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Soleimani Mashhadi I, Safarnejad MR, Shahmirzaie M, Aliahmadi A, Ghassempour A. Conjugation of Single-Chain Variable Fragment Antibody to Magnetic Nanoparticles and Screening of Fig Mosaic Virus by MALDI TOF Mass Spectrometry. Anal Chem 2020; 92:10460-10469. [DOI: 10.1021/acs.analchem.0c01119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ilnaz Soleimani Mashhadi
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| | - Mohammad Reza Safarnejad
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Morteza Shahmirzaie
- Pharmaceutical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Niayesh Highway, Valiasr Avenue, Tehran, Iran
| | - Atousa Aliahmadi
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| | - Alireza Ghassempour
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
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Kosoltanapiwat N, Reamtong O, Okabayashi T, Ampawong S, Rungruengkitkun A, Thiangtrongjit T, Thippornchai N, Leaungwutiwong P, Mahittikorn A, Mori H, Yoohanngoa T, Yamwong P. Mass spectrometry-based identification and whole-genome characterisation of the first pteropine orthoreovirus isolated from monkey faeces in Thailand. BMC Microbiol 2018; 18:135. [PMID: 30332986 PMCID: PMC6192116 DOI: 10.1186/s12866-018-1302-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 10/04/2018] [Indexed: 12/28/2022] Open
Abstract
Background The pteropine orthoreovirus (PRV) was isolated from monkey (Macaca fascicularis) faecal samples collected from human-inhabited areas in Lopburi Province, Thailand. These samples were initially obtained to survey for the presence of hepatitis E virus (HEV). Results Two virus isolates were retrieved by virus culture of 55 monkey faecal samples. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was successfully used to identify the viruses as the segmented dsRNA orthoreovirus. Phylogenetic analysis of the Lopburi orthoreovirus whole-genomes revealed relationships with the well-characterised PRVs Pulau (segment L1), Cangyuan (segments L2, M3 and S3), Melaka (segments L3 and M2), Kampar (segments M1 and S2) and Sikamat (segments S1 and S4) of Southeast Asia and China with nucleotide sequence identities of 93.5–98.9%. RT-PCR showed that PRV was detected in 10.9% (6/55) and HEV was detected in 25.5% (14/55) of the monkey faecal samples. Conclusions PRV was isolated from monkey faeces for the first time in Thailand via viral culture and LC-MS/MS. The genetic diversity of the virus genome segments suggested a re-assortment within the PRV species group. The overall findings emphasise that monkey faeces can be sources of zoonotic viruses, including PRV and HEV, and suggest the need for active virus surveillance in areas of human and monkey co-habitation to prevent and control emerging zoonotic diseases in the future. Electronic supplementary material The online version of this article (10.1186/s12866-018-1302-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand.
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Tamaki Okabayashi
- Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Gakuen-kibanadai-nishi-1-1, Miyazaki, 889-2192, Japan.,Mahidol-Osaka Center for Infectious Diseases (MOCID), Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Sumate Ampawong
- Department of Tropical Pathology, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Amporn Rungruengkitkun
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Tipparat Thiangtrongjit
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Narin Thippornchai
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Pornsawan Leaungwutiwong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Aongart Mahittikorn
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Hirotake Mori
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Thanada Yoohanngoa
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Prechaya Yamwong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
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Yefremova Y, Al-Majdoub M, Opuni KF, Koy C, Cui W, Yan Y, Gross M, Glocker MO. "De-novo" amino acid sequence elucidation of protein G'e by combined "top-down" and "bottom-up" mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:482-492. [PMID: 25560987 PMCID: PMC6130978 DOI: 10.1007/s13361-014-1053-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 11/20/2014] [Accepted: 11/20/2014] [Indexed: 06/04/2023]
Abstract
Mass spectrometric de-novo sequencing was applied to review the amino acid sequence of a commercially available recombinant protein G´ with great scientific and economic importance. Substantial deviations to the published amino acid sequence (Uniprot Q54181) were found by the presence of 46 additional amino acids at the N-terminus, including a so-called "His-tag" as well as an N-terminal partial α-N-gluconoylation and α-N-phosphogluconoylation, respectively. The unexpected amino acid sequence of the commercial protein G' comprised 241 amino acids and resulted in a molecular mass of 25,998.9 ± 0.2 Da for the unmodified protein. Due to the higher mass that is caused by its extended amino acid sequence compared with the original protein G' (185 amino acids), we named this protein "protein G'e." By means of mass spectrometric peptide mapping, the suggested amino acid sequence, as well as the N-terminal partial α-N-gluconoylations, was confirmed with 100% sequence coverage. After the protein G'e sequence was determined, we were able to determine the expression vector pET-28b from Novagen with the Xho I restriction enzyme cleavage site as the best option that was used for cloning and expressing the recombinant protein G'e in E. coli. A dissociation constant (K(d)) value of 9.4 nM for protein G'e was determined thermophoretically, showing that the N-terminal flanking sequence extension did not cause significant changes in the binding affinity to immunoglobulins.
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Affiliation(s)
- Yelena Yefremova
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | | | | | - Cornelia Koy
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Weidong Cui
- Washington University in St. Louis, St. Louis, Missouri, USA
| | - Yuetian Yan
- Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael Gross
- Washington University in St. Louis, St. Louis, Missouri, USA
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Running WE, Ni P, Kao CC, Reilly JP. Chemical reactivity of brome mosaic virus capsid protein. J Mol Biol 2012; 423:79-95. [PMID: 22750573 DOI: 10.1016/j.jmb.2012.06.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 06/01/2012] [Accepted: 06/20/2012] [Indexed: 12/12/2022]
Abstract
Viral particles are biological machines that have evolved to package, protect, and deliver the viral genome into the host via regulated conformational changes of virions. We have developed a procedure to modify lysine residues with S-methylthioacetimidate across the pH range from 5.5 to 8.5. Lysine residues that are not completely modified are involved in tertiary or quaternary structural interactions, and their extent of modification can be quantified as a function of pH. This procedure was applied to the pH-dependent structural transitions of brome mosaic virus (BMV). As the reaction pH increases from 5.5 to 8.5, the average number of modified lysine residues in the BMV capsid protein increases from 6 to 12, correlating well with the known pH-dependent swelling behavior of BMV virions. The extent of reaction of each of the capsid protein's lysine residues has been quantified at eight pH values using coupled liquid chromatography-tandem mass spectrometry. Each lysine can be assigned to one of three structural classes identified by inspection of the BMV virion crystal structure. Several lysine residues display reactivity that indicates their involvement in dynamic interactions that are not obvious in the crystal structure. The influence of several capsid protein mutants on the pH-dependent structural transition of BMV has also been investigated. Mutant H75Q exhibits an altered swelling transition accompanying solution pH increases. The H75Q capsids show increased reactivity at lysine residues 64 and 130, residues distal from the dimer interface occupied by H75, across the entire pH range.
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Affiliation(s)
- W E Running
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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5
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Croxatto A, Prod'hom G, Greub G. Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol Rev 2012; 36:380-407. [DOI: 10.1111/j.1574-6976.2011.00298.x] [Citation(s) in RCA: 581] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 07/06/2011] [Accepted: 07/07/2011] [Indexed: 11/30/2022] Open
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Luo H, Wylie SJ, Jones MGK. Identification of plant viruses using one-dimensional gel electrophoresis and peptide mass fingerprints. J Virol Methods 2010; 165:297-301. [PMID: 20170682 DOI: 10.1016/j.jviromet.2010.01.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 01/11/2010] [Accepted: 01/26/2010] [Indexed: 11/18/2022]
Abstract
A generic assay to detect and partially characterize unknown viruses from plants was developed. Proteins extracted from virus-infected and uninfected plants were separated in one dimension by SDS polyacrylamide gel electrophoresis. Differentially expressed protein bands were eluted after trypsin digestion and resulting peptide fragments separated according to their mass by matrix-assisted laser-desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. Resulting peptide mass fingerprints (PMF) were compared with those in protein databases. The assay was used to identify three known viruses: the potyviruses Zucchini yellow mosaic virus and Turnip mosaic virus, and an alfamovirus Alfalfa mosaic virus. It was also used to identify a virus that manifested symptoms in wild Cakile maritima plants, tentatively identified as Pelargonium zonate spot virus (PZSV) (genus Anulavirus) by its PMF, and then confirmed by nucleotide sequencing. The detection of PZSV constitutes a first record of this virus in Australia and in this host. It is proposed that this rapid and simple assay is a useful approach for analysis of plant samples known to harbor viruses that could not be identified using antisera or nucleic acid-based assays.
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Affiliation(s)
- H Luo
- Plant Biotechnology Research Group, Western Australian State Agricultural Biotechnology Centre, School of Biological Sciences and Biotechnology, Murdoch University, Perth, WA 6150, Australia
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Yi G, Vaughan RC, Yarbrough I, Dharmaiah S, Kao CC. RNA binding by the brome mosaic virus capsid protein and the regulation of viral RNA accumulation. J Mol Biol 2009; 391:314-26. [PMID: 19481091 PMCID: PMC2774812 DOI: 10.1016/j.jmb.2009.05.065] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2009] [Revised: 05/12/2009] [Accepted: 05/20/2009] [Indexed: 12/20/2022]
Abstract
Viral capsid proteins (CPs) can regulate gene expression and encapsulate viral RNAs. Low-level expression of the brome mosaic virus (BMV) CP was found to stimulate viral RNA accumulation, while higher levels inhibited translation and BMV RNA replication. Regulation of translation acts through an RNA element named the B box, which is also critical for the replicase assembly. The BMV CP has also been shown to preferentially bind to an RNA element named SLC that contains the core promoter for genomic minus-strand RNA synthesis. To further elucidate CP interaction with RNA, we used a reversible cross-linking-peptide fingerprinting assay to identify peptides in the capsid that contact the SLC, the B-box RNA, and the encapsidated RNA. Transient expression of three mutations made in residues within or close by the cross-linked peptides partially released the normal inhibition of viral RNA accumulation in agroinfiltrated Nicotiana benthamiana. Interestingly, two of the mutants, R142A and D148A, were found to retain the ability to down-regulate reporter RNA translation. These two mutants formed viral particles in inoculated leaves, but only R142A was able to move systemically in the inoculated plant. The R142A CP was found to have higher affinities for SLC and the B box compared with those of wild-type CP and to alter contacts to the RNA in the virion. These results better define how the BMV CP can interact with RNA and regulate different viral processes.
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Affiliation(s)
- Guanghui Yi
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Seifers DL, Martin TJ, Harvey TL, Fellers JP, Stack JP, Ryba-White M, Haber S, Krokhin O, Spicer V, Lovat N, Yamchuk A, Standing KG. Triticum mosaic virus: A New Virus Isolated from Wheat in Kansas. PLANT DISEASE 2008; 92:808-817. [PMID: 30769583 DOI: 10.1094/pdis-92-5-0808] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In 2006, a mechanically-transmissible and previously uncharacterized virus was isolated in Kansas from wheat plants with mosaic symptoms. The physiochemical properties of the virus were examined by purification on cesium chloride density gradients, electron microscopy, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), sequencing of the nucleotides and amino acids of the coat protein, and immunological reactivity. Purified preparations contained flexuous, rod-shaped particles that resembled potyviruses. The coat protein was estimated from SDS-PAGE to have a mass of approximately 35 kDa. Its amino acid sequence, as deduced from DNA sequencing of cloned, reverse-transcribed viral RNA and separately determined by time-of-flight mass spectrometry, was most closely related (49% similarity) to Sugarcane streak mosaic virus, a member of the Tritimovirus genus of the family Potyviridae. The virus gave strong positive reactions during enzyme-linked immunosorbent assays using polyclonal antibodies raised against purified preparations of the cognate virus but gave consistent negative reactions against antibodies to Wheat streak mosaic virus (WSMV), other wheat potyviruses, and the High Plains virus. When the virus was inoculated on the WSMV-resistant wheat cv. RonL, systemic symptoms appeared and plant growth was diminished significantly in contrast with WSMV-inoculated RonL. Taken together, the data support consideration of this virus as a new potyvirus, and the name Triticum mosaic virus (TriMV) is proposed.
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Affiliation(s)
- Dallas L Seifers
- Professors, Kansas State University, Agricultural Research Center-Hays, Hays 67601-9228
| | - T J Martin
- Professors, Kansas State University, Agricultural Research Center-Hays, Hays 67601-9228
| | - Tom L Harvey
- Professor, Department of Entomology, Kansas State University, Manhattan 66506
| | - John P Fellers
- United States Department of Agriculture-Agricultural Research Service-PSERU, Department of Plant Pathology, Manhattan, KS 66506
| | - James P Stack
- Department of Plant Pathology, Kansas State University, Manhattan
| | | | - Steve Haber
- Cereal Research Centre, Agriculture & Agri-Food Canada, Winnipeg, Manitoba, Canada
| | - Oleg Krokhin
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Victor Spicer
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nicole Lovat
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrej Yamchuk
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kenneth G Standing
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba, Canada
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9
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She YM, Krokhin O, Spicer V, Loboda A, Garland G, Ens W, Standing KG, Westmore JB. Formation of (bn-1 + H2O) ions by collisional activation of MALDI-formed peptide [M + H]+ ions in a QqTOF mass spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1024-37. [PMID: 17418589 PMCID: PMC1979097 DOI: 10.1016/j.jasms.2007.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Revised: 02/09/2007] [Accepted: 02/12/2007] [Indexed: 05/14/2023]
Abstract
Collisional activation of [M + H](+) parent ions from peptides of n amino acid residues may yield a rearrangement that involves loss of the C-terminal amino acid residue to produce (b(n-1) + H(2)O) daughters. We have studied this reaction by a retrospective examination of the m/z spectra of two collections of data. The first set comprised 398 peptides from coat protein digests of a number of plant viruses by various enzymes, where conditions in the tryptic digests were chosen so as to produce many missed cleavages. In this case, a large effect was observed-323 (b(n-1) + H(2)O) daughter ions (approximately 81%), including 185 (approximately 46%) "strong" decays with ratios (b(n-1) + H(2)O)/(b(n-1)) > 1. The second set comprised 1200 peptides, all from tryptic digests, which were carried out under more stringent conditions, resulting in relatively few missed cleavages. Even here, 190 (b(n-1) + H(2)O) ions (approximately 16%) were observed, including 87 (> 7%) "strong" decays, so the effect is still appreciable. The results suggest that the tendency for (b(n-1) + H(2)O) ion formation is promoted by the protonated side chain of a non-C-terminal basic amino acid residue, in the order arginine >> lysine > or = histidine, and that its (non-C-terminal) position is not critical. The results can be interpreted by a mechanism in which hydrogen bonding between the protonated side chain and the (n - 1) carbonyl oxygen facilitates loss of the C-terminal amino acid residue to give a product ion having a carboxyl group at the new C-terminus.
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Affiliation(s)
- Yi-Min She
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba, Canada
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10
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Abstract
Plant diseases caused by fungi, oomycetes, viruses, and bacteria are devastating both to the economy and to the food supply of a nation. Therefore, the development of new, rapid methods to identify these pathogens is a highly important area of research that is of international concern. MS-based proteomics has become a powerful and increasingly popular approach to not only identify these pathogens, but also to better understand their biology. However, there is a distinction between identifying a pathogen protein and identifying a pathogen based upon the detection of one of its proteins and this must be considered before the general application of MS for plant pathogen detection is made. There has been a recent push in the proteomics community to make data from large-scale proteomics experiments publicly available in the form of a centralized repository. Such a resource could enable the use of MS as a universal plant pathogen detection technology.
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Affiliation(s)
- Neerav D Padliya
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, USA
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Gopinath K, Dragnea B, Kao C. Interaction between Brome mosaic virus proteins and RNAs: effects on RNA replication, protein expression, and RNA stability. J Virol 2005; 79:14222-34. [PMID: 16254357 PMCID: PMC1280218 DOI: 10.1128/jvi.79.22.14222-14234.2005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Accepted: 08/20/2005] [Indexed: 11/20/2022] Open
Abstract
Brome mosaic virus (BMV) RNA replication has been examined in a number of systems, including Saccharomyces cerevisiae. We developed an efficient T-DNA-based gene delivery system using Agrobacterium tumefaciens to transiently express BMV RNAs in Nicotiana benthamiana. The expressed RNAs can systemically infect plants and provide material to extract BMV replicase that can perform template-dependent RNA-dependent RNA synthesis in vitro. We also expressed the four BMV-encoded proteins from nonreplicating RNAs and analyzed their effects on BMV RNA accumulation. The capsid protein that coinfiltrated with constructs expressing RNA1 and RNA2 suppressed minus-strand levels but increased plus-strand RNA accumulation. The replication proteins 1a and 2a could function in trans to replicate and transcribe the BMV RNAs. None of the BMV proteins or RNA could efficiently suppress posttranscriptional silencing. However, 1a expressed in trans will suppress the production of a recombinant green fluorescent protein expressed from the nontranslated portions of BMV RNA1 and RNA2, suggesting that 1a may regulate translation from BMV RNAs. BMV replicase proteins 1a did not affect the accumulation of the BMV RNAs in the absence of RNA replication, unlike the situation reported for S. cerevisiae. This work demonstrates that the Agrobacterium-mediated gene delivery system can be used to study the cis- and trans-acting requirements for BMV RNA replication in plants and that significant differences can exist for BMV RNA replication in different hosts.
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Affiliation(s)
- K Gopinath
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA
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Seifers DL, Harvey TL, Martin TJ, Haber S, She YM, Ens W, Standing KG, Salomon R, Gera A. Association of a Virus with Wheat Displaying Yellow Head Disease Symptoms in the Great Plains. PLANT DISEASE 2005; 89:888-895. [PMID: 30786523 DOI: 10.1094/pd-89-0888] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Wheat with yellow head disease (YHD) (yellow heads and mosaic leaf symptoms) has been observed in Kansas since 1997. A pathogen was transmitted from the infected wheat to maize by vascular puncture inoculation and to Nicotiana benthamiana by rub inoculation. The original infected wheat and infected maize and N. benthamiana test plants all produced a unique 32- to 34-kDa protein when analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Time-of-flight mass spectrometry analysis of the unique 32- to 34-kDa protein showed that the amino acid sequence was most closely related to the nucleoprotein of Rice hoja blanca virus, indicating that the virus causing YHD symptoms in wheat is a tenuivirus. Antiserum made to this protein failed to react with extracts made from healthy wheat or wheat infected with Wheat streak mosaic virus or the High Plains virus. The antiserum did react to extracts made from symptomatic wheat, maize, and N. benthamiana, shown by SDS-PAGE to contain the unique protein, and to extracts of wheat with YHD symptoms from Kansas, North Dakota, South Dakota, and Oklahoma. The name Wheat yellow head virus is proposed for this virus.
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Affiliation(s)
- Dallas L Seifers
- Professor, Kansas State University, Agricultural Research Center-Hays, 67601-9228
| | - Tom L Harvey
- Professor, Department of Entomology, Kansas State University, Manhattan 66506
| | - T J Martin
- Professor, Kansas State University, Agricultural Research Center-Hays
| | - Steve Haber
- Research Scientist, Cereal Research Center, Agriculture & Agri-Food Canada, 195 Dafoe Road, Winnipeg, Manitoba, Canada
| | | | - Werner Ens
- Professors, Department of Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kenneth G Standing
- Professors, Department of Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - A Gera
- Volcani Center, Bet-Dagan, Israel
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Fan X, She YM, Bagshaw RD, Callahan JW, Schachter H, Mahuran DJ. Identification of the hydrophobic glycoproteins of Caenorhabditis elegans. Glycobiology 2005; 15:952-64. [PMID: 15888633 DOI: 10.1093/glycob/cwi075] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Hydrophobic proteins such as integral membrane proteins are difficult to separate, and therefore to study, at a proteomics level. However, the Asn-linked (N-linked) carbohydrates (N-glycans) contained in membrane glycoproteins are important in differentiation, embryogenesis, inflammation, cancer and metastasis, and other vital cellular processes. Thus, the identification of these proteins and their sites of glycosylation in a well-characterized model organism is the first step toward understanding the mechanisms by which N-glycans and their associated proteins function in vivo. In this report, a proteomics method recently developed by our group was applied to identify 117 hydrophobic N-glycosylated proteins of Caenorhabditis elegans extracts by analysis of 195 glycopeptides containing 199 Asn-linked oligosaccharides. Most of the proteins identified are involved in cell adhesion, metabolism, or the transport of small molecules. In addition, there are 18 proteins for which no function is known or predictable by sequence homologies and two proteins which were previously predicted to exist only on the basis of genomic sequences in the C. elegans database. Because N-glycosylation is initiated in the lumen of the endoplasmic reticulum (ER), our data can be used to reassess the previously predicted subcellular localizations of these proteins. As well, the identification of N-glycosylation sites helps establish the membrane topology of the associated glycoproteins. Caenorhabditis elegans strains are presently available with mutations in 17 of the genes we have identified. The powerful genetic tools available for C. elegans can be used to make other strains with mutations in genes encoding N-glycosylated proteins and thereby determine N-glycan function.
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Affiliation(s)
- Xiaolian Fan
- Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
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Ackloo S, Loboda A. Applications of a matrix-assisted laser desorption/ionization orthogonal time-of-flight mass spectrometer. l. Metastable decay and collision-induced dissociation for sequencing peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:213-220. [PMID: 15593255 DOI: 10.1002/rcm.1775] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The use of a high-performance orthogonal time-of-flight (o-TOF) mass spectrometer for sequence analysis is described. The mass spectrometer is equipped with a matrix-assisted laser desorption/ionization (MALDI) source that operates at elevated pressure, 0.01-1 Torr. Ion fragmentation is controlled by varying the pressure of the buffer gas, the laser energy, the voltage difference between the MALDI target and the adjacent sampling cone, and between the cone and the quadrupole ion guide. The peptides were analyzed under optimal ionization conditions to obtain their molecular mass, and under conditions that promote ion dissociation via metastable decomposition or collision-induced dissociation (CID). The fragmentation spectra were used to obtain sequence information. Ion dissociation was promoted via three configurations of the ionization parameters. All methods yielded sequencing-grade b- and y-type ions. Two binary mixtures of peptides were used to demonstrate that: (1) external calibration provides a standard deviation (sigma) of 4 ppm with a mode of 9 ppm; and (2) that peptides with molecular masses that differ by a factor of two may be independently fragmented by appropriately choosing the CID energy and the low-mass cut-off. Analyses of tryptic digests employed liquid chromatography (LC), deposition of the eluant on a target, and finally MALDI-TOF mass spectrometry. The mass fingerprint and the (partial) sequence of the tryptic peptides were matched to their precursor protein via database searches.
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Affiliation(s)
- Suzanne Ackloo
- MDS Sciex, 71 Four Valley Drive, Concord, Ontario L4K 4V8, Canada.
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15
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Ens W, Standing KG. Hybrid Quadrupole/Time‐of‐Flight Mass Spectrometers for Analysis of Biomolecules. Methods Enzymol 2005; 402:49-78. [PMID: 16401506 DOI: 10.1016/s0076-6879(05)02002-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
The basic principles of quadrupole/time-of-flight (TOF) mass spectrometers are discussed. These instruments can be used for ions produced either by electrospray ionization (ESI) or by matrix-assisted laser desorption ionization (MALDI). In the most common configuration, the functions of collisional cooling, parent ion selection, and collision-induced dissociation are carried out successively in three separate quadrupoles. The ions are then injected orthogonally into a TOF spectrometer, which makes the m/z measurement. Thus, these hybrid instruments benefit from the versatile ability of quadrupoles to carry out various tasks and from the high performance of TOF spectrometers in both simple mass spectrometry (MS) and tandem (MS/MS) modes. Significantly, collisions in the initial quadrupole decouple the instrument almost completely from the ion production process, so the quadrupole/TOF spectrometer is a stable device that is relatively insensitive to variations in the ion source.
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Affiliation(s)
- Werner Ens
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, Canada
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16
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Seifers DL, She YM, Harvey TL, Martin TJ, Haber S, Ens W, Standing KG, Louie R, Gordon DT. Biological and Molecular Variability Among High Plains virus Isolates. PLANT DISEASE 2004; 88:824-829. [PMID: 30812509 DOI: 10.1094/pdis.2004.88.8.824] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The High Plains virus (HPV), vectored by the wheat curl mite (WCM) (Aceria tosichella), causes a severe disease of maize (Zea mays) in the U. S. High Plains. In the present study, five HPV isolates from five states were separated from co-infecting Wheat streak mosaic virus and their molecular and biological variability studied. Molecular studies involved time-of-flight mass spectrometry (TOFMS) to determine amino acid sequence variability of the 32-kDa nucleoprotein (32 np) of the isolates. Biological studies involved testing the ability of the five HPV isolates to infect a maize line previously shown to have resistance. Inoculations of the HPV isolates were conducted using vascular puncture inoculation (VPI) and viruliferous WCM. TOFMS analyses demonstrated an 18-amino acid sequence in the isolates at the N-terminus of the 32 np, the presence of amino acid sequence differences among the isolates, and variability among amino acid sequences of the 32 np of some isolates. Three of the five HPV isolates infected the resistant maize inbred, B73, using VPI, and two of the same three HPV isolates infected this line using WCM inoculation, albeit low numbers of plants were infected by each technique.
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Affiliation(s)
- Dallas L Seifers
- Professor, Kansas State University, Agricultural Research Center-Hays 67601-9228
| | - Y-M She
- Department of Physics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Tom L Harvey
- Professor, Department of Entomology, Kansas State University, Manhattan 66506
| | - T J Martin
- Professor, Kansas State University, Agricultural Research Center-Hays
| | - S Haber
- Cereal Research Centre, Agriculture & Agri-Food Canada, Winnipeg, Manitoba, Canada
| | - W Ens
- Department of Physics, University of Manitoba, Winnipeg
| | - K G Standing
- Department of Physics, University of Manitoba, Winnipeg
| | - Raymond Louie
- United States Department of Agriculture-Agricultural Research Service
| | - D T Gordon
- Professor, Emeritus, Department of Plant Pathology, The Ohio State University, Wooster 44691
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17
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She YM, Seifers DL, Haber S, Ens W, Standing KG. Characterization of the Agent of “High Plains Disease”. J Biol Chem 2004; 279:488-94. [PMID: 14561770 DOI: 10.1074/jbc.m308506200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The "32-kDa" protein specifically associated with high plains disease was characterized by time-of-flight mass spectrometry, after the agent had been isolated in pure culture by "vascular puncture inoculation," a novel mechanical means of transmission. Two isolates from different geographic locations each consisted of a mixture of subpopulations that were highly homologous to an amino acid sequence derived from a nucleotide sequence (U60141) deposited in GenBank trade mark by the Nebraska group as "the probable N-protein of high plains virus." However, the U60141 sequence was found to be incomplete; de novo sequencing of peptides produced by proteolytic digestions of the 32-kDa band from an SDS-PAGE separation showed that an additional 18 amino acid residues were present at the N terminus. BLAST (basic local alignment search tool) examination of the sequence showed no significant homology with any protein in the databases, indicating that the infectious agent of high plains disease is likely a member of a hitherto unclassified virus group.
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Affiliation(s)
- Yi-Min She
- Department of Physics & Astronomy, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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18
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She YM, Narindrasorasak S, Yang S, Spitale N, Roberts EA, Sarkar B. Identification of Metal-binding Proteins in Human Hepatoma Lines by Immobilized Metal Affinity Chromatography and Mass Spectrometry. Mol Cell Proteomics 2003; 2:1306-18. [PMID: 14534351 DOI: 10.1074/mcp.m300080-mcp200] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The metalloproteome is defined as the set of proteins that have metal-binding capacity by being metalloproteins or having metal-binding sites. A different metalloproteome may exist for each metal. Mass spectrometric characterization of metalloproteomes provides valuable information relating to cellular disposition of metals physiologically and in metal-associated diseases. We examined the Cu and Zn metalloproteomes in three human hepatoma lines: Hep G2 and Mz-Hep-1, which retain many functional characteristics of normal human hepatocytes, and SK-Hep-1, which is poorly differentiated. Additionally we studied a single specimen of normal human liver and Hep G2 cells depleted in vitro of cellular copper. We used matrix-assisted laser desorption ionization and electrospray ionization quadrupole time-of-flight mass spectrometry to analyze peptide sequences of tryptic digests obtained by either in-gel digestion of metal-binding proteins or peptides on an immobilized metal affinity chromatography column loaded with either Cu or Zn. Mainly high abundance proteins were identified. Cu-binding proteins identified included enolase, albumin, transferrin, and alcohol dehydrogenase as well as certain intracellular chaperone proteins. The Cu metalloproteome was not identical to the Zn metalloproteome. Peptide binding experiments demonstrated that Cu coordination prefers the order of residues histidine > methionine > cysteine. Although the Cu metalloproteome was similar from line to line, subtle differences were apparent. Gel profiling showed more extensive variation in expression of annexin II in SK-Hep-1 and Mz-Hep-1 than in Hep G2 and normal liver tissue. Glycerylphosphorylethanolamine was identified as a post-translational modification at residue Glu-301 of elongation factor 1-alpha in Hep G2. Intracellular copper depletion was associated with loss of the glycerylphosphoryl side group. These findings suggest that post-translational modification could be affected by intracellular actions of copper. Comparison of the Cu and Zn metalloproteomes in Hep G2 with a published general proteome of Hep G2 disclosed little overlap (Seow, T. K., et al. (2001) Proteomics 1, 1249-1263). Proteins in the metalloproteomes of human hepatocytes can be identified by these methods. Variations in these metalloproteomes may have important physiological relevance.
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Affiliation(s)
- Yi-Min She
- Program in Structural Biology and Biochemistry, The Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
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19
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Zhang W, Krutchinsky AN, Chait BT. "De novo" peptide sequencing by MALDI-quadrupole-ion trap mass spectrometry: a preliminary study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2003; 14:1012-1021. [PMID: 12954169 DOI: 10.1016/s1044-0305(03)00346-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Collision-induced dissociation of singly charged peptide ions produced by resonant excitation in a matrix-assisted laser desorption/ionization (MALDI) ion trap mass spectrometer yields relatively low complexity MS/MS spectra that exhibit highly preferential fragmentation, typically occurring adjacent to aspartyl, glutamyl, and prolyl residues. Although these spectra have proven to be of considerable utility for database-driven protein identification, they have generally been considered to contain insufficient information to be useful for extensive de novo sequencing. Here, we report a procedure for de novo sequencing of peptides that uses MS/MS data generated by an in-house assembled MALDI-quadrupole-ion trap mass spectrometer (Krutchinsky, Kalkum, and Chait Anal. Chem. 2001, 73, 5066-5077). Peptide sequences of up 14 amino acid residues in length have been deduced from digests of proteins separated by SDS-PAGE. Key to the success of the current procedure is an ability to obtain MS/MS spectra with high signal-to-noise ratios and to efficiently detect relatively low abundance fragment ions that result from the less favorable fragmentation pathways. The high signal-to-noise ratio yields sufficiently accurate mass differences to allow unambiguous amino acid sequence assignments (with a few exceptions), and the efficient detection of low abundance fragment ions allows continuous reads through moderately long stretches of sequence. Finally, we show how the aforementioned preferential cleavage property of singly charged ions can be used to facilitate the de novo sequencing process.
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Affiliation(s)
- Wenzhu Zhang
- The Rockefeller University, New York, New York 10021, USA
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20
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Cooper B, Eckert D, Andon NL, Yates JR, Haynes PA. Investigative proteomics: identification of an unknown plant virus from infected plants using mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2003; 14:736-41. [PMID: 12837595 DOI: 10.1016/s1044-0305(03)00125-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We describe the identification of a previously uncharacterized plant virus that is capable of infecting Nicotiana spp. and Arabidopsis thaliana. Protein extracts were first prepared from leaf tissue of uninfected tobacco plants, and the proteins were visualized with two-dimensional electrophoresis (2-DE). Matching gels were then run using protein extracts of a tobacco plant infected with tobacco mosaic virus (TMV). After visual comparison, the proteins spots that were differentially expressed in infected plant tissues were cut from the gels and analyzed by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). Tandem mass spectrometry data of individual peptides was searched with SEQUEST. Using this approach we demonstrated a successful proof-of-concept experiment by identifying TMV proteins present in the total protein extract. The same procedure was then applied to tobacco plants infected with a laboratory viral isolate of unknown identity. Several of the differentially expressed protein spots were identified as proteins of potato virus X (PVX), thus successfully identifying the causative agent of the uncharacterized viral infection. We believe this demonstrates that HPLC-MS/MS can be used to successfully characterize unknown viruses in infected plants.
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Affiliation(s)
- Bret Cooper
- Plant Health Department, Torrey Mesa Research Institute of Syngenta, San Diego, California, USA.
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21
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Krokhin O, Li Y, Andonov A, Feldmann H, Flick R, Jones S, Stroeher U, Bastien N, Dasuri KVN, Cheng K, Simonsen JN, Perreault H, Wilkins J, Ens W, Plummer F, Standing KG. Mass spectrometric characterization of proteins from the SARS virus: a preliminary report. Mol Cell Proteomics 2003; 2:346-56. [PMID: 12775768 PMCID: PMC7780042 DOI: 10.1074/mcp.m300048-mcp200] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A new coronavirus has been implicated as the causative agent of severe acute respiratory syndrome (SARS). We have used convalescent sera from several SARS patients to detect proteins in the culture supernatants from cells exposed to lavage another SARS patient. The most prominent protein in the supernatant was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a approximately 46-kDa species. This was found to be a novel nucleocapsid protein that matched almost exactly one predicted by an open reading frame in the recently published nucleotide sequence of the same virus isolate (>96% coverage). A second viral protein corresponding to the predicted approximately 139-kDa spike glycoprotein has also been examined by MALDI-TOF MS (42% coverage). After peptide N-glycosidase F digestion, 12 glycosylation sites in this protein were confirmed. The sugars attached to four of the sites were also identified. These results suggest that the nucleocapsid protein is a major immunogen that may be useful for early diagnostics, and that the spike glycoprotein may present a particularly attractive target for prophylactic intervention in combating SARS.
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Affiliation(s)
- Oleg Krokhin
- Department of Physics, University of Manitoba, Winnipeg MB R3T 2N2, Canada
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22
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Liang XZ, Lee BTK, Wong SM. Covariation in the capsid protein of hibiscus chlorotic ringspot virus induced by serial passaging in a host that restricts movement leads to avirulence in its systemic host. J Virol 2002; 76:12320-4. [PMID: 12414972 PMCID: PMC136860 DOI: 10.1128/jvi.76.23.12320-12324.2002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hibiscus chlorotic ringspot virus (HCRSV) from naturally infected Hibiscus rosa-sinensis L. loses virulence in its experimental systemic host Hibiscus cannabinus L. (kenaf) after serial passages in a local lesion host Chenopodium quinoa. Here we report the genetic changes responsible for the loss of virulence at the molecular level. A remarkable covariation of eight site-specific amino acids was found in the HCRSV capsid protein (CP) after serial passages in C. quinoa: Val(49)-->Ile, Ile(95)-->Val, Lys(270)-->Arg, Gly(272)-->Asp, Tyr(274)-->His, Ala(311)-->Asp, Asp(334)-->Ala, and Ala(335)-->Thr. Covariation of at least three of the eight amino acids, Val(49), Ile(95), and Lys(270), caused the virus to become avirulent in kenaf. Interestingly, the nature of the covariation was consistent and reproducible at each serial passage. These data indicate that the nonsynonymous substitutions of amino acids in the HCRSV CP after serial passages in C. quinoa are not likely to be random events but may be due to host-associated positive selection or accelerated genetic drift. The observed interdependence among the three amino acids leading to avirulence in kenaf may have implications for structural or functional relationships in this virus-host interaction.
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Affiliation(s)
- Xiao-Zhen Liang
- Department of Biological Sciences, The National University of Singapore, Singapore 117543, Republic of Singapore
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23
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She YM, Wang GQ, Loboda A, Ens W, Standing KG, Burczynski FJ. Sequencing of rat liver cytosolic proteins by matrix-assisted laser desorption ionization-quadrupole time-of-flight mass spectrometry following electrophoretic separation and extraction. Anal Biochem 2002; 310:137-47. [PMID: 12423631 DOI: 10.1016/s0003-2697(02)00321-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A new technique is described that enables the direct determination of the complete or partial amino acid sequence of cytosolic proteins separated by gel electrophoresis and allows for the further observation of disease- or drug-induced posttranslational modifications. The procedure uses a two-phase extraction strategy (ethyl acetate/ammonium bicarbonate) for the efficient separation of proteins/peptides from an electrophoretic matrix and subsequent sequence analysis by matrix-assisted laser desorption ionization-quadrupole time-of-flight mass spectrometry. The method was tested using hepatocyte cytosolic proteins and compared to a complementary approach using direct solvent extraction from in-gel digests. Although the latter procedure identified the proteins, it did not enable complete amino acid sequence determination. In contrast, high sequence coverage was obtained using the peptide extraction procedure, without any apparent dependence on protein size. The technique minimized the chemically inconsistent modifications generated from in-gel digestion, thus aiding mass spectrometric interpretation and valid protein sequence identification.
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Affiliation(s)
- Yi-Min She
- Department of Physics and Astronomy, Faculty of Science, University of Manitoba, Man, R3T 2N2, Winnipeg, Canada
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24
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Abstract
Mass spectrometry plays an essential role in proteomics analysis and research. In recent years, it has been increasingly recognized that a key to proteomics using mass spectrometry relies not only on the instrument itself, but also on the analytical strategies and front-end sample-handling techniques. The advances of separations and mass spectrometry are having an increasing impact on the discovery of disease biomarkers and the understanding of cellular processes.
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Affiliation(s)
- Wenjun Mo
- Barnett Institute and Department of Chemistry, Northeastern University, 341 Mugar Hall, 360 Huntington Avenue, Boston, Massachusetts 02115, USA
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25
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Abstract
Proteome characterization using mass spectrometry is essential for the systematic investigation of biological systems and for the study of gene function. Recent advances in this multifaceted field have occurred in four general areas: protein and peptide separation methodologies; selective labeling chemistries for quantitative measurement of peptide and protein abundances; characterization of post-translational protein modifications; and instrumentation.
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Affiliation(s)
- T J Griffin
- Institute for Systems Biology, 4225 Roosevelt Way NE, Suite 200, Seattle, WA 98105, USA.
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26
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Bibliography. Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2001; 36:1164-1171. [PMID: 11747111 DOI: 10.1002/jms.97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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27
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Chernushevich IV, Loboda AV, Thomson BA. An introduction to quadrupole-time-of-flight mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2001; 36:849-865. [PMID: 11523084 DOI: 10.1002/jms.207] [Citation(s) in RCA: 388] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A brief introduction is presented to the basic principles and application of a quadrupole-time-of-flight (TOF) tandem mass spectrometer. The main features of reflecting TOF instruments with orthogonal injection of ions are discussed. Their operation and performance are compared with those of triple quadrupoles with electrospray ionization and matrix-assisted laser desorption/ionization (MALDI) TOF mass spectrometers. Examples and recommendations are provided for all major operational modes: mass spectrometry (MS) and tandem MS (MS/MS), precursor ion scans and studies of non-covalent complexes. Basic algorithms for liquid chromatography/MS/MS automation are discussed and illustrated by two applications.
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28
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Fenselau C, Demirev PA. Characterization of intact microorganisms by MALDI mass spectrometry. MASS SPECTROMETRY REVIEWS 2001; 20:157-171. [PMID: 11835304 DOI: 10.1002/mas.10004] [Citation(s) in RCA: 537] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The application of MALDI mass spectrometry to desorb protein biomarkers from intact viruses, bacteria, fungus, and spores is the focus of this review. Instrumentation, sample collection, sample preparation, and algorithms for data analysis are summarized. Optimally these analyses should be carried out in less than five minutes. Successful applications are discussed from biotechnology, cell biology, and the pharmaceutical industry.
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Affiliation(s)
- C Fenselau
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
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