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Braga TT, Davanso MR, Mendes D, de Souza TA, de Brito AF, Cruz MC, Hiyane MI, de Lima DS, Nunes V, de Fátima Giarola J, Souto DEP, Próchnicki T, Lauterbach M, Biscaia SMP, de Freitas RA, Curi R, Pontillo A, Latz E, Camara NOS. Sensing soluble uric acid by Naip1-Nlrp3 platform. Cell Death Dis 2021; 12:158. [PMID: 33547278 PMCID: PMC7864962 DOI: 10.1038/s41419-021-03445-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/11/2021] [Accepted: 01/15/2021] [Indexed: 01/30/2023]
Abstract
Uric acid (UA), a product of purine nucleotide degradation able to initiate an immune response, represents a breakpoint in the evolutionary history of humans, when uricase, the enzyme required for UA cleavage, was lost. Despite being inert in human cells, UA in its soluble form (sUA) can increase the level of interleukin-1β (IL-1β) in murine macrophages. We, therefore, hypothesized that the recognition of sUA is achieved by the Naip1-Nlrp3 inflammasome platform. Through structural modelling predictions and transcriptome and functional analyses, we found that murine Naip1 expression in human macrophages induces IL-1β expression, fatty acid production and an inflammation-related response upon sUA stimulation, a process reversed by the pharmacological and genetic inhibition of Nlrp3. Moreover, molecular interaction experiments showed that Naip1 directly recognizes sUA. Accordingly, Naip may be the sUA receptor lost through the human evolutionary process, and a better understanding of its recognition may lead to novel anti-hyperuricaemia therapies.
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Affiliation(s)
- Tarcio Teodoro Braga
- Department of Basic Pathology, Federal University of Parana, Curitiba, PR, Brazil.
- Department of Immunology, Institute of Biomedical Sciences IV, University of São Paulo, São Paulo, SP, Brazil.
- Institute of Innate Immunity, University Hospitals Bonn, Bonn, Germany.
| | - Mariana Rodrigues Davanso
- Department of Immunology, Institute of Biomedical Sciences IV, University of São Paulo, São Paulo, SP, Brazil
- Institute of Innate Immunity, University Hospitals Bonn, Bonn, Germany
- Department of Physiology and Biophysics, Institute of Biomedical Sciences I, University of Sao Paulo, São Paulo, SP, Brazil
| | - Davi Mendes
- Department of Microbiology, Institute of Biomedical Sciences II, University of São Paulo, São Paulo, SP, Brazil
| | - Tiago Antonio de Souza
- Department of Microbiology, Institute of Biomedical Sciences II, University of São Paulo, São Paulo, SP, Brazil
| | | | - Mario Costa Cruz
- Department of Immunology, Institute of Biomedical Sciences IV, University of São Paulo, São Paulo, SP, Brazil
| | - Meire Ioshie Hiyane
- Department of Immunology, Institute of Biomedical Sciences IV, University of São Paulo, São Paulo, SP, Brazil
| | - Dhemerson Souza de Lima
- Department of Immunology, Institute of Biomedical Sciences IV, University of São Paulo, São Paulo, SP, Brazil
| | - Vinicius Nunes
- Department of Immunology, Institute of Biomedical Sciences IV, University of São Paulo, São Paulo, SP, Brazil
| | | | - Denio Emanuel Pires Souto
- Institute of Chemistry, University of Campinas, Campinas, SP, Brazil
- Department of Chemistry, Federal University of Parana, Curitiba, PR, Brazil
| | - Tomasz Próchnicki
- Institute of Innate Immunity, University Hospitals Bonn, Bonn, Germany
| | - Mario Lauterbach
- Institute of Innate Immunity, University Hospitals Bonn, Bonn, Germany
| | | | | | - Rui Curi
- Department of Physiology and Biophysics, Institute of Biomedical Sciences I, University of Sao Paulo, São Paulo, SP, Brazil
- Interdisciplinary Post-Graduate Program in Health Sciences, Cruzeiro do Sul University, São Paulo, Brazil
| | - Alessandra Pontillo
- Department of Immunology, Institute of Biomedical Sciences IV, University of São Paulo, São Paulo, SP, Brazil
| | - Eicke Latz
- Institute of Innate Immunity, University Hospitals Bonn, Bonn, Germany
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01655, USA
- Centre for Molecular Inflammation Research (CEMIR), Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Niels Olsen Saraiva Camara
- Department of Immunology, Institute of Biomedical Sciences IV, University of São Paulo, São Paulo, SP, Brazil
- Nephrology Division, Federal University of São Paulo, São Paulo, SP, Brazil
- Renal Physiopathology Laboratory, Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
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Brito AFD, Braconi CT, Weidmann M, Dilcher M, Alves JMP, Gruber A, Zanotto PMDA. The Pangenome of the Anticarsia gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV). Genome Biol Evol 2015; 8:94-108. [PMID: 26615220 PMCID: PMC4758234 DOI: 10.1093/gbe/evv231] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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] [Indexed: 01/05/2023] Open
Abstract
The alphabaculovirus Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is the world's most successful viral bioinsecticide. Through the 1980s and 1990s, this virus was extensively used for biological control of populations of Anticarsia gemmatalis (Velvetbean caterpillar) in soybean crops. During this period, genetic studies identified several variable loci in the AgMNPV; however, most of them were not characterized at the sequence level. In this study we report a full genome comparison among 17 wild-type isolates of AgMNPV. We found the pangenome of this virus to contain at least 167 hypothetical genes, 151 of which are shared by all genomes. The gene bro-a that might be involved in host specificity and carrying transporter is absent in some genomes, and new hypothetical genes were observed. Among these genes there is a unique rnf12-like gene, probably implicated in ubiquitination. Events of gene fission and fusion are common, as four genes have been observed as single or split open reading frames. Gains and losses of genomic fragments (from 20 to 900 bp) are observed within tandem repeats, such as in eight direct repeats and four homologous regions. Most AgMNPV genes present low nucleotide diversity, and variable genes are mainly located in a locus known to evolve through homologous recombination. The evolution of AgMNPV is mainly driven by small indels, substitutions, gain and loss of nucleotide stretches or entire coding sequences. These variations may cause relevant phenotypic alterations, which probably affect the infectivity of AgMNPV. This work provides novel information on genomic evolution of the AgMNPV in particular and of baculoviruses in general.
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Affiliation(s)
- Anderson Fernandes de Brito
- Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Carla Torres Braconi
- Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Manfred Weidmann
- Department of Virology, University Medical Center, Göttingen, Germany
| | - Meik Dilcher
- Department of Virology, University Medical Center, Göttingen, Germany
| | - João Marcelo Pereira Alves
- Department of Parasitology, Institute of Biomedical Sciences-ICB II, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Arthur Gruber
- Department of Parasitology, Institute of Biomedical Sciences-ICB II, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Paolo Marinho de Andrade Zanotto
- Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil
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Oliveira JV, de Brito AF, Braconi CT, de Melo Freire CC, Iamarino A, de Andrade Zanotto PM. Modularity and evolutionary constraints in a baculovirus gene regulatory network. BMC Syst Biol 2013; 7:87. [PMID: 24006890 PMCID: PMC3879405 DOI: 10.1186/1752-0509-7-87] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 08/15/2013] [Indexed: 12/25/2022]
Abstract
BACKGROUND The structure of regulatory networks remains an open question in our understanding of complex biological systems. Interactions during complete viral life cycles present unique opportunities to understand how host-parasite network take shape and behave. The Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is a large double-stranded DNA virus, whose genome may encode for 152 open reading frames (ORFs). Here we present the analysis of the ordered cascade of the AgMNPV gene expression. RESULTS We observed an earlier onset of the expression than previously reported for other baculoviruses, especially for genes involved in DNA replication. Most ORFs were expressed at higher levels in a more permissive host cell line. Genes with more than one copy in the genome had distinct expression profiles, which could indicate the acquisition of new functionalities. The transcription gene regulatory network (GRN) for 149 ORFs had a modular topology comprising five communities of highly interconnected nodes that separated key genes that are functionally related on different communities, possibly maximizing redundancy and GRN robustness by compartmentalization of important functions. Core conserved functions showed expression synchronicity, distinct GRN features and significantly less genetic diversity, consistent with evolutionary constraints imposed in key elements of biological systems. This reduced genetic diversity also had a positive correlation with the importance of the gene in our estimated GRN, supporting a relationship between phylogenetic data of baculovirus genes and network features inferred from expression data. We also observed that gene arrangement in overlapping transcripts was conserved among related baculoviruses, suggesting a principle of genome organization. CONCLUSIONS Albeit with a reduced number of nodes (149), the AgMNPV GRN had a topology and key characteristics similar to those observed in complex cellular organisms, which indicates that modularity may be a general feature of biological gene regulatory networks.
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Affiliation(s)
- Juliana Velasco Oliveira
- Department of Microbiology, Institute of Biomedical Sciences – ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo – USP, São Paulo, SP, Brazil
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas Caixa Postal 6170, 13083-970, Brazil
| | - Anderson Fernandes de Brito
- Department of Microbiology, Institute of Biomedical Sciences – ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo – USP, São Paulo, SP, Brazil
| | - Carla Torres Braconi
- Department of Microbiology, Institute of Biomedical Sciences – ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo – USP, São Paulo, SP, Brazil
| | - Caio César de Melo Freire
- Department of Microbiology, Institute of Biomedical Sciences – ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo – USP, São Paulo, SP, Brazil
| | - Atila Iamarino
- Department of Microbiology, Institute of Biomedical Sciences – ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo – USP, São Paulo, SP, Brazil
| | - Paolo Marinho de Andrade Zanotto
- Department of Microbiology, Institute of Biomedical Sciences – ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo – USP, São Paulo, SP, Brazil
- Departamento de Microbiologia, Instituto de Ciências Biomédicas - ICB II, Laboratório de Evolução Molecular e Bioinformática, Universidade de São Paulo - USP, Av. Prof. Lineu Prestes, 1374, São Paulo CEP: 05508-900, Brasil
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Villabona-Arenas CJ, de Brito AF, de Andrade Zanotto PM. Genomic mosaicism in two strains of Dengue virus type 3. Infect Genet Evol 2013; 18:202-12. [PMID: 23727343 DOI: 10.1016/j.meegid.2013.05.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 05/14/2013] [Accepted: 05/15/2013] [Indexed: 11/28/2022]
Abstract
Recombination is a significant factor driving genomic evolution, but it is not well understood in Dengue virus. We used phylogenetic methods to search for recombination in 636 Dengue virus type 3 (DENV-3) genomes and unveiled complex recombination patterns in two strains, which appear to be the outcome of recombination between genotype II and genotype I parental DENV-3 lineages. Our findings of genomic mosaic structures suggest that strand switching during RNA synthesis may be involved in the generation of genetic diversity in dengue viruses.
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Affiliation(s)
- Christian Julián Villabona-Arenas
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1734, CEP: 05508-000, São Paulo, SP, Brazil
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