1
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Kashina AS, Yates Iii JR. Identification of Arginylated Proteins by Mass Spectrometry. Methods Mol Biol 2023; 2620:139-152. [PMID: 37010760 DOI: 10.1007/978-1-0716-2942-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Here, we describe the method for the identification of arginylated proteins by mass spectrometry. This method has been originally applied to the identification of N-terminally added Arg on proteins and peptides and then expanded to the side chain modification which has been recently described by our groups. The key steps in this method include the use of the mass spectrometry instruments that can identify peptides with very high pass accuracy (Orbitrap) and apply stringent mass cutoffs during automated data analysis, followed by manual validation of the identified spectra. These methods can be used with both complex and purified protein samples and, to date, constitute the only reliable way to confirm arginylation at a particular site on a protein or peptide.
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Affiliation(s)
- Anna S Kashina
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - John R Yates Iii
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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2
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Kashina AS, Yates Iii JR. Analysis of Arginylated Peptides by Subtractive Edman Degradation. Methods Mol Biol 2023; 2620:153-155. [PMID: 37010761 DOI: 10.1007/978-1-0716-2942-0_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
During the early studies of N-terminal arginylation, Edman degradation was widely used to identify N-terminally added Arg on protein substrates. This old method is reliable, but highly depends on the purity and abundance of samples and can become misleading unless a highly purified highly arginylated protein can be obtained. Here, we report a mass spectrometry-based method that utilizes Edman degradation chemistry to identify arginylation in more complex and less abundant protein samples. This method can also apply to the analysis of other posttranslational modifications.
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Affiliation(s)
- Anna S Kashina
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - John R Yates Iii
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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3
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Shah SH, Schiapparelli LM, Ma Y, Yokota S, Atkins M, Xia X, Cameron EG, Huang T, Saturday S, Sun CB, Knasel C, Blackshaw S, Yates Iii JR, Cline HT, Goldberg JL. Quantitative transportomics identifies Kif5a as a major regulator of neurodegeneration. eLife 2022; 11:68148. [PMID: 35259089 PMCID: PMC8947766 DOI: 10.7554/elife.68148] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 03/07/2022] [Indexed: 11/29/2022] Open
Abstract
Many neurons in the adult central nervous system, including retinal ganglion cells (RGCs), degenerate and die after injury. Early axon protein and organelle trafficking failure is a key component in many neurodegenerative disorders yet changes to axoplasmic transport in disease models have not been quantified. We analyzed early changes in the protein ‘transportome’ from RGC somas to their axons after optic nerve injury and identified transport failure of an anterograde motor protein Kif5a early in RGC degeneration. We demonstrated that manipulating Kif5a expression affects anterograde mitochondrial trafficking in RGCs and characterized axon transport in Kif5a knockout mice to identify proteins whose axon localization was Kif5a-dependent. Finally, we found that knockout of Kif5a in RGCs resulted in progressive RGC degeneration in the absence of injury. Together with expression data localizing Kif5a to human RGCs, these data identify Kif5a transport failure as a cause of RGC neurodegeneration and point to a mechanism for future therapeutics.
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Affiliation(s)
- Sahil H Shah
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, United States
| | | | - Yuanhui Ma
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States
| | - Satoshi Yokota
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, United States
| | - Melissa Atkins
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, United States
| | - Xin Xia
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, United States
| | - Evan G Cameron
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, United States
| | - Thanh Huang
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Sarah Saturday
- Neuroscience Department, The Scripps Research Institute, La Jolla, United States
| | - Catalin B Sun
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, United States
| | - Cara Knasel
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, United States
| | - Seth Blackshaw
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States
| | - John R Yates Iii
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States
| | - Hollis T Cline
- Neuroscience Department, The Scripps Research Institute, La Jolla, United States
| | - Jeffrey L Goldberg
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, United States
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4
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Chen M, Kuhle B, Diedrich J, Liu Z, Moresco JJ, Yates Iii JR, Pan T, Yang XL. Cross-editing by a tRNA synthetase allows vertebrates to abundantly express mischargeable tRNA without causing mistranslation. Nucleic Acids Res 2020; 48:6445-6457. [PMID: 32484512 PMCID: PMC7337962 DOI: 10.1093/nar/gkaa469] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/19/2020] [Accepted: 05/31/2020] [Indexed: 01/18/2023] Open
Abstract
The accuracy in pairing tRNAs with correct amino acids by aminoacyl-tRNA synthetases (aaRSs) dictates the fidelity of translation. To ensure fidelity, multiple aaRSs developed editing functions that remove a wrong amino acid from tRNA before it reaches the ribosome. However, no specific mechanism within an aaRS is known to handle the scenario where a cognate amino acid is mischarged onto a wrong tRNA, as exemplified by AlaRS mischarging alanine to G4:U69-containing tRNAThr. Here, we report that the mischargeable G4:U69-containing tRNAThr are strictly conserved in vertebrates and are ubiquitously and abundantly expressed in mammalian cells and tissues. Although these tRNAs are efficiently mischarged, no corresponding Thr-to-Ala mistranslation is detectable. Mistranslation is prevented by a robust proofreading activity of ThrRS towards Ala-tRNAThr. Therefore, while wrong amino acids are corrected within an aaRS, a wrong tRNA is handled in trans by an aaRS cognate to the mischarged tRNA species. Interestingly, although Ala-tRNAThr mischarging is not known to occur in bacteria, Escherichia coli ThrRS also possesses robust cross-editing ability. We propose that the cross-editing activity of ThrRS is evolutionarily conserved and that this intrinsic activity allows G4:U69-containing tRNAThr to emerge and be preserved in vertebrates to have alternative functions without compromising translational fidelity.
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Affiliation(s)
- Meirong Chen
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA.,College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Bernhard Kuhle
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jolene Diedrich
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ze Liu
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - James J Moresco
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates Iii
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Xiang-Lei Yang
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
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5
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Antonucci L, Di Magno L, D'Amico D, Manni S, Serrao SM, Di Pastena F, Bordone R, Yurtsever ZN, Caimano M, Petroni M, Giorgi A, Schininà ME, Yates Iii JR, Di Marcotullio L, De Smaele E, Checquolo S, Capalbo C, Agostinelli E, Maroder M, Coni S, Canettieri G. Mitogen-activated kinase kinase kinase 1 inhibits hedgehog signaling and medulloblastoma growth through GLI1 phosphorylation. Int J Oncol 2018; 54:505-514. [PMID: 30483764 PMCID: PMC6317670 DOI: 10.3892/ijo.2018.4638] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/09/2018] [Indexed: 12/15/2022] Open
Abstract
The aberrant activation of hedgehog (HH) signaling is a leading cause of the development of medulloblastoma, a pediatric tumor of the cerebellum. The FDA-approved HH inhibitor, Vismodegib, which targets the transmembrane transducer SMO, has shown limited efficacy in patients with medulloblastoma, due to compensatory mechanisms that maintain an active HH-GLI signaling status. Thus, the identification of novel actionable mechanisms, directly affecting the activity of the HH-regulated GLI transcription factors is an important goal for these malignancies. In this study, using gene expression and reporter assays, combined with biochemical and cellular analyses, we demonstrate that mitogen-activated kinase kinase kinase 1 (MEKK1), the most upstream kinase of the mitogen-activated protein kinase (MAPK) phosphorylation modules, suppresses HH signaling by associating and phosphorylating GLI1, the most potent HH-regulated transcription factor. Phosphorylation occurred at multiple residues in the C-terminal region of GLI1 and was followed by an increased association with the cytoplasmic proteins 14-3-3. Of note, the enforced expression of MEKK1 or the exposure of medulloblastoma cells to the MEKK1 activator, Nocodazole, resulted in a marked inhibitory effect on GLI1 activity and tumor cell proliferation and viability. Taken together, the results of this study shed light on a novel regulatory mechanism of HH signaling, with potentially relevant implications in cancer therapy.
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Affiliation(s)
- Laura Antonucci
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Laura Di Magno
- Center for Life Nano Science at Sapienza, Italian Institute of Technology, 00161 Rome, Italy
| | - Davide D'Amico
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Simona Manni
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Silvia Maria Serrao
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Fiorella Di Pastena
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 04100 Latina, Italy
| | - Rosa Bordone
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Zuleyha Nihan Yurtsever
- Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University of Rome, 00161 Rome, Italy
| | - Miriam Caimano
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Marialaura Petroni
- Center for Life Nano Science at Sapienza, Italian Institute of Technology, 00161 Rome, Italy
| | - Alessandra Giorgi
- Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University of Rome, 00161 Rome, Italy
| | - Maria Eugenia Schininà
- Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University of Rome, 00161 Rome, Italy
| | - John R Yates Iii
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lucia Di Marcotullio
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Enrico De Smaele
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Saula Checquolo
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 04100 Latina, Italy
| | - Carlo Capalbo
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Enzo Agostinelli
- Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University of Rome, 00161 Rome, Italy
| | - Marella Maroder
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 04100 Latina, Italy
| | - Sonia Coni
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Gianluca Canettieri
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
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6
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Seixas A, Alzugaray MF, Tirloni L, Parizi LF, Pinto AFM, Githaka NW, Konnai S, Ohashi K, Yates Iii JR, Termignoni C, da Silva Vaz I. Expression profile of Rhipicephalus microplus vitellogenin receptor during oogenesis. Ticks Tick Borne Dis 2017; 9:72-81. [PMID: 29054547 DOI: 10.1016/j.ttbdis.2017.10.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/06/2017] [Accepted: 10/06/2017] [Indexed: 12/31/2022]
Abstract
The vitellogenin receptor (VgR), which belongs to the low-density lipoprotein receptors (LDLR) family, regulates the absorption of yolk protein accumulated in developing oocytes during oogenesis. In the present study, the full sequence of Rhipicephalus microplus VgR (RmVgR) and the partial sequence of Rhipicephalus appendiculatus VgR (RaVgR) ORF were determined and cloned. The RmVgR amino acid sequence contains the five highly conserved structural motifs characteristic of LDLR superfamily members, the same overall structure as observed in other species. Phylogenetic analysis separated VgRs in two major groups, corresponding to receptors from acarines and insects. Consistent with observations from other arthropods, RmVgR was specifically expressed in the ovarian tissue and its peak of expression occurs in females that are detaching from the host. Silencing with RmVgR dsRNA reduced VgR expression, which resulted in reduced fertility, evidenced by a decrease in the number of larvae. The present study confirms RmVgR is a specific receptor involved in yolk protein uptake and oocyte maturation in R. microplus, playing an important role in tick reproduction.
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Affiliation(s)
- Adriana Seixas
- Departamento de Farmacociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Rua Sarmento Leite, 245, Porto Alegre, RS, 90050-170, Brazil.
| | - María Fernanda Alzugaray
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Prédio 43421, Campus do Vale, Caixa Postal 15005, Porto Alegre, RS, 91501-970, Brazil; Departamento de Microbiología, Facultad de Veterinaria, Universidad de la Republica, Alberto Lasplaces 1550 a 1620, Montevideo, Código Postal 11600, Uruguay.
| | - Lucas Tirloni
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Prédio 43421, Campus do Vale, Caixa Postal 15005, Porto Alegre, RS, 91501-970, Brazil.
| | - Luis Fernando Parizi
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Prédio 43421, Campus do Vale, Caixa Postal 15005, Porto Alegre, RS, 91501-970, Brazil.
| | - Antonio Frederico Michel Pinto
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 90037 USA; Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, 90619-900, Brazil
| | - Naftaly Wang'ombe Githaka
- Tick Unit, Animal and Human Health Program, International Livestock Research Institute, P.O. Box 30709-00100, Nairobi, Kenya
| | - Satoru Konnai
- Department of Disease Control, Laboratory of Infectious Diseases, Graduate School of Veterinary Medicine, Hokkaido University, 060-0818, Sapporo, Hokkaido, Japan.
| | - Kazuhiko Ohashi
- Department of Disease Control, Laboratory of Infectious Diseases, Graduate School of Veterinary Medicine, Hokkaido University, 060-0818, Sapporo, Hokkaido, Japan.
| | - John R Yates Iii
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 90037 USA.
| | - Carlos Termignoni
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Prédio 43421, Campus do Vale, Caixa Postal 15005, Porto Alegre, RS, 91501-970, Brazil; Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos, 2600, Porto Alegre, RS, 90035-003, Brazil.
| | - Itabajara da Silva Vaz
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Prédio 43421, Campus do Vale, Caixa Postal 15005, Porto Alegre, RS, 91501-970, Brazil; Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9090, Porto Alegre, RS, 91540-000, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, Brazil.
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7
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Di Maggio LS, Tirloni L, Pinto AFM, Diedrich JK, Yates Iii JR, Benavides U, Carmona C, da Silva Vaz I, Berasain P. Across intra-mammalian stages of the liver f luke Fasciola hepatica: a proteomic study. Sci Rep 2016; 6:32796. [PMID: 27600774 PMCID: PMC5013449 DOI: 10.1038/srep32796] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/15/2016] [Indexed: 02/07/2023] Open
Abstract
Fasciola hepatica is the agent of fasciolosis, a foodborne zoonosis that affects livestock production and human health. Although flukicidal drugs are available, re-infection and expanding resistance to triclabendazole demand new control strategies. Understanding the molecular mechanisms underlying the complex interaction with the mammalian host could provide relevant clues, aiding the search for novel targets in diagnosis and control of fasciolosis. Parasite survival in the mammalian host is mediated by parasite compounds released during infection, known as excretory/secretory (E/S) products. E/S products are thought to protect parasites from host responses, allowing them to survive for a long period in the vertebrate host. This work provides in-depth proteomic analysis of F. hepatica intra-mammalian stages, and represents the largest number of proteins identified to date for this species. Functional classification revealed the presence of proteins involved in different biological processes, many of which represent original findings for this organism and are important for parasite survival within the host. These results could lead to a better comprehension of host-parasite relationships, and contribute to the development of drugs or vaccines against this parasite.
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Affiliation(s)
- Lucía Sánchez Di Maggio
- Unidad de Biología Parasitaria, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay.,Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lucas Tirloni
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Antonio F M Pinto
- Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Department of Chemical Physiology, The Scripps Research Institute, CA, Unites States of America
| | - Jolene K Diedrich
- Department of Chemical Physiology, The Scripps Research Institute, CA, Unites States of America
| | - John R Yates Iii
- Department of Chemical Physiology, The Scripps Research Institute, CA, Unites States of America
| | - Uruguaysito Benavides
- Departamento de Inmunología, Facultad de Veterinaria, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay
| | - Carlos Carmona
- Unidad de Biología Parasitaria, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay
| | - Itabajara da Silva Vaz
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Patricia Berasain
- Unidad de Biología Parasitaria, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay
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8
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Villela AD, Eichler P, Pinto AFM, Rodrigues-Junior V, Yates Iii JR, Bizarro CV, Basso LA, Santos DS. Gene replacement and quantitative mass spectrometry approaches validate guanosine monophosphate synthetase as essential for Mycobacterium tuberculosis growth. Biochem Biophys Rep 2015; 4:277-282. [PMID: 29124214 PMCID: PMC5669397 DOI: 10.1016/j.bbrep.2015.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/05/2015] [Accepted: 10/07/2015] [Indexed: 01/10/2023] Open
Abstract
Guanosine monophosphate synthetase (GMPS), encoded by guaA gene, is a key enzyme for guanine nucleotide biosynthesis in Mycobacterium tuberculosis. The guaA gene from several bacterial pathogens has been shown to be involved in virulence; however, no information about the physiological effect of direct guaA deletion in M. tuberculosis has been described so far. Here, we demonstrated that the guaA gene is essential for M. tuberculosis H37Rv growth. The lethal phenotype of guaA gene disruption was avoided by insertion of a copy of the ortholog gene from Mycobacterium smegmatis, indicating that this GMPS protein is functional in M. tuberculosis. Protein validation of the guaA essentiality observed by PCR was approached by shotgun proteomic analysis. A quantitative method was performed to evaluate protein expression levels, and to check the origin of common and unique peptides from M. tuberculosis and M. smegmatis GMPS proteins. These results validate GMPS as a molecular target for drug design against M. tuberculosis, and GMPS inhibitors might prove to be useful for future development of new drugs to treat human tuberculosis. The guaA gene is essential for M. tuberculosis H37Rv growth. The lethal phenotype of guaA gene disruption was avoided by the ortholog gene from M. smegmatis. Multiplexed LC–MS/MS analysis was performed to validate protein expression levels. The guaA essentiality was confirmed by gene replacement and quantitative mass spectrometry.
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Affiliation(s)
- Anne Drumond Villela
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul - PUCRS, Avenida Ipiranga, 6681, TecnoPUC 92A, 90619-900 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Medicina e Ciências da Saúde, PUCRS, Avenida Ipiranga, 6690, Hospital São Lucas, 90619-900 Porto Alegre, RS, Brazil
| | - Paula Eichler
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul - PUCRS, Avenida Ipiranga, 6681, TecnoPUC 92A, 90619-900 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Avenida Ipiranga, 6681, Prédio 12A, 90619-900 Porto Alegre, RS, Brazil
| | - Antonio Frederico Michel Pinto
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul - PUCRS, Avenida Ipiranga, 6681, TecnoPUC 92A, 90619-900 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Avenida Ipiranga, 6681, Prédio 12A, 90619-900 Porto Alegre, RS, Brazil
| | - Valnês Rodrigues-Junior
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul - PUCRS, Avenida Ipiranga, 6681, TecnoPUC 92A, 90619-900 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Medicina e Ciências da Saúde, PUCRS, Avenida Ipiranga, 6690, Hospital São Lucas, 90619-900 Porto Alegre, RS, Brazil
| | - John R Yates Iii
- Department of Chemical Physiology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA 92037, USA
| | - Cristiano Valim Bizarro
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul - PUCRS, Avenida Ipiranga, 6681, TecnoPUC 92A, 90619-900 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Avenida Ipiranga, 6681, Prédio 12A, 90619-900 Porto Alegre, RS, Brazil
| | - Luiz Augusto Basso
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul - PUCRS, Avenida Ipiranga, 6681, TecnoPUC 92A, 90619-900 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Medicina e Ciências da Saúde, PUCRS, Avenida Ipiranga, 6690, Hospital São Lucas, 90619-900 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Avenida Ipiranga, 6681, Prédio 12A, 90619-900 Porto Alegre, RS, Brazil
| | - Diógenes Santiago Santos
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul - PUCRS, Avenida Ipiranga, 6681, TecnoPUC 92A, 90619-900 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Avenida Ipiranga, 6681, Prédio 12A, 90619-900 Porto Alegre, RS, Brazil
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9
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Abstract
PatternLab for proteomics is a one-stop shop computational environment for analyzing shotgun proteomic data. Its modules provide means to pinpoint proteins/peptides that are differentially expressed and those that are unique to a state. It can also cluster the ones that share similar expression profiles in time-course experiments, as well as help in interpreting results according to Gene Ontology. PatternLab is user-friendly, simple, and provides a graphical user interface.
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Affiliation(s)
- Paulo C Carvalho
- Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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Usaite R, Wohlschlegel J, Venable JD, Park SK, Nielsen J, Olsson L, Yates Iii JR. Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression saccharomyces cerevisiae strains: the comparison of two quantitative methods. J Proteome Res 2008; 7:266-75. [PMID: 18173223 DOI: 10.1021/pr700580m] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The quantitative proteomic analysis of complex protein mixtures is emerging as a technically challenging but viable systems-level approach for studying cellular function. This study presents a large-scale comparative analysis of protein abundances from yeast protein lysates derived from both wild-type yeast and yeast strains lacking key components of the Snf1 kinase complex. Four different strains were grown under well-controlled chemostat conditions. Multidimensional protein identification technology followed by quantitation using either spectral counting or stable isotope labeling approaches was used to identify relative changes in the protein expression levels between the strains. A total of 2388 proteins were relatively quantified, and more than 350 proteins were found to have significantly different expression levels between the two strains of comparison when using the stable isotope labeling strategy. The stable isotope labeling based quantitative approach was found to be highly reproducible among biological replicates when complex protein mixtures containing small expression changes were analyzed. Where poor correlation between stable isotope labeling and spectral counting was found, the major reason behind the discrepancy was the lack of reproducible sampling for proteins with low spectral counts. The functional categorization of the relative protein expression differences that occur in Snf1-deficient strains uncovers a wide range of biological processes regulated by this important cellular kinase.
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Affiliation(s)
- Renata Usaite
- BioCentrum-DTU, Technical University of Denmark, Kgs. Lyngby, Denmark
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