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Gomes LGR, Dutra JCF, Profeta R, Dias MV, García GJY, Rodrigues DLN, Goés Neto A, Aburjaile FF, Tiwari S, Soares SC, Azevedo V, Jaiswal AK. Systematic review of reverse vaccinology and immunoinformatics data for non-viral sexually transmitted infections. AN ACAD BRAS CIENC 2023; 95:e20230617. [PMID: 38055447 DOI: 10.1590/0001-3765202320230617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/27/2023] [Indexed: 12/08/2023] Open
Abstract
Sexually Transmitted Infections (STIs) are a public health burden rising in developed and developing nations. The World Health Organization estimates nearly 374 million new cases of curable STIs yearly. Global efforts to control their spread have been insufficient in fulfilling their objective. As there is no vaccine for many of these infections, these efforts are focused on education and condom distribution. The development of vaccines for STIs is vital for successfully halting their spread. The field of immunoinformatics is a powerful new tool for vaccine development, allowing for the identification of vaccine candidates within a bacterium's genome and allowing for the design of new genome-based vaccine peptides. The goal of this review was to evaluate the usage of immunoinformatics in research focused on non-viral STIs, identifying fields where research efforts are concentrated. Here we describe gaps in applying these techniques, as in the case of Treponema pallidum and Trichomonas vaginalis.
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Affiliation(s)
- Lucas Gabriel R Gomes
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Joyce C F Dutra
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Microbiologia, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Rodrigo Profeta
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Mariana V Dias
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Glen J Y García
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Bioinformática, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Diego Lucas N Rodrigues
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
- Universidade Federal de Minas Gerais (UFMG), Escola de Veterinária, Departamento de Medicina Veterinária, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Aristóteles Goés Neto
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Microbiologia, Laboratório de Biologia Molecular e Computacional de Fungos, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Flávia F Aburjaile
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
- Universidade Federal de Minas Gerais (UFMG), Escola de Veterinária, Departamento de Medicina Veterinária, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Sandeep Tiwari
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
- Universidade Federal da Bahia, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, Ondina, 40170-115 Salvador, BA, Brazil
- Universidade Federal da Bahia, Instituto de Ciências da Saúde, Av. Reitor Miguel Calmon, s/n, Vale do Canela, 40110-902 Salvador, BA, Brazil
| | - Siomar C Soares
- Universidade Federal do Triângulo Mineiro (UFTM), Instituto de Ciências Biológicas e Naturais, Departamento de Microbiologia, Imunologia, e Parasitologia, Rua Vigário Carlos, 100, Abadia, 38025-180 Uberaba, MG, Brazil
| | - Vasco Azevedo
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Arun K Jaiswal
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Laboratório de Genética Celular e Molecular (LGCM), Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
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Velez LS, Aburjaile FF, Farias ARG, Baia ADB, Oliveira WJ, Silva AMF, Benko-Iseppon AM, Azevedo V, Brenig B, Ham JH, Souza EB, Gama MAS. Burkholderia semiarida sp. nov. and Burkholderia sola sp. nov., two novel B. cepacia complex species causing onion sour skin. Syst Appl Microbiol 2023; 46:126415. [PMID: 36933352 DOI: 10.1016/j.syapm.2023.126415] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/13/2023]
Abstract
Two putative novel Burkholderia cenocepacia lineages found in the semi-arid region of north-east Brazil causing onion sour skin were studied using genomic approaches to determine their taxonomic position. Four strains belonging to one novel lineage (CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171) and one strain (CCRMBC51) belonging to another novel lineage had their whole genome sequenced to carry out taxogenomic analyses. The phylogenomic tree built using the type (strain) genome server (TYGS) clustered the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171 into the same clade, while grouped the strain CCRMBC51 separately. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analysis showed values above 99.21 % and 93.2 %, respectively, among the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171, while ANI and dDDH values between these strains and the strain CCRMBC51 were below 94.49 % and 56.6 %, respectively. All these strains showed ANI and dDDH values below 94.78 % and 58.8 % concerning type strains of the B. cepacia complex (Bcc) species. The phylogenetic maximum likelihood tree constructed based on the multilocus sequence analysis of core genes (cMLSA) clustered the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171 and the strain CCRMBC51 in two exclusive clades, which did not cluster with any known species of the Bcc. Therefore, combined data from TYGS, ANI, dDDH, and cMLSA demonstrated that the strains represent two novel species of the Bcc, which we classified as Burkholderia semiarida sp. nov. and Burkholderia sola sp. nov., and proposed the strains CCRMBC74T (=IBSBF 3371 T = CBAS 905 T) and CCRMBC51T (=IBSBF3370T = CBAS 904 T) as type strains, respectively.
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Affiliation(s)
- Leandro S Velez
- Department of Agronomy, Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil
| | - Flávia F Aburjaile
- Preventive Veterinary Medicine Departament, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Antonio R G Farias
- Center of Excellence in Fungal Research, School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Ana D B Baia
- Department of Agronomy, Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil
| | - Willams J Oliveira
- Department of Agronomy, Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil
| | - Adriano M F Silva
- Department of Agronomy, Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil
| | - Ana M Benko-Iseppon
- Department of Genetics, Universidade Federal de Pernambuco, Recife, PE 50670-901, Brazil
| | - Vasco Azevedo
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Bertram Brenig
- Department of Molecular Biology of Livestock, Institute of Veterinary Medicine, Georg August University Göttingen, 37077 Göttingen, Germany
| | - Jong H Ham
- Department Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, United States
| | - Elineide B Souza
- Department of Biology, Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil
| | - Marco A S Gama
- Department of Agronomy, Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil.
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Carvalho RDO, Guédon E, Aburjaile FF, Azevedo V. Editorial: Probiogenomics of classic and next-generation probiotics. Front Microbiol 2022; 13:982642. [PMID: 36060755 PMCID: PMC9433118 DOI: 10.3389/fmicb.2022.982642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Rodrigo D. O. Carvalho
- Department of Biochemistry and Biophysics, Institute of Health Sciences, Universidade Federal da Bahia, Salvador, Brazil
| | | | - Flávia F. Aburjaile
- Preventive Veterinary Medicine Department, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Department of Genetics, Ecology, and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- *Correspondence: Vasco Azevedo
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Silveira SA, Fassio AV, Gonçalves-Almeida VM, de Lima EB, Barcelos YT, Aburjaile FF, Rodrigues LM, Meira W, de Melo-Minardi RC. VERMONT: Visualizing mutations and their effects on protein physicochemical and topological property conservation. BMC Proc 2014; 8:S4. [PMID: 25237391 PMCID: PMC4155615 DOI: 10.1186/1753-6561-8-s2-s4] [Citation(s) in RCA: 5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In this paper, we propose an interactive visualization called VERMONT which tackles the problem of visualizing mutations and infers their possible effects on the conservation of physicochemical and topological properties in protein families. More specifically, we visualize a set of structure-based sequence alignments and integrate several structural parameters that should aid biologists in gaining insight into possible consequences of mutations. VERMONT allowed us to identify patterns of position-specific properties as well as exceptions that may help predict whether specific mutations could damage protein function.
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Affiliation(s)
- Sabrina A Silveira
- Department of Computer Science, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6.627, 31270-901, Belo Horizonte, Brazil
| | - Alexandre V Fassio
- Department of Computer Science, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6.627, 31270-901, Belo Horizonte, Brazil.,Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6.627, 31270-901, Belo Horizonte, Brazil
| | - Valdete M Gonçalves-Almeida
- Department of Computer Science, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6.627, 31270-901, Belo Horizonte, Brazil
| | - Elisa B de Lima
- Department of Computer Science, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6.627, 31270-901, Belo Horizonte, Brazil.,Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6.627, 31270-901, Belo Horizonte, Brazil
| | - Yussif T Barcelos
- Department of Computer Science, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6.627, 31270-901, Belo Horizonte, Brazil
| | - Flávia F Aburjaile
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6.627, 31270-901, Belo Horizonte, Brazil
| | - Laerte M Rodrigues
- Department of Computer Science, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6.627, 31270-901, Belo Horizonte, Brazil.,Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6.627, 31270-901, Belo Horizonte, Brazil
| | - Wagner Meira
- Department of Computer Science, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6.627, 31270-901, Belo Horizonte, Brazil
| | - Raquel C de Melo-Minardi
- Department of Computer Science, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6.627, 31270-901, Belo Horizonte, Brazil
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