Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare

Bacterial genomes are composed of core and accessory genomes. The first is composed of housekeeping and essential genes, while the second is highly enriched in mobile genetic elements, including transposable elements (TEs). Insertion sequences (ISs), the smallest TEs, have an important role in genome evolution, and contribute to bacterial genome plasticity and adaptability. ISs can spread in a genome, presenting different locations in nearly related strains, and producing phenotypic variations. Few tools are available which can identify differentially located ISs (DLISs) on assembled genomes. Here, we introduce ISCompare, a new program to profile IS mobilization events in related bacterial strains using complete or draft genome assemblies. ISCompare was validated using artificial genomes with simulated random IS insertions and real sequences, achieving the same or better results than other available tools, with the advantage that ISCompare can analyze multiple ISs at the same time and outputs a list of candidate DLISs. ISCompare provides an easy and straightforward approach to look for differentially located ISs on bacterial genomes.Fil: Mogro, Ezequiel Gerardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Ambrosis, Nicolás Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Lozano, Mauricio Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentin

Phylogenomic analysis supports the reclassification of burkholderia novacaledonica as caballeronia novacaledonica comb. Nov.

Burkholderia novacaledonica is a Betaproteobacterial species isolated from ultramafic soils in New Caledonia. The characterization and classification of this species into the Burkholderia genus was done simultaneously with the proposal of the new genus Caballeronia, initially composed of closely related Burkholderia glathei-like species. Thereafter, some reports based on the use of phylogenetic marker genes suggested that B. novacaledonica forms part of Caballeronia genus. Lacking a formal validation, and with the availability of its genome sequence, a genome-based phylogeny of B. novacaledonica was obtained to unravel its taxonomic position in Burkholderia sensu lato. A partial gyrB gene phylogeny, extended multilocus sequence typing on homologous protein sequences, and genomic distance-based phylogeny, all support the placement of this species in the Caballeronia genus. Therefore, the reclassification of B. novacaledonica to Caballeronia novacaledonica comb. nov. is proposed.Fil: Lozano, Mauricio Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Mogro, Ezequiel Gerardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Draghi, Walter Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentin

Codon usage optimization in the prokaryotic tree of life: how synonymous codons are differentially selected in sequence domains with different expression levels and degrees of conservation

Prokaryote genomes exhibit a wide range of GC contents and codon usages, both resulting from an interaction between mutational bias and natural selection. In order to investigate the basis underlying specific codon changes, we performed a comprehensive analysis of 29 different prokaryote families. The analysis of core gene sets with increasing ancestries in each family lineage revealed that the codon usages became progressively more adapted to the tRNA pools. While, as previously reported, highly expressed genes presented the most optimized codon usage, the singletons contained the less selectively favored codons. The results showed that usually codons with the highest translational adaptation were preferentially enriched. In agreement with previous reports, a C bias in 2- to 3-fold pyrimidine-ending codons, and a U bias in 4-fold codons occurred in all families, irrespective of the global genomic GC content. Furthermore, the U biases suggested that U3-mRNA–U34-tRNA interactions were responsible for a prominent codon optimization in both the most ancestral core and the highly expressed genes. A comparative analysis of sequences that encode conserved (cr) or variable (vr) translated products, with each one being under high (HEP) and low (LEP) expression levels, demonstrated that the efficiency was more relevant (by a factor of 2) than accuracy to modeling codon usage. Finally, analysis of the third position of codons (GC3) revealed that in genomes with global GC contents higher than 35 to 40%, selection favored a GC3 increase, whereas in genomes with very low GC contents, a decrease in GC3 occurred. A comprehensive final model is presented in which all patterns of codon usage variations are condensed in four distinct behavioral groups. IMPORTANCE The prokaryotic genomes—the current heritage of the most ancient life forms on earth—are comprised of diverse gene sets, all characterized by varied origins, ancestries, and spatial-temporal expression patterns. Such genetic diversity has for a long time raised the question of how cells shape their coding strategies to optimize protein demands (i.e., product abundance) and accuracy (i.e., translation fidelity) through the use of the same genetic code in genomes with GC contents that range from less than 20 to more than 80%. Here, we present evidence on how codon usage is adjusted in the prokaryotic tree of life and on how specific biases have operated to improve translation. Through the use of proteome data, we characterized conserved and variable sequence domains in genes of either high or low expression level and quantitated the relative weight of efficiency and accuracy—as well as their interaction—in shaping codon usage in prokaryotes.Fil: López, José Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Lozano, Mauricio Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Fabre, Maria Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Lagares, Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentin

Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic

SARS-CoV-2, the seventh coronavirus known to infect humans, can cause severe life-threatening respiratory pathologies. To better understand SARS-CoV-2 evolution, genome-wide analyses have been made, including the general characterization of its codons usage profile. Here we present a bioinformatic analysis of the evolution of SARS-CoV-2 codon usage over time using complete genomes collected since December 2019. Our results show that SARS-CoV-2 codon usage pattern is antagonistic to, and it is getting farther away from that of the human host. Further, a selection of deoptimized codons over time, which was accompanied by a decrease in both the codon adaptation index and the effective number of codons, was observed. All together, these findings suggest that SARS-CoV-2 could be evolving, at least from the perspective of the synonymous codon usage, to become less pathogenic.Instituto de Biotecnología y Biología Molecula

Trabajos prácticos Bioinformática 2021

La Bioinformática es un área interdisciplinaria que se ocupa del análisis computacional de los sistemas biológicos, siendo una de sus ramas la aplicación de este tipo de análisis a los sistemas moleculares. Si bien una parte de la Bioinformática se ocupa del desarrollo de nuevas metodologías, en la actualidad contamos con un gran conjunto de herramientas computacionales que permiten sistematizar, extraer y analizar la información biológica contenida en secuencias moleculares tanto de ácidos nucleicos como de proteínas. Estas herramientas permiten entre otras cosas, predecir la estructura de proteínas, diseñar ligandos específicos como inhibidores o antibióticos, diseñar racionalmente proteínas, identificar sitios funcionales y predecir la función biológica. Así, la Bioinformática es un campo estrechamente relacionado con la biotecnología, la bioquímica, la biología molecular, la farmacología, y consecuentemente tiene incidencia en distintas áreas como por ejemplo la salud y el agro, tanto en el ámbito académico como industrial. La incorporación de estas herramientas acompañada del marco conceptual adecuado para su utilización y su articulación con resultados experimentales, son los principales objetivos de la asignatura optativa -y de postgrado- Bioinformática, perteneciente a la Licenciatura en Biotecnología y Biología Molecular dictada por el Área Biotecnología y Biología Molecular de la Facultad de Ciencias Exactas, Universidad Nacional de La Plata. Los docentes a cargo de la materia son el Profesor Gustavo Parisi y los JTPs Mauricio Lozano y María Leticia Ferrelli. El programa de la materia incluye los siguientes temas orientados principalmente al estudio de proteínas: estructura de proteínas, evolución biológica, estudios de similitud secuencial, utilización de bases de datos biológicas, estimación de la estructura de proteínas, estudios basados similitud estructural, modelado molecular, inferencia filogenética, e integración estructura-evolución (predicción de la función biológica). En el contexto de esta asignatura, y con el objetivo de que los estudiantes adquirieran una mayor experiencia práctica en las diferentes temáticas estudiadas, se realizó un trabajo práctico integrador desarrollado a lo largo de 12 clases, durante las cuales se profundizó en la caracterización de una proteína que fue elegida por los estudiantes bajo la supervisión de la cátedra. Como resultado del análisis bioinformático realizado se exigió a los estudiantes la presentación de un trabajo escrito individual, con el objetivo de fijar los conocimientos adquiridos, e introducir a los estudiantes en la escritura científica.Facultad de Ciencias Exacta

Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare

Motivation: Bacterial genomes are composed by a core and an accessory genome. The first composed of housekeeping and essential genes, while the second is composed, in its majority, of mobile genetic elements, including transposable elements (TEs). Insertion sequences (ISs), the smallest TEs, have an important role in genome evolution, and contribute to bacterial genome plasticity and adaptability. ISs can spread in a genome, presenting different locations in nearly related strains, and producing phenotypic variations. Few tools are available which can identify differentially located ISs (DLIS) on assembled genomes. Results: We developed ISCompare to profile IS mobilization events in related bacterial strains using complete or draft genome assemblies. ISCompare was validated using artificial genomes with simulated random IS insertions and real sequences, achieving the same or better results than other available tools, with the advantage that ISCompare can analyse multiple ISs at the same time and outputs a list of candidate DLIS. We think that ISCompare provides an easy and straightforward approach to look for differentially located ISs on bacterial genomes.Instituto de Biotecnología y Biología Molecula

Cold alkaline extraction of Elephant grass for optimal subsequent extraction of hemicelluloses and energy production

There is growing scientific and industrial interest in obtaining useful substances by fractionating lignocellulosic biomass from non-food plant crops for use by the bioenergy industry. The primary goals are to ensure process sustainability and to comply with the principles of circular economy. In this work, we optimized energy production from Elephant grass by previously using cold alkaline extraction to remove its hemicellulose fraction. Elephant grass contains a high proportion of lignin (20%) and hemicelluloses (27.4%), and therefore is an excellent alternative to wood materials for energy production by direct burning. Energy production was optimized to identify the best operating conditions among those tested, namely: alkali concentrations of 80–120 g NaOH L– 1, temperatures of 20–40 °C, and treatment times of 30–90 min. Using the optimum conditions thus established (viz., 100 g NaOH L– 1, 30 °C, and 30 min) raised the high heating value (HHV) to 19.151 MJ kg– 1 (i.e., by 4% relative to the starting material). Also, it allowed the content in elemental C to be preserved, that in H increased by 4.86% and, more environmentally significant, most sulphur (46.9%) to be removed from the solid phase upon treatment. Cold alkaline extraction of the raw material additionally enabled relatively selective separation of the hemicellulose fraction from the cellulose and lignin fractions. Thus, 30.1% of all hemicellulose was dissolved in the treatment liquor and made valorizable while 93.0% of cellulose and 82.1% of lignin present in the raw material remained in the solid phase.Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. Funding for open acces charge: Universidad de Huelva/CBUA. This study was funded by the Spanish Ministry of Economy and Competitiveness through the National Programme for Research Aimed at the Challenges of Society (CTQ201785251-C2-1and 2-R and PID2020-112875RB-C21), additional cofunding, in an 80:20 proportion, by FEDER (Project Green Asphalt, ref. 802C1800001) and the Andalusian Regional Government (Economy, Knowledge, Enterprises and University Council/IDEA Agency) and by micro-projects of research “Cátedra de la provincia” of the University of Huelva

Estudio bioinformático de la proteína Aurora kinasa A de <i>Bos taurus</i>

En la regulación del ciclo celular, las proteínas Aurora juegan un papel fundamental como reguladores de la segregación de cromosomas y la división celular. Debido a esto, su mal funcionamiento ha sido asociado al desarrollo de células malignas y hay interés en su utilización como blancos terapéuticos. En el presente trabajo se aplicaron diferentes herramientas bioinformáticas para obtener información secuencial y estructural de la proteína Aurora kinasa A, de la especie Bos taurus (Uniprot ID: Q2TA06). Esta presenta un dominio kinasa y una región N-ter desordenada. Además presenta un 88.8% de identidad con la proteína ortóloga humana, la cual se utilizó para construir el modelo de la proteína por homología. La estructura de la proteína permite observar un loop de activación y el sitio activo.Facultad de Ciencias Exacta