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da Silva-Januário ME, da Costa CS, Tavares LA, Oliveira AK, Januário YC, de Carvalho AN, Cassiano MHA, Rodrigues RL, Miller ME, Palameta S, Arns CW, Arruda E, Paes Leme AF, daSilva LLP. HIV-1 Nef Changes the Proteome of T Cells Extracellular Vesicles Depleting IFITMs and Other Antiviral Factors. Mol Cell Proteomics 2023; 22:100676. [PMID: 37940003 PMCID: PMC10746527 DOI: 10.1016/j.mcpro.2023.100676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 10/19/2023] [Accepted: 11/05/2023] [Indexed: 11/10/2023] Open
Abstract
Extracellular vesicles (EVs) are biomolecule carriers for intercellular communication in health and disease. Nef is a HIV virulence factor that is released from cells within EVs and is present in plasma EVs of HIV-1 infected individuals. We performed a quantitative proteomic analysis to fully characterize the Nef-induced changes in protein composition of T cell-derived EVs and identify novel host targets of HIV. Several proteins with well-described roles in infection or not previously associated with HIV pathogenesis were specifically modulated by Nef in EVs. Among the downregulated proteins are the interferon-induced transmembrane 1, 2, and 3 (IFITM1-3) proteins, broad-spectrum antiviral factors known to be cell-to-cell transferable by EVs. We demonstrate that Nef depletes IFITM1-3 from EVs by excluding these proteins from the plasma membrane and lipid rafts, which are sites of EVs biogenesis in T cells. Our data establish Nef as a modulator of EVs' global protein content and as an HIV factor that antagonizes IFITMs.
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Affiliation(s)
- Mara E da Silva-Januário
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Cristina S da Costa
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Lucas A Tavares
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Ana K Oliveira
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - Yunan C Januário
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Andreia N de Carvalho
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Murilo H A Cassiano
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Roger L Rodrigues
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Michael E Miller
- Instituto de Biologia, Universidade de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Soledad Palameta
- Instituto de Biologia, Universidade de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Clarice W Arns
- Instituto de Biologia, Universidade de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Eurico Arruda
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Adriana F Paes Leme
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - Luis L P daSilva
- Centro de Pesquisa em Virologia (CPV) and Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil.
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Martins-Santana L, Nora LC, Sanches-Medeiros A, Lovate GL, Cassiano MHA, Silva-Rocha R. Systems and Synthetic Biology Approaches to Engineer Fungi for Fine Chemical Production. Front Bioeng Biotechnol 2018; 6:117. [PMID: 30338257 PMCID: PMC6178918 DOI: 10.3389/fbioe.2018.00117] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/02/2018] [Indexed: 01/16/2023] Open
Abstract
Since the advent of systems and synthetic biology, many studies have sought to harness microbes as cell factories through genetic and metabolic engineering approaches. Yeast and filamentous fungi have been successfully harnessed to produce fine and high value-added chemical products. In this review, we present some of the most promising advances from recent years in the use of fungi for this purpose, focusing on the manipulation of fungal strains using systems and synthetic biology tools to improve metabolic flow and the flow of secondary metabolites by pathway redesign. We also review the roles of bioinformatics analysis and predictions in synthetic circuits, highlighting in silico systemic approaches to improve the efficiency of synthetic modules.
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Affiliation(s)
- Leonardo Martins-Santana
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
| | - Luisa C Nora
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
| | - Ananda Sanches-Medeiros
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
| | - Gabriel L Lovate
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
| | - Murilo H A Cassiano
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
| | - Rafael Silva-Rocha
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
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