, Seattle, WA 98154, USA
| | - Ashley Ziegler
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, NY 10023, USA
| | - Barney Yoo
- Department of Chemistry, Hunter College, City University of New York, New York, NY 10065, USA
| | - Xiaohong Yuan
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, NY 10023, USA
| | - Wenjia Li
- Department of Computer Science, New York Institute of Technology, New York, NY 10023, USA
| | - Shenglong Zhang
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, NY 10023, USA
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8
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Sandfort F, Knecht T, Pinkert T, Daniliuc CG, Glorius F. Site-Selective Thiolation of (Multi)halogenated Heteroarenes. J Am Chem Soc 2020; 142:6913-6919. [PMID: 32237706 DOI: 10.1021/jacs.0c01630] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A general and simple strategy for the site-selective thiolation of various pharmaceutically relevant electron-rich heteroarenes with thiols is reported. This mild and reliable photocatalytic protocol enables C-S coupling at the most electron-rich position of the (multi)halogenated substrates, complementing established methodologies. Experimental and computational studies suggest a radical chain mechanism with the key step being a homolytic aromatic substitution of the heteroaryl halide by an electrophilic thiyl radical, highlighting an underdeveloped reactivity mode.
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Affiliation(s)
- Frederik Sandfort
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Tobias Knecht
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Tobias Pinkert
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Constantin G Daniliuc
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Frank Glorius
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
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9
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Arnold RJ, Saraswat S, Reilly JP. Analysis of Methylation, Acetylation, and Other Modifications in Bacterial Ribosomal Proteins. Methods Mol Biol 2019; 1934:293-307. [PMID: 31256386 DOI: 10.1007/978-1-4939-9055-9_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A wide variety of posttranslational modifications of expressed proteins are known to occur in living organisms (Krishna R, Wold F. Post-translational modification of proteins. In: Meister A (ed) Advances in enzymology and related areas of molecular biology. Wiley, New York, 1993, pp 265-296). Although their presence in an organism cannot be predicted from the genome, these modifications can play critical roles in protein structure and function. The identification of posttranslational modifications is critical to our understanding of the functions of proteins involved in important biological pathways and mass spectrometry offers a fast, accurate method for observing them. A combined top-down/bottom-up approach can be used for identification and localization of posttranslational modifications of ribosomal proteins. This chapter describes procedures for analyzing Escherichia coli ribosomal proteins and their modifications by matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry. It also covers the analysis of gram-negative Caulobacter crescentus and gram-positive Bacillus subtilis ribosomal proteins by electrospray quadrupole time-of-flight (ESI-QTOF) mass spectrometry. Confirmation of the occurrence and localization of PTMs is obtained through mass spectrometric analysis of tryptic peptides.
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Affiliation(s)
- Randy J Arnold
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - Suraj Saraswat
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - James P Reilly
- Department of Chemistry, Indiana University, Bloomington, IN, USA.
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10
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Teders M, Henkel C, Anhäuser L, Strieth-Kalthoff F, Gómez-Suárez A, Kleinmans R, Kahnt A, Rentmeister A, Guldi D, Glorius F. The energy-transfer-enabled biocompatible disulfide–ene reaction. Nat Chem 2018; 10:981-988. [DOI: 10.1038/s41557-018-0102-z] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/29/2018] [Indexed: 12/17/2022]
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11
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Cuccui J, Terra VS, Bossé JT, Naegeli A, Abouelhadid S, Li Y, Lin CW, Vohra P, Tucker AW, Rycroft AN, Maskell DJ, Aebi M, Langford PR, Wren BW. The N-linking glycosylation system from Actinobacillus pleuropneumoniae is required for adhesion and has potential use in glycoengineering. Open Biol 2017; 7:rsob.160212. [PMID: 28077594 PMCID: PMC5303269 DOI: 10.1098/rsob.160212] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/28/2016] [Indexed: 12/16/2022] Open
Abstract
Actinobacillus pleuropneumoniae is a mucosal respiratory pathogen causing contagious porcine pleuropneumonia. Pathogenesis studies have demonstrated a major role for the capsule, exotoxins and outer membrane proteins. Actinobacillus pleuropneumoniae can also glycosylate proteins, using a cytoplasmic N-linked glycosylating enzyme designated NGT, but its transcriptional arrangement and role in virulence remains unknown. We investigated the NGT locus and demonstrated that the putative transcriptional unit consists of rimO, ngt and a glycosyltransferase termed agt. From this information we used the A. pleuropneumoniae glycosylation locus to decorate an acceptor protein, within Escherichia coli, with a hexose polymer that reacted with an anti-dextran antibody. Mass spectrometry analysis of a truncated protein revealed that this operon could add up to 29 repeat units to the appropriate sequon. We demonstrated the importance of NGT in virulence, by creating deletion mutants and testing them in a novel respiratory cell line adhesion model. This study demonstrates the importance of the NGT glycosylation system for pathogenesis and its potential biotechnological application for glycoengineering.
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Affiliation(s)
- Jon Cuccui
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Vanessa S Terra
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Janine T Bossé
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London W2 1PG, UK
| | - Andreas Naegeli
- Institute of Microbiology, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Sherif Abouelhadid
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Yanwen Li
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London W2 1PG, UK
| | - Chia-Wei Lin
- Institute of Microbiology, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Prerna Vohra
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Andrew N Rycroft
- The Royal Veterinary College, Hawkshead Campus, Hatfield, Hertfordshire AL9 7TA, UK
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Markus Aebi
- Institute of Microbiology, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London W2 1PG, UK
| | - Brendan W Wren
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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12
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Cuccui J, Terra VS, Bossé JT, Naegeli A, Abouelhadid S, Li Y, Lin CW, Vohra P, Tucker AW, Rycroft AN, Maskell DJ, Aebi M, Langford PR, Wren BW. The N-linking glycosylation system from Actinobacillus pleuropneumoniae is required for adhesion and has potential use in glycoengineering. Open Biol 2017. [PMID: 28077594 DOI: 10.1098/rsob.160212.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Actinobacillus pleuropneumoniae is a mucosal respiratory pathogen causing contagious porcine pleuropneumonia. Pathogenesis studies have demonstrated a major role for the capsule, exotoxins and outer membrane proteins. Actinobacillus pleuropneumoniae can also glycosylate proteins, using a cytoplasmic N-linked glycosylating enzyme designated NGT, but its transcriptional arrangement and role in virulence remains unknown. We investigated the NGT locus and demonstrated that the putative transcriptional unit consists of rimO, ngt and a glycosyltransferase termed agt. From this information we used the A. pleuropneumoniae glycosylation locus to decorate an acceptor protein, within Escherichia coli, with a hexose polymer that reacted with an anti-dextran antibody. Mass spectrometry analysis of a truncated protein revealed that this operon could add up to 29 repeat units to the appropriate sequon. We demonstrated the importance of NGT in virulence, by creating deletion mutants and testing them in a novel respiratory cell line adhesion model. This study demonstrates the importance of the NGT glycosylation system for pathogenesis and its potential biotechnological application for glycoengineering.
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Affiliation(s)
- Jon Cuccui
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Vanessa S Terra
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Janine T Bossé
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London W2 1PG, UK
| | - Andreas Naegeli
- Institute of Microbiology, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Sherif Abouelhadid
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Yanwen Li
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London W2 1PG, UK
| | - Chia-Wei Lin
- Institute of Microbiology, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Prerna Vohra
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Andrew N Rycroft
- The Royal Veterinary College, Hawkshead Campus, Hatfield, Hertfordshire AL9 7TA, UK
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Markus Aebi
- Institute of Microbiology, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London W2 1PG, UK
| | - Brendan W Wren
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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13
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Molle T, Moreau Y, Clemancey M, Forouhar F, Ravanat JL, Duraffourg N, Fourmond V, Latour JM, Gambarelli S, Mulliez E, Atta M. Redox Behavior of the S-Adenosylmethionine (SAM)-Binding Fe-S Cluster in Methylthiotransferase RimO, toward Understanding Dual SAM Activity. Biochemistry 2016; 55:5798-5808. [PMID: 27677419 DOI: 10.1021/acs.biochem.6b00597] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
RimO, a radical-S-adenosylmethionine (SAM) enzyme, catalyzes the specific C3 methylthiolation of the D89 residue in the ribosomal S12 protein. Two intact iron-sulfur clusters and two SAM cofactors both are required for catalysis. By using electron paramagnetic resonance, Mössbauer spectroscopies, and site-directed mutagenesis, we show how two SAM molecules sequentially bind to the unique iron site of the radical-SAM cluster for two distinct chemical reactions in RimO. Our data establish that the two SAM molecules bind the radical-SAM cluster to the unique iron site, and spectroscopic evidence obtained under strongly reducing conditions supports a mechanism in which the first molecule of SAM causes the reoxidation of the reduced radical-SAM cluster, impeding reductive cleavage of SAM to occur and allowing SAM to methylate a HS- ligand bound to the additional cluster. Furthermore, by using density functional theory-based methods, we provide a description of the reaction mechanism that predicts the attack of the carbon radical substrate on the methylthio group attached to the additional [4Fe-4S] cluster.
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Affiliation(s)
- Thibaut Molle
- Laboratoire de Chimie et Biologie des Métaux, team "Biocatalyse", Biosciences & Biotechnology Institute of Grenoble (BIG), BIG/LCBM/Biocat, UMR 5249 CEA/CNRS/UGA, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Yohann Moreau
- Laboratoire de Chimie et Biologie des Métaux, team "MCT" Biosciences & Biotechnology Institute of Grenoble (BIG), BIG/LCBM/MCT, UMR 5249 CEA/CNRS/UGA, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Martin Clemancey
- Laboratoire de Chimie et Biologie des Métaux, team "PMB" Biosciences & Biotechnology Institute of Grenoble (BIG), BIG/LCBM/PMB, UMR 5249 CEA/CNRS/UGA, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Farhad Forouhar
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University , New York, New York 10027, United States
| | - Jean-Luc Ravanat
- University Grenoble Alpes , INAC-SCIB, F-38000 Grenoble, France.,CEA , INAC-SyMMES, F-38000 Grenoble, France
| | - Nicolas Duraffourg
- Laboratoire de Chimie et Biologie des Métaux, team "Affond" Biosciences & Biotechnology Institute of Grenoble (BIG), BIG/LCBM/Affond, UMR 5249 CEA/CNRS/UGA, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Vincent Fourmond
- Aix-Marseille University , CNRS, BIP UMR 7281, 31 chemin J. Aiguier, 13402 Marseille Cedex 20, France
| | - Jean-Marc Latour
- Laboratoire de Chimie et Biologie des Métaux, team "PMB" Biosciences & Biotechnology Institute of Grenoble (BIG), BIG/LCBM/PMB, UMR 5249 CEA/CNRS/UGA, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Serge Gambarelli
- University Grenoble Alpes, INAC, SCIB/LRM , F-38000 Grenoble, France.,CEA, INAC, SCIB/LRM, F-38054 Grenoble, France
| | - Etienne Mulliez
- Laboratoire de Chimie et Biologie des Métaux, team "Biocatalyse", Biosciences & Biotechnology Institute of Grenoble (BIG), BIG/LCBM/Biocat, UMR 5249 CEA/CNRS/UGA, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Mohamed Atta
- Laboratoire de Chimie et Biologie des Métaux, team "Biocatalyse", Biosciences & Biotechnology Institute of Grenoble (BIG), BIG/LCBM/Biocat, UMR 5249 CEA/CNRS/UGA, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
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14
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Wang J, Woldring RP, Román-Meléndez GD, McClain AM, Alzua BR, Marsh ENG. Recent advances in radical SAM enzymology: new structures and mechanisms. ACS Chem Biol 2014; 9:1929-38. [PMID: 25009947 PMCID: PMC4168785 DOI: 10.1021/cb5004674] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
The radical S-adenosylmethionine
(SAM) superfamily of enzymes catalyzes
an amazingly diverse variety of reactions ranging from simple hydrogen
abstraction to complicated multistep rearrangements and insertions.
The reactions they catalyze are important for a broad range of biological
functions, including cofactor and natural product biosynthesis, DNA
repair, and tRNA modification. Generally conserved features of the
radical SAM superfamily include a CX3CX2C motif
that binds an [Fe4S4] cluster essential for
the reductive cleavage of SAM. Here, we review recent advances in
our understanding of the structure and mechanisms of these enzymes
that, in some cases, have overturned widely accepted mechanisms.
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Affiliation(s)
- Jiarui Wang
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Rory P. Woldring
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Alan M. McClain
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brian R. Alzua
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - E. Neil G. Marsh
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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15
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Sergeeva OV, Sergiev PV, Bogdanov AA, Dontsova OA. Ribosome: Lessons of a molecular factory construction. Mol Biol 2014. [DOI: 10.1134/s0026893314040116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Structural analysis of base substitutions in Thermus thermophilus 16S rRNA conferring streptomycin resistance. Antimicrob Agents Chemother 2014; 58:4308-17. [PMID: 24820088 DOI: 10.1128/aac.02857-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Streptomycin is a bactericidal antibiotic that induces translational errors. It binds to the 30S ribosomal subunit, interacting with ribosomal protein S12 and with 16S rRNA through contacts with the phosphodiester backbone. To explore the structural basis for streptomycin resistance, we determined the X-ray crystal structures of 30S ribosomal subunits from six streptomycin-resistant mutants of Thermus thermophilus both in the apo form and in complex with streptomycin. Base substitutions at highly conserved residues in the central pseudoknot of 16S rRNA produce novel hydrogen-bonding and base-stacking interactions. These rearrangements in secondary structure produce only minor adjustments in the three-dimensional fold of the pseudoknot. These results illustrate how antibiotic resistance can occur as a result of small changes in binding site conformation.
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17
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Broderick JB, Duffus B, Duschene KS, Shepard EM. Radical S-adenosylmethionine enzymes. Chem Rev 2014; 114:4229-317. [PMID: 24476342 PMCID: PMC4002137 DOI: 10.1021/cr4004709] [Citation(s) in RCA: 584] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Joan B. Broderick
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Benjamin
R. Duffus
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Kaitlin S. Duschene
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Eric M. Shepard
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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18
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Forouhar F, Arragain S, Atta M, Gambarelli S, Mouesca JM, Hussain M, Xiao R, Kieffer-Jaquinod S, Seetharaman J, Acton TB, Montelione GT, Mulliez E, Hunt JF, Fontecave M. Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases. Nat Chem Biol 2013; 9:333-8. [PMID: 23542644 DOI: 10.1038/nchembio.1229] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 03/05/2013] [Indexed: 11/09/2022]
Abstract
How living organisms create carbon-sulfur bonds during the biosynthesis of critical sulfur-containing compounds is still poorly understood. The methylthiotransferases MiaB and RimO catalyze sulfur insertion into tRNAs and ribosomal protein S12, respectively. Both belong to a subgroup of radical-S-adenosylmethionine (radical-SAM) enzymes that bear two [4Fe-4S] clusters. One cluster binds S-adenosylmethionine and generates an Ado• radical via a well-established mechanism. However, the precise role of the second cluster is unclear. For some sulfur-inserting radical-SAM enzymes, this cluster has been proposed to act as a sacrificial source of sulfur for the reaction. In this paper, we report parallel enzymological, spectroscopic and crystallographic investigations of RimO and MiaB, which provide what is to our knowledge the first evidence that these enzymes are true catalysts and support a new sulfation mechanism involving activation of an exogenous sulfur cosubstrate at an exchangeable coordination site on the second cluster, which remains intact during the reaction.
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Affiliation(s)
- Farhad Forouhar
- Northeast Structural Genomics Consortium, New York, New York, USA
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19
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Strader MB, Hervey WJ, Costantino N, Fujigaki S, Chen CY, Akal-Strader A, Ihunnah CA, Makusky AJ, Court DL, Markey SP, Kowalak JA. A coordinated proteomic approach for identifying proteins that interact with the E. coli ribosomal protein S12. J Proteome Res 2013; 12:1289-99. [PMID: 23305560 DOI: 10.1021/pr3009435] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial ribosomal protein S12 contains a universally conserved D88 residue on a loop region thought to be critically involved in translation due to its proximal location to the A site of the 30S subunit. While D88 mutants are lethal this residue has been found to be post-translationally modified to β-methylthioaspartic acid, a post-translational modification (PTM) identified in S12 orthologs from several phylogenetically distinct bacteria. In a previous report focused on characterizing this PTM, our results provided evidence that this conserved loop region might be involved in forming multiple proteins-protein interactions ( Strader , M. B. ; Costantino , N. ; Elkins , C. A. ; Chen , C. Y. ; Patel , I. ; Makusky , A. J. ; Choy , J. S. ; Court , D. L. ; Markey , S. P. ; Kowalak , J. A. A proteomic and transcriptomic approach reveals new insight into betamethylthiolation of Escherichia coli ribosomal protein S12. Mol. Cell. Proteomics 2011 , 10 , M110 005199 ). To follow-up on this study, the D88 containing loop was probed to identify candidate binders employing a two-step complementary affinity purification strategy. The first involved an endogenously expressed S12 protein containing a C-terminal tag for capturing S12 binding partners. The second strategy utilized a synthetic biotinylated peptide representing the D88 conserved loop region for capturing S12 loop interaction partners. Captured proteins from both approaches were detected by utilizing SDS-PAGE and one-dimensional liquid chromatography-tandem mass spectrometry. The results presented in this report revealed proteins that form direct interactions with the 30S subunit and elucidated which are likely to interact with S12. In addition, we provide evidence that two proteins involved in regulating ribosome and/or mRNA transcript levels under stress conditions, RNase R and Hfq, form direct interactions with the S12 conserved loop, suggesting that it is likely part of a protein binding interface.
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Affiliation(s)
- Michael Brad Strader
- Laboratory of Neurotoxicology, National Institute of Mental Health , Bethesda, Maryland 20892, United States
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20
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Lauber MA, Rappsilber J, Reilly JP. Dynamics of ribosomal protein S1 on a bacterial ribosome with cross-linking and mass spectrometry. Mol Cell Proteomics 2012; 11:1965-76. [PMID: 23033476 PMCID: PMC3518124 DOI: 10.1074/mcp.m112.019562] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 09/19/2012] [Indexed: 11/23/2022] Open
Abstract
Ribosomal protein S1 has been shown to be a significant effector of prokaryotic translation. The protein is in fact capable of efficiently initiating translation, regardless of the presence of a Shine-Dalgarno sequence in mRNA. Structural insights into this process have remained elusive, as S1 is recalcitrant to traditional techniques of structural analysis, such as x-ray crystallography. Through the application of protein cross-linking and high resolution mass spectrometry, we have detailed the ribosomal binding site of S1 and have observed evidence of its dynamics. Our results support a previous hypothesis that S1 acts as the mRNA catching arm of the prokaryotic ribosome. We also demonstrate that in solution the major domains of the 30S subunit are remarkably flexible, capable of moving 30-50Å with respect to one another.
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Affiliation(s)
- Matthew A. Lauber
- From the ‡Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Juri Rappsilber
- §Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, The University of Edinburgh, Edinburgh EH9 3JR, UK and Institut für Biotechnologie, Technische Universität Berlin, 13353 Berlin, Germany
| | - James P. Reilly
- From the ‡Department of Chemistry, Indiana University, Bloomington, Indiana 47405
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21
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Matallana-Surget S, Joux F, Wattiez R, Lebaron P. Proteome analysis of the UVB-resistant marine bacterium Photobacterium angustum S14. PLoS One 2012; 7:e42299. [PMID: 22870314 PMCID: PMC3411663 DOI: 10.1371/journal.pone.0042299] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 07/03/2012] [Indexed: 12/22/2022] Open
Abstract
The proteome of the marine bacterium Photobacterium angustum S14 was exposed to UVB and analyzed by the implementation of both the post-digest ICPL labeling method and 2D-DIGE technique using exponentially growing cells. A total of 40 and 23 proteins were quantified in all replicates using either the ICPL or 2D-DIGE methods, respectively. By combining both datasets from 8 biological replicates (4 biological replicates for each proteomics technique), 55 proteins were found to respond significantly to UVB radiation in P. angustum. A total of 8 UVB biomarkers of P. angustum were quantified in all replicates using both methods. Among them, the protein found to present the highest increase in abundance (almost a 3-fold change) was RecA, which is known to play a crucial role in the so-called recombinational repair process. We also observed a high number of antioxidants, transport proteins, metabolism-related proteins, transcription/translation regulators, chaperonins and proteases. We also discuss and compare the UVB response and global protein expression profiles obtained for two different marine bacteria with trophic lifestyles: the copiotroph P. angustum and oligotroph Sphingopyxis alaskensis.
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Affiliation(s)
- Sabine Matallana-Surget
- UPMC Univ Paris 06, UMR7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Banyuls/mer, France.
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22
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Bae N, Lödl M, Pollak A, Lubec G. Mass spectrometrical analysis of bilin-binding protein from the wing of Hebomoia glaucippe (Linnaeus, 1758) (Lepidoptera: Pieridae). Electrophoresis 2012; 33:1787-94. [DOI: 10.1002/elps.201100569] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Narkhyun Bae
- Department of Pediatrics; Medical University of Vienna; Vienna; Austria
| | - Martin Lödl
- Naturhistorisches Museum Wien; Vienna; Austria
| | - Arnold Pollak
- Department of Pediatrics; Medical University of Vienna; Vienna; Austria
| | - Gert Lubec
- Department of Pediatrics; Medical University of Vienna; Vienna; Austria
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23
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Atta M, Arragain S, Fontecave M, Mulliez E, Hunt JF, Luff JD, Forouhar F. The methylthiolation reaction mediated by the Radical-SAM enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1824:1223-30. [PMID: 22178611 DOI: 10.1016/j.bbapap.2011.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 11/28/2011] [Indexed: 01/29/2023]
Abstract
Over the past 10 years, considerable progress has been made in our understanding of the mechanistic enzymology of the Radical-SAM enzymes. It is now clear that these enzymes appear to be involved in a remarkably wide range of chemically challenging reactions. This review article highlights mechanistic and structural aspects of the methylthiotransferases (MTTases) sub-class of the Radical-SAM enzymes. The mechanism of methylthio insertion, now observed to be performed by three different enzymes is an exciting unsolved problem. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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Affiliation(s)
- Mohamed Atta
- Institut de Recherches en Technologie et Sciences pour le Vivant IRTSV-LCBM, UMR 5249 CEA/CNRS/UJF, CEA-Grenoble, 17 avenue des Martyrs, 38054, Grenoble Cedex 09, France.
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24
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Nesterchuk M, Sergiev P, Dontsova O. Posttranslational Modifications of Ribosomal Proteins in Escherichia coli. Acta Naturae 2011; 3:22-33. [PMID: 22649682 PMCID: PMC3347575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
А number of ribosomal proteins inEscherichia coliundergo posttranslational modifications. Six ribosomal proteins are methylated (S11, L3, L11, L7/L12, L16, and L33), three proteins are acetylated (S5, S18, and L7), and protein S12 is methylthiolated. Extra amino acid residues are added to protein S6. С-terminal amino acid residues are partially removed from protein L31. The functional significance of these modifications has remained unclear. These modifications are not vital to the cells, and it is likely that they have regulatory functions. This paper reviews all the known posttranslational modifications of ribosomal proteins inEscherichia coli. Certain enzymes responsible for the modifications and mechanisms of enzymatic reactions are also discussed.
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Affiliation(s)
- M.V. Nesterchuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University
- Faculty of Chemistry, Lomonosov Moscow State University
| | - P.V. Sergiev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University
- Faculty of Chemistry, Lomonosov Moscow State University
| | - O.A. Dontsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University
- Faculty of Chemistry, Lomonosov Moscow State University
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25
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Strader MB, Costantino N, Elkins CA, Chen CY, Patel I, Makusky AJ, Choy JS, Court DL, Markey SP, Kowalak JA. A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12. Mol Cell Proteomics 2010; 10:M110.005199. [PMID: 21169565 DOI: 10.1074/mcp.m110.005199] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
β-methylthiolation is a novel post-translational modification mapping to a universally conserved Asp 88 of the bacterial ribosomal protein S12. This S12 specific modification has been identified on orthologs from multiple bacterial species. The origin and functional significance was investigated with both a proteomic strategy to identify candidate S12 interactors and expression microarrays to search for phenotypes that result from targeted gene knockouts of select candidates. Utilizing an endogenous recombinant E. coli S12 protein with an affinity tag as bait, mass spectrometric analysis identified candidate S12 binding partners including RimO (previously shown to be required for this post-translational modification) and YcaO, a conserved protein of unknown function. Transcriptomic analysis of bacterial strains with deleted genes for RimO and YcaO identified an overlapping transcriptional phenotype suggesting that YcaO and RimO likely share a common function. As a follow up, quantitative mass spectrometry additionally indicated that both proteins dramatically impacted the modification status of S12. Collectively, these results indicate that the YcaO protein is involved in β-methylthiolation of S12 and its absence impairs the ability of RimO to modify S12. Additionally, the proteomic data from this study provides direct evidence that the E. coli specific β-methylthiolation likely occurs when S12 is assembled as part of a ribosomal subunit.
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Affiliation(s)
- Michael Brad Strader
- Laboratory of Neurotoxicology, National Institute of Mental Health, Bethesda, MD 20892, USA.
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26
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Atta M, Mulliez E, Arragain S, Forouhar F, Hunt JF, Fontecave M. S-Adenosylmethionine-dependent radical-based modification of biological macromolecules. Curr Opin Struct Biol 2010; 20:684-92. [PMID: 20951571 DOI: 10.1016/j.sbi.2010.09.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 09/14/2010] [Accepted: 09/15/2010] [Indexed: 11/26/2022]
Abstract
Proteins and RNA molecules enjoy a variety of chemically complex post-translational and post-transcriptional modifications. The chemistry at work in these reactions, which was considered to be exclusively ionic in nature has recently been shown to depend on radical mechanisms in some cases. The overwhelming majority of these radical-based reactions are catalyzed by 'Radical-SAM' enzymes. This review article highlights mechanistic and structural aspects of this class of reactions and indicates important research directions to be addressed.
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Affiliation(s)
- Mohamed Atta
- Institut de Recherches en Technologie et Sciences pour le Vivant IRTSV-LCBM, UMR 5249 CEA/CNRS/UJF, CEA-Grenoble, 17 avenue des Martyrs, 38054 Grenoble Cedex 09, France
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27
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Banerjee S, Mazumdar S. Non-covalent dimers of the lysine containing protonated peptide ions in gaseous state: electrospray ionization mass spectrometric study. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:1212-1219. [PMID: 20872902 DOI: 10.1002/jms.1817] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Study of the non-covalent molecular complexes in gas phase by electrospray ionization mass spectrometry (ESI-MS) represents a promising strategy to probe the intrinsic nature of these complexes. ESI-MS investigation of a series of synthetic octapeptides containing six alanine and two lysine residues differing only by their positions showed the formation of non-covalent dimers, which were preserved in the gas phase. Unlike the monomers, the dimers were found to show only singly protonated state. The decrease in the solvent polarity from water to alcohol showed enhanced propensity of formation of the dimer indicating that the electrostatic interaction plays a crucial role to stabilize the dimer. Selective functionalization studies showed that ε-NH(2) of lysine and C-terminal amide (-CONH(2)) facilitate the dimerization through intermolecular hydrogen bonding network.
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Affiliation(s)
- Shibdas Banerjee
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
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28
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Running WE, Reilly JP. Variation of the chemical reactivity of Thermus thermophilus HB8 ribosomal proteins as a function of pH. Proteomics 2010; 10:3669-87. [DOI: 10.1002/pmic.201000342] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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Lauber MA, Running WE, Reilly JP. B. subtilis ribosomal proteins: structural homology and post-translational modifications. J Proteome Res 2009; 8:4193-206. [PMID: 19653700 DOI: 10.1021/pr801114k] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribosomal proteins of the model gram-positive bacterium B. subtilis 168 were extensively characterized in a proteomic study. Mass spectra of the 52 proteins expected to be constitutive components of the 70S ribosome were recorded. Peptide MS/MS analysis with an average sequence coverage of 85% supported the identification of these proteins and facilitated the unambiguous assignment of post-translational modifications, including the methylation of S7, L11, and L16 and the N-terminal acetylation of S9. In addition, the high degree of structural homology between B. subtilis and other eubacterial ribosomal proteins was demonstrated through chemical labeling with S-methylthioacetimidate. One striking difference from previous characterizations of bacterial ribosomal proteins is that dozens of protein masses were found to be in error and not easily accounted for by post-translational modifications. This, in turn, led us to discover an inordinate number of sequencing errors in the reference genome of B. subtilis 168. We have found that these errors have been corrected in a recently revised version of the genome.
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Affiliation(s)
- Matthew A Lauber
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.
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30
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Arragain S, Garcia-Serres R, Blondin G, Douki T, Clemancey M, Latour JM, Forouhar F, Neely H, Montelione GT, Hunt JF, Mulliez E, Fontecave M, Atta M. Post-translational modification of ribosomal proteins: structural and functional characterization of RimO from Thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase. J Biol Chem 2009; 285:5792-801. [PMID: 20007320 DOI: 10.1074/jbc.m109.065516] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Post-translational modifications of ribosomal proteins are important for the accuracy of the decoding machinery. A recent in vivo study has shown that the rimO gene is involved in generation of the 3-methylthio derivative of residue Asp-89 in ribosomal protein S12 (Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. U. S. A. 105, 1826-1831). This reaction is formally identical to that catalyzed by MiaB on the C2 of adenosine 37 near the anticodon of several tRNAs. We present spectroscopic evidence that Thermotoga maritima RimO, like MiaB, contains two [4Fe-4S] centers, one presumably bound to three invariant cysteines in the central radical S-adenosylmethionine (AdoMet) domain and the other to three invariant cysteines in the N-terminal UPF0004 domain. We demonstrate that holo-RimO can specifically methylthiolate the aspartate residue of a 20-mer peptide derived from S12, yielding a mixture of mono- and bismethylthio derivatives. Finally, we present the 2.0 A crystal structure of the central radical AdoMet and the C-terminal TRAM (tRNA methyltransferase 2 and MiaB) domains in apo-RimO. Although the core of the open triose-phosphate isomerase (TIM) barrel of the radical AdoMet domain was conserved, RimO showed differences in domain organization compared with other radical AdoMet enzymes. The unusually acidic TRAM domain, likely to bind the basic S12 protein, is located at the distal edge of the radical AdoMet domain. The basic S12 protein substrate is likely to bind RimO through interactions with both the TRAM domain and the concave surface of the incomplete TIM barrel. These biophysical results provide a foundation for understanding the mechanism of methylthioation by radical AdoMet enzymes in the MiaB/RimO family.
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Affiliation(s)
- Simon Arragain
- Institut de Recherches en Technologie et Sciences pour le Vivant-Laboratoire de Chimie et Biologie des Métaux (iRTSV-LCBM), UMR 5249, CEA-CNRS-UJF, Commissariat à l'Energie Atomique Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 09, France
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Lee KH, Saleh L, Anton BP, Madinger CL, Benner JS, Iwig DF, Roberts RJ, Krebs C, Booker SJ. Characterization of RimO, a new member of the methylthiotransferase subclass of the radical SAM superfamily. Biochemistry 2009; 48:10162-74. [PMID: 19736993 DOI: 10.1021/bi900939w] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RimO, encoded by the yliG gene in Escherichia coli, has been recently identified in vivo as the enzyme responsible for the attachment of a methylthio group on the beta-carbon of Asp88 of the small ribosomal protein S12 [Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 1826-1831]. To date, it is the only enzyme known to catalyze methylthiolation of a protein substrate; the four other naturally occurring methylthio modifications have been observed on tRNA. All members of the methylthiotransferase (MTTase) family, to which RimO belongs, have been shown to contain the canonical CxxxCxxC motif in their primary structures that is typical of the radical S-adenosylmethionine (SAM) family of proteins. MiaB, the only characterized MTTase, and the enzyme experimentally shown to be responsible for methylthiolation of N(6)-isopentenyladenosine of tRNA in E. coli and Thermotoga maritima, has been demonstrated to harbor two distinct [4Fe-4S] clusters. Herein, we report in vitro biochemical and spectroscopic characterization of RimO. We show by analytical and spectroscopic methods that RimO, overproduced in E. coli in the presence of iron-sulfur cluster biosynthesis proteins from Azotobacter vinelandii, contains one [4Fe-4S](2+) cluster. Reconstitution of this form of RimO (RimO(rcn)) with (57)Fe and sodium sulfide results in a protein that contains two [4Fe-4S](2+) clusters, similar to MiaB. We also show by mass spectrometry that RimO(rcn) catalyzes the attachment of a methylthio group to a peptide substrate analogue that mimics the loop structure bearing aspartyl 88 of the S12 ribosomal protein from E. coli. Kinetic analysis of this reaction shows that the activity of RimO(rcn) in the presence of the substrate analogue does not support a complete turnover. We discuss the possible requirement for an assembled ribosome for fully active RimO in vitro. Our findings are consistent with those of other enzymes that catalyze sulfur insertion, such as biotin synthase, lipoyl synthase, and MiaB.
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Affiliation(s)
- Kyung-Hoon Lee
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Ferguson JT, Wenger CD, Metcalf WW, Kelleher NL. Top-down proteomics reveals novel protein forms expressed in Methanosarcina acetivorans. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1743-50. [PMID: 19577935 PMCID: PMC2832193 DOI: 10.1016/j.jasms.2009.05.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 04/29/2009] [Accepted: 05/23/2009] [Indexed: 05/12/2023]
Abstract
Using both automated nanospray and online liquid chromatography mass spectrometry LC-MS strategies, 99 proteins have been newly identified by top-down tandem mass spectrometry (MS/MS) in Methanosarcina acetivorans, the methanogen with the largest known genome [5.7 mega base pairs (Mb)] for an Archaeon. Because top-down MS/MS was used, 15 proteins were detected with mispredicted start sites along with an additional five from small open reading frames (SORFs). Beyond characterization of these more common discrepancies in genome annotation, one SORF resulted from a rare start codon (AUA) as the initiation site for translation of this protein. Also, a methylation on a 30S ribosomal protein (MA1259) was localized to Pro59-Val69, contrasting sharply from its homologue in Escherichia coli (rp S12) known to harbor an unusual beta-thiomethylated aspartic acid residue.
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Affiliation(s)
- Jonathan T Ferguson
- Department of Chemistry at University of Illinois at Urbana-Champaign, Urbana, Illinois 6180, USA
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Heredia-Moya J, Kirk KL. Synthesis of beta-(S-methyl)thioaspartic acid and derivatives. Bioorg Med Chem 2008; 16:5908-13. [PMID: 18468905 PMCID: PMC2587367 DOI: 10.1016/j.bmc.2008.04.069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Revised: 04/24/2008] [Accepted: 04/24/2008] [Indexed: 11/17/2022]
Abstract
Beta-(S-Methyl)thioaspartic acid occurs as a posttranslational modification at position 88 in Escherichia coli ribosomal protein S12, a position that is a mutational hotspot resulting in both antibiotic-resistant and antibiotic-sensitive phenotypes. Critical to research designed to determine the biological function of beta-(S-methyl)thioaspartic acid will be the availability of synthetic beta-(S-methyl)thioaspartic acid as well as derivatives designed for peptide incorporation. We report here the synthesis of beta-(S-methyl)thioaspartic acid and derivatives. The installation of the beta-methylthio moiety into the aspartic acid structure was accomplished by electrophilic sulfenylation of N-protected-l-aspartic acid derivatives with 2,4-dinitrophenyl methyl disulfide. Following this key transformation, we were able to prepare protected beta-(S-methyl)thioaspartic acid derivative suitable for peptide coupling.
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Affiliation(s)
- Jorge Heredia-Moya
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892. USA
| | - Kenneth L. Kirk
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892. USA
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Arnold RJ, Running W, Reilly JP. Analysis of methylation, acetylation, and other modifications in bacterial ribosomal proteins. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2008; 446:151-61. [PMID: 18373256 DOI: 10.1007/978-1-60327-084-7_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
A wide variety of post-translational modifications of expressed proteins are known to occur in living organisms (1). Although their presence in an organism cannot be predicted from the genome, these modifications can play critical roles in protein structure and function. The identification of post-translational modifications can be critical in understanding the functions of proteins involved in important biological pathways and mass spectrometry offers a fast, accurate method for observing them. This chapter describes the procedure for analyzing ribosomal proteins of Escherichia coli by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry and Caulobacter crescentus ribosomal proteins by electrospray quadrupole time-of-flight (ESI-QTOF) mass spectrometry.
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Affiliation(s)
- Randy J Arnold
- Department of Chemistry, Indiana University, Bloomington, IN, USA
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35
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Mendoza-Cózatl DG, Butko E, Springer F, Torpey JW, Komives EA, Kehr J, Schroeder JI. Identification of high levels of phytochelatins, glutathione and cadmium in the phloem sap of Brassica napus. A role for thiol-peptides in the long-distance transport of cadmium and the effect of cadmium on iron translocation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 54:249-59. [PMID: 18208526 PMCID: PMC2839885 DOI: 10.1111/j.1365-313x.2008.03410.x] [Citation(s) in RCA: 203] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Phytochelatins (PCs) are glutathione-derived peptides that function in heavy metal detoxification in plants and certain fungi. Recent research in Arabidopsis has shown that PCs undergo long-distance transport between roots and shoots. However, it remains unknown which tissues or vascular systems, xylem or phloem, mediate PC translocation and whether PC transport contributes to physiologically relevant long-distance transport of cadmium (Cd) between shoots and roots. To address these questions, xylem and phloem sap were obtained from Brassica napus to quantitatively analyze which thiol species are present in response to Cd exposure. High levels of PCs were identified in the phloem sap within 24 h of Cd exposure using combined mass spectrometry and fluorescence HPLC analyses. Unexpectedly, the concentration of Cd was more than four-fold higher in phloem sap compared to xylem sap. Cadmium exposure dramatically decreased iron levels in xylem and phloem sap whereas other essential heavy metals such as zinc and manganese remained unchanged. Data suggest that Cd inhibits vascular loading of iron but not nicotianamine. The high ratios [PCs]/[Cd] and [glutathione]/[Cd] in the phloem sap suggest that PCs and glutathione (GSH) can function as long-distance carriers of Cd. In contrast, only traces of PCs were detected in xylem sap. Our results suggest that, in addition to directional xylem Cd transport, the phloem is a major vascular system for long-distance source to sink transport of Cd as PC-Cd and glutathione-Cd complexes.
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Affiliation(s)
- David G. Mendoza-Cózatl
- Division of Biological Sciences, Cell and Developmental Biology Section, and Center for Molecular Genetics, University of California, San Diego, La Jolla, CA 92093-0116, USA
| | - Emerald Butko
- Division of Biological Sciences, Cell and Developmental Biology Section, and Center for Molecular Genetics, University of California, San Diego, La Jolla, CA 92093-0116, USA
| | - Franziska Springer
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam OT Golm, Germany
| | - Justin W. Torpey
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, USA
| | - Elizabeth A. Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, USA
| | - Julia Kehr
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam OT Golm, Germany
| | - Julian I. Schroeder
- Division of Biological Sciences, Cell and Developmental Biology Section, and Center for Molecular Genetics, University of California, San Diego, La Jolla, CA 92093-0116, USA
- For correspondence (fax +1 858 534 7108; )
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RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli. Proc Natl Acad Sci U S A 2008; 105:1826-31. [PMID: 18252828 DOI: 10.1073/pnas.0708608105] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribosomal protein S12 undergoes a unique posttranslational modification, methylthiolation of residue D88, in Escherichia coli and several other bacteria. Using mass spectrometry, we have identified the enzyme responsible for this modification in E. coli, the yliG gene product. This enzyme, which we propose be called RimO, is a radical-S-adenosylmethionine protein that bears strong sequence similarity to MiaB, which methylthiolates tRNA. We show that RimO and MiaB represent two of four subgroups of a larger, ancient family of likely methylthiotransferases, the other two of which are typified by Bacillus subtilis YqeV and Methanococcus jannaschii Mj0867, and we predict that RimO is unique among these subgroups in its modification of protein as opposed to tRNA. Despite this, RimO has not significantly diverged from the other three subgroups at the sequence level even within the C-terminal TRAM domain, which in the methyltransferase RumA is known to bind the RNA substrate and which we presume to be responsible for substrate binding and recognition in all four subgroups of methylthiotransferases. To our knowledge, RimO and MiaB represent the most extreme known case of resemblance between enzymes modifying protein and nucleic acid. The initial results presented here constitute a bioinformatics-driven prediction with preliminary experimental validation that should serve as the starting point for several interesting lines of further inquiry.
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Carroll AJ, Heazlewood JL, Ito J, Millar AH. Analysis of the Arabidopsis cytosolic ribosome proteome provides detailed insights into its components and their post-translational modification. Mol Cell Proteomics 2007; 7:347-69. [PMID: 17934214 DOI: 10.1074/mcp.m700052-mcp200] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Finding gene-specific peptides by mass spectrometry analysis to pinpoint gene loci responsible for particular protein products is a major challenge in proteomics especially in highly conserved gene families in higher eukaryotes. We used a combination of in silico approaches coupled to mass spectrometry analysis to advance the proteomics insight into Arabidopsis cytosolic ribosomal composition and its post-translational modifications. In silico digestion of all 409 ribosomal protein sequences in Arabidopsis defined the proportion of theoretical gene-specific peptides for each gene family and highlighted the need for low m/z cutoffs of MS ion selection for MS/MS to characterize low molecular weight, highly basic ribosomal proteins. We undertook an extensive MS/MS survey of the cytosolic ribosome using trypsin and, when required, chymotrypsin and pepsin. We then used custom software to extract and filter peptide match information from Mascot result files and implement high confidence criteria for calling gene-specific identifications based on the highest quality unambiguous spectra matching exclusively to certain in silico predicted gene- or gene family-specific peptides. This provided an in-depth analysis of the protein composition based on 1446 high quality MS/MS spectra matching to 795 peptide sequences from ribosomal proteins. These identified peptides from five gene families of ribosomal proteins not identified previously, providing experimental data on 79 of the 80 different types of ribosomal subunits. We provide strong evidence for gene-specific identification of 87 different ribosomal proteins from these 79 families. We also provide new information on 30 specific sites of co- and post-translational modification of ribosomal proteins in Arabidopsis by initiator methionine removal, N-terminal acetylation, N-terminal methylation, lysine N-methylation, and phosphorylation. These site-specific modification data provide a wealth of resources for further assessment of the role of ribosome modification in influencing translation in Arabidopsis.
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Affiliation(s)
- Adam J Carroll
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology and School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, 35 Stirling Highway, M316, Crawley 6009, Western Australia, Australia
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Sharma D, Cukras AR, Rogers EJ, Southworth DR, Green R. Mutational analysis of S12 protein and implications for the accuracy of decoding by the ribosome. J Mol Biol 2007; 374:1065-76. [PMID: 17967466 DOI: 10.1016/j.jmb.2007.10.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 09/26/2007] [Accepted: 10/02/2007] [Indexed: 10/22/2022]
Abstract
The fidelity of aminoacyl-tRNA selection by the ribosome depends on a conformational switch in the decoding center of the small ribosomal subunit induced by cognate but not by near-cognate aminoacyl-tRNA. The aminoglycosides paromomycin and streptomycin bind to the decoding center and induce related structural rearrangements that explain their observed effects on miscoding. Structural and biochemical studies have identified ribosomal protein S12 (as well as specific nucleotides in 16S ribosomal RNA) as a critical molecular contributor in distinguishing between cognate and near-cognate tRNA species as well as in promoting more global rearrangements in the small subunit, referred to as "closure." Here we use a mutational approach to define contributions made by two highly conserved loops in S12 to the process of tRNA selection. Most S12 variant ribosomes tested display increased levels of fidelity (a "restrictive" phenotype). Interestingly, several variants, K42A and R53A, were substantially resistant to the miscoding effects of paromomycin. Further characterization of the compromised paromomycin response identified a probable second, fidelity-modulating binding site for paromomycin in the 16S ribosomal RNA that facilitates closure of the small subunit and compensates for defects associated with the S12 mutations.
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Affiliation(s)
- Divya Sharma
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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40
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Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genes Dev 2007; 17:1362-77. [PMID: 17690205 PMCID: PMC1950905 DOI: 10.1101/gr.6427907] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Accepted: 06/12/2007] [Indexed: 11/24/2022]
Abstract
While bacterial genome annotations have significantly improved in recent years, techniques for bacterial proteome annotation (including post-translational chemical modifications, signal peptides, proteolytic events, etc.) are still in their infancy. At the same time, the number of sequenced bacterial genomes is rising sharply, far outpacing our ability to validate the predicted genes, let alone annotate bacterial proteomes. In this study, we use tandem mass spectrometry (MS/MS) to annotate the proteome of Shewanella oneidensis MR-1, an important microbe for bioremediation. In particular, we provide the first comprehensive map of post-translational modifications in a bacterial genome, including a large number of chemical modifications, signal peptide cleavages, and cleavages of N-terminal methionine residues. We also detect multiple genes that were missed or assigned incorrect start positions by gene prediction programs, and suggest corrections to improve the gene annotation. This study demonstrates that complementing every genome sequencing project by an MS/MS project would significantly improve both genome and proteome annotations for a reasonable cost.
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Affiliation(s)
- Nitin Gupta
- Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA.
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41
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Kaczanowska M, Rydén-Aulin M. Ribosome biogenesis and the translation process in Escherichia coli. Microbiol Mol Biol Rev 2007; 71:477-94. [PMID: 17804668 PMCID: PMC2168646 DOI: 10.1128/mmbr.00013-07] [Citation(s) in RCA: 275] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Translation, the decoding of mRNA into protein, is the third and final element of the central dogma. The ribosome, a nucleoprotein particle, is responsible and essential for this process. The bacterial ribosome consists of three rRNA molecules and approximately 55 proteins, components that are put together in an intricate and tightly regulated way. When finally matured, the quality of the particle, as well as the amount of active ribosomes, must be checked. The focus of this review is ribosome biogenesis in Escherichia coli and its cross-talk with the ongoing protein synthesis. We discuss how the ribosomal components are produced and how their synthesis is regulated according to growth rate and the nutritional contents of the medium. We also present the many accessory factors important for the correct assembly process, the list of which has grown substantially during the last few years, even though the precise mechanisms and roles of most of the proteins are not understood.
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Affiliation(s)
- Magdalena Kaczanowska
- Department of Genetics, Microbiology, and Toxicology, Stockholm University, S-10691 Stockholm, Sweden
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Abstract
Methylation is one of the most common protein modifications. Many different prokaryotic and eukaryotic proteins are methylated, including proteins involved in translation, including ribosomal proteins (RPs) and translation factors (TFs). Positions of the methylated residues in six Escherichia coli RPs and two Saccharomyces cerevisiae RPs have been determined. At least two RPs, L3 and L12, are methylated in both organisms. Both prokaryotic and eukaryotic elongation TFs (EF1A) are methylated at lysine residues, while both release factors are methylated at glutamine residues. The enzymes catalysing methylation reactions, protein methyltransferases (MTases), generally use S-adenosylmethionine as the methyl donor to add one to three methyl groups that, in case of arginine, can be asymetrically positioned. The biological significance of RP and TF methylation is poorly understood, and deletions of the MTase genes usually do not cause major phenotypes. Apparently methylation modulates intra- or intermolecular interactions of the target proteins or affects their affinity for RNA, and, thus, influences various cell processes, including transcriptional regulation, RNA processing, ribosome assembly, translation accuracy, protein nuclear trafficking and metabolism, and cellular signalling. Differential methylation of specific RPs and TFs in a number of organisms at different physiological states indicates that this modification may play a regulatory role.
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Affiliation(s)
- Bogdan Polevoda
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA.
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Kim TY, Brun YV, Reilly JP. Effects of tryptic peptide esterification in MALDI mass spectrometry. Anal Chem 2007; 77:4185-93. [PMID: 15987125 DOI: 10.1021/ac0481250] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of esterification on MALDI ion yield is investigated by using alcohols having different aliphatic chain lengths. For peptides whose ionization yields increase with derivatization, more hydrophobic alcohols tend to yield greater peak enhancements. The completeness of the reaction increases from propanol to methanol. Undesired solvolysis of the amide group in the side chain of Asn or Gln leads to unexpected ester products. Ethanol is suggested as the optimal alcohol for esterification in proteomics experiments since it yields almost complete esterification without substantial solvolysis. Ethanol esterification was employed to facilitate the identification of gel-separated proteins.
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Affiliation(s)
- Tae-Young Kim
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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Karty JA, Running WE, Reilly JP. Two dimensional liquid phase separations of proteins using online fractionation and concentration between chromatographic dimensions. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 847:103-13. [PMID: 17056305 DOI: 10.1016/j.jchromb.2006.09.043] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2006] [Revised: 08/04/2006] [Accepted: 09/21/2006] [Indexed: 11/21/2022]
Abstract
Multi-dimensional liquid chromatography is often presented as an alternative to two-dimensional (2-D) gel electrophoresis for separating complex protein mixtures. The vast majority of analytical-scale 2-D LC systems have employed either off-line fractionation or stepped gradients in the first dimension separation. The latter severely restrict flexibility in setting up the first dimension gradient. We propose a novel two-dimensional LC system that employs online fractionation of proteins into a series of small reversed phase trapping columns. These traps effectively decouple the two separation dimensions and avoid problems associated with off-line fraction collection. Flexibility in determining the gradient programs for the two separations is thus enhanced. The reduced diameter of the trapping columns concentrates analyte between chromatographic dimensions. The apparatus is coupled with online electrospray time-of-flight mass spectrometry to characterize ribosomal proteins of Caulobacter crescentus.
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Affiliation(s)
- Jonathan A Karty
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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Running WE, Ravipaty S, Karty JA, Reilly JP. A top-down/bottom-up study of the ribosomal proteins of Caulobacter crescentus. J Proteome Res 2007; 6:337-47. [PMID: 17203977 PMCID: PMC2536757 DOI: 10.1021/pr060306q] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribosomes from the Gram-negative alpha-proteobacterium Caulobacter crescentus were isolated using standard methods. Proteins were separated using a two-dimensional liquid chromatographic system that allowed the analysis of whole proteins by direct coupling to an ESI-QTOF mass spectrometer and of proteolytic digests by a number of mass spectrometric methods. The masses of 53 of 54 ribosomal proteins were directly measured. Protein identifications and proposed post-translational modifications were supported by proteolysis with trypsin, endoprotease Glu-C, and exoproteases carboxypeptidases Y and P. Tryptic peptide mass maps show an average sequence coverage of 62%, and carboxypeptidase C-terminal sequence tagging provided unambiguous identification of the small, highly basic proteins of the large subunit. C. crescentus presents some post-translational modifications that are similar to those of Escherichia coli (e.g., N-terminal acetylation of S9 and S18) along with some unique variations, such as a near absence of L7 and extensive modification of L11. The comprehensive description of this organism's ribosomal proteome provides a foundation for the study of ribosome structure, dependence of post-translational modifications on growth conditions, and the evolution of subcellular organelles.
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Affiliation(s)
- William E Running
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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Chi A, Bai DL, Geer LY, Shabanowitz J, Hunt DF. Analysis of intact proteins on a chromatographic time scale by electron transfer dissociation tandem mass spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2007; 259:197-203. [PMID: 17364019 PMCID: PMC1826913 DOI: 10.1016/j.ijms.2006.09.030] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Direct analysis of intact proteins on a chromatographic time scale is demonstrated on a modified linear ion trap mass spectrometer using sequential ion/ion reactions, electron transfer and proton transfer, to dissociate the sample and to convert the resulting peptide fragments to a mixture of singly and doubly charged species. Proteins are converted to gas-phase, multiply-charged, positive ions by electrospray ionization and then allowed to react with fluoranthene radical anions. Electron transfer to the multiply charged protein promotes random fragmentation of amide bonds along the protein backbone. Multiply charged fragment ions are then deprotonated in a second ion/ion reaction with even-electron benzoate anions. M/z values for the resulting singly and doubly charged ions are used to read a sequence of 15-40 amino acids at both the N-terminus and the C-terminus of the protein. This information, along with the measured mass of the intact protein, are employed to identify known proteins and to detect the presence of post-translational modifications. In this study, we analyze intact proteins from the Escherchia coli 70S ribosomal protein complex and identify 46 of the 55 known unique components in a single, 90 min, on-line, chromatography experiment. Truncated versions of the above proteins along with several post-translational modifications are also detected.
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47
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Carr JF, Hamburg DM, Gregory ST, Limbach PA, Dahlberg AE. Effects of streptomycin resistance mutations on posttranslational modification of ribosomal protein S12. J Bacteriol 2006; 188:2020-3. [PMID: 16484214 PMCID: PMC1426572 DOI: 10.1128/jb.188.5.2020-2023.2006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ribosomal protein S12 contains a highly conserved aspartic acid residue that is posttranslationally beta-methylthiolated. Using mass spectrometry, we have determined the modification states of several S12 mutants of Thermus thermophilus and conclude that beta-methylthiolation is not a determinant of the streptomycin phenotype.
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Affiliation(s)
- Jennifer F Carr
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
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48
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Suh MJ, Hamburg DM, Gregory ST, Dahlberg AE, Limbach PA. Extending ribosomal protein identifications to unsequenced bacterial strains using matrix-assisted laser desorption/ionization mass spectrometry. Proteomics 2006; 5:4818-31. [PMID: 16287167 PMCID: PMC2603143 DOI: 10.1002/pmic.200402111] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A protocol has been developed that allows protein identifications using available DNA-based or protein sequences from a reference strain of a bacterial species to be extended to bacterial strains for which no prior DNA-based or protein sequence information exists. The protocol is predicated on careful isolation of a specific sub-cellular group of proteins. In this study, ribosomal proteins were chosen due to their high relative abundance and similarity in copy number per cell. After isolation of ribosomal proteins, MALDI-MS is used to acquire accurate protein molecular weights. An iterative comparison of reference protein molecular weights and identities is made to the resulting data, allowing for the straightforward identification of ribosomal proteins from any non-reference strains. This approach can reveal differences between proteins at the amino acid or post-translational level. The protocol was developed, validated and applied to ribosomal proteins from three strains of the extreme thermophile Thermus thermophilus. This approach revealed that nearly 60% of the ribosomal proteins from all three strains are identical. The extension of protein identification to additional bacterial strains can be useful in phylogenetic studies as well as in biomarker identification.
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Affiliation(s)
- Moo-Jin Suh
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Daisy-Malloy Hamburg
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Steven T. Gregory
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Albert E. Dahlberg
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
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49
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Strader MB, Verberkmoes NC, Tabb DL, Connelly HM, Barton JW, Bruce BD, Pelletier DA, Davison BH, Hettich RL, Larimer FW, Hurst GB. Characterization of the 70S Ribosome from Rhodopseudomonas palustris Using an Integrated “Top-Down” and “Bottom-Up” Mass Spectrometric Approach. J Proteome Res 2004; 3:965-78. [PMID: 15473684 DOI: 10.1021/pr049940z] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a comprehensive mass spectrometric approach that integrates intact protein molecular mass measurement ("top-down") and proteolytic fragment identification ("bottom-up") to characterize the 70S ribosome from Rhodopseudomonas palustris. Forty-two intact protein identifications were obtained by the top-down approach and 53 out of the 54 orthologs to Escherichia coli ribosomal proteins were identified from bottom-up analysis. This integrated approach simplified the assignment of post-translational modifications by increasing the confidence of identifications, distinguishing between isoforms, and identifying the amino acid positions at which particular post-translational modifications occurred. Our combined mass spectrometry data also allowed us to check and validate the gene annotations for three ribosomal proteins predicted to possess extended C-termini. In particular, we identified a highly repetitive C-terminal "alanine tail" on L25. This type of low complexity sequence, common to eukaryotic proteins, has previously not been reported in prokaryotic proteins. To our knowledge, this is the most comprehensive protein complex analysis to date that integrates two MS techniques.
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Affiliation(s)
- Michael Brad Strader
- Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6131, USA
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50
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Anderson LB, Ouellette AJA, Eaton-Rye J, Maderia M, MacCoss MJ, Yates JR, Barry BA. Evidence for a Post-Translational Modification, Aspartyl Aldehyde, in a Photosynthetic Membrane Protein. J Am Chem Soc 2004; 126:8399-405. [PMID: 15237995 DOI: 10.1021/ja0478781] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In oxygenic photosynthesis, photosystem II (PSII) carries out the oxidation of water and reduction of plastoquinone. Three PSII subunits contain reactive groups that covalently bind amines and phenylhydrazine. It has been proposed that these reactive groups are carbonyl-containing, co- or post-translationally modified amino acids. To identify modified amino acid residues in one of the PSII subunits (CP47), tandem mass spectrometry was performed. Modified residues were affinity-tagged with either biotin-LC-hydrazide or biocytin hydrazide, which are known to label carbonyl groups. The affinity-tagged subunit was isolated by denaturing gel electrophoresis, and tryptic peptides were then subjected to affinity purification and tandem mass spectrometry. This procedure identified a hydrazide-labeled peptide, which has the sequence XKEGR. This result is supported by quantitative results acquired from peptide mapping and methylamine labeling. The gene sequence and these tandem data predict that the first amino acid, X, which is labeled with the hydrazide reagent, is a modified form of aspartic acid. On the basis of these data, we propose that D348 of the CP47 subunit is post- or co-translationally modified to give a novel amino acid side chain, aspartyl aldehyde.
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Affiliation(s)
- Lorraine B Anderson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, USA
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