Examinando por Autor "Valdés, Jorge"

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    Acidithiobacillus ferrooxidans metabolism: From genome sequence to industrial applications
    (BMC, 2008-12-11) Valdés, Jorge; Pedroso, Inti; Quatrini, Raquel; Dodson, Robert J.; Tettelin, Herve; Blake II, Robert; Eisen, Jonathan A.; Holmes, David S.
    Background: Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, γ-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1-2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism. Results: The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes. Conclusion: Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential. © 2008 Valdés et al; licensee BioMed Central Ltd.
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    Análisis genómico-transcripcional de la respuesta del patógeno de peces Piscirickettsia salmonis frente a antibióticos utilizados en la industria acuícola
    (Universidad Andrés Bello, 2016) Méndez Méndez, Tamara Belén; Valdés, Jorge; Fuentes, Dere
    La bacteria intracelular Piscirickettsia salmonis (P. salmonis) es el agente causal de la Septicemia Rickettsial del Salmón (SRS), la cual afecta cultivos principalmente en etapas de mar. Cada año aumenta la cantidad de antibióticos utilizados por la industria acuícola como método de tratamiento, generando condiciones en el ambiente que permitan la selección de cepas resistentes a estos. Estudios sugieren que incluso la exposición a bajas concentraciones de antibióticos podría seleccionar bacterias resistentes. En el caso de P. salmonis, a la fecha es limitada la información de los mecanismos moleculares que determinan la resistencia a diversos antibióticos. El objetivo general de este trabajo es identificar genes de P. salmonis potencialmente involucrados en procesos de resistencia a antibióticos y analizar sus niveles de expresión. Los objetivos específicos son: i) Identificar y analizar proteínas predichas potencialmente involucrados en la expulsión y metabolización de antibióticos en los genomas de diferentes cepas de P. salmonis, ii) Identificar la Concentración Mínima Inhibitoria (CIM) para diferentes antibióticos en las cepas de P. salmonis bajo estudio, iii) Evaluar la expresión de genes potencialmente involucrados en procesos de resistencia antibiótica frente a concentraciones subinhibitorias del antibiótico florfenicol y iv) Integrar información con datos disponibles en bases de datos públicas y generar un modelo preliminar de resistencia antibiótica en P salmonis. Los resultados de determinación de la concentración mínima inhibitoria utilizando antibióticos regularmente usados en la industria indican que existen distintos grados de inhibición frente a un gradiente de concentración de antibióticos, diferencias que se hacen más marcadas entre cepas ambientales y de referencia. Con el objetivo de explicar estas diferencias se clasificaron y compararon, mediante herramientas bioinformáticas, genes potencialmente involucrados en resistencia entre los genomas secuenciados de las cepas de P. salmonis bajo estudio. Nuestros resultados indican que no existen grandes diferencias entre los genes identificados, ya que todas las cepas poseen una amplia maquinaria genética que le permitiría sobrevivir frente a diferentes clases de antibióticos. Como las cepas cuentan con un paquete genético similar, se evaluó diferencias en la expresión de genes seleccionados como potencialmente determinantes en resistencia frente a concentraciones sub-inhibitorias. Se observaron diferencias significativas en la expresión de algunos de estos genes, lo que se podría asociar a posibles determinantes en las cepas ambientales, expuestas constantemente a las condiciones operacionales descritas (concentraciones sub-inhibitorias del antibiótico florfenicol). Finalmente se concluye que las diferencias observadas en la respuesta de cepas ambientales y de referencia podrían dar pie a estudios más representativos para la generación de nuevos enfoques en el estudio de mecanismos de resistencia a antibióticos en ambientes marinos de producción intensiva.
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    Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus
    (Public Library of Science, 2013-11-08) Acuña, Lillian G.; Cárdenas, Juan Pablo; Covarrubias, Paulo C.; Haristoy, Juan José; Flores, Rodrigo; Nuñez, Harold; Riadi, Gonzalo; Shmaryahu, Amir; Valdés, Jorge; Dopson, Mark; Rawlings, Douglas E.; Banfield, Jillian F.
    Background: Acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the Acidithiobacillales. As such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. In this study, we explore the genomic diversity of A. caldus strains using a combination of bioinformatic and experimental techniques, thus contributing first insights into the elucidation of the species pangenome. Principal Findings: Comparative sequence analysis of A. caldus ATCC 51756 and SM-1 indicate that, despite sharing a conserved and highly syntenic genomic core, both strains have unique gene complements encompassing nearly 20% of their respective genomes. The differential gene complement of each strain is distributed between the chromosomal compartment, one megaplasmid and a variable number of smaller plasmids, and is directly associated to a diverse pool of mobile genetic elements (MGE). These include integrative conjugative and mobilizable elements, genomic islands and insertion sequences. Some of the accessory functions associated to these MGEs have been linked previously to the flexible gene pool in microorganisms inhabiting completely different econiches. Yet, others had not been unambiguously mapped to the flexible gene pool prior to this report and clearly reflect strain-specific adaption to local environmental conditions. Significance: For many years, and because of DNA instability at low pH and recurrent failure to genetically transform acidophilic bacteria, gene transfer in acidic environments was considered negligible. Findings presented herein imply that a more or less conserved pool of actively excising MGEs occurs in the A. caldus population and point to a greater frequency of gene exchange in this econiche than previously recognized. Also, the data suggest that these elements endow the species with capacities to withstand the diverse abiotic and biotic stresses of natural environments, in particular those associated with its extreme econiche. © 2013 Acuña et al.
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    Biochemical, genomic and structural characteristics of the Acr3 pump in Exiguobacterium strains isolated from arsenic-rich Salar de Huasco sediments
    (Frontiers Media S.A., 2022-11) Castro-Severyn, Juan; Pardo-Esté, Coral; Araya-Durán, Ingrid; Gariazzo, Valentina; Cabezas, Carolina; Valdés, Jorge; Remonsellez, Francisco; Saavedra, Claudia P.
    Arsenic is a highly toxic metalloid of major concern for public safety. However, microorganisms have several resistance mechanisms, particularly the expression of arsenic pumps is a critical component for bacterial ability to expel it and decrease intracellular toxicity. In this study, we aimed to characterize the biochemical, structural, and genomic characteristics of the Acr3 pump among a group of Exiguobacterium strains isolated from different sites of the arsenic-rich Salar de Huasco (SH) ecosystem. We also determined whether the differences in As(III) resistance levels presented by the strains could be attributed to changes in the sequence or structure of this protein. In this context, we found that based on acr3 sequences the strains isolated from the SH grouped together phylogenetically, even though clustering based on gene sequence identity did not reflect the strain’s geographical origin. Furthermore, we determined the genetic context of the acr3 sequences and found that there are two versions of the organization of acr3 gene clusters, that do not reflect the strain’s origin nor arsenic resistance level. We also contribute to the knowledge regarding structure of the Acr3 protein and its possible implications on the functionality of the pump, finding that although important and conserved components of this family of proteins are present, there are several changes in the amino acidic sequences that may affect the interactions among amino acids in the 3D model, which in fact are evidenced as changes in the structure and residues contacts. Finally, we demonstrated through heterologous expression that the Exiguobacterium Acr3 pump does indeed improve the organisms As resistance level, as evidenced in the complemented E. coli strains. The understanding of arsenic detoxification processes in prokaryotes has vast biotechnological potential and it can also provide a lot of information to understand the processes of evolutionary adaptation. Copyright © 2022 Castro-Severyn, Pardo-Esté, Araya-Durán, Gariazzo, Cabezas, Valdés, Remonsellez and Saavedra.
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    Spatial co-occurrence patterns of benthic microbial assemblage in response to trace metals in the Atacama Desert Coastline
    (Frontiers Media S.A., 2023-01) Zárate, Ana; Molina, Verónica; Valdés, Jorge; Icaza, Gonzalo; Vega, Sue Ellen; Castillo, Alexis; Ugalde, Juan A.; Dorador, Cristina
    Taxonomic and functional microbial communities may respond differently to anthropogenic coastal impacts, but ecological quality monitoring assessments using environmental DNA and RNA (eDNA/eRNA) in response to pollution are poorly understood. In the present study, we investigated the utility of the co-occurrence network approach’s to comprehensively explore both structure and potential functions of benthic marine microbial communities and their responses to Cu and Fe fractioning from two sediment deposition coastal zones of northern Chile via 16S rRNA gene metabarcoding. The results revealed substantial differences in the microbial communities, with the predominance of two distinct module hubs based on study zone. This indicates that habitat influences microbial co-occurrence networks. Indeed, the discriminant analysis allowed us to identify keystone taxa with significant differences in eDNA and eRNA comparison between sampled zones, revealing that Beggiatoaceae, Carnobacteriaceae, and Nitrosococcaceae were the primary representatives from Off Loa, whereas Enterobacteriaceae, Corynebacteriaceae, Latescibacteraceae, and Clostridiaceae were the families responsible for the observed changes in Mejillones Bay. The quantitative evidence from the multivariate analyses supports that the benthic microbial assemblages’ features were linked to specific environments associated with Cu and Fe fractions, mainly in the Bay. Furthermore, the predicted functional microbial structure suggested that transporters and DNA repair allow the communities to respond to metals and endure the interacting variable environmental factors like dissolved oxygen, temperature, and salinity. Moreover, some active taxa recovered are associated with anthropogenic impact, potentially harboring antibiotic resistance and other threats in the coastal zone. Overall, the method of scoping eRNA in parallel with eDNA applied here has the capacity to significantly enhance the spatial and functional understanding of real-time microbial assemblages and, in turn, would have the potential to increase the acuity of biomonitoring programs key to responding to immediate management needs for the marine environment. Copyright © 2023 Zárate, Molina, Valdés, Icaza, Vega, Castillo, Ugalde and Dorador.
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    Sulfur metabolism in the extreme acidophile Acidithiobacillus caldus
    (Frontiers Research Foundation, 2011-02) Mangold, Stefanie; Valdés, Jorge; Holmes, David S.; Dopson, Mark
    Given the challenges to life at low pH, an analysis of inorganic sulfur compound (ISC) oxidation was initiated in the chemolithoautotrophic extremophile Acidithiobacillus caldus. A. caldus is able to metabolize elemental sulfur and a broad range of ISCs. It has been implicated in the production of environmentally damaging acidic solutions as well as participating in industrial bioleaching operations where it forms part of microbial consortia used for the recovery of metal ions. Based upon the recently published A. caldus type strain genome sequence, a bioinformatic reconstruction of elemental sulfur and ISC metabolism predicted genes included: sulfide-quinone reductase (sqr), tetrathionate hydrolase (tth), two sox gene clusters potentially involved in thiosulfate oxidation (soxABXYZ), sulfur oxygenase reductase (sor), and various electron transport components. RNA transcript profiles by semi quantitative reverse transcription PCR suggested up-regulation of sox genes in the presence of tetrathionate. Extensive gel based proteomic comparisons of total soluble and membrane enriched protein fractions during growth on elemental sulfur and tetrathionate identified differential protein levels from the two Sox clusters as well as several chaperone and stress proteins up-regulated in the presence of elemental sulfur. Proteomics results also suggested the involvement of heterodisulfide reductase (HdrABC) in A. caldus ISC metabolism. A putative new function of Hdr in acidophiles is discussed. Additional proteomic analysis evaluated protein expression differences between cells grown attached to solid, elemental sulfur versus planktonic cells. This study has provided insights into sulfur metabolism of this acidophilic chemolithotroph and gene expression during attachment to solid elemental sulfur. © 2011 Mangold, Valdés, Holmes and Dopson.