Examinando por Autor "Holmes, David S."
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Ítem 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.Ítem AFAL: a web service for profiling amino acids surrounding ligands in proteins(Journal of Computer-Aided Molecular Design. Volume 28, Issue 11, Pages 1069 - 1076. November 2014, 2014-11) Arenas-Salinas, Mauricio; Ortega-Salazar, Samuel; Gonzales-Nilo, Fernando; Pohl, Ehmke; Holmes, David S.; Quatrini, RaquelWith advancements in crystallographic technology and the increasing wealth of information populating structural databases, there is an increasing need for prediction tools based on spatial information that will support the characterization of proteins and protein–ligand interactions. Herein, a new web service is presented termed amino acid frequency around ligand (AFAL) for determining amino acids type and frequencies surrounding ligands within proteins deposited in the Protein Data Bank and for assessing the atoms and atom-ligand distances involved in each interaction (availability: http://structuralbio.utalca.cl/AFAL/index.html). AFAL allows the user to define a wide variety of filtering criteria (protein family, source organism, resolution, sequence redundancy and distance) in order to uncover trends and evolutionary differences in amino acid preferences that define interactions with particular ligands. Results obtained from AFAL provide valuable statistical information about amino acids that may be responsible for establishing particular ligand–protein interactions. The analysis will enable investigators to compare ligand-binding sites of different proteins and to uncover general as well as specific interaction patterns from existing data. Such patterns can be used subsequently to predict ligand binding in proteins that currently have no structural information and to refine the interpretation of existing protein models. The application of AFAL is illustrated by the analysis of proteins interacting with adenosine-5′-triphosphate.Ítem AlterORF: A database of alternate open reading frames(Oxford University Press, 2008-01) Pedroso, Inti; Rivera, Gustavo; Lazo, Felipe; Chacón, Max; Ossandón, Francisco; Veloso, Felipe A.; Holmes, David S.AlterORF is a searchable database that contains information regarding alternate open reading frames (ORFs) for over 1.5 million genes in 481 prokaryotic genomes. The objective of the database is to provide a platform for improving genome annotation and to serve as an aid for the identification of prokaryotic genes that potentially encode proteins in more than one reading frame. The AlterORF Database can be accessed through a web interface at www.alterorf.cl. © 2007 The Author(s).Ítem Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans(2007-04) Quatrini, Raquel; Lefimil, Claudia; Veloso, Felipe A.; Pedroso, Inti; Holmes, David S.; Jedlicki, EugeniaThe γ-proteobacterium Acidithiobacillus ferrooxidans lives in extremely acidic conditions (pH 2) and, unlike most organisms, is confronted with an abundant supply of soluble iron. It is also unusual in that it oxidizes iron as an energy source. Consequently, it faces the challenging dual problems of (i) maintaining intracellular iron homeostasis when confronted with extremely high environmental loads of iron and (ii) of regulating the use of iron both as an energy source and as a metabolic micronutrient. A combined bioinformatic and experimental approach was undertaken to identify Fur regulatory sites in the genome of A. ferrooxidans and to gain insight into the constitution of its Fur regulon. Fur regulatory targets associated with a variety of cellular functions including metal trafficking (e.g. feoPABC, tdr, tonBexbBD, copB, cdf), utilization (e.g. fdx, nif, transcriptional regulation (e.g. phoB, irr, iscR) and redox balance (grx), trx, gst) were identified. Selected predicted Fur regulatory sites were confirmed by FURTA, EMSA and in vitro transcription analyses. This study provides the first model for a Fur-binding site consensus sequence in an acidophilic iron-oxidizing microorganism and lays the foundation for future studies aimed at deepening our understanding of the regulatory networks that control iron uptake, homeostasis and oxidation in extreme acidophiles. © 2007 The Author(s).Ítem Differential expression of two bc1 complexes in the strict acidophilic chemolithoautotrophic bacterium Acidithiobacillus ferrooxidans suggests a model for their respective roles in iron or sulfur oxidation(2007-01) Bruscella, Patrice; Appia-Ayme, Corinne; Levicán, Gloria; Ratouchniak, Jeanine; Jedlicki, Eugenia; Holmes, David S.; Bonnefoy, ViolaineThree strains of the strict acidophilic chemolithoautotrophic Acidithiobacillus ferrooxidans, including the type strain ATCC 23270, contain a petllABC gene cluster that encodes the three proteins, cytochrome c1, cytochrome b and a Rieske protein, that constitute a bc1, electron-transfer complex. RT-PCR and Northern blotting show that the petllABC cluster is co-transcribed with cycA, encoding a cytochrome c belonging to the c4 family, sdrA, encoding a putative short-chain dehydrogenase, and hip, encoding a high potential iron-sulfur protein, suggesting that the six genes constitute an operon, termed the petll operon. Previous results indicated that A. ferrooxidans contains a second pet operon, termed the petl operon, which contains a gene cluster that is similarly organized except that it lacks hip. Real-time PCR and Northern blot experiments demonstrate that petl is transcribed mainly in cells grown in medium containing iron, whereas petll is transcribed in cells grown in media containing sulfur or iron. Primer extension experiments revealed possible transcription initiation sites for the petl and petll operons. A model is presented in which petl is proposed to encode the bc1, complex, functioning in the uphill flow of electrons from iron to NAD(P), whereas petll is suggested to be involved in electron transfer from sulfur (or formate) to oxygen (or ferric iron). A. ferrooxidans is the only organism, to date, to exhibit two functional bc1 complexes. © 2007 SGM.Ítem Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile(BIOMED CENTRAL, 2016-02) Issotta, Francisco; Galleguillos, Pedro A.; Moya-Beltrán, Ana; Davis-Belmar, Carol S.; Rautenbach, George; Covarrubias, Paulo C.; Acosta, Mauricio; Ossandon, Francisco J.; Contador, Yasna; Holmes, David S.; Marín-Eliantonio, Sabrina; Quatrini, Raquel; Demergasso, CeciliaLeptospirillum ferriphilum Sp-Cl is a Gram negative, thermotolerant, curved, rod- shaped bacterium, isolated from an industrial bioleaching operation in northern Chile, where chalcocite is the major copper mineral and copper hydroxychloride atacamite is present in variable proportions in the ore. This strain has unique features as compared to the other members of the species, namely resistance to elevated concentrations of chloride, sulfate and metals. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 2,475,669 bp draft genome is arranged into 74 scaffolds of 74 contigs. A total of 48 RNA genes and 2,834 protein coding genes were predicted from its annotation; 55 % of these were assigned a putative function. Release of the genome sequence of this strain will provide further understanding of the mechanisms used by acidophilic bacteria to endure high osmotic stress and high chloride levels and of the role of chloride-tolerant iron-oxidizers in industrial bioleaching operations.Ítem Draft genome sequence of the nominated type strain of "Ferrovum myxofaciens," an acidophilic, iron-oxidizing betaproteobacterium(American Society for Microbiology, 2014) Moya-Beltrán, Ana; Cárdenas, Juan Pablo; Covarrubias, Paulo C.; Issotta, Francisco; Ossandon, Francisco J.; Grail, Barry M.; Holmes, David S.; Quatrini, Raquel; Johnson, D. BarrieFerrovum myxofaciens” is an iron-oxidizing betaproteobacterium with widespread distribution in acidic low-temperature en vironments, such as acid mine drainage streams. Here, we describe the genomic features of this novel acidophile and investigate the relevant metabolic pathways that enable its survival in these environments.Ítem Estudio bioinformático del sobrelapamiento génico en procariontes(Universidad Andrés Bello, 2013) Ossandón Cabrera, Francisco Javier; Holmes, David S.; Facultad de Ciencias BiológicasLa existencia de genes que comparten secuencias de ADN, a través de la codificación en diferentes marcos de lectura, ha sido firmemente establecida en muchos genomas, especialmente en virus pero también en especies procariontes. Hay 3 tipos de sobrelapamiento dependiendo de la orientación relativa de los genes, sin embargo, esta tesis solamente explora aquellos sobrelapamientos generados por genes convergentes , en donde ambos genes se ubican en hebras opuestas del ADN y comparten sus extremos 3' ( --7 ~ ). Los primeros intentos de detectar genes sobrelapados convergentes se vieron seriamente obstaculizados por la presencia de un número significativo de anotaciones incorrectas de genes en bases de datos públicas como la del National Center for Biotechnology lnformation (NCBI). Debido a esto, antes de proceder a un análisis a gran escala de genes sobrelapados , fue indispensable mejorar la anotación de genes existente, lo cual se volvió un eje fundamental de la tesis. El primer paso de esta tesis consistió en desarrollar una base de datos llamada AlterORF, que contuviera todos los genes anotados de más de 900 especies procariontes junto a la predicción de sus marcos de lectura abiertos (ORFs, "open reading trames") alternativos. Se predijeron los dominios conservados de todos los ORFs por medio de similitud de secuencias con registros provenientes de distintas bases de datos, y los resultados proporcionaron evidencia de genes no detectados previamente y evidencia de ORFs predichos incorrectamente. El segundo paso de esta tesis consistió en llevar la corrección de anotaciones de genomas procariontes al siguiente nivel, a través del desarrollo y validación de una herramienta de anotación automática propia (ORFminer). Las anotaciones generadas mediante esta herramienta mostraron en un aumento significativo de la predicción de ORFs, predicción de función para muchas proteínas hipotéticas, y reducción en el número de proteínas hipotéticas predichas. y comparten sus extremos 3' (3 t). El tercer paso de esta tesis consistió en el regreso al anál isis original del sobrelapamiento de genes. El anál isis llevó al sorprendente descubrimiento de que las Arqueas tienen , en promedio, frecuencias de sobrelapamiento convergente significativamente mayores que las Bacterias. Además, se detectó una asociación positiva entre frecuencias altas y especies que viven a altas temperaturas . Una evaluación adicional de ambos re inos por separado mostró que esta asociación se presentaba en especies de Bacterias termófilas (25% de ellas se ubican en el 10% • superior de las frecuencias de sobrelapamiento observadas), pero en menor grado que el observado en especies de Arqueas termófilas (87% de ellas se ubican en el 10% superior de las frecuencias de sobrelapamiento observadas). Luego, se seleccionó un grupo de genes sobrelapados que excluía proteínas hipotéticas y poseía un largo significativo de sobrelapamiento de al menos 30 nucleótidos. Su análisis mostró que para los sobrelapamientos convergentes más comunes, el marco de lectura relativo preferido es +1 /-3 (donde el segundo nucleótido de un codón coincide con el tercer nucleótido del codón opuesto). Una posible explicación por esta preferencia es que ese marco de lectura relativo es el que permite el mayor número de reemplazos de aminoácidos en la reg ión sobrelapante de un gen, sin afectar la secuencia aminoacídica de la región sobrelapada del otro gen. Además, el análisis de los dominios que más frecuentemente participan en sobrelapamientos mostró que ellos poseen funciones de regulación , transporte y transducción de señales. Finalmente, un par de genes sobrelapados fue seleccionado para examinar su potencial mecanismo de formación del sobrelapamiento. Los resultados permitieron la predicción de una sucesión de eventos evolutivos que podrían haber llevado a la formación del sobrelapamiento convergente. Aunque este análisis se restringió a un solo ejemplo , se propone que el mecanismo podría ser aplicado a todos los casos de sobrelapamiento convergente de genes.Ítem Expression and activity of the Calvin-Benson-Bassham cycle transcriptional regulator CbbR from Acidithiobacillus ferrooxidans in Ralstonia eutropha(Oxford University Press, 2015-08) Esparza, Mario; Jedlicki, Eugenia; Dopson, Mark; Holmes, David S.Autotrophic fixation of carbon dioxide into cellular carbon occurs via several pathways but quantitatively, the Calvin-Benson-Bassham cycle is the most important. CbbR regulates the expression of the cbb genes involved in CO2 fixation via the Calvin-Benson-Bassham cycle in a number of autotrophic bacteria. A gene potentially encoding CbbR (cbbRAF) has been predicted in the genome of the chemolithoautotrophic, extreme acidophile Acidithiobacillus ferrooxidans. However, this microorganism is recalcitrant to genetic manipulation impeding the experimental validation of bioinformatic predictions. Two novel functional assays were devised to advance our understanding of cbbRAF function using the mutated facultative autotroph Ralstonia eutropha H14 ΔcbbR as a surrogate host to test gene function: (i) cbbRAF was expressed in R. eutropha and was able to complement ΔcbbR; and (ii) CbbRAF was able to regulate the in vivo activity of four A. ferrooxidans cbb operon promoters in R. eutropha. These results open up the use of R. eutropha as a surrogate host to explore cbbRAF activity. © FEMS 2015.Ítem Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans(BioMed Central Ltd., 2009-08-24) Quatrini, Raquel; Appia-Ayme, Corinne; Denis, Yann; Jedlicki, Eugenia; Holmes, David S.; Bonnefoy, ViolaineBackground: Acidithiobacillus ferrooxidans gains energy from the oxidation of ferrous iron and various reduced inorganic sulfur compounds at very acidic pH. Although an initial model for the electron pathways involved in iron oxidation has been developed, much less is known about the sulfur oxidation in this microorganism. In addition, what has been reported for both iron and sulfur oxidation has been derived from different A. ferrooxidans strains, some of which have not been phylogenetically characterized and some have been shown to be mixed cultures. It is necessary to provide models of iron and sulfur oxidation pathways within one strain of A. ferrooxidans in order to comprehend the full metabolic potential of the pangenome of the genus. Results: Bioinformatic-based metabolic reconstruction supported by microarray transcript profiling and quantitative RT-PCR analysis predicts the involvement of a number of novel genes involved in iron and sulfur oxidation in A. ferrooxidans ATCC23270. These include for iron oxidation: cup (copper oxidase-like), ctaABT (heme biogenesis and insertion), nuoI and nuoK (NADH complex subunits), sdrA1 (a NADH complex accessory protein) and atpB and atpE (ATP synthetase F0 subunits). The following new genes are predicted to be involved in reduced inorganic sulfur compounds oxidation: a gene cluster (rhd, tusA, dsrE, hdrC, hdrB, hdrA, orf2, hdrC, hdrB) encoding three sulfurtransferases and a heterodisulfide reductase complex, sat potentially encoding an ATP sulfurylase and sdrA2 (an accessory NADH complex subunit). Two different regulatory components are predicted to be involved in the regulation of alternate electron transfer pathways: 1) a gene cluster (ctaRUS) that contains a predicted iron responsive regulator of the Rrf2 family that is hypothesized to regulate cytochrome aa3 oxidase biogenesis and 2) a two component sensor-regulator of the RegB-RegA family that may respond to the redox state of the quinone pool. Conclusion: Bioinformatic analysis coupled with gene transcript profiling extends our understanding of the iron and reduced inorganic sulfur compounds oxidation pathways in A. ferrooxidans and suggests mechanisms for their regulation. The models provide unified and coherent descriptions of these processes within the type strain, eliminating previous ambiguity caused by models built from analyses of multiple and divergent strains of this microorganism. © 2009 Quatrini et al; licensee BioMed Central Ltd.Ítem Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile “Ferrovum”(FRONTIERS MEDIA, 2016) Ullrich, Sophie R.; González, Carolina; Poehlein, Anja; Tischler, Judith S.; Daniel, Rolf; Schlömann, Michael; Holmes, David S.; Mühling, MartinAcid mine drainage (AMD), associated with active and abandoned mining sites, is a habitat for acidophilic microorganisms that gain energy from the oxidation of reduced sulfur compounds and ferrous iron and that thrive at pH below 4. Members of the recently proposed genus "Ferrovurn" are the first acidophilic iron oxidizers to be described within the Betaproteobacteria. Although they have been detected as typical community members in AMD habitats worldwide, knowledge of their phylogenetic and metabolic diversity is scarce. Genomics approaches appear to be most promising in addressing this lacuna since isolation and cultivation of "Ferrovurn" has proven to be extremely difficult and has so far only been successful for the designated type strain-Ferrovum myxofaciens" P3G. In this study, the genomes of two novel strains of "Ferrovurn" (PN-J185 and Z-31) derived from water samples of a mine water treatment plant were sequenced. These genomes were compared with those of "Ferrovum" sp. JA12 that also originated from the mine water treatment plant, and of the type strain (P3G). Phylogenomic scrutiny suggests that the four strains represent three "Ferrovum" species that cluster in two groups (1 and 2). Comprehensive analysis of their predicted metabolic pathways revealed that these groups harbor characteristic metabolic profiles, notably with respect to motility, chemotaxis, nitrogen metabolism, biofilm formation and their potential strategies to cope with the acidic environment. For example, while the "F myxofaciens" strains (group 1) appear to be motile and diazotrophic, the non-motile group 2 strains have the predicted potential to use a greater variety of fixed nitrogen sources. Furthermore, analysis of their genome synteny provides first insights into their genome evolution, suggesting that horizontal gene transfer and genome reduction in the group 2 strains by loss of genes encoding complete metabolic pathways or physiological features contributed to the observed diversification.Ítem Genes and pathways for CO2fixation in the obligate, chemolithoautotrophic acidophile, Acidithiobacillus ferrooxidans, Carbon fixation in A. ferrooxidans(BMC, 2010) Esparza, Mario; Crdenas, Juan Pablo; Bowien, Botho; Jedlicki, Eugenia; Holmes, David S.Background. Acidithiobacillus ferrooxidans is chemolithoautotrophic -proteobacterium that thrives at extremely low pH (pH 1-2). Although a substantial amount of information is available regarding CO2uptake and fixation in a variety of facultative autotrophs, less is known about the processes in obligate autotrophs, especially those living in extremely acidic conditions, prompting the present study. Results. Four gene clusters (termed cbb1-4) in the A. ferrooxidans genome are predicted to encode enzymes and structural proteins involved in carbon assimilation via the Calvin-Benson- Bassham (CBB) cycle including form I of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO, EC 4.1.1.39) and the CO2- concentrating carboxysomes. RT-PCR experiments demonstrated that each gene cluster is a single transcriptional unit and thus is an operon. Operon cbb1 is divergently transcribed from a gene, cbbR, encoding the LysR-type transcriptional regulator CbbR that has been shown in many organisms to regulate the expression of RubisCO genes. Sigma70-like -10 and -35 promoter boxes and potential CbbR-binding sites (T-N11-A/TNA-N7TNA) were predicted in the upstream regions of the four operons. Electrophoretic mobility shift assays (EMSAs) confirmed that purified CbbR is able to bind to the upstream regions of the cbb1, cbb2 and cbb3 operons, demonstrating that the predicted CbbR-binding sites are functional in vitro. However, CbbR failed to bind the upstream region of the cbb4 operon that contains cbbP, encoding phosphoribulokinase (EC 2.7.1.19). Thus, other factors not present in the assay may be required for binding or the region lacks a functional CbbR-binding site. The cbb3 operon contains genes predicted to encode anthranilate synthase components I and II, catalyzing the formation of anthranilate and pyruvate from chorismate. This suggests a novel regulatory connection between CO 2fixation and tryptophan biosynthesis. The presence of a form II RubisCO could promote the ability of A. ferrooxidans to fix CO2at different concentrations of CO2. Conclusions. A. ferrooxidans has features of cbb gene organization for CO2-assimilating functions that are characteristic of obligate chemolithoautotrophs and distinguish this group from facultative autotrophs. The most conspicuous difference is a separate operon for the cbbP gene. It is hypothesized that this organization may provide greater flexibility in the regulation of expression of genes involved in inorganic carbon assimilation. © 2010 Esparza et al; licensee BioMed Central Ltd.Ítem Genome analysis of the biotechnologically relevant acidophilic iron oxidising strain JA12 indicates phylogenetic and metabolic diversity within the novel genus "Ferrovum"(Public Library of Science, 2016-01) Ullrich, Sophie R.; Poehlein, Anja; Tischler, Judith S.; González, Carolina; Ossandon, Francisco J.; Daniel, Rolf; Holmes, David S.; Schlömann, Michael; Mühling, MartinBackground: Members of the genus "Ferrovum" are ubiquitously distributed in acid mine drainage (AMD) waters which are characterised by their high metal and sulfate loads. So far isolation and microbiological characterisation have only been successful for the designated type strain "Ferrovum myxofaciens" P3G. Thus, knowledge about physiological characteristics and the phylogeny of the genus "Ferrovum" is extremely scarce. Objective: In order to access the wider genetic pool of the genus "Ferrovum" we sequenced the genome of a "Ferrovum"-containing mixed culture and successfully assembled the almost complete genome sequence of the novel "Ferrovum" strain JA12. Phylogeny and lifestyle: The genome-based phylogenetic analysis indicates that strain JA12 and the type strain represent two distinct "Ferrovum" species. "Ferrovum" strain JA12 is characterised by an unusually small genome in comparison to the type strain and other iron oxidising bacteria. The prediction of nutrient assimilation pathways suggests that "Ferrovum" strain JA12 maintains a chemolithoautotrophic lifestyle utilising carbon dioxide and bicarbonate, ammonium and urea, sulfate, phosphate and ferrous iron as carbon, nitrogen, sulfur, phosphorous and energy sources, respectively. Unique Metabolic Features: The potential utilisation of urea by "Ferrovum" strain JA12 is moreover remarkable since it may furthermore represent a strategy among extreme acidophiles to cope with the acidic environment. Unlike other acidophilic chemolithoautotrophs "Ferrovum" strain JA12 exhibits a complete tricarboxylic acid cycle, a metabolic feature shared with the closer related neutrophilic iron oxidisers among the Betaproteobacteria including Sideroxydans lithotrophicus and Thiobacillus denitrificans. Furthermore, the absence of characteristic redox proteins involved in iron oxidation in the well-studied acidophiles Acidithiobacillus ferrooxidans (rusticyanin) and Acidithiobacillus ferrivorans (iron oxidase) indicates the existence of a modified pathway in "Ferrovum" strain JA12. Therefore, the results of the present study extend our understanding of the genus "Ferrovum" and provide a comprehensive framework for future comparative genome and metagenome studies. © 2016 Ullrich et al.Ítem Integrative Genomics Sheds Light on Evolutionary Forces Shaping the Acidithiobacillia Class Acidophilic Lifestyle(Frontiers Media S.A., 2022-02-15) González-Rosales, Carolina; Vergara, Eva; Dopson, Mark; Valdés, Jorge H.; Holmes, David S.Extreme acidophiles thrive in environments rich in protons (pH values <3) and often high levels of dissolved heavy metals. They are distributed across the three domains of the Tree of Life including members of the Proteobacteria. The Acidithiobacillia class is formed by the neutrophilic genus Thermithiobacillus along with the extremely acidophilic genera Fervidacidithiobacillus, Igneacidithiobacillus, Ambacidithiobacillus, and Acidithiobacillus. Phylogenomic reconstruction revealed a division in the Acidithiobacillia class correlating with the different pH optima that suggested that the acidophilic genera evolved from an ancestral neutrophile within the Acidithiobacillia. Genes and mechanisms denominated as “first line of defense” were key to explaining the Acidithiobacillia acidophilic lifestyle including preventing proton influx that allows the cell to maintain a near-neutral cytoplasmic pH and differ from the neutrophilic Acidithiobacillia ancestors that lacked these systems. Additional differences between the neutrophilic and acidophilic Acidithiobacillia included the higher number of gene copies in the acidophilic genera coding for “second line of defense” systems that neutralize and/or expel protons from cell. Gain of genes such as hopanoid biosynthesis involved in membrane stabilization at low pH and the functional redundancy for generating an internal positive membrane potential revealed the transition from neutrophilic properties to a new acidophilic lifestyle by shaping the Acidithiobacillaceae genomic structure. The presence of a pool of accessory genes with functional redundancy provides the opportunity to “hedge bet” in rapidly changing acidic environments. Although a core of mechanisms for acid resistance was inherited vertically from an inferred neutrophilic ancestor, the majority of mechanisms, especially those potentially involved in resistance to extremely low pH, were obtained from other extreme acidophiles by horizontal gene transfer (HGT) events. Copyright © 2022 González-Rosales, Vergara, Dopson, Valdés and Holmes.Ítem Metagenomic analysis reveals adaptations to a cold-adapted lifestyle in a low-temperature acid mine drainage stream(Oxford University Press, 2015-04) Liljeqvist, Maria; Ossandon, Francisco J.; González, Carolina; Rajan, Sukithar; Stell, Adam; Valdes, Jorge; Holmes, David S.; Dopson, MarkAn acid mine drainage (pH 2.5-2.7) stream biofilm situated 250 m below ground in the low-temperature (6-10°C)Kristineberg mine, northern Sweden, contained a microbial community equipped for growth at low temperature and acidicpH. Metagenomic sequencing of the biofilm and planktonic fractions identified the most abundant microorganism to besimilar to the psychrotolerant acidophile, Acidithiobacillus ferrivorans. In addition, metagenome contigs were most similar toother Acidithiobacillus species, an Acidobacteria-like species, and a Gallionellaceae-like species. Analyses of the metagenomesindicated functional characteristics previously characterized as related to growth at low temperature including cold-shockproteins, several pathways for the production of compatible solutes and an anti-freeze protein. In addition, genes werepredicted to encode functions related to pH homeostasis and metal resistance related to growth in the acidicmetal-containing mine water. Metagenome analyses identified microorganisms capable of nitrogen fixation and exhibitinga primarily autotrophic lifestyle driven by the oxidation of the ferrous iron and inorganic sulfur compounds contained in thesulfidic mine waters. The study identified a low diversity of abundant microorganisms adapted to a low-temperature acidicenvironment as well as identifying some of the strategies the microorganisms employ to grow in this extreme environment. © FEMS 2015.Ítem Metal resistance or tolerance? Acidophiles confront high metal loads via both abiotic and biotic mechanisms(Frontiers Research Foundation, 2014-04) Dopson, Mark; Ossandon, Francisco J.; Lövgren, Lars; Holmes, David S.All metals are toxic at high concentrations and consequently their intracellular concentrations must be regulated. Extremely acidophilic microorganisms have an optimum growth of pH < 3 and proliferate in natural and anthropogenic low pH environments. Some acidophiles are involved in the catalysis of sulfide mineral dissolution, resulting in high concentrations of metals in solution. Acidophiles are often described as highly metal resistant via mechanisms such as multiple and/or more efficient active resistance systems than are present in neutrophiles. However, this is not the case for all acidophiles and we contend that their growth in high metal concentrations is partially due to an intrinsic tolerance as a consequence of the environment in which they live. In this perspective, we highlight metal tolerance via complexation of free metals by sulfate ions and passive tolerance to metal influx via an internal positive cytoplasmic transmembrane potential. These tolerance mechanisms have been largely ignored in past studies of acidophile growth in the presence of metals and should be taken into account. © 2014 Dopson, Ossandon, Laóvgren and Holmes.Ítem Metal resistance or tolerance? Acidophiles confront high metal loads via both abiotic and biotic mechanisms(Frontiers Media S.A., 2014-04) Dopson, Mark; Ossandon, Francisco J.; Lövgren, Lars; Holmes, David S.All metals are toxic at high concentrations and consequently their intracellular concentrations must be regulated. Extremely acidophilic microorganisms have an optimum growth of pH < 3 and proliferate in natural and anthropogenic low pH environments. Some acidophiles are involved in the catalysis of sulfide mineral dissolution, resulting in high concentrations of metals in solution. Acidophiles are often described as highly metal resistant via mechanisms such as multiple and/or more efficient active resistance systems than are present in neutrophiles. However, this is not the case for all acidophiles and we contend that their growth in high metal concentrations is partially due to an intrinsic tolerance as a consequence of the environment in which they live. In this perspective, we highlight metal tolerance via complexation of free metals by sulfate ions and passive tolerance to metal influx via an internal positive cytoplasmic transmembrane potential. These tolerance mechanisms have been largely ignored in past studies of acidophile growth in the presence of metals and should be taken into account. © 2014 Dopson, Ossandon, Laóvgren and Holmes.Ítem Metal resistance or tolerance? Acidophiles confront high metal loads via both abiotic and biotic mechanisms(Frontiers Media S.A., 2014-04) Dopson, Mark; Ossandon, Francisco J.; Lövgren, Lars; Holmes, David S.All metals are toxic at high concentrations and consequently their intracellular concentrations must be regulated. Extremely acidophilic microorganisms have an optimum growth of pH < 3 and proliferate in natural and anthropogenic low pH environments. Some acidophiles are involved in the catalysis of sulfide mineral dissolution, resulting in high concentrations of metals in solution. Acidophiles are often described as highly metal resistant via mechanisms such as multiple and/or more efficient active resistance systems than are present in neutrophiles. However, this is not the case for all acidophiles and we contend that their growth in high metal concentrations is partially due to an intrinsic tolerance as a consequence of the environment in which they live. In this perspective, we highlight metal tolerance via complexation of free metals by sulfate ions and passive tolerance to metal influx via an internal positive cytoplasmic transmembrane potential. These tolerance mechanisms have been largely ignored in past studies of acidophile growth in the presence of metals and should be taken into account. © 2014 Dopson, Ossandon, Laóvgren and Holmes.Ítem Multi Locus Sequence Typing scheme for Acidithiobacillus caldus strain evaluation and differentiation(Elsevier Masson s.r.l., 2014) Nuñez, Harold; Loyola, David; Cárdenas, Juan Pablo; Holmes, David S.; Johnson, D. Barrie; Quatrini, RaquelPhenotypic, metabolic and genetic properties of several Acidithiobacillus caldus strains indicate the existence of as yet undefined levels of variation within the species. Inspite of this, intraspecies genetic diversity has not yet been explored in detail. In this study, the design and implementation of a Multi Locus Sequence Typing (MLST) scheme for At. caldus is described. This represents the first MLST-based study applied to industrial isolates of the species. Seven informative and discriminant MLST markers were selected using a sequence-driven approach and a custom-designed bioinformatic pipeline. The allelic profiles of thirteen At. caldus strains from diverse geographical origins and industrial settings were derived using this scheme. MLST-based population structure analysis indicated only moderate amounts of genetic diversity within the set of strains, further supporting their current assignment to a single species. Also, no clear evidence for geographical isolation could be derived from this study. However, the prevalence of sequence type 1 in heap leaching industrial settings support the view that bioprocess conditions and dynamics may have a strong influence on At. caldus (microbial) microdiversity patterns. The MLST scheme presented herein is a valuable tool for the identification and classification of strains of At. caldus for either ecological or evolutionary studies and possibly also for industrial monitoring purposes. © 2014 The Authors.Ítem Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins(NLM (Medline), 2017-03) Valdebenito-Maturana, Braulio; Reyes-Suarez, Jose Antonio; Henriquez, Jaime; Holmes, David S.; Quatrini, Raquel; Pohl, Ehmke; Arenas-Salinas, MauricioThe electrostatic potential plays a key role in many biological processes like determining the affinity of a ligand to a given protein target, and they are responsible for the catalytic activity of many enzymes. Understanding the effect that amino acid mutations will have on the electrostatic potential of a protein, will allow a thorough understanding of which residues are the most important in a protein. MutantElec, is a friendly web application for in silico generation of site-directed mutagenesis of proteins and the comparison of electrostatic potential between the wild type protein and the mutant(s), based on the three-dimensional structure of the protein. The effect of the mutation is evaluated using different approach to the traditional surface map. MutantElec provides a graphical display of the results that allows the visualization of changes occurring at close distance from the mutation and thus uncovers the local and global impact of a specific change. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.