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Fleith RC, Lobo FP, Dos Santos PF, Rocha MM, Bordignon J, Strottmann DM, Patricio DO, Pavanelli WR, Lo Sarzi M, Santos CND, Ferguson BJ, Mansur DS. Genome-wide analyses reveal a highly conserved Dengue virus envelope peptide which is critical for virus viability and antigenic in humans. Sci Rep 2016; 6:36339. [PMID: 27805018 PMCID: PMC5090869 DOI: 10.1038/srep36339] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/14/2016] [Indexed: 12/15/2022] Open
Abstract
Targeting regions of proteins that show a high degree of structural conservation has been proposed as a method of developing immunotherapies and vaccines that may bypass the wide genetic variability of RNA viruses. Despite several attempts, a vaccine that protects evenly against the four circulating Dengue virus (DV) serotypes remains elusive. To find critical conserved amino acids in dengue viruses, 120 complete genomes of each serotype were selected at random and used to calculate conservation scores for nucleotide and amino acid sequences. The identified peptide sequences were analysed for their structural conservation and localisation using crystallographic data. The longest, surface exposed, highly conserved peptide of Envelope protein was found to correspond to amino acid residues 250 to 270. Mutation of this peptide in DV1 was lethal, since no replication of the mutant virus was detected in human cells. Antibodies against this peptide were detected in DV naturally infected patients indicating its potential antigenicity. Hence, this study has identified a highly conserved, critical peptide in DV that is a target of antibodies in infected humans.
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Affiliation(s)
- Renata C Fleith
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Parasitology, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Francisco P Lobo
- Department of General Biology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Paula F Dos Santos
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Parasitology, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Mariana M Rocha
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Parasitology, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Juliano Bordignon
- Laboratory of Molecular Virology, Instituto Carlos Chagas, Curitiba, Brazil
| | - Daisy M Strottmann
- Laboratory of Molecular Virology, Instituto Carlos Chagas, Curitiba, Brazil
| | - Daniel O Patricio
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Parasitology, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | | | | | - Claudia N D Santos
- Laboratory of Molecular Virology, Instituto Carlos Chagas, Curitiba, Brazil
| | | | - Daniel S Mansur
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Parasitology, Universidade Federal de Santa Catarina, Florianópolis, Brazil
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4
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Hongo JA, de Castro GM, Cintra LC, Zerlotini A, Lobo FP. POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes. BMC Genomics 2015; 16:567. [PMID: 26231214 PMCID: PMC4521464 DOI: 10.1186/s12864-015-1765-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 07/10/2015] [Indexed: 11/29/2022] Open
Abstract
Background Detection of genes evolving under positive Darwinian evolution in genome-scale data is nowadays a prevailing strategy in comparative genomics studies to identify genes potentially involved in adaptation processes. Despite the large number of studies aiming to detect and contextualize such gene sets, there is virtually no software available to perform this task in a general, automatic, large-scale and reliable manner. This certainly occurs due to the computational challenges involved in this task, such as the appropriate modeling of data under analysis, the computation time to perform several of the required steps when dealing with genome-scale data and the highly error-prone nature of the sequence and alignment data structures needed for genome-wide positive selection detection. Results We present POTION, an open source, modular and end-to-end software for genome-scale detection of positive Darwinian selection in groups of homologous coding sequences. Our software represents a key step towards genome-scale, automated detection of positive selection, from predicted coding sequences and their homology relationships to high-quality groups of positively selected genes. POTION reduces false positives through several sophisticated sequence and group filters based on numeric, phylogenetic, quality and conservation criteria to remove spurious data and through multiple hypothesis corrections, and considerably reduces computation time thanks to a parallelized design. Our software achieved a high classification performance when used to evaluate a curated dataset of Trypanosoma brucei paralogs previously surveyed for positive selection. When used to analyze predicted groups of homologous genes of 19 strains of Mycobacterium tuberculosis as a case study we demonstrated the filters implemented in POTION to remove sources of errors that commonly inflate errors in positive selection detection. A thorough literature review found no other software similar to POTION in terms of customization, scale and automation. Conclusion To the best of our knowledge, POTION is the first tool to allow users to construct and check hypotheses regarding the occurrence of site-based evidence of positive selection in non-curated, genome-scale data within a feasible time frame and with no human intervention after initial configuration. POTION is available at http://www.lmb.cnptia.embrapa.br/share/POTION/. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1765-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jorge A Hongo
- Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Campinas, São Paulo, 13083-886, Brazil.
| | - Giovanni M de Castro
- Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Campinas, São Paulo, 13083-886, Brazil.
| | - Leandro C Cintra
- Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Campinas, São Paulo, 13083-886, Brazil.
| | - Adhemar Zerlotini
- Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Campinas, São Paulo, 13083-886, Brazil.
| | - Francisco P Lobo
- Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Campinas, São Paulo, 13083-886, Brazil.
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6
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Ruiz JC, D'Afonseca V, Silva A, Ali A, Pinto AC, Santos AR, Rocha AAMC, Lopes DO, Dorella FA, Pacheco LGC, Costa MP, Turk MZ, Seyffert N, Moraes PMRO, Soares SC, Almeida SS, Castro TLP, Abreu VAC, Trost E, Baumbach J, Tauch A, Schneider MPC, McCulloch J, Cerdeira LT, Ramos RTJ, Zerlotini A, Dominitini A, Resende DM, Coser EM, Oliveira LM, Pedrosa AL, Vieira CU, Guimarães CT, Bartholomeu DC, Oliveira DM, Santos FR, Rabelo ÉM, Lobo FP, Franco GR, Costa AF, Castro IM, Dias SRC, Ferro JA, Ortega JM, Paiva LV, Goulart LR, Almeida JF, Ferro MIT, Carneiro NP, Falcão PRK, Grynberg P, Teixeira SMR, Brommonschenkel S, Oliveira SC, Meyer R, Moore RJ, Miyoshi A, Oliveira GC, Azevedo V. Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains. PLoS One 2011; 6:e18551. [PMID: 21533164 PMCID: PMC3078919 DOI: 10.1371/journal.pone.0018551] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 03/11/2011] [Indexed: 02/02/2023] Open
Abstract
Background Corynebacterium pseudotuberculosis, a Gram-positive, facultative intracellular pathogen, is the etiologic agent of the disease known as caseous lymphadenitis (CL). CL mainly affects small ruminants, such as goats and sheep; it also causes infections in humans, though rarely. This species is distributed worldwide, but it has the most serious economic impact in Oceania, Africa and South America. Although C. pseudotuberculosis causes major health and productivity problems for livestock, little is known about the molecular basis of its pathogenicity. Methodology and Findings We characterized two C. pseudotuberculosis genomes (Cp1002, isolated from goats; and CpC231, isolated from sheep). Analysis of the predicted genomes showed high similarity in genomic architecture, gene content and genetic order. When C. pseudotuberculosis was compared with other Corynebacterium species, it became evident that this pathogenic species has lost numerous genes, resulting in one of the smallest genomes in the genus. Other differences that could be part of the adaptation to pathogenicity include a lower GC content, of about 52%, and a reduced gene repertoire. The C. pseudotuberculosis genome also includes seven putative pathogenicity islands, which contain several classical virulence factors, including genes for fimbrial subunits, adhesion factors, iron uptake and secreted toxins. Additionally, all of the virulence factors in the islands have characteristics that indicate horizontal transfer. Conclusions These particular genome characteristics of C. pseudotuberculosis, as well as its acquired virulence factors in pathogenicity islands, provide evidence of its lifestyle and of the pathogenicity pathways used by this pathogen in the infection process. All genomes cited in this study are available in the NCBI Genbank database (http://www.ncbi.nlm.nih.gov/genbank/) under accession numbers CP001809 and CP001829.
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Affiliation(s)
- Jerônimo C. Ruiz
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Vívian D'Afonseca
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Artur Silva
- Department of Genetics, Federal University of Pará, Belém, Pará, Brazil
| | - Amjad Ali
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Anne C. Pinto
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Anderson R. Santos
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Aryanne A. M. C. Rocha
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Débora O. Lopes
- Health Sciences Center, Federal University of São João Del Rei, Divinópilis, Minas Gerais, Brazil
| | - Fernanda A. Dorella
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Luis G. C. Pacheco
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Biointeraction Sciences, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Marcília P. Costa
- Department of Veterinary Medicine, State University of Ceará, Fortaleza, Ceará, Brazil
| | - Meritxell Z. Turk
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Núbia Seyffert
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Pablo M. R. O. Moraes
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Siomar C. Soares
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sintia S. Almeida
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Thiago L. P. Castro
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vinicius A. C. Abreu
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Eva Trost
- Department of Genetics, University of Bielefeld, CeBiTech, Bielefeld, Nordrhein-Westfale, Germany
| | - Jan Baumbach
- Department of Computer Science, Max-Planck-Institut für Informatik, Saarbrücken, Saarlan, Germany
| | - Andreas Tauch
- Department of Genetics, University of Bielefeld, CeBiTech, Bielefeld, Nordrhein-Westfale, Germany
| | | | - John McCulloch
- Department of Genetics, Federal University of Pará, Belém, Pará, Brazil
| | | | | | - Adhemar Zerlotini
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Anderson Dominitini
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Daniela M. Resende
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
- Department of Pharmaceutical Sciences, Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Elisângela M. Coser
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Luciana M. Oliveira
- Department of Phisics, Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - André L. Pedrosa
- Department of Pharmaceutical Sciences, Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
- Department of Biological Sciences, Federal University of Triangulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Carlos U. Vieira
- Department of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Cláudia T. Guimarães
- Brazilian Agricultural Research Corporation (EMBRAPA), Sete Lagoas, Minas Gerais, Brazil
| | - Daniela C. Bartholomeu
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Diana M. Oliveira
- Department of Veterinary Medicine, State University of Ceará, Fortaleza, Ceará, Brazil
| | - Fabrício R. Santos
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Élida Mara Rabelo
- Department of Parasitology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Francisco P. Lobo
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Glória R. Franco
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ana Flávia Costa
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ieso M. Castro
- Department of Pharmacy, Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Sílvia Regina Costa Dias
- Department of Parasitology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Jesus A. Ferro
- Department of Technology, State University of São Paulo, Jaboticabal, São Paulo, Brazil
| | - José Miguel Ortega
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Luciano V. Paiva
- Department of Chemistry, Federal University of Lavras, Lavras, Minas Gerais, Brazil
| | - Luiz R. Goulart
- Department of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Juliana Franco Almeida
- Department of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Maria Inês T. Ferro
- Department of Technology, State University of São Paulo, Jaboticabal, São Paulo, Brazil
| | - Newton P. Carneiro
- Brazilian Agricultural Research Corporation (EMBRAPA), Sete Lagoas, Minas Gerais, Brazil
| | - Paula R. K. Falcão
- Brazilian Agricultural Research Corporation (EMBRAPA), Campinas, São Paulo, Brazil
| | - Priscila Grynberg
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Santuza M. R. Teixeira
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sérgio Brommonschenkel
- Department of Plant Pathology, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - Sérgio C. Oliveira
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Roberto Meyer
- Department of Biointeraction Sciences, Federal University of Bahia, Salvador, Bahia, Brazil
| | | | - Anderson Miyoshi
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Guilherme C. Oliveira
- Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
- Center of Excellence in Bioinformatics, National Institute of Science and Technology, Research Center René Rachou, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- * E-mail:
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10
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Waisberg M, Lobo FP, Cerqueira GC, Passos LKJ, Carvalho OS, Franco GR, El-Sayed NM. Microarray analysis of gene expression induced by sexual contact in Schistosoma mansoni. BMC Genomics 2007; 8:181. [PMID: 17578584 PMCID: PMC1929073 DOI: 10.1186/1471-2164-8-181] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2007] [Accepted: 06/20/2007] [Indexed: 12/04/2022] Open
Abstract
Background The parasitic trematode Schistosoma mansoni is one of the major causative agents of Schistosomiasis, a disease that affects approximately 200 million people, mostly in developing countries. Since much of the pathology is associated with eggs laid by the female worm, understanding the mechanisms involved in oogenesis and sexual maturation is an important step towards the discovery of new targets for effective drug therapy. It is known that the adult female worm only develops fully in the presence of a male worm and that the rates of oviposition and maturation of eggs are significantly increased by mating. In order to study gene transcripts associated with sexual maturation and oviposition, we compared the gene expression profiles of sexually mature and immature parasites using DNA microarrays. Results For each experiment, three amplified RNA microarray hybridizations and their dye swaps were analyzed. Our results show that 265 transcripts are differentially expressed in adult females and 53 in adult males when mature and immature worms are compared. Of the genes differentially expressed, 55% are expressed at higher levels in paired females while the remaining 45% are more expressed in unpaired ones and 56.6% are expressed at higher levels in paired male worms while the remaining 43.4% are more expressed in immature parasites. Real-time RT-PCR analysis validated the microarray results. Several new maturation associated transcripts were identified. Genes that were up-regulated in single-sex females were mostly related to energy generation (i.e. carbohydrate and protein metabolism, generation of precursor metabolites and energy, cellular catabolism, and organelle organization and biogenesis) while genes that were down-regulated related to RNA metabolism, reactive oxygen species metabolism, electron transport, organelle organization and biogenesis and protein biosynthesis. Conclusion Our results confirm previous observations related to gene expression induced by sexual maturation in female schistosome worms. They also increase the list of S. mansoni maturation associated transcripts considerably, therefore opening new and exciting avenues for the study of the conjugal biology and development of new drugs against schistosomes.
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Affiliation(s)
- Michael Waisberg
- Laboratório de Genética Bioquímica, Departmento de Imunologia e Bioquímica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Parasite Genomics, The Institute for Genomic Research, Rockville, MD, USA
| | - Francisco P Lobo
- Laboratório de Genética Bioquímica, Departmento de Imunologia e Bioquímica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gustavo C Cerqueira
- Department of Parasite Genomics, The Institute for Genomic Research, Rockville, MD, USA
- Laboratório de Genética Molecular de Tripanosomatídeos, Departamento de Imunologia e Bioquímica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Liana KJ Passos
- Centro de Pesquisas René Rachou, Fundação Osvaldo Cruz, Belo Horizonte, MG, Brazil
| | - Omar S Carvalho
- Centro de Pesquisas René Rachou, Fundação Osvaldo Cruz, Belo Horizonte, MG, Brazil
| | - Glória R Franco
- Laboratório de Genética Bioquímica, Departmento de Imunologia e Bioquímica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Najib M El-Sayed
- Department of Parasite Genomics, The Institute for Genomic Research, Rockville, MD, USA
- Department of Cell Biology and Molecular Genetics and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
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