1
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Martins AMA, D M Santos M, C Camillo-Andrade A, Leite AL, Souza JS, Sánchez S, Muotri AR, Carvalho PC, Yates JR. Integrating DIA Single-Cell Proteomics Data with the DiagnoMass Proteomic Hub for Biological Insights. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39258941 DOI: 10.1021/jasms.4c00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Single-cell proteomics has emerged as a powerful technology for unraveling the complexities of cellular heterogeneity, enabling insights into individual cell functions and pathologies. One of the primary challenges in single-cell proteomics is data generation, where low mass spectral signals often preclude the triggering of MS2 events. This challenge is addressed by Data Independent Acquisition (DIA), a data acquisition strategy that does not depend on peptide ion isotopic signatures to generate an MS2 event. In this study, we present data generated from the integration of DIA single-cell proteomics with a version of the DiagnoMass Proteomic Hub that was adapted to handle DIA data. DiagnoMass employs a hierarchical clustering methodology that enables the identification of tandem mass spectral clusters that are discriminative of biological conditions, thereby reducing the reliance on search engine biases for identifications. Nevertheless, a search engine (in this work, DIA-NN) can be integrated with DiagnoMass for spectral annotation. We used single-cell proteomic data from iPSC-derived neuroprogenitor cell cultures as a test study of this integrated approach. We were able to differentiate between control and Rett Syndrome patient cells to discern the proteomic variances potentially contributing to the disease's pathology. Our research confirms that the DiagnoMass-DIA synergy significantly enhances the identification of discriminative proteomic signatures, highlighting critical biological variations such as the presence of unique spectra that could be related to Rett Syndrome pathology.
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Affiliation(s)
- Aline M A Martins
- Departments of Molecular Medicine and Neurobiology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR302, La Jolla, California 92037, United States
| | - Marlon D M Santos
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, R. Professor Algacyr Munhoz Mader, 3775 Curitiba, PR, Brazil
- Analytical Biochemistry and Proteomics Unit, Instituto de Investigaciones Biológicas Clemente Estable, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
| | - Amanda C Camillo-Andrade
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, R. Professor Algacyr Munhoz Mader, 3775 Curitiba, PR, Brazil
| | - Aline Lima Leite
- Bruker Daltonics Corporation, USA, 40 Manning Rd, Billerica, Massachusetts 01821, United States
| | - Janaina Sena Souza
- Department of Pediatrics, Sanford Consortium for Regenerative Medicine, UCSD, 2880 Torrey Pines Scenic Dr, La Jolla, California 92037, United States
| | - Sandra Sánchez
- Department of Pediatrics, Sanford Consortium for Regenerative Medicine, UCSD, 2880 Torrey Pines Scenic Dr, La Jolla, California 92037, United States
| | - Alysson R Muotri
- Department of Pediatrics, Sanford Consortium for Regenerative Medicine, UCSD, 2880 Torrey Pines Scenic Dr, La Jolla, California 92037, United States
| | - Paulo Costa Carvalho
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, R. Professor Algacyr Munhoz Mader, 3775 Curitiba, PR, Brazil
| | - John R Yates
- Departments of Molecular Medicine and Neurobiology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR302, La Jolla, California 92037, United States
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2
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Reis-de-Oliveira G, Carregari VC, Sousa GRDRD, Martins-de-Souza D. OmicScope unravels systems-level insights from quantitative proteomics data. Nat Commun 2024; 15:6510. [PMID: 39095347 PMCID: PMC11297029 DOI: 10.1038/s41467-024-50875-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 07/13/2024] [Indexed: 08/04/2024] Open
Abstract
Shotgun proteomics analysis presents multifaceted challenges, demanding diverse tool integration for insights. Addressing this complexity, OmicScope emerges as an innovative solution for quantitative proteomics data analysis. Engineered to handle various data formats, it performs data pre-processing - including joining replicates, normalization, data imputation - and conducts differential proteomics analysis for both static and longitudinal experimental designs. Empowered by Enrichr with over 224 databases, OmicScope performs Over Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA). Additionally, its Nebula module facilitates meta-analysis from independent datasets, providing a systems biology approach for enriched insights. Complete with a data visualization toolkit and accessible as Python package and a web application, OmicScope democratizes proteomics analysis, offering an efficient and high-quality pipeline for researchers.
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Affiliation(s)
- Guilherme Reis-de-Oliveira
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil.
- Research Center, Boldrini Children's Hospital, Campinas, SP, Brazil.
| | - Victor Corasolla Carregari
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil.
- University of Campinas (UNICAMP), Campinas, SP, Brazil.
- Instituto Nacional de Biomarcadores Em Neuropsiquiatria (INBION) Conselho Nacional de Desenvolvimento Científico E Tecnológico, São Paulo, Brazil.
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, SP, Brazil.
- D'Or Institute for Research and Education (IDOR), São Paulo, Brazil.
- INCT in Modelling Human Complex Diseases with 3D Platforms (Model3D), São Paulo, Brazil.
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3
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Kurt L, Clasen MA, Biembengut ÍV, Ruwolt M, Liu F, Gozzo FC, Lima DB, Carvalho PC. RawVegetable 2.0: Refining XL-MS Data Acquisition through Enhanced Quality Control. J Proteome Res 2024; 23:3141-3148. [PMID: 38301217 PMCID: PMC11301677 DOI: 10.1021/acs.jproteome.3c00791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/03/2024]
Abstract
We present RawVegetable 2.0, a software tailored for assessing mass spectrometry data quality and fine-tuned for cross-linking mass spectrometry (XL-MS) applications. Building upon the capabilities of its predecessor, RawVegetable 2.0 introduces four main modules, each providing distinct and new functionalities: 1) Pair Finder, which identifies ion doublets characteristic of cleavable cross-linking experiments; 2) Diagnostic Peak Finder, which locates potential reporter ions associated with a specific cross-linker; 3) Precursor Signal Ratio, which computes the ratio between precursor intensity and the total signal in an MS/MS scan; and 4) Xrea, which evaluates spectral quality by analyzing the heterogeneity of peak intensities within a spectrum. These modules collectively streamline the process of optimizing mass spectrometry data acquisition for both Proteomics and XL-MS experiments. RawVegetable 2.0, along with a comprehensive tutorial is freely accessible for academic use at: http://patternlabforproteomics.org/rawvegetable2.
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Affiliation(s)
- Louise
Ulrich Kurt
- Laboratory
for Structural and Computational Proteomics, Carlos Chagas Institute - Fiocruz Parana, Curitiba, Parana 81310-020, Brazil
| | - Milan Avila Clasen
- Laboratory
for Structural and Computational Proteomics, Carlos Chagas Institute - Fiocruz Parana, Curitiba, Parana 81310-020, Brazil
| | - Ísis Venturi Biembengut
- Laboratory
for Structural and Computational Proteomics, Carlos Chagas Institute - Fiocruz Parana, Curitiba, Parana 81310-020, Brazil
| | - Max Ruwolt
- Department
of Chemical Biology, Leibniz - Forschungsinstitut
für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Fan Liu
- Department
of Chemical Biology, Leibniz - Forschungsinstitut
für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Fabio César Gozzo
- Dalton
Mass Spectrometry Laboratory, Unicamp, Campinas, Sao Paulo 13083-970, Brazil
| | - Diogo Borges Lima
- Department
of Chemical Biology, Leibniz - Forschungsinstitut
für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Paulo Costa Carvalho
- Laboratory
for Structural and Computational Proteomics, Carlos Chagas Institute - Fiocruz Parana, Curitiba, Parana 81310-020, Brazil
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4
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Gomes JGDS, Brandão LC, Pinheiro DP, Pontes LQ, Carneiro RF, Quintela BCSF, Marinho ACM, Furtado GP, Rocha BAM. Kinetics characterization of a low immunogenic recombinant l-asparaginase from Phaseolus vulgaris with cytotoxic activity against leukemia cells. Int J Biol Macromol 2024; 275:133731. [PMID: 38986978 DOI: 10.1016/j.ijbiomac.2024.133731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/15/2024] [Accepted: 07/06/2024] [Indexed: 07/12/2024]
Abstract
l-asparaginases play a crucial role in the treatment of acute lymphoblastic leukemia (ALL), a type of cancer that mostly affects children and teenagers. However, it is common for these molecules to cause adverse reactions during treatment. These downsides ignite the search for novel asparaginases to mitigate these problems. Thus, this work aimed to produce and characterize a recombinant asparaginase from Phaseolus vulgaris (Asp-P). In this study, Asp-P was expressed in Escherichia coli with high yields and optimum activity at 40 °C, pH 9.0. The enzyme Km and Vmax values were 7.05 mM and 1027 U/mg, respectively. Asp-P is specific for l-asparagine, showing no activity against l-glutamine and other amino acids. The enzyme showed a higher cytotoxic effect against Raji than K562 cell lines, but only at high concentrations. In silico analysis indicated that Asp-P has lower immunogenicity than a commercial enzyme. Asp-P induced biofilm formation by Candida sp. due to sublethal dose, showing an underexplored potential of asparaginases. The absence of glutaminase activity, lower immunogenicity and optimal activity similar to physiological temperature conditions are characteristics that indicate Asp-P as a potential new commercial enzyme in the treatment of ALL and its underexplored application in the treatment of other diseases.
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Affiliation(s)
| | - Larisse Cadeira Brandão
- Departament of Fishing Engineering, Federal University of Ceara, Fortaleza, Brazil; Oswaldo Cruz Foundation - Fiocruz Ceara, Eusebio, Ceara, Brazil
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5
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Camillo-Andrade AC, Santos MDM, Nuevo PS, Lajas ABL, Sales LA, Leyva A, Fischer JSG, Duran R, Carvalho PC. Intra-Individual Paired Mass Spectrometry Dataset for Decoding Solar-Induced Proteomic Changes in Facial Skin. Sci Data 2024; 11:441. [PMID: 38702328 PMCID: PMC11068864 DOI: 10.1038/s41597-024-03231-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 04/04/2024] [Indexed: 05/06/2024] Open
Abstract
Photoaging is the premature aging of the skin caused by prolonged exposure to solar radiation. The visual alterations manifest as wrinkles, reduced skin elasticity, uneven skin tone, as well as other signs that surpass the expected outcomes of natural aging. Beyond these surface changes, there is a complex interplay of molecular alterations, encompassing shifts in cellular function, DNA damage, and protein composition disruptions. This data descriptor introduces a unique dataset derived from ten individuals, each with a minimum of 18 years of professional experience as a driver, who are asymmetrically and chronically exposed to solar radiation due to their driving orientation. Skin samples were independently collected from each side of the face using a microdermabrasion-like procedure and analyzed on an Exploris 240 mass spectrometer. Our adapted proteomic statistical framework leverages the sample pairing to provide robust insights. This dataset delves into the molecular differences in exposed skin and serves as a foundational resource for interdisciplinary research in photodermatology, targeted skincare treatments, and computational modelling of skin health.
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Affiliation(s)
- Amanda C Camillo-Andrade
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Curitiba, Paraná, Brazil
- Analytical Biochemistry and Proteomics Unit, Instituto de Investigaciones Biológicas Clemente Estable, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Asthetics and Cosmetics, Positivo University, Curitiba, Paraná, Brazil
| | - Marlon D M Santos
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Curitiba, Paraná, Brazil
- Analytical Biochemistry and Proteomics Unit, Instituto de Investigaciones Biológicas Clemente Estable, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Patrícia S Nuevo
- Asthetics and Cosmetics, Positivo University, Curitiba, Paraná, Brazil
| | - Ana B L Lajas
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Curitiba, Paraná, Brazil
| | - Lucas A Sales
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Curitiba, Paraná, Brazil
| | - Alejandro Leyva
- Analytical Biochemistry and Proteomics Unit, Instituto de Investigaciones Biológicas Clemente Estable, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Juliana S G Fischer
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Curitiba, Paraná, Brazil
| | - Rosario Duran
- Analytical Biochemistry and Proteomics Unit, Instituto de Investigaciones Biológicas Clemente Estable, Institut Pasteur de Montevideo, Montevideo, Uruguay.
| | - Paulo C Carvalho
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Curitiba, Paraná, Brazil.
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6
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D M Santos M, C Camillo-Andrade A, Rodriguez A, Durán R. A Module for Analyzing Interactomes via APEX-MS Integrated into PatternLab for Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1055-1058. [PMID: 38606722 DOI: 10.1021/jasms.3c00382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Proximity labeling techniques, such as APEX-MS, provide valuable insights into proximal interactome mapping; however, the verification of biotinylated peptides is not straightforward. With this as motivation, we present a new module integrated into PatternLab for proteomics to enable APEX-MS data interpretation by targeting diagnostic fragment ions associated with APEX modifications. We reanalyzed a previously published APEX-MS data set and report a significant number of biotinylated peptides and, consequently, a confident set of proximal proteins. As the module is part of the widely adopted PatternLab for proteomics software suite, it offers users a comprehensive, easy, and integrated solution for data analysis. Given the broad utility of the APEX-MS technique in various biological contexts, we anticipate that our module will be a valuable asset to researchers, facilitating and enhancing interactome studies. PatternLab's APEX, including a usage protocol, is available at http://patternlabforproteomics.org/apex.
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Affiliation(s)
- Marlon D M Santos
- Analytical Biochemistry and Proteomics Unit, Instituto de Investigaciones Biológicas Clemente Estable, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz-Paraná, R. Professor Algacyr Munhoz Mader, 3775 Curitiba, PR, Brazil
| | - Amanda C Camillo-Andrade
- Analytical Biochemistry and Proteomics Unit, Instituto de Investigaciones Biológicas Clemente Estable, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz-Paraná, R. Professor Algacyr Munhoz Mader, 3775 Curitiba, PR, Brazil
| | - Azalia Rodriguez
- Analytical Biochemistry and Proteomics Unit, Instituto de Investigaciones Biológicas Clemente Estable, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
- Facultad de Química, Universidad de la República, Av. Gral. Flores 2124, 11800 Montevideo, Uruguay
| | - Rosario Durán
- Analytical Biochemistry and Proteomics Unit, Instituto de Investigaciones Biológicas Clemente Estable, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
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7
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de Oliveira HC, Santos MDM, Camillo-Andrade AC, Castelli RF, Dos Reis FCG, Carvalho PC, Rodrigues ML. Proteomics reveals that the antifungal activity of fenbendazole against Cryptococcus neoformans requires protein kinases. Int J Antimicrob Agents 2024; 63:107157. [PMID: 38548248 DOI: 10.1016/j.ijantimicag.2024.107157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/09/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024]
Abstract
Cryptococcus neoformans is responsible for over 100 000 deaths annually, and the treatment of this fungal disease is expensive and not consistently effective. Unveiling new therapeutic avenues is crucial. Previous studies have suggested that the anthelmintic drug fenbendazole is an affordable and nontoxic candidate to combat cryptococcosis. However, its mechanism of anticryptococcal activity has been only superficially investigated. In this study, we examined the global cellular response of C. neoformans to fenbendazole using a proteomic approach (data are available via ProteomeXchange with identifier PXD047041). Fenbendazole treatment mostly impacted the abundance of proteins related to metabolic pathways, RNA processing, and intracellular traffic. Protein kinases, in particular, were significantly affected by fenbendazole treatment. Experimental validation of the proteomics data using a collection of C. neoformans mutants led to the identification of critical roles of five protein kinases in fenbendazole's antifungal activity. In fact, mutants lacking the expression of genes encoding Chk1, Tco2, Tco3, Bub1, and Sch9 kinases demonstrated greater resistance to fenbendazole compared to wild-type cells. In combination with the standard antifungal drug amphotericin B, fenbendazole reduced the cryptococcal burden in mice. These findings not only contribute to the elucidation of fenbendazole's mode of action but also support its use in combination therapy with amphotericin B. In conclusion, our data suggest that fenbendazole holds promise for further development as an anticryptococcal agent.
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Affiliation(s)
| | - Marlon D M Santos
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil; Analytical Biochemistry and Proteomics Unit. IIBCE/Institut Pasteur de Montevideo, Uruguay
| | - Amanda C Camillo-Andrade
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil; Analytical Biochemistry and Proteomics Unit. IIBCE/Institut Pasteur de Montevideo, Uruguay
| | - Rafael F Castelli
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
| | - Flavia C G Dos Reis
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil; Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Paulo C Carvalho
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
| | - Marcio L Rodrigues
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil; Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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8
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Castelli RF, Pereira A, Honorato L, Valdez A, de Oliveira HC, Bazioli JM, Garcia AWA, Klimeck TDF, Reis FCG, Camillo-Andrade AC, Santos MDM, Carvalho PC, Zaragoza O, Staats CC, Nimrichter L, Fill TP, Rodrigues ML. Corrected and republished from: "Extracellular Vesicle Formation in Cryptococcus deuterogattii Impacts Fungal Virulence". Infect Immun 2024; 92:e0003724. [PMID: 38470135 PMCID: PMC11003230 DOI: 10.1128/iai.00037-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 03/13/2024] Open
Abstract
Small molecules are components of fungal extracellular vesicles (EVs), but their biological roles are only superficially known. NOP16 is a eukaryotic gene that is required for the activity of benzimidazoles against Cryptococcus deuterogattii. In this study, during the phenotypic characterization of C. deuterogattii mutants expected to lack NOP16 expression, we observed a reduced EV production. Whole-genome sequencing, RNA-Seq, and cellular proteomics revealed that, contrary to our initial findings, these mutants expressed Nop16 but exhibited altered expression of 14 genes potentially involved in sugar transport. Based on this observation, we designated these mutant strains as Past1 and Past2, representing potentially altered sugar transport. Analysis of the small molecule composition of EVs produced by wild-type cells and the Past1 and Past2 mutant strains revealed not only a reduced number of EVs but also an altered small molecule composition. In a Galleria mellonella model of infection, the Past1 and Past2 mutant strains were hypovirulent. The hypovirulent phenotype was reverted when EVs produced by wild-type cells, but not mutant EVs, were co-injected with the mutant cells in G. mellonella. These results connect EV biogenesis, cargo, and cryptococcal virulence.
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Affiliation(s)
- Rafael F. Castelli
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
- Programa de Pós-Graduação em Biologia Parasitária, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Alana Pereira
- Instituto de Química, Universidade de Campinas, São Paulo, Brazil
| | - Leandro Honorato
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alessandro Valdez
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Jaqueline M. Bazioli
- Instituto de Química, Universidade de Campinas, São Paulo, Brazil
- Faculty of Pharmaceutical Sciences, State University of Campinas, Campinas, São Paulo, Brazil
| | - Ane W. A. Garcia
- Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Flavia C. G. Reis
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
- Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Marlon D. M. Santos
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
- Analytical Biochemistry and Proteomics Unit. IIBCE/Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Paulo C. Carvalho
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
| | - Oscar Zaragoza
- Mycology Reference Laboratory. National Centre for Microbiology. Instituto de Salud Carlos III, Madrid, Spain
- Center for Biomedical Research in Network in Infectious Diseases, CB21/13/00105, Instituto de Salud Carlos III, Madrid, Spain
| | - Charley C. Staats
- Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Leonardo Nimrichter
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Taícia P. Fill
- Instituto de Química, Universidade de Campinas, São Paulo, Brazil
| | - Marcio L. Rodrigues
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, Brazil
- Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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9
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Plouviez M, Dubreucq E. Key Proteomics Tools for Fundamental and Applied Microalgal Research. Proteomes 2024; 12:13. [PMID: 38651372 PMCID: PMC11036299 DOI: 10.3390/proteomes12020013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Microscopic, photosynthetic prokaryotes and eukaryotes, collectively referred to as microalgae, are widely studied to improve our understanding of key metabolic pathways (e.g., photosynthesis) and for the development of biotechnological applications. Omics technologies, which are now common tools in biological research, have been shown to be critical in microalgal research. In the past decade, significant technological advancements have allowed omics technologies to become more affordable and efficient, with huge datasets being generated. In particular, where studies focused on a single or few proteins decades ago, it is now possible to study the whole proteome of a microalgae. The development of mass spectrometry-based methods has provided this leap forward with the high-throughput identification and quantification of proteins. This review specifically provides an overview of the use of proteomics in fundamental (e.g., photosynthesis) and applied (e.g., lipid production for biofuel) microalgal research, and presents future research directions in this field.
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Affiliation(s)
- Maxence Plouviez
- School of Agriculture and Environment, Massey University, Palmerston North 4410, New Zealand
- The Cawthron Institute, Nelson 7010, New Zealand
| | - Eric Dubreucq
- Agropolymer Engineering and Emerging Technologies, L’Institut Agro Montpellier, 34060 Montpellier, France;
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10
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Brasileiro-Martins LM, Cavalcante SA, Nascimento TP, Silva-Neto AV, Mariano Santos MD, Camillo-Andrade AC, da Gama Fischer JDS, Ferreira CC, Oliveira LB, Sartim MA, Costa AG, Pucca MB, Wen FH, Moura-da-Silva AM, Sachett J, Carvalho PC, de Aquino PF, Monteiro WM. Urinary proteomics reveals biological processes related to acute kidney injury in Bothrops atrox envenomings. PLoS Negl Trop Dis 2024; 18:e0012072. [PMID: 38536893 PMCID: PMC11020875 DOI: 10.1371/journal.pntd.0012072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/16/2024] [Accepted: 03/14/2024] [Indexed: 04/18/2024] Open
Abstract
Acute kidney injury (AKI) is a critical systemic complication caused by Bothrops envenoming, a neglected health problem in the Brazilian Amazon. Understanding the underlying mechanisms leading to AKI is crucial for effectively mitigating the burden of this complication. This study aimed to characterize the urinary protein profile of Bothrops atrox snakebite victims who developed AKI. We analyzed three groups of samples collected on admission: healthy subjects (controls, n = 10), snakebite victims who developed AKI (AKI, n = 10), and those who did not evolve to AKI (No-AKI, n = 10). Using liquid-chromatography tandem mass spectrometry, we identified and quantified (label-free) 1190 proteins. A panel of 65 proteins was identified exclusively in the urine of snakebite victims, with 32 exclusives to the AKI condition. Proteins more abundant or exclusive in AKI's urine were associated with acute phase response, endopeptidase inhibition, complement cascade, and inflammation. Notable proteins include serotransferrin, SERPINA-1, alpha-1B-glycoprotein, and NHL repeat-containing protein 3. Furthermore, evaluating previously reported biomarkers candidates for AKI and renal injury, we found retinol-binding protein, beta-2-microglobulin, cystatin-C, and hepcidin to be significant in cases of AKI induced by Bothrops envenoming. This work sheds light on physiological disturbances caused by Bothrops envenoming, highlighting potential biological processes contributing to AKI. Such insights may aid in better understanding and managing this life-threatening complication.
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Affiliation(s)
- Lisele Maria Brasileiro-Martins
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
| | | | - Thaís Pinto Nascimento
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
- Leonidas and Maria Deane Institute, Oswaldo Cruz Foundation, Manaus, Brazil
| | - Alexandre Vilhena Silva-Neto
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
| | - Marlon Dias Mariano Santos
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Brazil
| | - Amanda C. Camillo-Andrade
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Brazil
| | | | | | | | - Marco Aurelio Sartim
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
- Department of Research, Nilton Lins University, Manaus, Brazil
| | - Allyson Guimarães Costa
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
- Nursing School, Amazonas Federal University, Manaus, Brazil
| | - Manuela B. Pucca
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University, Araraquara, Brazil
| | - Fan Hui Wen
- Immunopathology Laboratory, Butantan Institute, São Paulo, Brazil
| | | | - Jacqueline Sachett
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- Immunopathology Laboratory, Butantan Institute, São Paulo, Brazil
| | - Paulo Costa Carvalho
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Brazil
| | | | - Wuelton M. Monteiro
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
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11
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da Silva EMG, Fischer JSG, Souza IDLS, Andrade ACC, Souza LDCE, Andrade MKD, Carvalho PC, Souza RLR, Vital MABF, Passetti F. Proteomic Analysis of a Rat Streptozotocin Model Shows Dysregulated Biological Pathways Implicated in Alzheimer's Disease. Int J Mol Sci 2024; 25:2772. [PMID: 38474019 DOI: 10.3390/ijms25052772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/14/2024] Open
Abstract
Alzheimer's Disease (AD) is an age-related neurodegenerative disorder characterized by progressive memory loss and cognitive impairment, affecting 35 million individuals worldwide. Intracerebroventricular (ICV) injection of low to moderate doses of streptozotocin (STZ) in adult male Wistar rats can reproduce classical physiopathological hallmarks of AD. This biological model is known as ICV-STZ. Most studies are focused on the description of behavioral and morphological aspects of the ICV-STZ model. However, knowledge regarding the molecular aspects of the ICV-STZ model is still incipient. Therefore, this work is a first attempt to provide a wide proteome description of the ICV-STZ model based on mass spectrometry (MS). To achieve that, samples from the pre-frontal cortex (PFC) and hippocampus (HPC) of the ICV-STZ model and control (wild-type) were used. Differential protein abundance, pathway, and network analysis were performed based on the protein identification and quantification of the samples. Our analysis revealed dysregulated biological pathways implicated in the early stages of late-onset Alzheimer's disease (LOAD), based on differentially abundant proteins (DAPs). Some of these DAPs had their mRNA expression further investigated through qRT-PCR. Our results shed light on the AD onset and demonstrate the ICV-STZ as a valid model for LOAD proteome description.
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Affiliation(s)
- Esdras Matheus Gomes da Silva
- Instituto Carlos Chagas, FIOCRUZ, Curitiba 81310-020, PR, Brazil
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-361, RJ, Brazil
| | | | | | | | | | | | - Paulo C Carvalho
- Instituto Carlos Chagas, FIOCRUZ, Curitiba 81310-020, PR, Brazil
| | | | | | - Fabio Passetti
- Instituto Carlos Chagas, FIOCRUZ, Curitiba 81310-020, PR, Brazil
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12
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Santos LGC, Parreira VDSC, da Silva EMG, Santos MDM, Fernandes ADF, Neves-Ferreira AGDC, Carvalho PC, Freitas FCDP, Passetti F. SpliceProt 2.0: A Sequence Repository of Human, Mouse, and Rat Proteoforms. Int J Mol Sci 2024; 25:1183. [PMID: 38256255 PMCID: PMC10816255 DOI: 10.3390/ijms25021183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/15/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
SpliceProt 2.0 is a public proteogenomics database that aims to list the sequence of known proteins and potential new proteoforms in human, mouse, and rat proteomes. This updated repository provides an even broader range of computationally translated proteins and serves, for example, to aid with proteomic validation of splice variants absent from the reference UniProtKB/SwissProt database. We demonstrate the value of SpliceProt 2.0 to predict orthologous proteins between humans and murines based on transcript reconstruction, sequence annotation and detection at the transcriptome and proteome levels. In this release, the annotation data used in the reconstruction of transcripts based on the methodology of ternary matrices were acquired from new databases such as Ensembl, UniProt, and APPRIS. Another innovation implemented in the pipeline is the exclusion of transcripts predicted to be susceptible to degradation through the NMD pathway. Taken together, our repository and its applications represent a valuable resource for the proteogenomics community.
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Affiliation(s)
- Letícia Graziela Costa Santos
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
| | - Vinícius da Silva Coutinho Parreira
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
| | - Esdras Matheus Gomes da Silva
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (FIOCRUZ), Av. Brazil 4036, Campus Maré, Rio de Janeiro 21040-361, RJ, Brazil
| | - Marlon Dias Mariano Santos
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
| | - Alexander da Franca Fernandes
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
| | - Ana Gisele da Costa Neves-Ferreira
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (FIOCRUZ), Av. Brazil 4036, Campus Maré, Rio de Janeiro 21040-361, RJ, Brazil
| | - Paulo Costa Carvalho
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
| | - Flávia Cristina de Paula Freitas
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luis, Km 235, São Carlos 13565-905, SP, Brazil
| | - Fabio Passetti
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
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13
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Moro CF, Nogueira FCS, Almeida CGM, Real-Guerra R, Dalberto PF, Bizarro CV, Ligabue-Braun R, Carlini CR. One enzyme, many faces: urease is also canatoxin. J Biomol Struct Dyn 2023; 41:10750-10761. [PMID: 36546698 DOI: 10.1080/07391102.2022.2158938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
Ureases catalyze the hydrolysis of urea into carbamate and ammonia. Well-conserved proteins, most plant ureases are hexamers of a single chain subunit, like the most abundant isoform of the jack bean (Canavalia ensiformis) urease (JBU). Canatoxin (CNTX) was originally isolated from these seeds as a neurotoxic protein, and later characterized as an isoform of JBU with lower molecular mass and enzyme activity. Inactive CNTX oligomers form upon storage and stabilization of CNTX was achieved by treatment with low concentration of formaldehyde, avoiding its oligomerization. Here, nano-LC-MS/MS-based peptide analysis of CNTX revealed 804 amino acids identical to those of JBU's sequence (840 amino acids). De novo sequencing of CNTX revealed 15 different peptides containing substitution of amino acid residues, denoting CNTX as a product of a paralog gene of JBU. The MS/MS analysis of formaldehyde-treated CNTX showed that amino acid residues located at the trimer-trimer interface of JBU's hexamer were modified. The data confirmed that CNTX is an isoform of JBU and elucidated that stabilization by formaldehyde treatment occurs by modification of amino acids at the protein's surface that prevents the formation of the hexamer and of higher molecular mass inactive aggregates. HIGHLIGHTSCanatoxin (CNTX) is an isoform of jack bean urease (JBU, hexamer of 90 kDa chains)MS/MS sequencing of CNTX showed 804 amino acids identical in JBU (840 residues)Formaldehyde treatment of CNTX stabilizes its toxicity and avoids oligomerizationModified amino acid residues in CNTX are at the trimer-trimer interface of JBUCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Carlo Frederico Moro
- Graduate Program in Medicine and Health Sciences, Pontificia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Fábio C S Nogueira
- Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Carlos Gabriel Moreira Almeida
- Graduate Program in Medicine and Health Sciences, Pontificia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Rafael Real-Guerra
- Interdisciplinary Department, Universidade Federal do Rio Grande do Sul, Tramandaí, RS, Brazil
| | - Pedro Ferrari Dalberto
- Graduate Program in Cellular and Molecular Biology, Pontificia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Cristiano V Bizarro
- Graduate Program in Cellular and Molecular Biology, Pontificia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
- National Institute of Science and Technology in Tuberculosis (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Rodrigo Ligabue-Braun
- Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Celia R Carlini
- Brain Institute-Instituto do Cérebro do Rio Grande do Sul (INSCER), Porto Alegre, RS, Brazil
- National Institute of Science and Technology in Brain Diseases, Excitotoxity and Neuroprotection (INCT-EN), Porto Alegre, RS, Brazil
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14
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Deng W, Zhong Z, Tong Y, Liu J, Wang X, Xu L, Li Y, Chen X, Wei Q, Rao J. 4D DIA-PRM proteomic study identifying modulated pathways and biomarkers associated with pelvic organ prolapse. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1230:123916. [PMID: 37922782 DOI: 10.1016/j.jchromb.2023.123916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/19/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
Pelvic organ prolapse (POP) is a highly disabling condition that negatively affects the quality of life of millions of women worldwide. However, the underlying mechanisms associated with the development and progression of the disease remain poorly understood. Here, an untargeted four-dimensional data-independent acquisition (4D DIA)-based proteomics approach was applied to vaginal wall tissue samples from POP (n = 19) and control (n = 8) patients to identify potential diagnostic biomarker(s) for POP and examine the molecular mechanisms underlying the disease. Of the 5713 tissue proteins that were detected, 1957 proteins were significantly changed in POP patients. Further bioinformatics analysis revealed that multiple biological processes including protein digestion & absorption, retrograde endocannabinoid signaling, tyrosine metabolism, and nucleotide metabolism were significantly enriched and associated with the pathogenesis of POP. Interestingly, 16 of these differentially expressed proteins associated with four pathways were also identified by targeted parallel reaction monitoring (PRM) proteomics analysis on the same 27 tissue samples. Changes in 94 % (15/16) of these proteins were consistent with the 4D DIA data. Furthermore, most proteins displayed good diagnostic accuracy with high area under the curve (AUC) values (AUC>0.8). Specifically, five proteins including ELN, COL6A2, ENTPD1, AOC3, and COX7A2 distinguished between POP and control patients with very high accuracy (AUC ≥ 0.95) in both 4D DIA and PRM analyses, and may therefore be potential diagnostic biomarkers for POP. In summary, the present study not only provided several potential biomarker(s) for effective POP diagnosis, but extended our knowledge of the key regulatory pathways associated with the disease.
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Affiliation(s)
- Wei Deng
- Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, Zhejiang Province, China; Jiangxi Provincial Maternal and Child Health Hospital, Nanchang 330006, Jiangxi Province, China
| | - Zhifeng Zhong
- Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, Zhejiang Province, China
| | - Yuehong Tong
- Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, Zhejiang Province, China
| | - Jun Liu
- Jiangxi Provincial Maternal and Child Health Hospital, Nanchang 330006, Jiangxi Province, China
| | - Xiaofen Wang
- Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, Zhejiang Province, China
| | - Lili Xu
- Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, Zhejiang Province, China
| | - Yufeng Li
- Department of Joint Surgery, People's Hospital of Ganxian District, Ganzhou, Jiangxi, 341100, China
| | - Xiaodan Chen
- Jiangxi Cancer Hospital, The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Clinical Research Center for Cancer, Nanchang 330029, Jiangxi Province, China
| | - Qingfeng Wei
- Jiangxi Cancer Hospital, The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Clinical Research Center for Cancer, Nanchang 330029, Jiangxi Province, China.
| | - Jun Rao
- Jiangxi Cancer Hospital, The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Clinical Research Center for Cancer, Nanchang 330029, Jiangxi Province, China.
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15
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Lin AD, Fischer JDSDG, Santos MDM, Camillo-Andrade AC, Kurt LU, Souza TACB, Lajas ABL, Rivera B, Portela M, Duran R, Mira MT, Pillonetto M, Carvalho PC. Beyond the identifiable proteome: Delving into the proteomics of polymyxin-resistant and non-resistant Acinetobacter baumannii from Brazilian hospitals. J Proteomics 2023; 289:105012. [PMID: 37748533 DOI: 10.1016/j.jprot.2023.105012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023]
Abstract
This work discloses a unique, comprehensive proteomic dataset of Acinetobacter baumannii strains, both resistant and non-resistant to polymyxin B, isolated in Brazil generated using Orbitrap Fusion Lumos. From nearly 4 million tandem mass spectra, the software DiagnoMass produced 240,685 quality-filtered mass spectral clusters, of which PatternLab for proteomics identified 44,553 peptides mapping to 3479 proteins. Crucially, DiagnoMass shortlisted 3550 and 1408 unique mass spectral clusters for the resistant and non-resistant strains, respectively, with only about a third with sequences (and PTMs) identified by PatternLab. Further open-search attempts via FragPipe yielded an additional ∼20% identifications, suggesting the remaining unidentified spectra likely arise from complex combinations of post-translational modifications and amino-acid substitutions. This highlights the untapped potential of the dataset for future discoveries, particularly given the importance of PTMs, which remain elusive to nucleotide sequencing approaches but are crucial for understanding biological mechanisms. Our innovative approach extends beyond the identifications that are typically subjected to the bias of a search engine; we discern which spectral clusters are differential and subject them to increased scrutiny, akin to spectral library matching by comparing captured spectra to themselves. Our analysis reveals adaptations in the resistant strain, including enhanced detoxification, altered protein synthesis, and metabolic adjustments. SIGNIFICANCE: We present comprehensive proteomic profiles of non-resistant and resistant Acinetobacter baumannii from Brazilian Hospitals strains, and highlight the presence of discriminative and yet unidentified mass spectral clusters. Our work emphasizes the importance of exploring this overlooked data, as it could hold the key to understanding the complex dynamics of antibiotic resistance. This approach not only informs antimicrobial stewardship efforts but also paves the way for the development of innovative diagnostic tools. Thus, our findings have profound implications for the field, as far as methods for providing a new perspective on diagnosing antibiotic resistance as well as classifying proteomes in general.
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Affiliation(s)
- Amanda Dal Lin
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, Brazil; Laboratório Experimental Multiuso, Pontifícia Universidade Católica do Paraná, Brazil
| | - Juliana de S da G Fischer
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, Brazil
| | - Marlon D M Santos
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, Brazil; Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo/IIBCE, Montevideo, Uruguay
| | - Amanda Caroline Camillo-Andrade
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, Brazil; Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo/IIBCE, Montevideo, Uruguay
| | - Louise Ulrich Kurt
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, Brazil
| | - Tatiana A C B Souza
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, Brazil
| | - Ana Beatriz Lyrio Lajas
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, Brazil
| | - Bernardina Rivera
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo/IIBCE, Montevideo, Uruguay
| | - Magdalena Portela
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo/IIBCE, Montevideo, Uruguay
| | - Rosario Duran
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo/IIBCE, Montevideo, Uruguay
| | - Marcelo Távora Mira
- Laboratório Experimental Multiuso, Pontifícia Universidade Católica do Paraná, Brazil
| | - Marcelo Pillonetto
- Laboratório Experimental Multiuso, Pontifícia Universidade Católica do Paraná, Brazil; Laboratório Central do Estado do Paraná, Brazil.
| | - Paulo Costa Carvalho
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz - Paraná, Brazil.
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16
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Martinez M, Petit J, Leyva A, Sogues A, Megrian D, Rodriguez A, Gaday Q, Ben Assaya M, Portela MM, Haouz A, Ducret A, Grangeasse C, Alzari PM, Durán R, Wehenkel AM. Eukaryotic-like gephyrin and cognate membrane receptor coordinate corynebacterial cell division and polar elongation. Nat Microbiol 2023; 8:1896-1910. [PMID: 37679597 PMCID: PMC10522489 DOI: 10.1038/s41564-023-01473-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 08/11/2023] [Indexed: 09/09/2023]
Abstract
The order Corynebacteriales includes major industrial and pathogenic Actinobacteria such as Corynebacterium glutamicum or Mycobacterium tuberculosis. These bacteria have multi-layered cell walls composed of the mycolyl-arabinogalactan-peptidoglycan complex and a polar growth mode, thus requiring tight coordination between the septal divisome, organized around the tubulin-like protein FtsZ, and the polar elongasome, assembled around the coiled-coil protein Wag31. Here, using C. glutamicum, we report the discovery of two divisome members: a gephyrin-like repurposed molybdotransferase (Glp) and its membrane receptor (GlpR). Our results show how cell cycle progression requires interplay between Glp/GlpR, FtsZ and Wag31, showcasing a crucial crosstalk between the divisome and elongasome machineries that might be targeted for anti-mycobacterial drug discovery. Further, our work reveals that Corynebacteriales have evolved a protein scaffold to control cell division and morphogenesis, similar to the gephyrin/GlyR system that mediates synaptic signalling in higher eukaryotes through network organization of membrane receptors and the microtubule cytoskeleton.
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Affiliation(s)
- Mariano Martinez
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Julienne Petit
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Alejandro Leyva
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Adrià Sogues
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, VIB, Vrije Universiteit Brussel, Brussels, Belgium
| | - Daniela Megrian
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Azalia Rodriguez
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Quentin Gaday
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Mathildeb Ben Assaya
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Maria Magdalena Portela
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Ahmed Haouz
- Plate-forme de cristallographie, C2RT-Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Adrien Ducret
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, Lyon, France
| | - Pedro M Alzari
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Rosario Durán
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.
| | - Anne Marie Wehenkel
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France.
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17
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Pinto AFM, Diedrich JK, Moresco JJ, Yates JR. Differential Precipitation of Proteins: A Simple Protein Fractionation Strategy to Gain Biological Insights with Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2025-2033. [PMID: 37527410 DOI: 10.1021/jasms.3c00182] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Differential precipitation of proteins (DiffPOP) is a simple technique for fractionating complex protein mixtures. Using stepwise addition of acidified methanol, ten distinct subsets of proteins can be selectively precipitated by centrifugation and identified by mass spectrometry-based proteomics. We have previously shown that the ability of a protein to resist precipitation can be altered by drug binding, which enabled us to identify a novel drug-target interaction. Here, we show that the addition of DiffPOP to a standard LC-MS proteomics workflow results in a three-dimensional separation of peptides that increases protein coverage and peptide identifications. Importantly, DiffPOP reveals solubility differences between proteoforms, potentially providing valuable insights that are typically lost in bottom-up proteomics.
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Affiliation(s)
- Antonio F M Pinto
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037, United States
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
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18
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Pandeswari PB, Isaac AE, Sabareesh V. Database Creator for Mass Analysis of Peptides and Proteins, DC-MAPP: A Standalone Tool for Simplifying Manual Analysis of Mass Spectral Data to Identify Peptide/Protein Sequences. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1962-1969. [PMID: 37526995 DOI: 10.1021/jasms.3c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Proteomic studies typically involve the use of different types of software for annotating experimental tandem mass spectrometric data (MS/MS) and thereby simplifying the process of peptide and protein identification. For such annotations, these softwares calculate the m/z values of the peptide/protein precursor and fragment ions, for which a database of protein sequences must be provided as an input file. The calculated m/z values are stored as another database, which the user usually cannot view. Database Creator for Mass Analysis of Peptides and Proteins (DC-MAPP) is a novel standalone software that can create custom databases for "viewing" the calculated m/z values of precursor and fragment ions, prior to the database search. It contains three modules. Peptide/Protein sequences as per user's choice can be entered as input to the first module for creating a custom database. In the second module, m/z values must be queried-in, which are searched within the custom database to identify protein/peptide sequences. The third module is suited for peptide mass fingerprinting, which can be used to analyze both ESI and MALDI mass spectral data. The feature of "viewing" the custom database can be helpful not only for better understanding the search engine processes, but also for designing multiple reaction monitoring (MRM) methods. Post-translational modifications and protein isoforms can also be analyzed. Since, DC-MAPP relies on the protein/peptide "sequences" for creating custom databases, it may not be applicable for the searches involving spectral libraries. Python language was used for implementation, and the graphical user interface was built with Page/Tcl, making this tool more user-friendly. It is freely available at https://vit.ac.in/DC-MAPP/.
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Affiliation(s)
- Pandi Boomathi Pandeswari
- Centre for Bio-Separation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu - 632014, India
| | - Arnold Emerson Isaac
- Bioinformatics Programming Laboratory, School of Bio Sciences & Technology (SBST), VIT, Vellore, Tamil Nadu - 632014, India
| | - Varatharajan Sabareesh
- Centre for Bio-Separation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu - 632014, India
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19
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Carrión F, Rammauro F, Olivero‐Deibe N, Fló M, Portela MM, Lima A, Durán R, Pritsch O, Bianchi S. Soluble SARS-CoV-2 RBD and human ACE2 peptidase domain produced in Drosophila S2 cells show functions evoking virus-cell interface. Protein Sci 2023; 32:e4721. [PMID: 37405395 PMCID: PMC10382795 DOI: 10.1002/pro.4721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/06/2023] [Accepted: 07/03/2023] [Indexed: 07/06/2023]
Abstract
The interaction between the receptor-binding domain (RBD) of the spike glycoprotein of SARS-CoV-2 and the peptidase domain of the human angiotensin-converting enzyme 2 (ACE2) allows the first specific contact at the virus-cell interface making it the main target of neutralizing antibodies. Here, we show a unique and cost-effective protocol using Drosophila S2 cells to produce both RBD and soluble human ACE2 peptidase domain (shACE2) as thermostable proteins, purified via Strep-tag with yields >40 mg L-1 in a laboratory scale. Furthermore, we demonstrate its binding with KD values in the lower nanomolar range (independently of Strep-tag removal) and its capability to be blocked by serum antibodies in a competition ELISA with Strep-Tactin-HRP as a proof-of-concept. In addition, we assess the capacity of RBD to bind native dimeric ACE2 overexpressed in human cells and its antigen properties with specific serum antibodies. Finally, for completeness, we analyzed RBD microheterogeneity associated with glycosylation and negative charges, with negligible effect on binding either with antibodies or shACE2. Our system represents an accessible and reliable tool for designing in-house surrogate virus neutralization tests (sVNTs), enabling the rapid characterization of neutralizing humoral responses elicited against vaccines or infection, especially in the absence of facilities to conduct virus neutralization tests. Moreover, our biophysical and biochemical characterization of RBD and shACE2 produced in S2 cells lays the groundwork for adapting to different variants of concern (VOCs) to study humoral responses elicited against different VOCs and vaccine formulations.
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Affiliation(s)
- Federico Carrión
- Laboratorio de InmunovirologíaInstitut Pasteur de MontevideoMontevideoUruguay
| | - Florencia Rammauro
- Laboratorio de InmunovirologíaInstitut Pasteur de MontevideoMontevideoUruguay
- Facultad de Medicina, Departamento de InmunobiologíaUniversidad de la RepúblicaMontevideoUruguay
| | | | - Martín Fló
- Laboratorio de InmunovirologíaInstitut Pasteur de MontevideoMontevideoUruguay
- Facultad de Medicina, Departamento de InmunobiologíaUniversidad de la RepúblicaMontevideoUruguay
| | - María Magdalena Portela
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo & Instituto de Investigaciones Biológicas Clemente EstableMontevideoUruguay
- Facultad de CienciasUniversidad de la RepúblicaMontevideoUruguay
| | - Analía Lima
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo & Instituto de Investigaciones Biológicas Clemente EstableMontevideoUruguay
| | - Rosario Durán
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo & Instituto de Investigaciones Biológicas Clemente EstableMontevideoUruguay
| | - Otto Pritsch
- Laboratorio de InmunovirologíaInstitut Pasteur de MontevideoMontevideoUruguay
- Facultad de Medicina, Departamento de InmunobiologíaUniversidad de la RepúblicaMontevideoUruguay
| | - Sergio Bianchi
- Departamento de Fisiopatología, Laboratorio de Biomarcadores Moleculares, Hospital de ClínicasUniversidad de la RepúblicaMontevideoUruguay
- Laboratorio de Genómica FuncionalInstitut Pasteur de MontevideoMontevideoUruguay
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20
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Margenat M, Betancour G, Irving V, Costábile A, García-Cedrés T, Portela MM, Carrión F, Herrera FE, Villarino A. Characteristics of Mycobacterium tuberculosis PtpA interaction and activity on the alpha subunit of human mitochondrial trifunctional protein, a key enzyme of lipid metabolism. Front Cell Infect Microbiol 2023; 13:1095060. [PMID: 37424790 PMCID: PMC10325834 DOI: 10.3389/fcimb.2023.1095060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/29/2023] [Indexed: 07/11/2023] Open
Abstract
During Mycobacterium tuberculosis (Mtb) infection, the virulence factor PtpA belonging to the protein tyrosine phosphatase family is delivered into the cytosol of the macrophage. PtpA interacts with numerous eukaryotic proteins modulating phagosome maturation, innate immune response, apoptosis, and potentially host-lipid metabolism, as previously reported by our group. In vitro, the human trifunctional protein enzyme (hTFP) is a bona fide PtpA substrate, a key enzyme of mitochondrial β-oxidation of long-chain fatty acids, containing two alpha and two beta subunits arranged in a tetramer structure. Interestingly, it has been described that the alpha subunit of hTFP (ECHA, hTFPα) is no longer detected in mitochondria during macrophage infection with the virulent Mtb H37Rv. To better understand if PtpA could be the bacterial factor responsible for this effect, in the present work, we studied in-depth the PtpA activity and interaction with hTFPα. With this aim, we performed docking and in vitro dephosphorylation assays defining the P-Tyr-271 as the potential target of mycobacterial PtpA, a residue located in the helix-10 of hTFPα, previously described as relevant for its mitochondrial membrane localization and activity. Phylogenetic analysis showed that Tyr-271 is absent in TFPα of bacteria and is present in more complex eukaryotic organisms. These results suggest that this residue is a specific PtpA target, and its phosphorylation state is a way of regulating its subcellular localization. We also showed that phosphorylation of Tyr-271 can be catalyzed by Jak kinase. In addition, we found by molecular dynamics that PtpA and hTFPα form a stable protein complex through the PtpA active site, and we determined the dissociation equilibrium constant. Finally, a detailed study of PtpA interaction with ubiquitin, a reported PtpA activator, showed that additional factors are required to explain a ubiquitin-mediated activation of PtpA. Altogether, our results provide further evidence supporting that PtpA could be the bacterial factor that dephosphorylates hTFPα during infection, potentially affecting its mitochondrial localization or β-oxidation activity.
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Affiliation(s)
- Mariana Margenat
- Instituto de Biología, Sección Bioquímica, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Gabriela Betancour
- Instituto de Biología, Sección Bioquímica, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Vivian Irving
- Instituto de Biología, Sección Bioquímica, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Alicia Costábile
- Instituto de Biología, Sección Bioquímica, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Tania García-Cedrés
- Instituto de Biología, Sección Bioquímica, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - María Magdalena Portela
- Instituto de Biología, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo and Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Federico Carrión
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Fernando E. Herrera
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas-Universidad Nacional del Litoral – CONICET, Santa Fe, Argentina
| | - Andrea Villarino
- Instituto de Biología, Sección Bioquímica, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
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21
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DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters. J Proteomics 2023; 277:104853. [PMID: 36804625 DOI: 10.1016/j.jprot.2023.104853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
Abstract
MOTIVATION There are several well-established paradigms for identifying and pinpointing discriminative peptides/proteins using shotgun proteomic data; examples are peptide-spectrum matching, de novo sequencing, open searches, and even hybrid approaches. Such an arsenal of complementary paradigms can provide deep data coverage, albeit some unidentified discriminative peptides remain. RESULTS We present DiagnoMass, software tool that groups similar spectra into spectral clusters and then shortlists those clusters that are discriminative for biological conditions. DiagnoMass then communicates with proteomic tools to attempt the identification of such clusters. We demonstrate the effectiveness of DiagnoMass by analyzing proteomic data from Escherichia coli, Salmonella, and Shigella, listing many high-quality discriminative spectral clusters that had thus far remained unidentified by widely adopted proteomic tools. DiagnoMass can also classify proteomic profiles. We anticipate the use of DiagnoMass as a vital tool for pinpointing biomarkers. AVAILABILITY DiagnoMass and related documentation, including a usage protocol, are available at http://www.diagnomass.com.
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22
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Clasen MA, Santos MDM, Kurt LU, Fischer J, Camillo-Andrade AC, Sales LA, de Arruda Campos Brasil de Souza T, Lima DB, Gozzo FC, Valente RH, Duran R, Barbosa VC, Carvalho PC. PatternLab V Handles Multiplex Spectra in Shotgun Proteomic Searches and Increases Identification. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:794-796. [PMID: 36947430 DOI: 10.1021/jasms.3c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Complex protein mixtures typically generate many tandem mass spectra produced by different peptides coisolated in the gas phase. Widely adopted proteomic data analysis environments usually fail to identify most of these spectra, succeeding at best in identifying only one of the multiple cofragmenting peptides. We present PatternLab V (PLV), an updated version of PatternLab that integrates the YADA 3 deconvolution algorithm to handle such cases efficiently. In general, we expect an increase of 10% in spectral identifications when dealing with complex proteomic samples. PLV is freely available at http://patternlabforproteomics.org.
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Affiliation(s)
- Milan A Clasen
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz-Parana 81310-020, Brazil
| | - Marlon D M Santos
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz-Parana 81310-020, Brazil
| | - Louise Ulrich Kurt
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz-Parana 81310-020, Brazil
| | - Juliana Fischer
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz-Parana 81310-020, Brazil
| | - Amanda C Camillo-Andrade
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz-Parana 81310-020, Brazil
| | - Lucas Albuquerque Sales
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz-Parana 81310-020, Brazil
| | | | - Diogo Borges Lima
- Department of Structural Biology, Leibniz─Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Fabio C Gozzo
- Dalton Mass Spectrometry Laboratory, Unicamp, Campinas 13083-970, Brazil
| | - Richard Hemmi Valente
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Rosario Duran
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo/IIBCE, Montevideo 11400, Uruguay
| | - Valmir C Barbosa
- Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro 21941-914, Brazil
| | - Paulo C Carvalho
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz-Parana 81310-020, Brazil
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23
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Alves GB, de Oliveira EE, Jumbo LOV, dos Santos GR, dos Santos MM, Ootani MA, Ribeiro BM, Aguiar RWDS. Genomic–proteomic analysis of a novel Bacillus thuringiensis strain: toxicity against two lepidopteran pests, abundance of Cry1Ac5 toxin, and presence of InhA1 virulence factor. Arch Microbiol 2023; 205:143. [PMID: 36967401 DOI: 10.1007/s00203-023-03479-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/28/2023]
Abstract
Bacillus thuringiensis (Bt) is a biological alternative to the indiscriminate use of chemical insecticides in agriculture. Due to resistance development on insect pests to Bt crops, isolating novel Bt strains is a strategy for screening new pesticidal proteins or strains containing toxin profile variety that can delay resistance. Besides, the combined genomic and proteomic approaches allow identifying pesticidal proteins and virulence factors accurately. Here, the genome of a novel Bt strain (Bt TOL651) was sequenced, and the proteins from the spore-crystal mixture were identified by proteomic analysis. Toxicity bioassays with the spore-crystal mixture against larvae of Diatraea saccharalis and Anticarsia gemmatalis, key pests of sugarcane and soybean, respectively, were performed. The toxicity of Bt TOL651 varies with the insect; A. gemmatalis (LC50 = 1.45 ng cm-2) is more susceptible than D. saccharalis (LC50 = 73.77 ng cm-2). Phylogenetic analysis of the gyrB gene indicates that TOL651 is related to Bt kenyae strains. The genomic analysis revealed the presence of cry1Aa18, cry1Ac5, cry1Ia44, and cry2Aa9 pesticidal genes. Virulence factor genes such as phospholipases (plcA, piplc), metalloproteases (inhA), hemolysins (cytK, hlyIII, hblA, hblC, hblD), and enterotoxins (nheA, nheB, nheC) were also identified. The combined use of the genomic and proteomic data indicated the expression of Cry1Aa18, Cry1Ac5, and Cry2Aa9 proteins, with Cry1Ac5 being the most abundant. InhA1 also was expressed and may contribute to Bt TOL651 pathogenicity. These results provide Bt TOL651 as a new tool for the biocontrol of lepidopteran pests.
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24
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Almeida MA, Bernardes-Engemann AR, Coelho RA, Lugones CJG, de Andrade IB, Corrêa-Junior D, de Oliveira SSC, Dos Santos ALS, Frases S, Rodrigues ML, Valente RH, Zancopé-Oliveira RM, Almeida-Paes R. Mebendazole Inhibits Histoplasma capsulatum In Vitro Growth and Decreases Mitochondrion and Cytoskeleton Protein Levels. J Fungi (Basel) 2023; 9:jof9030385. [PMID: 36983553 PMCID: PMC10051957 DOI: 10.3390/jof9030385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/13/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Histoplasmosis is a frequent mycosis in people living with HIV/AIDS and other immunocompromised hosts. Histoplasmosis has high rates of mortality in these patients if treatment is unsuccessful. Itraconazole and amphotericin B are used to treat histoplasmosis; however, both antifungals have potentially severe pharmacokinetic drug interactions and toxicity. The present study determined the minimal inhibitory and fungicidal concentrations of mebendazole, a drug present in the NIH Clinical Collection, to establish whether it has fungicidal or fungistatic activity against Histoplasma capsulatum. Protein extracts from H. capsulatum yeasts, treated or not with mebendazole, were analyzed by proteomics to understand the metabolic changes driven by this benzimidazole. Mebendazole inhibited the growth of 10 H. capsulatum strains, presenting minimal inhibitory concentrations ranging from 5.0 to 0.08 µM. Proteomics revealed 30 and 18 proteins exclusively detected in untreated and mebendazole-treated H. capsulatum yeast cells, respectively. Proteins related to the tricarboxylic acid cycle, cytoskeleton, and ribosomes were highly abundant in untreated cells. Proteins related to the nitrogen, sulfur, and pyrimidine metabolisms were enriched in mebendazole-treated cells. Furthermore, mebendazole was able to inhibit the oxidative metabolism, disrupt the cytoskeleton, and decrease ribosomal proteins in H. capsulatum. These results suggest mebendazole as a drug to be repurposed for histoplasmosis treatment.
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Affiliation(s)
- Marcos Abreu Almeida
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
| | - Andrea Reis Bernardes-Engemann
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
| | - Rowena Alves Coelho
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
| | - Camila Jantoro Guzman Lugones
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
| | - Iara Bastos de Andrade
- Laboratório de Biofísica de Fungos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Dario Corrêa-Junior
- Laboratório de Biofísica de Fungos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Simone Santiago Carvalho de Oliveira
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - André Luis Souza Dos Santos
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Rede Micologia RJ, Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Rio de Janeiro 21941-901, Brazil
| | - Susana Frases
- Laboratório de Biofísica de Fungos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Rede Micologia RJ, Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Rio de Janeiro 21941-901, Brazil
| | | | - Richard Hemmi Valente
- Laboratório de Toxinologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
| | - Rosely Maria Zancopé-Oliveira
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
| | - Rodrigo Almeida-Paes
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
- Rede Micologia RJ, Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Rio de Janeiro 21941-901, Brazil
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25
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Martinez M, Petit J, Leyva A, Sogues A, Megrian D, Rodriguez A, Gaday Q, Ben Assaya M, Portela M, Haouz A, Ducret A, Grangeasse C, Alzari PM, Durán R, Wehenkel A. Eukaryotic-like gephyrin and cognate membrane receptor coordinate corynebacterial cell division and polar elongation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526586. [PMID: 36778425 PMCID: PMC9915583 DOI: 10.1101/2023.02.01.526586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The order Corynebacteriales includes major industrial and pathogenic actinobacteria such as Corynebacterium glutamicum or Mycobacterium tuberculosis . Their elaborate multi-layered cell wall, composed primarily of the mycolyl-arabinogalactan-peptidoglycan complex, and their polar growth mode impose a stringent coordination between the septal divisome, organized around the tubulin-like protein FtsZ, and the polar elongasome, assembled around the tropomyosin-like protein Wag31. Here, we report the identification of two new divisome members, a gephyrin-like repurposed molybdotransferase (GLP) and its membrane receptor (GLPR). We show that the interplay between the GLPR/GLP module, FtsZ and Wag31 is crucial for orchestrating cell cycle progression. Our results provide a detailed molecular understanding of the crosstalk between two essential machineries, the divisome and elongasome, and reveal that Corynebacteriales have evolved a protein scaffold to control cell division and morphogenesis similar to the gephyrin/GlyR system that in higher eukaryotes mediates synaptic signaling through network organization of membrane receptors and the microtubule cytoskeleton.
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Affiliation(s)
- M. Martinez
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - J. Petit
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - A. Leyva
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - A. Sogues
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - D. Megrian
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - A. Rodriguez
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Q. Gaday
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - M. Ben Assaya
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - M. Portela
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - A. Haouz
- Plate-forme de cristallographie, C2RT-Institut Pasteur, CNRS, UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - A. Ducret
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - C. Grangeasse
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - P. M. Alzari
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - R. Durán
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - A. Wehenkel
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
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26
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Otávio KS, Passos JRS, Silva RF, Lima LF, Cadenas J, Paes VM, Correia HHV, Ferreira ACA, Canafístula FG, Bezerra MJB, Oliveira LLB, Carvalho GGC, Paier CRK, Pessoa C, Guerreiro DG, Moraes MEA, Figueiredo JR, Moura AA. Comprehensive proteomic profiling of early antral follicles from sheep. Anim Reprod Sci 2023; 248:107153. [PMID: 36502761 DOI: 10.1016/j.anireprosci.2022.107153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022]
Abstract
The present study evaluates the proteome of early antral follicles from Ovis aries. Fifty follicles were collected from ovaries of adult ewes and extracted proteins were trypsin-digested, desalted and analyzed by LC-MS/MS. Genes were screened for potential modulation by miRNAs and protein data, subjected to functional enrichment analysis. Label-free mass spectrometry allowed the identification of 2503 follicle proteins, confirming vimentin, actin, lamin, heat shock proteins and histones as the most abundant ones. In silico analyses indicated that miRNAs modulate the expression of genes coding proteins of the sheep follicles involved in cell cycle, cell differentiation, aging, apoptosis, cell death, adipocyte differentiation, cell division. The most important biological processes associated with the follicle proteins were innate immune response, translation, adaptive immune response and protein folding, while molecular functions linked to the proteome of sheep antral follicles related to metal ion binding, ATP binding, oxygen binding, RNA binding and GTP binding, among others. Upload of 2503 Uniport accession codes through DAVID platform matched 1274 genes, associated with translation, metabolic process, proteolysis involved in cellular protein catabolic process, zona pellucida receptor complex and others. KEEG pathways analysis indicated genes correlated with ovine follicular development, with major pathways listed as carbon metabolism, biosynthesis of amino acids, glutathione metabolism, oxidative phosphorylation, fatty acid degradation and oocyte meiosis. This represents a comprehensive atlas of proteins expressed in sheep early antral follicles and will contribute to future identification of biomarkers for follicular development and oocyte maturation.
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Affiliation(s)
- Kamila S Otávio
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | - José R S Passos
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | - Renato F Silva
- School of Veterinary Medicine, State University of Ceará, Fortaleza, Brazil
| | - Laritza F Lima
- School of Veterinary Medicine, State University of Ceará, Fortaleza, Brazil
| | - Jesús Cadenas
- School of Veterinary Medicine, State University of Ceará, Fortaleza, Brazil
| | - Victor M Paes
- School of Veterinary Medicine, State University of Ceará, Fortaleza, Brazil
| | - Hudson H V Correia
- School of Veterinary Medicine, State University of Ceará, Fortaleza, Brazil
| | | | | | | | - Laís L B Oliveira
- Drug Research and Development Center, School of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Guilherme G C Carvalho
- Drug Research and Development Center, School of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Carlos R K Paier
- Drug Research and Development Center, School of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Claudia Pessoa
- Drug Research and Development Center, School of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Denise G Guerreiro
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | - Maria Elisabete A Moraes
- Drug Research and Development Center, School of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | | | - Arlindo A Moura
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil; Drug Research and Development Center, School of Medicine, Federal University of Ceará, Fortaleza, Brazil.
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27
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Clasen MA, Kurt LU, Santos MDM, Lima DB, Liu F, Gozzo FC, Barbosa VC, Carvalho PC. Increasing confidence in proteomic spectral deconvolution through mass defect. Bioinformatics 2022; 38:5119-5120. [PMID: 36130273 DOI: 10.1093/bioinformatics/btac638] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/24/2022] [Accepted: 09/19/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Confident deconvolution of proteomic spectra is critical for several applications such as de novo sequencing, cross-linking mass spectrometry and handling chimeric mass spectra. RESULTS In general, all deconvolution algorithms may eventually report mass peaks that are not compatible with the chemical formula of any peptide. We show how to remove these artifacts by considering their mass defects. We introduce Y.A.D.A. 3.0, a fast deconvolution algorithm that can remove peaks with unacceptable mass defects. Our approach is effective for polypeptides with less than 10 kDa, and its essence can be easily incorporated into any deconvolution algorithm. AVAILABILITY AND IMPLEMENTATION Y.A.D.A. 3.0 is freely available for academic use at http://patternlabforproteomics.org/yada3. SUPPLEMENTARY INFORMATION Supplementary information is available at Bioinformatics online.
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Affiliation(s)
- Milan A Clasen
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz-Paraná 81310-020, Brazil
| | - Louise U Kurt
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz-Paraná 81310-020, Brazil
| | - Marlon D M Santos
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz-Paraná 81310-020, Brazil
| | - Diogo B Lima
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Fan Liu
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Fabio C Gozzo
- Dalton Mass Spectrometry Laboratory, Unicamp, Campinas 13083-970, Brazil
| | - Valmir C Barbosa
- Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro 21941-972, Brazil
| | - Paulo C Carvalho
- Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz-Paraná 81310-020, Brazil
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da Silva EMG, Rebello KM, Choi YJ, Gregorio V, Paschoal AR, Mitreva M, McKerrow JH, Neves-Ferreira AGDC, Passetti F. Identification of Novel Genes and Proteoforms in Angiostrongylus costaricensis through a Proteogenomic Approach. Pathogens 2022; 11:1273. [PMID: 36365024 PMCID: PMC9694666 DOI: 10.3390/pathogens11111273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/15/2022] [Accepted: 10/20/2022] [Indexed: 07/22/2023] Open
Abstract
RNA sequencing (RNA-Seq) and mass-spectrometry-based proteomics data are often integrated in proteogenomic studies to assist in the prediction of eukaryote genome features, such as genes, splicing, single-nucleotide (SNVs), and single-amino-acid variants (SAAVs). Most genomes of parasite nematodes are draft versions that lack transcript- and protein-level information and whose gene annotations rely only on computational predictions. Angiostrongylus costaricensis is a roundworm species that causes an intestinal inflammatory disease, known as abdominal angiostrongyliasis (AA). Currently, there is no drug available that acts directly on this parasite, mostly due to the sparse understanding of its molecular characteristics. The available genome of A. costaricensis, specific to the Costa Rica strain, is a draft version that is not supported by transcript- or protein-level evidence. This study used RNA-Seq and MS/MS data to perform an in-depth annotation of the A. costaricensis genome. Our prediction improved the reference annotation with (a) novel coding and non-coding genes; (b) pieces of evidence of alternative splicing generating new proteoforms; and (c) a list of SNVs between the Brazilian (Crissiumal) and the Costa Rica strain. To the best of our knowledge, this is the first time that a multi-omics approach has been used to improve the genome annotation of A. costaricensis. We hope this improved genome annotation can assist in the future development of drugs, kits, and vaccines to treat, diagnose, and prevent AA caused by either the Brazil strain (Crissiumal) or the Costa Rica strain.
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Affiliation(s)
- Esdras Matheus Gomes da Silva
- Instituto Carlos Chagas, Fiocruz, Curitiba 81350-010, PR, Brazil
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Karina Mastropasqua Rebello
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
- Laboratory of Integrated Studies in Protozoology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
| | - Young-Jun Choi
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Vitor Gregorio
- Bioinformatics and Pattern Recognition Group (Bioinfo-CP), Department of Computer Science (DACOM), Federal University of Technology-Parana (UTFPR), Cornélio Procópio 86300-000, PR, Brazil
| | - Alexandre Rossi Paschoal
- Bioinformatics and Pattern Recognition Group (Bioinfo-CP), Department of Computer Science (DACOM), Federal University of Technology-Parana (UTFPR), Cornélio Procópio 86300-000, PR, Brazil
| | - Makedonka Mitreva
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - James H. McKerrow
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA 92093, USA
| | | | - Fabio Passetti
- Instituto Carlos Chagas, Fiocruz, Curitiba 81350-010, PR, Brazil
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29
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Chacon DS, Santos MDM, Bonilauri B, Vilasboa J, da Costa CT, da Silva IB, Torres TDM, de Araújo TF, Roque ADA, Pilon AC, Selegatto DM, Freire RT, Reginaldo FPS, Voigt EL, Zuanazzi JAS, Scortecci KC, Cavalheiro AJ, Lopes NP, Ferreira LDS, dos Santos LV, Fontes W, de Sousa MV, Carvalho PC, Fett-Neto AG, Giordani RB. Non-target molecular network and putative genes of flavonoid biosynthesis in Erythrina velutina Willd., a Brazilian semiarid native woody plant. FRONTIERS IN PLANT SCIENCE 2022; 13:947558. [PMID: 36161018 PMCID: PMC9493460 DOI: 10.3389/fpls.2022.947558] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/26/2022] [Indexed: 06/16/2023]
Abstract
Erythrina velutina is a Brazilian native tree of the Caatinga (a unique semiarid biome). It is widely used in traditional medicine showing anti-inflammatory and central nervous system modulating activities. The species is a rich source of specialized metabolites, mostly alkaloids and flavonoids. To date, genomic information, biosynthesis, and regulation of flavonoids remain unknown in this woody plant. As part of a larger ongoing research goal to better understand specialized metabolism in plants inhabiting the harsh conditions of the Caatinga, the present study focused on this important class of bioactive phenolics. Leaves and seeds of plants growing in their natural habitat had their metabolic and proteomic profiles analyzed and integrated with transcriptome data. As a result, 96 metabolites (including 43 flavonoids) were annotated. Transcripts of the flavonoid pathway totaled 27, of which EvCHI, EvCHR, EvCHS, EvCYP75A and EvCYP75B1 were identified as putative main targets for modulating the accumulation of these metabolites. The highest correspondence of mRNA vs. protein was observed in the differentially expressed transcripts. In addition, 394 candidate transcripts encoding for transcription factors distributed among the bHLH, ERF, and MYB families were annotated. Based on interaction network analyses, several putative genes of the flavonoid pathway and transcription factors were related, particularly TFs of the MYB family. Expression patterns of transcripts involved in flavonoid biosynthesis and those involved in responses to biotic and abiotic stresses were discussed in detail. Overall, these findings provide a base for the understanding of molecular and metabolic responses in this medicinally important species. Moreover, the identification of key regulatory targets for future studies aiming at bioactive metabolite production will be facilitated.
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Affiliation(s)
- Daisy Sotero Chacon
- Department of Pharmacy, Federal University of Rio Grande do Norte (UFRN), Natal, RN, Brazil
| | | | - Bernardo Bonilauri
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States
| | - Johnatan Vilasboa
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Cibele Tesser da Costa
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Taffarel de Melo Torres
- Bioinformatics, Biostatistics and Computer Biology Nucleus, Rural Federal University of the Semiarid, Mossoró, RN, Brazil
| | | | - Alan de Araújo Roque
- Institute for Sustainable Development and Environment, Dunas Park Herbarium, Natal, RN, Brazil
| | - Alan Cesar Pilon
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil
| | - Denise Medeiros Selegatto
- Zimmermann Group, European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Rafael Teixeira Freire
- Signal and Information Processing for Sensing Systems, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Eduardo Luiz Voigt
- Department of Cell Biology and Genetics, Center for Biosciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | | | - Kátia Castanho Scortecci
- Department of Cell Biology and Genetics, Center for Biosciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | | | - Norberto Peporine Lopes
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil
| | | | - Leandro Vieira dos Santos
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia, DF, Brazil
| | - Marcelo Valle de Sousa
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia, DF, Brazil
| | - Paulo Costa Carvalho
- Computational and Structural Proteomics Laboratory, Carlos Chagas Institute, Fiocruz, PR, Brazil
| | - Arthur Germano Fett-Neto
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Raquel Brandt Giordani
- Department of Pharmacy, Federal University of Rio Grande do Norte (UFRN), Natal, RN, Brazil
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30
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Spermatozoa and seminal plasma proteomics: too many molecules, too few markers. The case of bovine and porcine semen. Anim Reprod Sci 2022; 247:107075. [DOI: 10.1016/j.anireprosci.2022.107075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/06/2022] [Accepted: 09/20/2022] [Indexed: 11/22/2022]
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Combination of E- and NS1-Derived DNA Vaccines: The Immune Response and Protection Elicited in Mice against DENV2. Viruses 2022; 14:v14071452. [PMID: 35891431 PMCID: PMC9323404 DOI: 10.3390/v14071452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/16/2022] Open
Abstract
The occurrence of dengue disease has increased radically in recent decades. Previously, we constructed the pE1D2 and pcTPANS1 DNA vaccines encoding the DENV2 envelope (E) and non-structural 1 (NS1) proteins, respectively. To decrease the number of plasmids in a tetravalent candidate vaccine, we constructed a bicistronic plasmid, pNS1/E/D2, encoding these two proteins simultaneously. We evaluated the protective immunity induced in mice vaccinated with the pNS1/E/D2 candidate and compared to the responses elicited by immunization with the former vaccines isolated or in combination. We transfected BHK-21 cells with the different plasmids and detected recombinant proteins by immunofluorescence and mass spectrometry assays to confirm antigen expression. BALB/c mice were inoculated with the DNA vaccines followed by a lethal DENV2 challenge. ELISA, PRNT50, and IFN-gamma ELISPOT assays were performed for the investigation of the humoral and cellular responses. We observed the concomitant expression of NS1 and E proteins in pNS1/E/D2-transfected cells. All E-based vaccines induced anti-E and neutralizing antibodies. However, anti-NS1 antibodies were only observed after immunization with the pcTPANS1 administered alone or combined with pE1D2. In contrast, splenocytes from pNS1/E/D2- or pcTPANS1 + pE1D2-vaccinated animals responded to NS1- and E-derived synthetic peptides. All the DNA vaccines conferred protection against DENV2.
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32
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Bittencourt CB, Carvalho da Silva TL, Rodrigues Neto JC, Vieira LR, Leão AP, de Aquino Ribeiro JA, Abdelnur PV, de Sousa CAF, Souza MT. Insights from a Multi-Omics Integration (MOI) Study in Oil Palm (Elaeis guineensis Jacq.) Response to Abiotic Stresses: Part One—Salinity. PLANTS 2022; 11:plants11131755. [PMID: 35807707 PMCID: PMC9269341 DOI: 10.3390/plants11131755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 12/13/2022]
Abstract
Oil palm (Elaeis guineensis Jacq.) is the number one source of consumed vegetable oil nowadays. It is cultivated in areas of tropical rainforest, where it meets its natural condition of high rainfall throughout the year. The palm oil industry faces criticism due to a series of practices that was considered not environmentally sustainable, and it finds itself under pressure to adopt new and innovative procedures to reverse this negative public perception. Cultivating this oilseed crop outside the rainforest zone is only possible using artificial irrigation. Close to 30% of the world’s irrigated agricultural lands also face problems due to salinity stress. Consequently, the research community must consider drought and salinity together when studying to empower breeding programs in order to develop superior genotypes adapted to those potential new areas for oil palm cultivation. Multi-Omics Integration (MOI) offers a new window of opportunity for the non-trivial challenge of unraveling the mechanisms behind multigenic traits, such as drought and salinity tolerance. The current study carried out a comprehensive, large-scale, single-omics analysis (SOA), and MOI study on the leaves of young oil palm plants submitted to very high salinity stress. Taken together, a total of 1239 proteins were positively regulated, and 1660 were negatively regulated in transcriptomics and proteomics analyses. Meanwhile, the metabolomics analysis revealed 37 metabolites that were upregulated and 92 that were downregulated. After performing SOA, 436 differentially expressed (DE) full-length transcripts, 74 DE proteins, and 19 DE metabolites underwent MOI analysis, revealing several pathways affected by this stress, with at least one DE molecule in all three omics platforms used. The Cysteine and methionine metabolism (map00270) and Glycolysis/Gluconeogenesis (map00010) pathways were the most affected ones, each one with 20 DE molecules.
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Affiliation(s)
- Cleiton Barroso Bittencourt
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras 37200-000, Brazil; (C.B.B.); (T.L.C.d.S.); (L.R.V.)
| | - Thalliton Luiz Carvalho da Silva
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras 37200-000, Brazil; (C.B.B.); (T.L.C.d.S.); (L.R.V.)
| | | | - Letícia Rios Vieira
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras 37200-000, Brazil; (C.B.B.); (T.L.C.d.S.); (L.R.V.)
| | - André Pereira Leão
- Embrapa Agroenergia, Brasília 70770-901, Brazil; (J.C.R.N.); (A.P.L.); (J.A.d.A.R.); (P.V.A.)
| | | | | | | | - Manoel Teixeira Souza
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras 37200-000, Brazil; (C.B.B.); (T.L.C.d.S.); (L.R.V.)
- Embrapa Agroenergia, Brasília 70770-901, Brazil; (J.C.R.N.); (A.P.L.); (J.A.d.A.R.); (P.V.A.)
- Correspondence: ; Tel.: +55-61-3448-3210
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