Publications by authors named "Verónica Cambiazo"

46 Publications

Global Proteomic Profiling of and Salmon Macrophage-Like Cells during Intracellular Infection.

Microorganisms 2020 Nov 24;8(12). Epub 2020 Nov 24.

Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile.

is an intracellular bacterial fish pathogen that causes piscirickettsiosis, a disease with numerous negative impacts in the Chilean salmon farming industry. Although transcriptomic studies of and its host have been performed, dual host-pathogen proteomic approaches during infection are still missing. Considering that gene expression does not always correspond with observed phenotype, and bacteriological culture studies inadequately reflect infection conditions, to improve the existing knowledge for the pathogenicity of , we present here a global proteomic profiling of macrophage-like cell cultures infected with LF-89. The proteomic analyses identified several proteins from two temporally different stages of macrophages infection, some of them related to key functions for bacterial survival in other intracellular pathogens. Metabolic differences were observed in early-stage infection bacteria, compared to late-stage infections. Virulence factors related to membrane, lipopolysaccharide (LPS) and surface component modifications, cell motility, toxins, and secretion systems also varied between the infection stages. Pilus proteins, beta-hemolysin, and the type VI secretion system (T6SS) were characteristic of the early-infection stage, while fimbria, upregulation of 10 toxins or effector proteins, and the Dot/Icm type IV secretion system (T4SS) were representative of the late-infection stage bacteria. Previously described virulence-related genes in plasmids were identified by proteomic assays during infection in SHK-1 cells, accompanied by an increase of mobile-related elements. By comparing the infected and un-infected proteome of SHK-1 cells, we observed changes in cellular and redox homeostasis; innate immune response; microtubules and actin cytoskeleton organization and dynamics; alteration in phagosome components, iron transport, and metabolism; and amino acids, nucleoside, and nucleotide metabolism, together with an overall energy and ATP production alteration. Our global proteomic profiling and the current knowledge of the infection process allowed us to propose a model of the macrophage- interaction.
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http://dx.doi.org/10.3390/microorganisms8121845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7760863PMC
November 2020

Fungal Diversity Analysis of Grape Musts from Central Valley-Chile and Characterization of Potential New Starter Cultures.

Microorganisms 2020 Jun 24;8(6). Epub 2020 Jun 24.

Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7810000, Chile.

Autochthonous microorganisms are an important source of the distinctive metabolites that influence the chemical profile of wine. However, little is known about the diversity of fungal communities associated with grape musts, even though they are the source of local yeast strains with potential capacities to become starters during fermentation. By using internal transcribed spacer (ITS) amplicon sequencing, we identified the taxonomic structure of the yeast community in unfermented and fermented musts of a typical L. var. Sauvignon blanc from the Central Valley of Chile throughout two consecutive seasons of production. Unsurprisingly, represented the most abundant fungal genus in unfermented and fermented musts, mainly due to the contribution of (42.7%) and (80%). Unfermented musts were highly variable between seasons and showed higher values of fungal diversity than fermented musts. Since microbial physiological characterization is primarily achieved in culture, we isolated nine species belonging to six genera of fungi from the unfermented must samples. All isolates were characterized for their potential capacities to be used as new starters in wine. Remarkably, only could co-exist with a commercial strain under fermentative conditions, representing a feasible candidate strain for wine production.
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http://dx.doi.org/10.3390/microorganisms8060956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7356840PMC
June 2020

PCR-RFLP Detection and Genogroup Identification of in Field Samples.

Pathogens 2020 May 8;9(5). Epub 2020 May 8.

Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile.

, the causative agent of piscirickettsiosis, is genetically divided into two genomic groups, named after the reference strains as LF-89-like or EM-90-like. Phenotypic differences have been detected between the genogroups, including antibiotic susceptibilities, host specificities and pathogenicity. In this study, we aimed to develop a rapid, sensitive and cost-effective assay for the differentiation of the genogroups. Using an in silico analysis of the 16S rDNA digestion patterns, we have designed a genogroup-specific assay based on PCR-restriction fragment length polymorphism (RFLP). An experimental validation was carried out by comparing the restriction patterns of 13 strains and 57 field samples obtained from the tissues of dead or moribund fish. When the bacterial composition of a set of field samples, for which we detected mixtures of bacterial DNA, was analyzed by a high-throughput sequencing of the 16S rRNA gene amplicons, a diversity of taxa could be identified, including pathogenic and commensal bacteria. Despite the presence of mixtures of bacterial DNA, the characteristic digestion pattern of the genogroups could be detected in the field samples without the need of a microbiological culture and bacterial isolation.
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http://dx.doi.org/10.3390/pathogens9050358DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7281544PMC
May 2020

Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment.

Sci Rep 2020 03 27;10(1):5560. Epub 2020 Mar 27.

Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile.

The Atacama Desert is the most arid desert on Earth, focus of important research activities related to microbial biodiversity studies. In this context, metabolic characterization of arid soil bacteria is crucial to understand their survival strategies under extreme environmental stress. We investigated whether strain-specific features of two Microbacterium species were involved in the metabolic ability to tolerate/adapt to local variations within an extreme desert environment. Using an integrative systems biology approach we have carried out construction and comparison of genome-scale metabolic models (GEMs) of two Microbacterium sp., CGR1 and CGR2, previously isolated from physicochemically contrasting soil sites in the Atacama Desert. Despite CGR1 and CGR2 belong to different phylogenetic clades, metabolic pathways and attributes are highly conserved in both strains. However, comparison of the GEMs showed significant differences in the connectivity of specific metabolites related to pH tolerance and CO production. The latter is most likely required to handle acidic stress through decarboxylation reactions. We observed greater GEM connectivity within Microbacterium sp. CGR1 compared to CGR2, which is correlated with the capacity of CGR1 to tolerate a wider pH tolerance range. Both metabolic models predict the synthesis of pigment metabolites (β-carotene), observation validated by HPLC experiments. Our study provides a valuable resource to further investigate global metabolic adaptations of bacterial species to grow in soils with different abiotic factors within an extreme environment.
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http://dx.doi.org/10.1038/s41598-020-62130-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101325PMC
March 2020

Transcriptomic Changes of During Intracellular Growth in a Salmon Macrophage-Like Cell Line.

Front Cell Infect Microbiol 2019 9;9:426. Epub 2020 Jan 9.

Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile.

is the causative agent of Piscirickettsiosis, a systemic infection of salmonid fish species. infects and survives in its host cell, a process that correlates with the expression of virulence factors including components of the type IVB secretion system. To gain further insights into the cellular and molecular mechanism behind the adaptive response of during host infection, we established an model of infection using the SHK-1 cell line from Atlantic salmon head kidney. The results indicated that in comparison to uninfected SHK-1 cells, infection significantly decreased cell viability after 10 days along with a significant increment of genome equivalents. At that time, the intracellular bacteria were localized within a spacious cytoplasmic vacuole. By using a whole-genome microarray of LF-89, the transcriptome of this bacterium was examined during intracellular growth in the SHK-1 cell line and exponential growth in broth. Transcriptome analysis revealed a global shutdown of translation during intracellular growth and suggested an induction of the stringent response. Accordingly, key genes of the stringent response pathway were up-regulated during intracellular growth as well as at stationary phase bacteria, suggesting a role of the stringent response on bacterial virulence. Our results also reinforce the participation of the Dot/Icm type IVB secretion system during infection and reveals many unexplored genes with potential roles in the adaptation to intracellular growth. Finally, we proposed that intracellular alternates between a replicative phase and a stationary phase in which the stringent response is activated.
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http://dx.doi.org/10.3389/fcimb.2019.00426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6964531PMC
September 2020

Cryptic Plasmids: Source of Mobile DNA and Virulence Factors.

Pathogens 2019 Nov 28;8(4). Epub 2019 Nov 28.

Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile.

Four large cryptic plasmids were identified in the salmon pathogen reference strain LF-89. These plasmids appeared highly novel, with less than 7% nucleotidic identity to the nr plasmid database. Plasmid copy number analysis revealed that they are harbored in chromosome equivalent ratios. In addition to plasmid-related genes (plasmidial autonomous replication, partitioning, maintenance, and mobilization genes), mobile genetic elements such as transposases, integrases, and prophage sequences were also identified in plasmids. However, bacterial lysis was not observed upon the induction of prophages. A total of twelve putative virulence factors (VFs) were identified, in addition to two global transcriptional regulators, the widely conserved CsrA protein and the regulator Crp/Fnr. Eleven of the putative VFs were overexpressed during infection in two salmon-derived cellular infection models, supporting their role as VFs. The ubiquity of these plasmids was also confirmed by sequence similarity in the genomes of other strains. The ontology of plasmids suggests a role in bacterial fitness and adaptation to the environment as they encode proteins related to mobilization, nutrient transport and utilization, and bacterial virulence. Further functional characterization of plasmids may improve our knowledge regarding virulence and mobile elements in this intracellular pathogen.
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http://dx.doi.org/10.3390/pathogens8040269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6963756PMC
November 2019

Soil Bacterial Communities From the Chilean Andean Highlands: Taxonomic Composition and Culturability.

Front Bioeng Biotechnol 2019 5;7:10. Epub 2019 Feb 5.

Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.

The Atacama Desert is a highly complex, extreme ecosystem which harbors microorganisms remarkable for their biotechnological potential. Here, a soil bacterial prospection was carried out in the high Altiplano region of the Atacama Desert (>3,800 m above sea level; m a.s.l.), where direct anthropogenic interference is minimal. We studied: (1) soil bacterial community composition using high-throughput sequencing of the 16S rRNA gene and (2) bacterial culturability, by using a soil extract medium (SEM) under a factorial design of three factors: temperature (15 and 30°C), nutrient content (high and low nutrient disposal) and oxygen availability (presence and absence). A total of 4,775 OTUs were identified and a total of 101 isolates were selected for 16S rRNA sequencing, 82 of them corresponded to unique or non-redundant sequences. To expand our view of the Altiplano landscape and to obtain a better representation of its microbiome, we complemented our Operational Taxonomic Units (OTUs) and isolate collection with data from other previous data from our group and obtained a merged set of OTUs and isolates that we used to perform our study. Taxonomic comparisons between culturable microbiota and metabarcoding data showed an overrepresentation of the phylum Firmicutes (44% of isolates vs. 2% of OTUs) and an underrepresentation of Proteobacteria (8% of isolates vs. 36% of OTUs). Within the Next Generation Sequencing (NGS) results, 33% of the OTUs were unknown up to genus, revealing an important proportion of putative new species in this environment. Biochemical characterization and analysis extracted from the literature indicated that an important number of our isolates had biotechnological potential. Also, by comparing our results with similar studies on other deserts, the Altiplano highland was most similar to a cold arid desert. In summary, our study contributes to expand the knowledge of soil bacterial communities in the Atacama Desert and complements the pipeline to isolate selective bacteria that could represent new potential biotechnological resources.
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http://dx.doi.org/10.3389/fbioe.2019.00010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6371850PMC
February 2019

Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans.

Sci Rep 2019 02 14;9(1):2132. Epub 2019 Feb 14.

FONDAP Center for Genome Regulation, Santiago, Chile.

Whole human genome sequencing initiatives help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations, and the information of the genomic structure of Native Americans, especially those from the Southern Cone is scant. Here we present annotation and variant discovery from high-quality complete genome sequences of a cohort of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile. We found approximately 3.1 × 10 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs events. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a sample from a marginally admixed population from the Southern Cone, whose main genetic component derives from Native American ancestors. Additionally, we found that HUI genomes contain variants in genes associated with 5 of the 6 leading causes of noncommunicable diseases in Chile, which may have an impact on the risk of prevalent diseases in Chilean and Amerindian populations. Our data represents a useful resource that can contribute to population-based studies and for the design of early diagnostics or prevention tools for Native and admixed Latin American populations.
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http://dx.doi.org/10.1038/s41598-019-39391-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6376018PMC
February 2019

Bacterial communities associated to Chilean altiplanic native plants from the Andean grasslands soils.

Sci Rep 2019 01 31;9(1):1042. Epub 2019 Jan 31.

FONDAP Center for Genome Regulation, Santiago, Chile.

The rhizosphere is considered the primary place for soil microbiome differentiation and plays a key role in plant survival, especially for those subjected to environmental stress. Using high-throughput sequencing of the 16S rRNA gene, we analyzed and compared soil bacterial communities associated to four of the most abundant high altitude native plant species of the Chilean Andean grasslands. We examined three soil compartments: the rhizosphere (bacteria firmly attached to the roots), the rhizosphere-surrounding soil (bacteria loosely attached to the roots) and the bulk soil (plant-free soil). The rhizosphere microbiome was in all cases the least diverse, exposing that the bulk soil was a more complex environment. Taxonomic analysis revealed an abrupt change between the rhizosphere and the rest of the non-rhizospheric soils. Thus, while rhizobacterial communities were enriched in Proteobacteria (mainly Alphaproteobacteria), Actinobacteria (mostly Blastocatellia) dominated in bulk soils. Finally, we detected certain taxonomic rhizosphere signatures, which could be attributed to a particular genotype. Overall, our results indicate that the thin layer of soil surrounding the roots constitute a distinctive soil environment. This study contributes to expand the knowledge about soil bacterial communities in the Chilean highlands and takes the first step to understand the processes that might lead to the rhizosphere differentiation in that area.
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http://dx.doi.org/10.1038/s41598-018-37776-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6355873PMC
January 2019

The Role of Fur in the Transcriptional and Iron Homeostatic Response of .

Front Microbiol 2018 17;9:1580. Epub 2018 Jul 17.

Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.

The ferric uptake regulator (Fur) plays a major role in controlling the expression of iron homeostasis genes in bacterial organisms. In this work, we fully characterized the capacity of Fur to reconfigure the global transcriptional network and influence iron homeostasis in . The characterization of the Fur regulon from indicated that this protein (Fur) regulated the expression of genes involved in iron uptake systems, conferring to the system a high level of efficiency and specificity to respond under different iron exposure conditions. An RNAseq assay coupled with a systems biology approach allowed us to identify the first global transcriptional network activated by different iron treatments (excess and limited), with and without the presence of Fur. The results showed that changes in iron availability activated a complex network of transcriptional factors in , among them global regulators such as LysR, ArgR, GalRS, and local regulators, LexA and CopY, which were also stimulated by copper and zinc treatments. The deletion of Fur impacted the expression of genes encoding for ABC transporters, energy production and [Fe-S] proteins, which optimized detoxification and iron uptake under iron excess and limitation, respectively. Finally, considering the close relationship between iron homeostasis and pathogenesis, our data showed that the absence of Fur increased the internal concentration of iron in the bacterium and also affected its ability to produce biofilm. These results open new alternatives in the field of infection mechanisms of .
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http://dx.doi.org/10.3389/fmicb.2018.01580DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056675PMC
July 2018

The dorsoventral patterning of embryos: insights into BMP/Dpp evolution from the base of the lower cyclorraphan flies.

Evodevo 2018 16;9:13. Epub 2018 May 16.

1Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano 5524, Santiago, Chile.

Background: In the last few years, accumulated information has indicated that the evolution of an extra-embryonic membrane in dipterans was accompanied by changes in the gene regulatory network controlled by the BMP/Dpp pathway, which is responsible for dorsal patterning in these insects. However, only comparative analysis of gene expression levels between distant species with two extra-embryonic membranes, like or , and has been conducted. Analysis of gene expression in ancestral species, which evolved closer to the amnioserosa origin, could provide new insights into the evolution of dorsoventral patterning in dipterans.

Results: Here we describe the spatial expression of several key and downstream elements of the Dpp pathway and show the compared patterns of expression between and embryos, both dipterans with amnioserosa. Most of the analyzed gene showed a high degree of expression conservation, however, we found several differences in the gene expression pattern of orthologs for and . Bioinformatics analysis of the promoter of both genes indicated that the variations could be related to the gain of several binding sites for the transcriptional factor Dorsal in the promoter and Snail in the . These altered expressions could explain the unclear formation of the pMad gradient in the embryo, compared to the formation of the gradient in

Conclusion: Gene expression changes during the dorsal-ventral patterning in insects contribute to the differentiation of extra-embryonic tissues as a consequence of changes in the gene regulatory network controlled by BMP/Dpp. In this work, in early embryos, we identified the expression pattern of several genes members involved in the dorsoventral specification of the embryo. We believe that these data can contribute to understanding the evolution of the BMP/Dpp pathway, the regulation of BMP ligands, and the formation of a Dpp gradient in higher cyclorraphan flies.
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http://dx.doi.org/10.1186/s13227-018-0102-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5956798PMC
May 2018

Microbiome analysis and bacterial isolation from Lejía Lake soil in Atacama Desert.

Extremophiles 2018 Jul 23;22(4):665-673. Epub 2018 Apr 23.

Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile.

As a consequence of the severe climatic change affecting our entire world, many lakes in the Andes Cordillera are likely to disappear within a few decades. One of these lakes is Lejía Lake, located in the central Atacama Desert. The objectives of this study were: (1) to characterize the bacterial community from Lejía Lake shore soil (LLS) using 16S rRNA sequencing and (2) to test a culture-based approach using a soil extract medium (SEM) to recover soil bacteria. This extreme ecosystem was dominated by three phyla: Bacteroidetes, Proteobacteria, and Firmicutes with 29.2, 28.2 and 28.1% of the relative abundance, respectively. Using SEM, we recovered 7.4% of the operational taxonomic units from LLS, all of which belonged to the same three dominant phyla from LLS (6.9% of Bacteroidetes, 77.6% of Proteobacteria, and 15.3% of Firmicutes). In addition, we used SEM to recover isolates from LLS and supplemented the culture medium with increasing salt concentrations to isolate microbial representatives of salt tolerance (Halomonas spp.). The results of this study complement the list of microbial taxa diversity from the Atacama Desert and assess a pipeline to isolate selective bacteria that could represent useful elements for biotechnological approaches.
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http://dx.doi.org/10.1007/s00792-018-1027-6DOI Listing
July 2018

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience.

Sci Rep 2018 04 12;8(1):5875. Epub 2018 Apr 12.

Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.

Understanding the factors that modulate bacterial community assembly in natural soils is a longstanding challenge in microbial community ecology. In this work, we compared two microbial co-occurrence networks representing bacterial soil communities from two different sections of a pH, temperature and humidity gradient occurring along a western slope of the Andes in the Atacama Desert. In doing so, a topological graph alignment of co-occurrence networks was used to determine the impact of a shift in environmental variables on OTUs taxonomic composition and their relationships. We observed that a fraction of association patterns identified in the co-occurrence networks are persistent despite large environmental variation. This apparent resilience seems to be due to: (1) a proportion of OTUs that persist across the gradient and maintain similar association patterns within the community and (2) bacterial community ecological rearrangements, where an important fraction of the OTUs come to fill the ecological roles of other OTUs in the other network. Actually, potential functional features suggest a fundamental role of persistent OTUs along the soil gradient involving nitrogen fixation. Our results allow identifying factors that induce changes in microbial assemblage configuration, altering specific bacterial soil functions and interactions within the microbial communities in natural environments.
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http://dx.doi.org/10.1038/s41598-018-23931-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5897386PMC
April 2018

Analysis of Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing.

Front Microbiol 2017 11;8:2462. Epub 2017 Dec 11.

Mathomics, Center for Mathematical Modeling, Universidad de Chile, Santiago, Chile.

is an intracellular bacterial fish pathogen that causes piscirickettsiosis, a disease with highly adverse impact in the Chilean salmon farming industry. The development of effective treatment and control methods for piscireckttsiosis is still a challenge. To meet it the number of studies on has grown in the last couple of years but many aspects of the pathogen's biology are still poorly understood. Studies on its metabolism are scarce and only recently a metabolic model for reference strain LF-89 was developed. We present a new genome-scale model for LF-89 with more than twice as many genes as in the previous model and incorporating specific elements of the fish pathogen metabolism. Comparative analysis with models of different bacterial pathogens revealed a lower flexibility in metabolic network. Through constraint-based analysis, we determined essential metabolites required for its growth and showed that it can benefit from different carbon sources tested experimentally in new defined media. We also built an additional model for strain A1-15972, and together with an analysis of pangenome, we identified metabolic features that differentiate two main species clades. Both models constitute a knowledge-base for metabolism and can be used to guide the efficient culture of the pathogen and the identification of specific drug targets.
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http://dx.doi.org/10.3389/fmicb.2017.02462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5732189PMC
December 2017

The bioleaching potential of a bacterial consortium.

Bioresour Technol 2016 Oct 6;218:659-66. Epub 2016 Jul 6.

Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Department of Mathematical Engineering, Universidad de Chile, Beauchef 851, 5th Floor, Santiago, Chile. Electronic address:

This work presents the molecular foundation of a consortium of five efficient bacteria strains isolated from copper mines currently used in state of the art industrial-scale biotechnology. The strains Acidithiobacillus thiooxidans Licanantay, Acidiphilium multivorum Yenapatur, Leptospirillum ferriphilum Pañiwe, Acidithiobacillus ferrooxidans Wenelen and Sulfobacillus thermosulfidooxidans Cutipay were selected for genome sequencing based on metal tolerance, oxidation activity and bioleaching of copper efficiency. An integrated model of metabolic pathways representing the bioleaching capability of this consortium was generated. Results revealed that greater efficiency in copper recovery may be explained by the higher functional potential of L. ferriphilum Pañiwe and At. thiooxidans Licanantay to oxidize iron and reduced inorganic sulfur compounds. The consortium had a greater capacity to resist copper, arsenic and chloride ion compared to previously described biomining strains. Specialization and particular components in these bacteria provided the consortium a greater ability to bioleach copper sulfide ores.
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http://dx.doi.org/10.1016/j.biortech.2016.07.012DOI Listing
October 2016

Target genes of Dpp/BMP signaling pathway revealed by transcriptome profiling in the early D.melanogaster embryo.

Gene 2016 Oct 7;591(1):191-200. Epub 2016 Jul 7.

Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Libano 5524, Santiago, Chile; Fondap Center for Genome Regulation (CGR), Chile. Electronic address:

In the early Drosophila melanogaster embryo, the gene regulatory network controlled by Dpp signaling is involved in the subdivision of dorsal ectoderm into the presumptive dorsal epidermis and amnioserosa. In this work, we aimed to identify new Dpp downstream targets involved in dorsal ectoderm patterning. We used oligonucleotide D. melanogaster microarrays to identify the set of genes that are differential expressed between wild type embryos and embryos that overexpress Dpp (nos-Gal4>UAS-dpp) during early stages of embryo development. By using this approach, we identified 358 genes whose relative abundance significantly increased in response to Dpp overexpression. Among them, we found the entire set of known Dpp target genes that function in dorsal ectoderm patterning (zen, doc, hnt, pnr, ush, tup, and others) in addition to several up-regulated genes of unknown functions. Spatial expression pattern of up-regulated genes in response to Dpp overexpression as well as their opposing transcriptional responses to Dpp loss- and gain-of-function indicated that they are new candidate target genes of Dpp signaling pathway. We further analyse one of the candidate genes, CG13653, which is expressed at the dorsal-most cells of the embryo during a restricted period of time. CG13653 orthologs were not detected in basal lineages of Dipterans, which unlike D. melanogaster develop two extra-embryonic membranes, amnion and serosa. We characterized the enhancer region of CG13653 and revealed that CG13653 is directly regulated by Dpp signaling pathway.
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http://dx.doi.org/10.1016/j.gene.2016.07.015DOI Listing
October 2016

Genomic-Based Restriction Enzyme Selection for Specific Detection of Piscirickettsia salmonis by 16S rDNA PCR-RFLP.

Front Microbiol 2016 9;7:643. Epub 2016 May 9.

Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile; Fondap Center for Genoma RegulationSantiago, Chile; Laboratorio de Genómica Aplicada, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile.

The gram negative facultative bacterium P. salmonis is the etiological agent of Salmonid Rickettsial Septicaemia (SRS), a severe disease that causes important economic losses in the global salmon farmer industry. Despite efforts to control this disease, the high frequency of new epizootic events indicate that the vaccine and antibiotics treatments have limited effectiveness, therefore the preventive and diagnostic approaches must be improved. A comparison of several methodologies for SRS diagnostic indicate differences in their specificity and its capacity to detect other bacteria coexisting with P. salmonis in culture media (contamination) and fish samples (coinfection), aspects relevant for research, vaccine development and clinical diagnostic. By computer-simulation analyses, we identified a group of restriction enzymes that generate unique P. salmonis 16S rDNA band patterns, distinguishable from all other bacteria. From this information, we designed and developed a PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism) assay, which was validated using 16S rDNA universal primers and restriction enzyme PmaCI for the amplification and digestion, respectively. Experimental validation was performed by comparing the restriction pattern of P. salmonis with the restriction patterns generated by bacteria that cohabit with P. salmonis (fish bacterial isolates and culture media contaminants). Our results indicate that the restriction enzyme selection pipeline was suitable to design a more specific, sensible, faster and cheaper assay than the currently used P. salmonis detection methodologies.
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http://dx.doi.org/10.3389/fmicb.2016.00643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860512PMC
May 2016

Complete genome sequence of Microbacterium sp. CGR1, bacterium tolerant to wide abiotic conditions isolated from the Atacama Desert.

J Biotechnol 2015 Dec 29;216:149-50. Epub 2015 Oct 29.

Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano 5524 Santiago, Chile; Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada 2085 Santiago, Chile. Electronic address:

Microbacterium sp. CGR1 (RGM2230) is an isolate from the Atacama Desert that displays a wide pH, salinity and temperature tolerance. This strain exhibits riboflavin overproducer features and traits for developing an environmental arsenic biosensor. Here, we report the complete genome sequence of this strain, which represents the first genome of the genus Microbacterium sequenced and assembled in a single contig. The genome contains 3,634,864bp, 3299 protein-coding genes, 45 tRNAs, six copies of 5S-16S-23S rRNA and a high genome average GC-content of 68.04%.
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http://dx.doi.org/10.1016/j.jbiotec.2015.10.020DOI Listing
December 2015

Spatial and temporal distribution of Patched-related protein in the Drosophila embryo.

Gene Expr Patterns 2015 Sep-Nov;19(1-2):120-8. Epub 2015 Oct 23.

Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile and Fondap Center for Genome Regulation (CGR), Santiago, Chile. Electronic address:

Patched-related (Ptr) encodes a protein with 12 potential transmembrane domains and a sterol-sensing domain that is closely related in predicted topology and domain organization to Patched, the canonical receptor of the Hedgehog pathway. Here we describe the production of an antibody specific for Drosophila Ptr and analyse its spatial and temporal distribution in the embryo. We find that at early developmental stages Ptr is predominantly localized at cell periphery but later on it becomes strongly and almost exclusively expressed in hemocytes. Interestingly Ptr null mutant embryos died without hatching. Our findings suggest that Ptr plays an essential function in Drosophila development, perhaps as a new receptor of embryonic hemocytes.
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http://dx.doi.org/10.1016/j.gep.2015.10.002DOI Listing
September 2016

Identification and molecular characterization of five putative toxins from the venom gland of the snake Philodryas chamissonis (Serpentes: Dipsadidae).

Toxicon 2015 Dec 26;108:19-31. Epub 2015 Sep 26.

Laboratorio de Neuroetología, Programa de Fisiología y Biofísica, Facultad de Medicina, Universidad de Chile, Casilla 70005, Correo 7, Santiago, Chile; Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PB1066 Blinder, 0316 Oslo, Norway. Electronic address:

Philodryas chamissonis is a rear-fanged snake endemic to Chile. Its bite produces mild to moderate symptoms with proteolytic and anti-coagulant effects. Presently, the composition of the venom, as well as, the biochemical and structural characteristics of its toxins, remains unknown. In this study, we cloned and reported the first full-length sequences of five toxin-encoding genes from the venom gland of this species: Type III snake venom metalloprotease (SVMP), snake venom serine protease (SVSP), Cysteine-rich secretory protein (CRISP), α and β subunits of C-type lectin-like protein (CLP) and C-type natriuretic peptide (NP). These genes are highly expressed in the venom gland and their sequences exhibited a putative signal peptide, suggesting that these are components of the venom. These putative toxins had different evolutionary relationships with those reported for some front-fanged snakes, being SVMP, SVSP and CRISP of P. chamissonis closely related to the toxins present in Elapidae species, while NP was more related to those of Viperidae species. In addition, analyses suggest that the α and β subunits of CLP of P. chamissonis might have a α-subunit scaffold in common with Viperidae species, whose highly variable C-terminal region might have allowed the diversification in α and β subunits. Our results provide the first molecular description of the toxins possibly implicated in the envenomation of prey and humans by the bite of P. chamissonis.
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http://dx.doi.org/10.1016/j.toxicon.2015.09.032DOI Listing
December 2015

Complete genome sequence of Piscirickettsia salmonis LF-89 (ATCC VR-1361) a major pathogen of farmed salmonid fish.

J Biotechnol 2015 Oct 26;212:30-1. Epub 2015 Jul 26.

Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano 5524, Santiago, Chile; Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada 2085, Santiago, Chile. Electronic address:

Piscirickettsia salmonis, the causative agent of salmonid rickettsial septicemia (SRS), is a significant threat to the healthy and sustainable production of salmonid farming industry. This Gram-negative bacterium, originally isolated from a coho salmon in Southern Chile, produces a systemic infection characterized by colonization of several fish organs. P. salmonis is able to infect, survive, and replicate inside salmonid macrophages however little is known about its mechanisms of pathogenesis. Here, we present the whole genome sequence and annotation of the P. salmonis reference strain LF-89 (ATCC VR-1361). The genome contains one circular chromosome of 3,184,851 bp and three plasmids, pPSLF89-1 (180,124 bp), pPSLF89-2 (33,516 bp) and pPSLF89-3 (51,573 bp). A total of 2850 protein-coding genes, 56 tRNAs and six copies of 5S-16S-23S rRNA.
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http://dx.doi.org/10.1016/j.jbiotec.2015.07.017DOI Listing
October 2015

Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system.

BMC Genomics 2015 Jul 4;16:495. Epub 2015 Jul 4.

Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago, Chile.

Background: Piscirickettsiosis or Salmonid Rickettsial Septicaemia (SRS) is a bacterial disease that has a major economic impact on the Chilean salmon farming industry. Despite the fact that Piscirickettsia salmonis has been recognized as a major fish pathogen for over 20 years, the molecular strategies underlying the fish response to infection and the bacterial mechanisms of pathogenesis are poorly understood. We analysed and compared the head kidney transcriptional response of Atlantic salmon (Salmo salar) families with different levels of susceptibility to P. salmonis infection in order to reveal mechanisms that might confer infection resistance.

Results: We ranked forty full-sibling Atlantic salmon families according to accumulated mortality after a challenge with P. salmonis and selected the families with the lowest and highest cumulative mortalities for microarray gene expression analysis. A comparison of the response to P. salmonis infection between low and high susceptibility groups identified biological processes presumably involved in natural resistance to the pathogen. In particular, expression changes of genes linked to cellular iron depletion, as well as low iron content and bacterial load in the head kidney of fish from low susceptibility families, suggest that iron-deprivation is an innate immunity defence mechanism against P. salmonis. To complement these results, we predicted a set of iron acquisition genes from the P. salmonis genome. Identification of putative Fur boxes and expression of the genes under iron-depleted conditions revealed that most of these genes form part of the Fur regulon of P. salmonis.

Conclusions: This study revealed, for the first time, differences in the transcriptional response to P. salmonis infection among Atlantic salmon families with varied levels of susceptibility to the infection. These differences correlated with changes in the abundance of transcripts encoding proteins directly and indirectly involved in the immune response; changes that highlighted the role of nutritional immunity through iron deprivation in host defence mechanisms against P. salmonis. Additionally, we found that P. salmonis has several mechanisms for iron acquisition, suggesting that this bacterium can obtain iron from different sources, including ferric iron through capturing endogenous and exogenous siderophores and ferrous iron. Our results contribute to determining the underlying resistance mechanisms of Atlantic salmon to P. salmonis infection and to identifying future treatment strategies.
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http://dx.doi.org/10.1186/s12864-015-1716-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4490697PMC
July 2015

Interplay between copper and zinc homeostasis through the transcriptional regulator Zur in Enterococcus faecalis.

Metallomics 2015 Jul 23;7(7):1137-45. Epub 2015 Apr 23.

Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile.

By integrating the microarray expression data and a global E. faecalis transcriptional network we identified a sub-network activated by zinc and copper. Our analyses indicated that the transcriptional response of the bacterium to copper and zinc exposure involved the activation of two modules, module I that contains genes implicated in zinc homeostasis, including the Zur transcriptional repressor, and module II containing a set of genes associated with general stress response and basal metabolism. Bacterial exposure to zinc and copper led to the repression of the zinc uptake systems of module I. Upon deletion of Zur, exposure to different zinc and copper conditions induced complementary homeostatic mechanisms (ATPase efflux proteins) to control the intracellular concentrations of zinc. The transcriptional activation of zinc homeostasis genes by zinc and copper reveals a functional interplay between these two metals, in which exposure to copper also impacts on the zinc homeostasis. Finally, we present a new zinc homeostasis model in E. faecalis, positioning this bacterium as one of the most complete systems biology model in metals described to date.
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http://dx.doi.org/10.1039/c5mt00043bDOI Listing
July 2015

Comparative gene expression analysis of Dtg, a novel target gene of Dpp signaling pathway in the early Drosophila melanogaster embryo.

Gene 2014 Feb 7;535(2):210-7. Epub 2013 Dec 7.

Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano 5524, Santiago, Chile; Fondap Center for Genome Regulation (CGR), Universidad de Chile, Santiago, Chile. Electronic address:

In the early Drosophila melanogaster embryo, Dpp, a secreted molecule that belongs to the TGF-β superfamily of growth factors, activates a set of downstream genes to subdivide the dorsal region into amnioserosa and dorsal epidermis. Here, we examined the expression pattern and transcriptional regulation of Dtg, a new target gene of Dpp signaling pathway that is required for proper amnioserosa differentiation. We showed that the expression of Dtg was controlled by Dpp and characterized a 524-bp enhancer that mediated expression in the dorsal midline, as well as, in the differentiated amnioserosa in transgenic reporter embryos. This enhancer contained a highly conserved region of 48-bp in which bioinformatic predictions and in vitro assays identified three Mad binding motifs. Mutational analysis revealed that these three motifs were necessary for proper expression of a reporter gene in transgenic embryos, suggesting that short and highly conserved genomic sequences may be indicative of functional regulatory regions in D. melanogaster genes. Dtg orthologs were not detected in basal lineages of Dipterans, which unlike D. melanogaster develop two extra-embryonic membranes, amnion and serosa, nevertheless Dtg orthologs were identified in the transcriptome of Musca domestica, in which dorsal ectoderm patterning leads to the formation of a single extra-embryonic membrane. These results suggest that Dtg was recruited as a new component of the network that controls dorsal ectoderm patterning in the lineage leading to higher Cyclorrhaphan flies, such as D. melanogaster and M. domestica.
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http://dx.doi.org/10.1016/j.gene.2013.11.032DOI Listing
February 2014

Physiological copper exposure in Jurkat cells induces changes in the expression of genes encoding cholesterol biosynthesis proteins.

Biometals 2013 Dec 30;26(6):1033-40. Epub 2013 Oct 30.

Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile.

Copper is an essential micronutrient that functions as an enzymatic cofactor in a wide range of cellular processes. Although adequate Cu levels are essential for normal metabolism, excess Cu can be toxic to cells. Cellular responses to copper deficiency and overload involve changes in the expression of genes directly and indirectly involved in copper metabolism. However little is known on the effect of physiological copper concentration on gene expression changes. In the current study we aimed to establish whether the expression of genes encoding enzymes related to cholesterol (hmgcs1, hmgcr, fdft) and fatty acid biosynthesis and LDL receptor can be induced by an iso-physiological copper concentration. The iso-physiological copper concentration was determined as the bioavailable plasmatic copper in a healthy adult population. In doing so, two blood cell lines (Jurkat and THP-1) were exposed for 6 or 24 h to iso- or supraphysiological copper concentrations. Our results indicated that in cells exposed to an iso-physiological copper concentration the early induction of genes involved in lipid metabolism was not mediated by copper itself but by the modification of the cellular redox status. Thus our results contributed to understand the involvement of copper in the regulation of cholesterol metabolism under physiological conditions.
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http://dx.doi.org/10.1007/s10534-013-9680-9DOI Listing
December 2013

Transcriptomic response of Enterococcus faecalis to iron excess.

Biometals 2012 Aug 24;25(4):737-47. Epub 2012 Mar 24.

Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile.

Iron is an essential nutrient for sustaining bacterial growth; however, little is known about the molecular mechanisms that govern gene expression during the homeostatic response to iron availability. In this study we analyzed the global transcriptional response of Enterococcus faecalis to a non-toxic iron excess in order to identify the set of genes that respond to an increment of intracellular iron. Our results showed an up-regulation of transcriptional regulators of the Fur family (PerR and ZurR), the cation efflux family (CzcD) and ferredoxin, while proton-dependent Mn/Fe (MntH) transporters and the universal stress protein (UspA) were down-regulated. This indicated that E. faecalis was able to activate a transcriptional response while growing in the presence of an excess of non-toxic iron, assuring the maintenance of iron homeostasis. Gene expression analysis of E. faecalis treated with H(2)O(2) indicated that a fraction of the transcriptional changes induced by iron appears to be mediated by oxidative stress. A comparison of our transcriptomic data with a recently reported set of differentially expressed genes in E. faecalis grown in blood, revealed an important fraction of common genes. In particular, genes associated to oxidative stress were up-regulated in both conditions, while genes encoding the iron uptake system (feo and ycl operons) were up-regulated when cells were grown in blood. This suggested that blood cultures mimic an iron deficit, and was corroborated by measuring feo and ycl expression in E. faecalis treated with the iron chelating agent 2,2-dipyridil. In summary, our group identified an adaptive transcriptional mechanism in response to metal ion stress in E. faecalis, providing a foundation for future in-depth functional studies of the iron-activated regulatory network.
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http://dx.doi.org/10.1007/s10534-012-9539-5DOI Listing
August 2012

Yeast-based assay identifies novel Shh/Gli target genes in vertebrate development.

BMC Genomics 2012 Jan 3;13. Epub 2012 Jan 3.

Faculty of Sciences, Universidad de Chile, Santiago, Chile.

Background: The increasing number of developmental events and molecular mechanisms associated with the Hedgehog (Hh) pathway from Drosophila to vertebrates, suggest that gene regulation is crucial for diverse cellular responses, including target genes not yet described. Although several high-throughput, genome-wide approaches have yielded information at the genomic, transcriptional and proteomic levels, the specificity of Gli binding sites related to direct target gene activation still remain elusive. This study aims to identify novel putative targets of Gli transcription factors through a protein-DNA binding assay using yeast, and validating a subset of targets both in-vitro and in-vivo. Testing in different Hh/Gli gain- and loss-of-function scenarios we here identified known (e.g., ptc1) and novel Hh-regulated genes in zebrafish embryos.

Results: The combined yeast-based screening and MEME/MAST analysis were able to predict Gli transcription factor binding sites, and position mapping of these sequences upstream or in the first intron of promoters served to identify new putative target genes of Gli regulation. These candidates were validated by qPCR in combination with either the pharmacological Hh/Gli antagonist cyc or the agonist pur in Hh-responsive C3H10T1/2 cells. We also used small-hairpin RNAs against Gli proteins to evaluate targets and confirm specific Gli regulation their expression. Taking advantage of mutants that have been identified affecting different components of the Hh/Gli signaling system in the zebrafish model, we further analyzed specific novel candidates. Studying Hh function with pharmacological inhibition or activation complemented these genetic loss-of-function approaches. We provide evidence that in zebrafish embryos, Hh signaling regulates sfrp2, neo1, and c-myc expression in-vivo.

Conclusion: A recently described yeast-based screening allowed us to identify new Hh/Gli target genes, functionally important in different contexts of vertebrate embryonic development.
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http://dx.doi.org/10.1186/1471-2164-13-2DOI Listing
January 2012

Genome wide identification of Acidithiobacillus ferrooxidans (ATCC 23270) transcription factors and comparative analysis of ArsR and MerR metal regulators.

Biometals 2012 Feb 10;25(1):75-93. Epub 2011 Aug 10.

Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Libano 5524, Santiago, Chile.

Acidithiobacillus ferrooxidans is a chemolithoautotrophic acidophilic bacterium that obtains its energy from the oxidation of ferrous iron, elemental sulfur, or reduced sulfur minerals. This capability makes it of great industrial importance due to its applications in biomining. During the industrial processes, A. ferrooxidans survives to stressing circumstances in its environment, such as an extremely acidic pH and high concentration of transition metals. In order to gain insight into the organization of A. ferrooxidans regulatory networks and to provide a framework for further studies in bacterial growth under extreme conditions, we applied a genome-wide annotation procedure to identify 87 A. ferrooxidans transcription factors. We classified them into 19 families that were conserved among diverse prokaryotic phyla. Our annotation procedure revealed that A. ferrooxidans genome contains several members of the ArsR and MerR families, which are involved in metal resistance and detoxification. Analysis of their sequences revealed known and potentially new mechanism to coordinate gene-expression in response to metal availability. A. ferrooxidans inhabit some of the most metal-rich environments known, thus transcription factors identified here seem to be good candidates for functional studies in order to determine their physiological roles and to place them into A. ferrooxidans transcriptional regulatory networks.
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http://dx.doi.org/10.1007/s10534-011-9484-8DOI Listing
February 2012

Genome-wide transcriptome analysis of the adaptive response of Enterococcus faecalis to copper exposure.

Biometals 2010 Dec 25;23(6):1105-12. Epub 2010 Jun 25.

Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Libano 5524, Macul, Santiago, Chile.

In this work we investigated the adaptive response of E. faecalis to Cu and the role of CopY, a Cu-dependent repressor, in the regulation of Cu metabolism. In doing so, we examined the whole-genome transcriptional response of E. faecalis wild-type (WT) and a ΔcopY strain exposed to non-toxic Cu excess. The results indicated that after Cu exposure, most of the genes that displayed a significant change in their expression levels in the WT strain (135 of the 145 up-regulated genes and 115 of the 142 down-regulated genes) were also differentially expressed in the E. faecalis ΔcopY strain. This extensive overlap in the transcriptional response, suggested that additional transcription factors mediate the response of E. faecalis to Cu. As a first step to analyze this possibility, we selected among the up-regulated genes five genes encoding putative transcriptional regulators and determined their expression levels at different times after Cu exposure. The temporal expression of these regulators was different from that of copY, which reached its maximum at the earliest time measured. Nevertheless, transcription elongation factor GreA, and members of Rrf2, Cro/CI and SorC/DeoR transcription factor families were induced shortly after Cu exposure, suggesting that these proteins are able to complement the role of CopY in the regulatory network activated by Cu. To our knowledge, this is the first report on the global transcriptional response to Cu in a member of this taxonomic group.
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http://dx.doi.org/10.1007/s10534-010-9356-7DOI Listing
December 2010

Gene expression profiling analysis of copper homeostasis in Arabidopsis thaliana.

Biochem Biophys Res Commun 2010 Mar 1;393(2):248-52. Epub 2010 Feb 1.

INTA, Universidad de Chile, Macul, Santiago, Chile.

As a result of copper essentiality for life, plants and most other organisms have developed a conserved and complex network of proteins to handling Cu in order to prevent its deficit and to avoid its potentially toxic effects. To better understand regulation of Cu homeostasis in plants, we use adult plant of Arabidopsis thaliana to provide an integrated view of how Cu status affects the expression of genes involved in cellular Cu homoeostasis. In doing so, we use real-time RT-PCR to compare shoot and roots transcriptional responses to Cu. We measure changes in the abundance of transcripts encoding transporters, chaperones and P-type ATPases and correlated those changes with variation of Cu content in both tissues. Our results indicated that in both tissues transcript levels of COPT2, 4, and ZIP2 transporters and CCH chaperone were significantly down-regulated comparing to controls plants in response to Cu excess. In contrast, Cu chaperones ATX1, CCS, COX17-1 including two putative mitochondrial chaperones (At3g08950; At1g02410) were up-regulated under similar conditions. Regarding P-type ATPases, a reduction of HMA1, PAA1, PAA2, and RAN1 transcript levels in shoot after Cu exposure was observed, while HMA5 transcripts increased exclusively in roots. In plants growing under Cu-deficient conditions, COPT2, ZIP2, HMA1, andPAA2, were significantly up-regulated in shoots. Thus, our results indicated a common transcriptional regulation pattern of transporters and chaperone components, in particular transcriptional changes of COPT2, ZIP2, and CCH showed an inverse relation with Cu content suggesting that these proteins are required to avoid excess and deficit of Cu.
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http://dx.doi.org/10.1016/j.bbrc.2010.01.111DOI Listing
March 2010
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