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Zhang Y, Cai Q, Luo Y, Zhang Y, Li H. Integrated top-down and bottom-up proteomics mass spectrometry for the characterization of endogenous ribosomal protein heterogeneity. J Pharm Anal 2023; 13:63-72. [PMID: 36820077 PMCID: PMC9937802 DOI: 10.1016/j.jpha.2022.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Ribosomes are abundant, large RNA-protein complexes that are the sites of all protein synthesis in cells. Defects in ribosomal proteins (RPs), including proteoforms arising from genetic variations, alternative splicing of RNA transcripts, post-translational modifications and alterations of protein expression level, have been linked to a diverse range of diseases, including cancer and aging. Comprehensive characterization of ribosomal proteoforms is challenging but important for the discovery of potential disease biomarkers or protein targets. In the present work, using E. coli 70S RPs as an example, we first developed a top-down proteomics approach on a Waters Synapt G2 Si mass spectrometry (MS) system, and then applied it to the HeLa 80S ribosome. The results were complemented by a bottom-up approach. In total, 50 out of 55 RPs were identified using the top-down approach. Among these, more than 30 RPs were found to have their N-terminal methionine removed. Additional modifications such as methylation, acetylation, and hydroxylation were also observed, and the modification sites were identified by bottom-up MS. In a HeLa 80S ribosomal sample, we identified 98 ribosomal proteoforms, among which multiple truncated 80S ribosomal proteoforms were observed, the type of information which is often overlooked by bottom-up experiments. Although their relevance to diseases is not yet known, the integration of top-down and bottom-up proteomics approaches paves the way for the discovery of proteoform-specific disease biomarkers or targets.
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Affiliation(s)
- Ying Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Qinghua Cai
- Henan Engineering Laboratory for Mammary Bioreactor, School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Yuxiang Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yu Zhang
- The Shennong Laboratory, Zhengzhou, 450002, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
- Corresponding author. School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
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2
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Xu C, Shen Y, Li C, Lu F, Zhang MD, Meeley RB, McCarty DR, Tan BC. Emb15 encodes a plastid ribosomal assembly factor essential for embryogenesis in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:214-227. [PMID: 33450100 DOI: 10.1111/tpj.15160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Ribosome assembly factors guide the complex process by which ribosomal proteins and the ribosomal RNAs form a functional ribosome. However, the assembly of plant plastid ribosomes is poorly understood. In the present study, we discovered a maize (Zea mays) plastid ribosome assembly factor based on our characterization of the embryo defective 15 (emb15) mutant. Loss of function of Emb15 retards embryo development at an early stage, but does not substantially affect the endosperm, and causes an albino phenotype in other genetic backgrounds. EMB15 localizes to plastids and possesses a ribosome maturation factor M (RimM) domain in the N-terminus and a predicted UDP-GlcNAc pyrophosphorylase domain in the C-terminus. The EMB15 RimM domain originated in bacteria and the UDP-GlcNAc pyrophosphorylase domain originated in fungi; these two domains came together in the ancestor of land plants during evolution. The N-terminus of EMB15 complemented the growth defect of an Escherichia coli strain with a RimM deletion and rescued the albino phenotype of emb15 homozygous mutants. The RimM domain mediates the interaction between EMB15 and the plastid ribosomal protein PRPS19. Plastid 16S rRNA maturation is also significantly impaired in emb15. These observations suggest that EMB15 functions in maize seed development as a plastid ribosome assembly factor, and the C-terminal domain is not important under normal conditions.
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Affiliation(s)
- Chunhui Xu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao Campus, Qingdao, 266237, China
| | - Yun Shen
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao Campus, Qingdao, 266237, China
| | - Cuiling Li
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao Campus, Qingdao, 266237, China
| | - Fan Lu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao Campus, Qingdao, 266237, China
| | - Meng-Di Zhang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao Campus, Qingdao, 266237, China
| | - Robert B Meeley
- DuPont Pioneer AgBiotech Research, Johnston, Iowa, 50131-1004, USA
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao Campus, Qingdao, 266237, China
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3
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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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4
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Małecki J, Dahl HA, Moen A, Davydova E, Falnes PØ. The METTL20 Homologue from Agrobacterium tumefaciens Is a Dual Specificity Protein-lysine Methyltransferase That Targets Ribosomal Protein L7/L12 and the β Subunit of Electron Transfer Flavoprotein (ETFβ). J Biol Chem 2016; 291:9581-95. [PMID: 26929405 DOI: 10.1074/jbc.m115.709261] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Indexed: 12/31/2022] Open
Abstract
Human METTL20 is a mitochondrial, lysine-specific methyltransferase that methylates the β-subunit of electron transfer flavoprotein (ETFβ). Interestingly, putative METTL20 orthologues are found in a subset of α-proteobacteria, including Agrobacterium tumefaciens Using an activity-based approach, we identified in bacterial extracts two substrates of recombinant METTL20 from A. tumefaciens (AtMETTL20), namely ETFβ and the ribosomal protein RpL7/L12. We show that AtMETTL20, analogous to the human enzyme, methylates ETFβ on Lys-193 and Lys-196 both in vitro and in vivo ETF plays a key role in mediating electron transfer from various dehydrogenases, and we found that its electron transferring ability was diminished by AtMETTL20-mediated methylation of ETFβ. Somewhat surprisingly, AtMETTL20 also catalyzed monomethylation of RpL7/L12 on Lys-86, a common modification also found in many bacteria that lack METTL20. Thus, we here identify AtMETTL20 as the first enzyme catalyzing RpL7/L12 methylation. In summary, here we have identified and characterized a novel bacterial lysine-specific methyltransferase with unprecedented dual substrate specificity within the seven β-strand class of lysine-specific methyltransferases, as it targets two apparently unrelated substrates, ETFβ and RpL7/L12. Moreover, the present work establishes METTL20-mediated methylation of ETFβ as the first lysine methylation event occurring in both bacteria and humans.
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Affiliation(s)
- Jędrzej Małecki
- From the Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
| | - Helge-André Dahl
- From the Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
| | - Anders Moen
- From the Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
| | - Erna Davydova
- From the Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
| | - Pål Ø Falnes
- From the Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
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5
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Cannon JR, Cammarata M, Robotham SA, Cotham VC, Shaw JB, Fellers RT, Early BP, Thomas PM, Kelleher NL, Brodbelt JS. Ultraviolet photodissociation for characterization of whole proteins on a chromatographic time scale. Anal Chem 2014; 86:2185-92. [PMID: 24447299 PMCID: PMC3958131 DOI: 10.1021/ac403859a] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/21/2014] [Indexed: 02/01/2023]
Abstract
Intact protein characterization using mass spectrometry thus far has been achieved at the cost of throughput. Presented here is the application of 193 nm ultraviolet photodissociation (UVPD) for top down identification and characterization of proteins in complex mixtures in an online fashion. Liquid chromatographic separation at the intact protein level coupled with fast UVPD and high-resolution detection resulted in confident identification of 46 unique sequences compared to 44 using HCD from prepared Escherichia coli ribosomes. Importantly, nearly all proteins identified in both the UVPD and optimized HCD analyses demonstrated a substantial increase in confidence in identification (as defined by an average decrease in E value of ∼40 orders of magnitude) due to the higher number of matched fragment ions. Also shown is the potential for high-throughput characterization of intact proteins via liquid chromatography (LC)-UVPD-MS of molecular weight-based fractions of a Saccharomyces cerevisiae lysate. In total, protein products from 215 genes were identified and found in 292 distinct proteoforms, 168 of which contained some type of post-translational modification.
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Affiliation(s)
- Joe R. Cannon
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Michael
B. Cammarata
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Scott A. Robotham
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Victoria C. Cotham
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Jared B. Shaw
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Ryan T. Fellers
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Bryan P. Early
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Paul M. Thomas
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Jennifer S. Brodbelt
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
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6
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Ladror DT, Frey BL, Scalf M, Levenstein ME, Artymiuk JM, Smith LM. Methylation of yeast ribosomal protein S2 is elevated during stationary phase growth conditions. Biochem Biophys Res Commun 2014; 445:535-41. [PMID: 24486316 DOI: 10.1016/j.bbrc.2014.01.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 01/14/2014] [Indexed: 01/12/2023]
Abstract
Ribosomes, as the center of protein translation in the cell, require careful regulation via multiple pathways. While regulation of ribosomal synthesis and function has been widely studied on the transcriptional and translational "levels," the biological roles of ribosomal post-translational modifications (PTMs) are largely not understood. Here, we explore this matter by using quantitative mass spectrometry to compare the prevalence of ribosomal methylation and acetylation for yeast in the log phase and the stationary phase of growth. We find that of the 27 modified peptides identified, two peptides experience statistically significant changes in abundance: a 1.9-fold decrease in methylation for k(Me)VSGFKDEVLETV of ribosomal protein S1B (RPS1B), and a 10-fold increase in dimethylation for r(DiMe)GGFGGR of ribosomal protein S2 (RPS2). While the biological role of RPS1B methylation has largely been unexplored, RPS2 methylation is a modification known to have a role in processing and export of ribosomal RNA. This suggests that yeast in the stationary phase increase methylation of RPS2 in order to regulate ribosomal synthesis. These results demonstrate the utility of mass spectrometry for quantifying dynamic changes in ribosomal PTMs.
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Affiliation(s)
- Daniel T Ladror
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Brian L Frey
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Mark E Levenstein
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Jacklyn M Artymiuk
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
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7
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Tamura H, Hotta Y, Sato H. Novel accurate bacterial discrimination by MALDI-time-of-flight MS based on ribosomal proteins coding in S10-spc-alpha operon at strain level S10-GERMS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1185-1193. [PMID: 23686278 DOI: 10.1007/s13361-013-0627-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 01/15/2013] [Accepted: 03/03/2013] [Indexed: 06/02/2023]
Abstract
Matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is one of the most widely used mass-based approaches for bacterial identification and classification because of the simple sample preparation and extremely rapid analysis within a few minutes. To establish the accurate MALDI-TOF MS bacterial discrimination method at strain level, the ribosomal subunit proteins coded in the S10-spc-alpha operon, which encodes half of the ribosomal subunit protein and is highly conserved in eubacterial genomes, were selected as reliable biomarkers. This method, named the S10-GERMS method, revealed that the strains of genus Pseudomonas were successfully identified and discriminated at species and strain levels, respectively; therefore, the S10-GERMS method was further applied to discriminate the pathovar of P. syringae. The eight selected biomarkers (L24, L30, S10, S12, S14, S16, S17, and S19) suggested the rapid discrimination of P. syringae at the strain (pathovar) level. The S10-GERMS method appears to be a powerful tool for rapid and reliable bacterial discrimination and successful phylogenetic characterization. In this article, an overview of the utilization of results from the S10-GERMS method is presented, highlighting the characterization of the Lactobacillus casei group and discrimination of the bacteria of genera Bacillus and Sphingopyxis despite only two and one base difference in the 16S rRNA gene sequence, respectively.
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Affiliation(s)
- Hiroto Tamura
- School of Agriculture, Meijo University, Shiogamaguchi, Tenpaku-ku, Nagoya, Japan,
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8
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Jaffee EG, Lauber MA, Running WE, Reilly JP. In Vitro and In Vivo Chemical Labeling of Ribosomal Proteins: A Quantitative Comparison. Anal Chem 2012; 84:9355-61. [DOI: 10.1021/ac302115m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ethan G. Jaffee
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7000,
United States
| | - Matthew A. Lauber
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7000,
United States
| | - William E. Running
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7000,
United States
| | - James P. Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7000,
United States
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9
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Zhou W, Liotta LA, Petricoin EF. The spectra count label-free quantitation in cancer proteomics. Cancer Genomics Proteomics 2012; 9:135-142. [PMID: 22593248 PMCID: PMC3761408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
Abstract
Mass spectrometry is used routinely for large-scale protein identification from complex biological mixtures. Recently, relative quantitation approach on the basis of spectra count has been applied in several cancer proteomic studies. In this review, we examine the mechanism of this technique and highlight several important parameters associated with its application.
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Affiliation(s)
- Weidong Zhou
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10900 University Blvd, MS 1A9, Manassas, VA 20110, USA.
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10
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Kim JS, Shin M, Song JS, An S, Kim HJ. C-terminal de novo sequencing of peptides using oxazolone-based derivatization with bromine signature. Anal Biochem 2011; 419:211-6. [DOI: 10.1016/j.ab.2011.08.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 07/14/2011] [Accepted: 08/06/2011] [Indexed: 10/17/2022]
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11
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Ansong C, Tolić N, Purvine SO, Porwollik S, Jones M, Yoon H, Payne SH, Martin JL, Burnet MC, Monroe ME, Venepally P, Smith RD, Peterson SN, Heffron F, McClelland M, Adkins JN. Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium. BMC Genomics 2011; 12:433. [PMID: 21867535 PMCID: PMC3174948 DOI: 10.1186/1471-2164-12-433] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 08/25/2011] [Indexed: 12/22/2022] Open
Abstract
Background Complete and accurate genome annotation is crucial for comprehensive and systematic studies of biological systems. However, determining protein-coding genes for most new genomes is almost completely performed by inference using computational predictions with significant documented error rates (> 15%). Furthermore, gene prediction programs provide no information on biologically important post-translational processing events critical for protein function. Results We experimentally annotated the bacterial pathogen Salmonella Typhimurium 14028, using "shotgun" proteomics to accurately uncover the translational landscape and post-translational features. The data provide protein-level experimental validation for approximately half of the predicted protein-coding genes in Salmonella and suggest revisions to several genes that appear to have incorrectly assigned translational start sites, including a potential novel alternate start codon. Additionally, we uncovered 12 non-annotated genes missed by gene prediction programs, as well as evidence suggesting a role for one of these novel ORFs in Salmonella pathogenesis. We also characterized post-translational features in the Salmonella genome, including chemical modifications and proteolytic cleavages. We find that bacteria have a much larger and more complex repertoire of chemical modifications than previously thought including several novel modifications. Our in vivo proteolysis data identified more than 130 signal peptide and N-terminal methionine cleavage events critical for protein function. Conclusion This work highlights several ways in which application of proteomics data can improve the quality of genome annotations to facilitate novel biological insights and provides a comprehensive proteome map of Salmonella as a resource for systems analysis.
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Affiliation(s)
- Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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12
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Zhang L, Reilly JP. De novo sequencing of tryptic peptides derived from Deinococcus radiodurans ribosomal proteins using 157 nm photodissociation MALDI TOF/TOF mass spectrometry. J Proteome Res 2010; 9:3025-34. [PMID: 20377247 DOI: 10.1021/pr901206j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Vacuum ultraviolet photodissociation of peptide ions in a matrix assisted laser desorption ionization (MALDI) tandem time-of-flight (TOF) mass spectrometer is used to characterize peptide mixtures derived from Deinococcus radiodurans ribosomal proteins. Tryptic peptides from 52 proteins were separated by reverse-phase liquid chromatography and spotted onto a MALDI plate. From 192 sample spots, 492 peptide ions were isolated, fragmented by both photodissociation and postsource decay (PSD), and then de novo sequenced. Three-hundred seventy-two peptides yielded sequences with 5 or more amino acids. Homology searches of these sequences against the whole bacterial proteome identified 49 ribosomal proteins, 45 of which matched with two or more peptides. Peptide de novo sequencing identified slightly more proteins than conventional database searches using Mascot and was particularly advantageous in identifying unexpected peptide modifications. In the present analysis, 52 peptide modifications were identified by de novo sequencing, most of which were not recognized by database searches.
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Affiliation(s)
- Liangyi Zhang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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13
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Hotta Y, Teramoto K, Sato H, Yoshikawa H, Hosoda A, Tamura H. Classification of Genus Pseudomonas by MALDI-TOF MS Based on Ribosomal Protein Coding in S10−spc−alpha Operon at Strain Level. J Proteome Res 2010; 9:6722-8. [DOI: 10.1021/pr100868d] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yudai Hotta
- School of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan, Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Advanced Technology Division, JEOL Ltd., Tokyo 196-8558, Japan, and Department of Life, Environmental and Material Science, FIT, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan
| | - Kanae Teramoto
- School of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan, Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Advanced Technology Division, JEOL Ltd., Tokyo 196-8558, Japan, and Department of Life, Environmental and Material Science, FIT, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan
| | - Hiroaki Sato
- School of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan, Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Advanced Technology Division, JEOL Ltd., Tokyo 196-8558, Japan, and Department of Life, Environmental and Material Science, FIT, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan
| | - Hiromichi Yoshikawa
- School of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan, Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Advanced Technology Division, JEOL Ltd., Tokyo 196-8558, Japan, and Department of Life, Environmental and Material Science, FIT, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan
| | - Akifumi Hosoda
- School of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan, Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Advanced Technology Division, JEOL Ltd., Tokyo 196-8558, Japan, and Department of Life, Environmental and Material Science, FIT, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan
| | - Hiroto Tamura
- School of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan, Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Advanced Technology Division, JEOL Ltd., Tokyo 196-8558, Japan, and Department of Life, Environmental and Material Science, FIT, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan
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14
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Wang N, Li L. Reproducible microwave-assisted acid hydrolysis of proteins using a household microwave oven and its combination with LC-ESI MS/MS for mapping protein sequences and modifications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1573-1587. [PMID: 20547072 DOI: 10.1016/j.jasms.2010.04.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 04/21/2010] [Accepted: 04/22/2010] [Indexed: 05/29/2023]
Abstract
A new set-up for microwave-assisted acid hydrolysis (MAAH) with high efficiency and reproducibility to degrade proteins into peptides for mass spectrometry analysis is described. It is based on the use of an inexpensive domestic microwave oven and can be used for low volume protein solution digestion. This set-up has been combined with liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry (LC-ESI QTOF MS) for mapping protein sequences and characterizing phosphoproteins. It is demonstrated that for bovine serum albumin (BSA), with a molecular mass of about 67,000 Da, 1292 peptides (669 unique sequences) can be detected from a 2 microg hydrolysate generated by trifluoroacetic acid (TFA) MAAH. These peptides cover the entire protein sequence, allowing the identification of an amino acid substitution in a natural variant of BSA. It is shown that for a simple phosphoprotein containing one phosphoform, beta-casein, direct analysis of the hydrolysate generates a comprehensive peptide map that can be used to identify all five known phosphorylation sites. For characterizing a complex phosphoprotein consisting of different phosphoforms with varying numbers of phosphate groups and/or phosphorylation sites, such as bovine alpha(S1)-casein, immobilized metal-ion affinity chromatography (IMAC) is used to enrich the phosphopeptides from the hydrolysate, followed by LC-ESI MS analysis. The MS/MS data generated from the initial hydrolysate and the phosphopeptide-enriched fraction, in combination with MS analysis of the intact protein sample, allow us to reveal the presence of three different phosphoforms of bovine alpha(S1)-casein and assign the phosphorylation sites to each phosphoform with high confidence.
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Affiliation(s)
- Nan Wang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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15
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Kellie JF, Tran JC, Lee JE, Ahlf DR, Thomas HM, Ntai I, Catherman AD, Durbin KR, Zamdborg L, Vellaichamy A, Thomas PM, Kelleher NL. The emerging process of Top Down mass spectrometry for protein analysis: biomarkers, protein-therapeutics, and achieving high throughput. MOLECULAR BIOSYSTEMS 2010; 6:1532-9. [PMID: 20711533 DOI: 10.1039/c000896f] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Top Down mass spectrometry (MS) has emerged as an alternative to common Bottom Up strategies for protein analysis. In the Top Down approach, intact proteins are fragmented directly in the mass spectrometer to achieve both protein identification and characterization, even capturing information on combinatorial post-translational modifications. Just in the past two years, Top Down MS has seen incremental advances in instrumentation and dedicated software, and has also experienced a major boost from refined separations of whole proteins in complex mixtures that have both high recovery and reproducibility. Combined with steadily advancing commercial MS instrumentation and data processing, a high-throughput workflow covering intact proteins and polypeptides up to 70 kDa is directly visible in the near future.
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Affiliation(s)
- John F Kellie
- Technology Development Team, Center for Top Down Proteomics, University of Illinois at Urbana-Champaign, USA
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16
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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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17
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Liu X, Reilly JP. Correlating the Chemical Modification of Escherichia coli Ribosomal Proteins with Crystal Structure Data. J Proteome Res 2009; 8:4466-78. [DOI: 10.1021/pr9002382] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaohui Liu
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405
| | - James P. Reilly
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405
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18
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Running WE, Reilly JP. Ribosomal Proteins of Deinococcus radiodurans: Their Solvent Accessibility and Reactivity. J Proteome Res 2009; 8:1228-46. [DOI: 10.1021/pr800544y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- William E. Running
- Department of Chemistry, Indiana University, Bloomington, Indiana, 47405
| | - James P. Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana, 47405
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19
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Jungblut PR, Holzhütter HG, Apweiler R, Schlüter H. The speciation of the proteome. Chem Cent J 2008; 2:16. [PMID: 18638390 PMCID: PMC2492845 DOI: 10.1186/1752-153x-2-16] [Citation(s) in RCA: 186] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 07/18/2008] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION In proteomics a paradox situation developed in the last years. At one side it is basic knowledge that proteins are post-translationally modified and occur in different isoforms. At the other side the protein expression concept disclaims post-translational modifications by connecting protein names directly with function. DISCUSSION Optimal proteome coverage is today reached by bottom-up liquid chromatography/mass spectrometry. But quantification at the peptide level in shotgun or bottom-up approaches by liquid chromatography and mass spectrometry is completely ignoring that a special peptide may exist in an unmodified form and in several-fold modified forms. The acceptance of the protein species concept is a basic prerequisite for meaningful quantitative analyses in functional proteomics. In discovery approaches only top-down analyses, separating the protein species before digestion, identification and quantification by two-dimensional gel electrophoresis or protein liquid chromatography, allow the correlation between changes of a biological situation and function. CONCLUSION To obtain biological relevant information kinetics and systems biology have to be performed at the protein species level, which is the major challenge in proteomics today.
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Affiliation(s)
- Peter R Jungblut
- Max Planck Institute for Infection Biology, Core Facility Protein Analysis, Berlin, Germany
| | | | - Rolf Apweiler
- European Bioinformatics Institute, Cambridge CB10 1SD, UK
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20
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Williamson JR. Biophysical studies of bacterial ribosome assembly. Curr Opin Struct Biol 2008; 18:299-304. [PMID: 18541423 DOI: 10.1016/j.sbi.2008.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Accepted: 05/07/2008] [Indexed: 11/28/2022]
Abstract
The assembly of the bacterial ribosome involves the association of over 50 proteins to 3 large RNA molecules, and it represents a major metabolic activity for rapidly growing bacteria. The availability of atomic structures of the ribosome and the application of biochemical and biophysical methods have led to rapid progress in understanding the mechanistic details of ribosome assembly. The basic steps required to assemble a ribosome are outlined, and the contributions of mass spectrometry, computational methods, and RNA-folding studies in understanding these steps are detailed. This complex process takes place with both sequential and parallel processing that is coordinated to ensure efficient and complete assembly of ribosomes to meet the demands of cell growth.
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Affiliation(s)
- James R Williamson
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States.
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21
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Zhang L, Reilly JP. Use of 157-nm photodissociation to probe structures of y- and b-type ions produced in collision-induced dissociation of peptide ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:695-702. [PMID: 18325783 DOI: 10.1016/j.jasms.2008.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Revised: 01/22/2008] [Accepted: 01/24/2008] [Indexed: 05/26/2023]
Abstract
y- and b-type fragment ions produced in the collisional dissociation of arginine-terminated peptide ions are photodissociated with 157-nm light in a linear trap. y-type ions are shown to have the same structure as that of intact peptides of the same sequence with the ionizing proton located at the most basic residue(s). For generic b-type ions, the ionizing proton is shown to be sequestered at the N-terminal arginine, which is consistent with the proposed oxazolone structure.
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Affiliation(s)
- Liangyi Zhang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-4001, USA
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22
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Mohammed S, Lorenzen K, Kerkhoven R, Breukelen BV, Vannini A, Cramer P, Heck AJR. Multiplexed Proteomics Mapping of Yeast RNA Polymerase II and III Allows Near-Complete Sequence Coverage and Reveals Several Novel Phosphorylation Sites. Anal Chem 2008; 80:3584-92. [DOI: 10.1021/ac7024283] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Gene Center Munich and Center for Integrated Protein Science CiPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Kristina Lorenzen
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Gene Center Munich and Center for Integrated Protein Science CiPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Robert Kerkhoven
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Gene Center Munich and Center for Integrated Protein Science CiPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Bas van Breukelen
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Gene Center Munich and Center for Integrated Protein Science CiPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Alessandro Vannini
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Gene Center Munich and Center for Integrated Protein Science CiPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Patrick Cramer
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Gene Center Munich and Center for Integrated Protein Science CiPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Gene Center Munich and Center for Integrated Protein Science CiPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
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23
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Bunger MK, Cargile BJ, Ngunjiri A, Bundy JL, Stephenson JL. Automated Proteomics of E. coli via Top-Down Electron-Transfer Dissociation Mass Spectrometry. Anal Chem 2008; 80:1459-67. [DOI: 10.1021/ac7018409] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maureen K. Bunger
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709
| | - Benjamin J. Cargile
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709
| | - Anne Ngunjiri
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709
| | - Jonathan L. Bundy
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709
| | - James L. Stephenson
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709
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24
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Teramoto K, Sato H, Sun L, Torimura M, Tao H, Yoshikawa H, Hotta Y, Hosoda A, Tamura H. Phylogenetic Classification of Pseudomonas putida Strains by MALDI-MS Using Ribosomal Subunit Proteins as Biomarkers. Anal Chem 2007; 79:8712-9. [DOI: 10.1021/ac701905r] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kanae Teramoto
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
| | - Hiroaki Sato
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
| | - Liwei Sun
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
| | - Masaki Torimura
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
| | - Hiroaki Tao
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
| | - Hiromichi Yoshikawa
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
| | - Yudai Hotta
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
| | - Akifumi Hosoda
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
| | - Hiroto Tamura
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
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25
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Teramoto K, Sato H, Sun L, Torimura M, Tao H. A Simple Intact Protein Analysis by MALDI-MS for Characterization of Ribosomal Proteins of Two Genome-Sequenced Lactic Acid Bacteria and Verification of Their Amino Acid Sequences. J Proteome Res 2007; 6:3899-907. [PMID: 17854216 DOI: 10.1021/pr070218l] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rapid identification of bacteria by a bioinformatics-based approach, which processes the mass spectra observed by matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS), relies on the calculated masses of ribosomal subunit proteins as biomarkers predicted from amino acid sequences found in protein sequence databases. To verify the actual state of the registered sequence information, a simple intact protein analysis by MALDI-MS using cell lysates as samples was applied to the characterization of ribosomal proteins from genome-sequenced Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus strains. This method avoided the risk of loss of some subunit proteins and the formation of disulfide bonds during the purification of ribosomal proteins. By comparing this with the MALDI mass spectra of different strains and carrying out manual inspection of sequence information, a total of five errors in N-terminal amino acid sequences were identified. After sequence correction, approximately 40 out of 53 subunit proteins could be assigned, considering N-terminal methionine loss only as a post-translational modification. These show promise for use as practical biomarkers for the rapid identification of S. thermophilus and L. bulgaricus. After verification of these amino acid sequences, mass differences relative to those of genome-sequenced strains have the potential for distinguishing bacteria at the strain level.
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Affiliation(s)
- Kanae Teramoto
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8569, Japan
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