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1.
PLoS One ; 13(5): e0197511, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-29799863

RESUMEN

Pesticides are one of the most widely used pest and disease control measures in plant crops and their indiscriminate use poses a direct risk to the health of populations and environment around the world. As a result, there is a great need for the development of new, less toxic molecules to be employed against plant pathogens. In this work, we employed an in silico approach to study the genes coding for enzymes of the genomes of three commercially important plants, soybean (Glycine max), tomato (Solanum lycopersicum) and corn (Zea mays), as well as 15 plant pathogens (4 bacteria and 11 fungi), focusing on revealing a set of essential and non-homologous isofunctional enzymes (NISEs) that could be prioritized as drug targets. By combining sequence and structural data, we obtained an initial set of 568 cases of analogy, of which 97 were validated and further refined, revealing a subset of 29 essential enzymatic activities with a total of 119 different structural forms, most belonging to central metabolic routes, including the carbohydrate metabolism, the metabolism of amino acids, among others. Further, another subset of 26 enzymatic activities possess a tertiary structure specific for the pathogen, not present in plants, men and Apis mellifera, which may be of importance for the development of specific enzymatic inhibitors against plant diseases that are less harmful to humans and the environment.


Asunto(s)
Lycopersicon esculentum/microbiología , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/prevención & control , Soja/microbiología , Zea mays/microbiología , Animales , Antiinfecciosos/química , Antiinfecciosos/farmacología , Bacterias/efectos de los fármacos , Bacterias/enzimología , Bacterias/genética , Simulación por Computador , Productos Agrícolas/microbiología , Descubrimiento de Drogas , Hongos/efectos de los fármacos , Hongos/enzimología , Hongos/genética , Genoma Bacteriano , Genoma Fúngico , Humanos , Plaguicidas/farmacología , Plaguicidas/toxicidad , Fitomejoramiento
2.
Genome Biol Evol ; 9(6): 1624-1636, 2017 06 01.
Artículo en Inglés | MEDLINE | ID: mdl-28854631

RESUMEN

Since enzymes catalyze almost all chemical reactions that occur in living organisms, it is crucial that genes encoding such activities are correctly identified and functionally characterized. Several studies suggest that the fraction of enzymatic activities in which multiple events of independent origin have taken place during evolution is substantial. However, this topic is still poorly explored, and a comprehensive investigation of the occurrence, distribution, and implications of these events has not been done so far. Fundamental questions, such as how analogous enzymes originate, why so many events of independent origin have apparently occurred during evolution, and what are the reasons for the coexistence in the same organism of distinct enzymatic forms catalyzing the same reaction, remain unanswered. Also, several isofunctional enzymes are still not recognized as nonhomologous, even with substantial evidence indicating different evolutionary histories. In this work, we begin to investigate the biological significance of the cooccurrence of nonhomologous isofunctional enzymes in human metabolism, characterizing functional analogous enzymes identified in metabolic pathways annotated in the human genome. Our hypothesis is that the coexistence of multiple enzymatic forms might not be interpreted as functional redundancy. Instead, these enzymatic forms may be implicated in distinct (and probably relevant) biological roles.


Asunto(s)
Enzimas/genética , Enzimas/metabolismo , Catálisis , Evolución Molecular , Genoma Humano , Humanos , Redes y Vías Metabólicas
3.
Genome Announc ; 3(5)2015 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-26430044

RESUMEN

Mycobacterium tuberculosis of the Bejing subtype (MtbB) is transmitted efficiently in high burden countries for this genotype. A higher virulence was associated with isolates of the "modern" Beijing genotype sub-lineages when compared to "ancient" ones. Here, we report the full genomes of the strain representing these two genotypes from Brazil, a country with a low incidence of MtbB.

4.
Appl Biochem Biotechnol ; 175(4): 2124-65, 2015 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-25448632

RESUMEN

Streptococcus pneumoniae is a major cause of morbidity and mortality worldwide. Virulence-associated proteins common and conserved among all capsular types now represent the best strategy to combat pneumococcal infections. Our aim was to identify conserved targets in pneumococci that showed positive prediction for lipoprotein and extracellular subcellular location using bioinformatics programs and verify the distribution and the degree of conservation of these targets in pneumococci. These targets can be considered potential vaccine candidate to be evaluated in the future. A set of 13 targets were analyzed and confirmed the presence in all pneumococci tested. These 13 genes were highly conserved showing around >96 % of amino acid and nucleotide identity, but they were also present and show high identity in the closely related species Streptococcus mitis, Streptococcus oralis, and Streptococcus pseudopneumoniae. S. oralis clusters away from S. pneumoniae, while S. pseudopneumoniae and S. mitis cluster closer. The divergence between the selected targets was too small to be observed consistently in phylogenetic groups between the analyzed genomes of S. pneumoniae. The proteins analyzed fulfill two of the initial criteria of a vaccine candidate: targets are present in a variety of different pneumococci strains including different serotypes and are conserved among the samples evaluated.


Asunto(s)
Proteínas Bacterianas/inmunología , Genoma Bacteriano , Infecciones Neumocócicas/prevención & control , Streptococcus mitis/inmunología , Streptococcus oralis/inmunología , Streptococcus pneumoniae/inmunología , Streptococcus/inmunología , Antibacterianos/uso terapéutico , Proteínas Bacterianas/genética , Secuencia de Bases , Biología Computacional , Secuencia Conservada , Bases de Datos de Proteínas , Farmacorresistencia Bacteriana Múltiple/genética , Farmacorresistencia Bacteriana Múltiple/inmunología , Humanos , Anotación de Secuencia Molecular , Datos de Secuencia Molecular , Filogenia , Infecciones Neumocócicas/tratamiento farmacológico , Infecciones Neumocócicas/inmunología , Infecciones Neumocócicas/microbiología , Vacunas Neumococicas/genética , Vacunas Neumococicas/inmunología , Polimorfismo Genético , Streptococcus/clasificación , Streptococcus/efectos de los fármacos , Streptococcus/aislamiento & purificación , Streptococcus mitis/clasificación , Streptococcus mitis/efectos de los fármacos , Streptococcus mitis/aislamiento & purificación , Streptococcus oralis/clasificación , Streptococcus oralis/efectos de los fármacos , Streptococcus oralis/aislamiento & purificación , Streptococcus pneumoniae/clasificación , Streptococcus pneumoniae/efectos de los fármacos , Streptococcus pneumoniae/aislamiento & purificación
5.
Evol Bioinform Online ; 10: 131-53, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-25336895

RESUMEN

Leishmaniasis is an infectious disease caused by Leishmania species. Leishmania amazonensis is a New World Leishmania species belonging to the Mexicana complex, which is able to cause all types of leishmaniasis infections. The L. amazonensis reference strain MHOM/BR/1973/M2269 was sequenced identifying 8,802 codifying sequences (CDS), most of them of hypothetical function. Comparative analysis using six Leishmania species showed a core set of 7,016 orthologs. L. amazonensis and Leishmania mexicana share the largest number of distinct orthologs, while Leishmania braziliensis presented the largest number of inparalogs. Additionally, phylogenomic analysis confirmed the taxonomic position for L. amazonensis within the "Mexicana complex", reinforcing understanding of the split of New and Old World Leishmania. Potential non-homologous isofunctional enzymes (NISE) were identified between L. amazonensis and Homo sapiens that could provide new drug targets for development.

6.
Bioinform Biol Insights ; 8: 93-108, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-24899802

RESUMEN

For this report, we analyzed protein secondary structures in relation to the statistics of three nucleotide codon positions. The purpose of this investigation was to find which properties of the ribosome, tRNA or protein level, could explain the purine bias (Rrr) as it is observed in coding DNA. We found that the Rrr pattern is the consequence of a regularity (the codon structure) resulting from physicochemical constraints on proteins and thermodynamic constraints on ribosomal machinery. The physicochemical constraints on proteins mainly come from the hydropathy and molecular weight (MW) of secondary structures as well as the energy cost of amino acid synthesis. These constraints appear through a network of statistical correlations, such as (i) the cost of amino acid synthesis, which is in favor of a higher level of guanine in the first codon position, (ii) the constructive contribution of hydropathy alternation in proteins, (iii) the spatial organization of secondary structure in proteins according to solvent accessibility, (iv) the spatial organization of secondary structure according to amino acid hydropathy, (v) the statistical correlation of MW with protein secondary structures and their overall hydropathy, (vi) the statistical correlation of thymine in the second codon position with hydropathy and the energy cost of amino acid synthesis, and (vii) the statistical correlation of adenine in the second codon position with amino acid complexity and the MW of secondary protein structures. Amino acid physicochemical properties and functional constraints on proteins constitute a code that is translated into a purine bias within the coding DNA via tRNAs. In that sense, the Rrr pattern within coding DNA is the effect of information transfer on nucleotide composition from protein to DNA by selection according to the codon positions. Thus, coding DNA structure and ribosomal machinery co-evolved to minimize the energy cost of protein coding given the functional constraints on proteins.

7.
Vet Microbiol ; 162(1): 207-13, 2013 Feb 22.
Artículo en Inglés | MEDLINE | ID: mdl-22999523

RESUMEN

This report describes the complete genomic sequence and taxonomic position of BPV type 13. The BPV13 genome was amplified using the multiply primed rolling-circle amplification technique and long-template PCR employing two specific primers. The two long PCR fragments obtained were cloned and sequenced via primer walking. The complete genomic sequence of the BPV13 contains 7961 bp encoding eight proteins, E1, E2, E4, E5, E6, E7, L1, and L2. Similarly to the E5 gene in BPVs 1 and 2, the putative BPV13 E5 ORF encodes a small transforming protein that contains a hydrophobic transmembrane domain. Meanwhile, the retinoblastoma tumor suppressor-binding domain is absent in the putative BPV13 E7 protein. The presence of these two specific molecular features has been recognized as a distinct marker for the development of fibropapilloma in artiodactyl PV-induced lesions. The phylogenetic analysis demonstrated that BPV13 is a new member of the Deltapapillomavirus genus, to be classified as the third representative of the Delta 4 species. The characterization of the genomic sequence of this novel PV will aid in the interpretation of the pathologies described to be related to this virus and provide support for the development of diagnostic tools for epidemiological surveillance of BPV13 in its potential natural hosts.


Asunto(s)
Enfermedades de los Bovinos/virología , Deltapapillomavirus/clasificación , Deltapapillomavirus/genética , Infecciones por Papillomavirus/veterinaria , Secuencia de Aminoácidos , Animales , Bovinos , ADN Viral/análisis , ADN Viral/química , ADN Viral/genética , Femenino , Genoma Viral , Datos de Secuencia Molecular , Proteínas Oncogénicas Virales/análisis , Proteínas Oncogénicas Virales/química , Proteínas Oncogénicas Virales/genética , Sistemas de Lectura Abierta , Infecciones por Papillomavirus/virología , Filogenia , Reacción en Cadena de la Polimerasa/veterinaria , Alineación de Secuencia
8.
Enzyme Res ; 2011: 543912, 2011.
Artículo en Inglés | MEDLINE | ID: mdl-21808726

RESUMEN

Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi (Tritryps) are unicellular protozoa that cause leishmaniasis, sleeping sickness and Chagas' disease, respectively. Most drugs against them were discovered through the screening of large numbers of compounds against whole parasites. Nonhomologous isofunctional enzymes (NISEs) may present good opportunities for the identification of new putative drug targets because, though sharing the same enzymatic activity, they possess different three-dimensional structures thus allowing the development of molecules against one or other isoform. From public data of the Tritryps' genomes, we reconstructed the Genetic Information Processing Pathways (GIPPs). We then used AnEnPi to look for the presence of these enzymes between Homo sapiens and Tritryps, as well as specific enzymes of the parasites. We identified three candidates (ECs 3.1.11.2 and 6.1.1.-) in these pathways that may be further studied as new therapeutic targets for drug development against these parasites.

9.
J Med Microbiol ; 60(Pt 10): 1441-6, 2011 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-21596907

RESUMEN

We performed genotyping of Mycobacterium leprae present in skin biopsy samples that were collected during the first and the second disease occurrences from eight leprosy patients, seven of whom were diagnosed as suffering from disease relapse. Sequence analysis of part of the M. leprae rpoB, folP1, gyrB and gyrA genes did not show genetic change that supported the presence of drug-resistant bacilli. However, we observed a synonymous nucleotide change at position 297 of gyrA among five of these patients, one presenting C to T (CgyrAT) and four presenting T to C (TgyrAC) at this position. Additional genotyping by analysis of the four short tandem repeats GAA, GTA9, AT17 and TA18 showed that the gyrA single nucleotide polymorphism change was accompanied by a change in short tandem repeat genotype. Our data suggest that leprosy relapse in these patients, living in an area endemic for leprosy, could be caused by M. leprae with a genotype different from the one that caused initial disease.


Asunto(s)
Lepra/epidemiología , Lepra/microbiología , Tipificación Molecular , Mycobacterium leprae/clasificación , Mycobacterium leprae/genética , Adulto , Anciano , Proteínas Bacterianas/genética , Biopsia , Brasil/epidemiología , Femenino , Genotipo , Humanos , Masculino , Persona de Mediana Edad , Mycobacterium leprae/aislamiento & purificación , Recurrencia , Secuencias Repetitivas de Ácidos Nucleicos , Análisis de Secuencia de ADN , Piel/microbiología
10.
Bioinformatics ; 26(5): 705-7, 2010 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-20089515

RESUMEN

MOTIVATION: Many analyses in modern biological research are based on comparisons between biological sequences, resulting in functional, evolutionary and structural inferences. When large numbers of sequences are compared, heuristics are often used resulting in a certain lack of accuracy. In order to improve and validate results of such comparisons, we have performed radical all-against-all comparisons of 4 million protein sequences belonging to the RefSeq database, using an implementation of the Smith-Waterman algorithm. This extremely intensive computational approach was made possible with the help of World Community Grid, through the Genome Comparison Project. The resulting database, ProteinWorldDB, which contains coordinates of pairwise protein alignments and their respective scores, is now made available. Users can download, compare and analyze the results, filtered by genomes, protein functions or clusters. ProteinWorldDB is integrated with annotations derived from Swiss-Prot, Pfam, KEGG, NCBI Taxonomy database and gene ontology. The database is a unique and valuable asset, representing a major effort to create a reliable and consistent dataset of cross-comparisons of the whole protein content encoded in hundreds of completely sequenced genomes using a rigorous dynamic programming approach. AVAILABILITY: The database can be accessed through http://proteinworlddb.org


Asunto(s)
Bases de Datos de Proteínas , Genómica/métodos , Proteínas/química , Alineación de Secuencia/métodos , Programas Informáticos , Algoritmos , Genoma , Filogenia , Proteínas/genética
11.
Appl Bioinformatics ; 5(1): 49-53, 2006.
Artículo en Inglés | MEDLINE | ID: mdl-16539538

RESUMEN

UNLABELLED: The widely used programs BLAST (in this article, 'BLAST' includes both the National Center for Biotechnology Information [NCBI] BLAST and the Washington University version WU BLAST) and FASTA for similarity searches in nucleotide and protein databases usually result in copious output. However, when large query sets are used, human inspection rapidly becomes impractical. BioParser is a Perl program for parsing BLAST and FASTA reports. Making extensive use of the BioPerl toolkit, the program filters, stores and returns components of these reports in either ASCII or HTML format. BioParser is also capable of automatically feeding a local MySQL database with the parsed information, allowing subsequent filtering of hits and/or alignments with specific attributes. For this reason, BioParser is a valuable tool for large-scale similarity analyses by improving the access to the information present in BLAST or FASTA reports, facilitating extraction of useful information of large sets of sequence alignments, and allowing for easy handling and processing of the data. AVAILABILITY: BioParser is licensed under the Creative Commons Attribution-NonCommercial-NoDerivs 2.0 license terms (http://creativecommons.org/licenses/by-nc-nd/2.0/) and is available upon request. Additional information can be found at the BioParser website (http://www.dbbm.fiocruz.br/BioParser.html).


Asunto(s)
Sistemas de Administración de Bases de Datos , Bases de Datos de Proteínas , Almacenamiento y Recuperación de la Información/métodos , Alineación de Secuencia/métodos , Análisis de Secuencia de Proteína/métodos , Programas Informáticos , Interfaz Usuario-Computador , Secuencia de Aminoácidos , Gráficos por Computador , Datos de Secuencia Molecular
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