DSpace Angular :: Browsing by Author "Vidal, Elena A."

Browsing by Author "Vidal, Elena A."

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A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride
(2021) Olivares-Yanez, Consuelo; Sanchez, Evelyn; Perez-Lara, Gabriel; Seguel, Aldo; Camejo, Pamela Y.; Larrondo, Luis F.; Vidal, Elena A.; Canessa, Paulo
Botrytis cinerea and Trichoderma atroviride are two relevant fungi in agricultural systems. To gain insights into these organisms' transcriptional gene regulatory networks (GRNs), we generated a manually curated transcription factor (TF) dataset for each of them, followed by a GRN inference utilizing available sequence motifs describing DNA-binding specificity and global gene expression data. As a proof of concept of the usefulness of this resource to pinpoint key transcriptional regulators, we employed publicly available transcriptomics data and a newly generated dual RNA-seq dataset to build context-specific Botrytis and Trichoderma GRNs under two different biological paradigms: exposure to continuous light and Botrytis-Trichoderma confrontation assays. Network analysis of fungal responses to constant light revealed striking differences in the transcriptional landscape of both fungi. On the other hand, we found that the confrontation of both microorganisms elicited a distinct set of differentially expressed genes with changes in T. atroviride exceeding those in B. cinerea. Using our regulatory network data, we were able to determine, in both fungi, central TFs involved in this interaction response, including TFs controlling a large set of extracellular peptidases in the biocontrol agent T. atroviride. In summary, our work provides a comprehensive catalog of transcription factors and regulatory interactions for both organisms. This catalog can now serve as a basis for generating novel hypotheses on transcriptional regulatory circuits in different experimental contexts. (C) 2021 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.
B3 Transcription Factors Determine Iron Distribution and FERRITIN Gene Expression in Embryo but Do Not Control Total Seed Iron Content
(2022) Grant-Grant, Susana; Schaffhauser, Macarena; Baeza-Gonzalez, Pablo; Gao, Fei; Conejero, Genevieve; Vidal, Elena A.; Gaymard, Frederic; Dubos, Christian; Curie, Catherine; Roschzttardtz, Hannetz
Iron is an essential micronutrient for humans and other organisms. Its deficiency is one of the leading causes of anemia worldwide. The world health organization has proposed that an alternative to increasing iron content in food is through crop biofortification. One of the most consumed part of crops is the seed, however, little is known about how iron accumulation in seed occurs and how it is regulated. B3 transcription factors play a critical role in the accumulation of storage compounds such as proteins and lipids. Their role in seed maturation has been well characterized. However, their relevance in accumulation and distribution of micronutrients like iron remains unknown. In Arabidopsis thaliana and other plant models, three master regulators belonging to the B3 transcription factors family have been identified: FUSCA3 (FUS3), LEAFY COTYLEDON2 (LEC2), and ABSCISIC ACID INSENSITIVE 3 (ABI3). In this work, we studied how seed iron homeostasis is affected in B3 transcription factors mutants using histological and molecular approaches. We determined that iron distribution is modified in abi3, lec2, and fus3 embryo mutants. For abi3-6 and fus3-3 mutant embryos, iron was less accumulated in vacuoles of cells surrounding provasculature compared with wild type embryos. lec2-1 embryos showed no difference in the pattern of iron distribution in hypocotyl, but a dramatic decrease of iron was observed in cotyledons. Interestingly, for the three mutant genotypes, total iron content in dry mutant seeds showed no difference compared to wild type. At the molecular level, we showed that genes encoding the iron storage ferritins proteins are misregulated in mutant seeds. Altogether our results support a role of the B3 transcription factors ABI3, LEC2, and FUS3 in maintaining iron homeostasis in Arabidopsis embryos.
BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data
(2020) Moraga, Carol; Sanchez, Evelyn; Ferrarini, Mariana Galvão; Gutiérrez Ilabaca, Rodrigo Antonio; Vidal, Elena A.; Sagot, Marie-France
MicroRNAs (miRNAs) are small non-coding RNAs that are key players in the regulation of gene expression. In the last decade, with the increasing accessibility of high-throughput sequencing technologies, different methods have been developed to identify miRNAs, most of which rely on pre-existing reference genomes. However, when a reference genome is absent or is not of high quality, such identification becomes more difficult. In this context, we developed BrumiR, an algorithm that is able to discover miRNAs directly and exclusively from sRNA-seq data. We benchmarked BrumiR with datasets encompassing animal and plant species using real and simulated sRNA-seq experiments. The results demonstrate that BrumiR reaches the highest recall for miRNA discovery, while at the same time being much faster and more efficient than the state-of-the-art tools evaluated. The latter allows BrumiR to analyze a large number of sRNA-seq experiments, from plants or animals species. Moreover, BrumiR detects additional information regarding other expressed sequences (sRNAs, isomiRs, etc.), thus maximizing the biological insight gained from sRNA-seq experiments. Finally, when a reference genome is available, BrumiR provides a new mapping tool (BrumiR2ref) that performs an a posteriori exhaustive search to identify the precursor sequences. The code of BrumiR is freely available at https://github.com/camoragaq/BrumiR.
Comprehensive re-analysis of hairpin small RNAs in fungi reveals loci with conserved links
(2022) Johnson, Nathan R.; Larrondo, Luis F.; Alvarez, Jose M.; Vidal, Elena A.
RNA interference is an ancient mechanism with many regulatory roles in eukaryotic genomes, with small RNAs acting as their functional element. While there is a wide array of classes of small-RNA-producing loci, those resulting from stem-loop structures (hairpins) have received profuse attention. Such is the case of microRNAs (miRNAs), which have distinct roles in plants and animals. Fungi also produce small RNAs, and several publications have identified miRNAs and miRNA-like (mi/milRNA) hairpin RNAs in diverse fungal species using deep sequencing technologies. Despite this relevant source of information, relatively little is known about mi/milRNA features in fungi, mostly due to a lack of established criteria for their annotation. To systematically assess mi/milRNA characteristics and annotation confidence, we searched for publications describing mi/milRNA loci and re-assessed the annotations for 41 fungal species. We extracted and normalized the annotation data for 1727 reported mi/milRNA loci and determined their abundance profiles, concluding that less than half of the reported loci passed basic standards used for hairpin RNA discovery. We found that fungal mi/milRNA are generally more similar in size to animal miRNAs and were frequently associated with protein-coding genes. The compiled genomic analyses identified 25 mi/milRNA loci conserved in multiple species. Our pipeline allowed us to build a general hierarchy of locus quality, identifying more than 150 loci with high-quality annotations. We provide a centralized annotation of identified mi/milRNA hairpin RNAs in fungi which will serve as a resource for future research and advance in understanding the characteristics and functions of mi/milRNAs in fungal organisms.
Gene networks for nitrogen sensing, signaling, and response in Arabidopsis thaliana
(2010) Vidal, Elena A.; Tamayo, Karem P.; Gutierrez, Rodrigo A.
Nitrogen (N) is an essential macronutrient for plants. In nature, N cycles between different inorganic and organic forms some of which can serve as nutrients for plants. The inorganic N forms nitrate and ammonium are the most important sources of N for plants. However, plants can also uptake and use organic N forms such as amino acids and urea. Besides their nutritional role, nitrate and other forms of N can also act as signals that regulate the expression of hundreds of genes causing modulation of plant metabolism, physiology, growth, and development. Although many genes and processes affected by changes in external or internal N have been identified, the molecular mechanisms involved in N sensing and signaling are still poorly understood. Classic reverse and forward genetics and more recently the advent of genomic and systems approaches have helped to characterize some of the components of the signaling pathways directing Arabidopsis responses to N. Here, we provide an update on recent advances to identify the components involved in N sensing and signaling in Arabidopsis and their importance for the plant response to N. (C) 2010 John Wiley & Sons, Inc. WIREs Syst Biol Med 2010 2 683-693
Growth Developmental Defects of Mitochondrial Iron Transporter 1 and 2 Mutants in Arabidopsis in Iron Sufficient Conditions
(2023) Vargas, Joaquin; Gomez, Isabel; Vidal, Elena A.; Lee, Chun Pong; Millar, A. Harvey; Jordana, Xavier; Roschzttardtz, Hannetz
Iron is the most abundant micronutrient in plant mitochondria, and it has a crucial role in biochemical reactions involving electron transfer. It has been described in Oryza sativa that Mitochondrial Iron Transporter (MIT) is an essential gene and that knockdown mutant rice plants have a decreased amount of iron in their mitochondria, strongly suggesting that OsMIT is involved in mitochondrial iron uptake. In Arabidopsis thaliana, two genes encode MIT homologues. In this study, we analyzed different AtMIT1 and AtMIT2 mutant alleles, and no phenotypic defects were observed in individual mutant plants grown in normal conditions, confirming that neither AtMIT1 nor AtMIT2 are individually essential. When we generated crosses between the Atmit1 and Atmit2 alleles, we were able to isolate homozygous double mutant plants. Interestingly, homozygous double mutant plants were obtained only when mutant alleles of Atmit2 with the T-DNA insertion in the intron region were used for crossings, and in these cases, a correctly spliced AtMIT2 mRNA was generated, although at a low level. Atmit1 Atmit2 double homozygous mutant plants, knockout for AtMIT1 and knockdown for AtMIT2, were grown and characterized in iron-sufficient conditions. Pleiotropic developmental defects were observed, including abnormal seeds, an increased number of cotyledons, a slow growth rate, pinoid stems, defects in flower structures, and reduced seed set. A RNA-Seq study was performed, and we could identify more than 760 genes differentially expressed in Atmit1 Atmit2. Our results show that Atmit1 Atmit2 double homozygous mutant plants misregulate genes involved in iron transport, coumarin metabolism, hormone metabolism, root development, and stress-related response. The phenotypes observed, such as pinoid stems and fused cotyledons, in Atmit1 Atmit2 double homozygous mutant plants may suggest defects in auxin homeostasis. Unexpectedly, we observed a possible phenomenon of T-DNA suppression in the next generation of Atmit1 Atmit2 double homozygous mutant plants, correlating with increased splicing of the AtMIT2 intron containing the T-DNA and the suppression of the phenotypes observed in the first generation of the double mutant plants. In these plants with a suppressed phenotype, no differences were observed in the oxygen consumption rate of isolated mitochondria; however, the molecular analysis of gene expression markers, AOX1a, UPOX, and MSM1, for mitochondrial and oxidative stress showed that these plants express a degree of mitochondrial perturbation. Finally, we could establish by a targeted proteomic analysis that a protein level of 30% of MIT2, in the absence of MIT1, is enough for normal plant growth under iron-sufficient conditions.
Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots
(2013) Vidal, Elena A.; Moyano, Tomas C.; Krouk, Gabriel; Katari, Manpreet S.; Tanurdzic, Milos; McCombie, W. Richard; Coruzzi, Gloria M.; Gutierrez, Rodrigo A.
Background: Nitrate and other nitrogen metabolites can act as signals that regulate global gene expression in plants. Adaptive changes in plant morphology and physiology triggered by changes in nitrate availability are partly explained by these changes in gene expression. Despite several genome-wide efforts to identify nitrate-regulated genes, no comprehensive study of the Arabidopsis root transcriptome under contrasting nitrate conditions has been carried out.
Nitrate in 2020: Thirty years from transport to signaling networks
(2020) Vidal, Elena A.; Alvarez, José M.; Araus, Viviana; Riveras Hernández, Eleodoro Javier; Brooks, Matthew D.; Krouk, Gabriel; Ruffel, Sandrine; Lejay, Laurence; Crawford, Nigel M.; Coruzzi, Gloria M.; Gutiérrez Ilabaca, Rodrigo Antonio
Nitrogen (N) is an essential macronutrient for plants and a major limiting factor for plant growth and crop production. Nitrate is the main source of N available to plants in agricultural soils and in many natural environments. Sustaining agricultural productivity is of paramount importance in the current scenario of increasing world population, diversification of crop uses, and climate change. Plant productivity for major crops around the world, however, is still supported by excess application of N-rich fertilizers with detrimental economic and environmental impacts. Thus, understanding how plants regulate nitrate uptake and metabolism is key for developing new crops with enhanced N use efficiency and to cope with future world food demands. The study of plant responses to nitrate has gained considerable interest over the last 30 years. This review provides an overview of key findings in nitrate research, spanning biochemistry, molecular genetics, genomics, and systems biology. We discuss how we have reached our current view of nitrate transport, local and systemic nitrate sensing/signaling, and the regulatory networks underlying nitrate-controlled outputs in plants. We hope this summary will serve not only as a timeline and information repository but also as a baseline to define outstanding questions for future research.
Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate
(2022) Contreras-Lopez, Orlando; Vidal, Elena A.; Riveras, Eleodoro; Alvarez, Jose M.; Moyano, Tomas C.; Sparks, Erin E.; Medina, Joaquin; Pasquino, Angelo; Benfey, Philip N.; Coruzzi, Gloria M.; Gutierrez, Rodrigo A.
Nitrate is a nutrient and a potent signal that impacts global gene expression in plants. However, the regulatory factors controlling temporal and cell type-specific nitrate responses remain largely unknown. We assayed nitrate-responsive transcriptome changes in five major root cell types of the Arabidopsis thaliana root as a function of time. We found that gene-expression response to nitrate is dynamic and highly localized and predicted cell type- specific transcription factor (TF)-target interactions. Among cell types, the endodermis stands out as having the largest and most connected nitrate-regulatory gene network. ABF2 and ABF3 are major hubs for transcriptional responses in the endodermis cell layer. We experimentally validated TF-target interactions for ABF2 and ABF3 by chromatin immunoprecipitation followed by sequenc-ing and a cell-based system to detect TF regulation genome-wide. Validated targets of ABF2 and ABF3 account for more than 50% of the nitrate-responsive transcriptome in the endodermis. Moreover, ABF2 and ABF3 are involved in nitrate-induced lateral root growth. Our approach offers an unprecedented spatiotemporal resolution of the root response to nitrate and identifies important compo-nents of cell-specific gene regulatory networks.
TGA class II transcription factors are essential to restrict oxidative stress in response to UV-B stress in Arabidopsis
(2021) Herrera Vásquez, Ariel Esteban; Fonseca Cárdenas, Alejandro Alfredo; Ugalde Valdivia, José Manuel; Lamig Giannini, Liliana Andrea; Seguel Avello, Aldo Luis; Moyano Yugovic, Tomás Custodio; Gutiérrez Ilabaca, Rodrigo Antonio; Salinas, Paula; Vidal, Elena A.; Holuigue Barros, Loreto
Plants possess a robust metabolic network for sensing and controlling reactive oxygen species (ROS) levels upon stress conditions. Evidence shown here supports a role for TGA class II transcription factors as critical regulators of genes controlling ROS levels in the tolerance response to UV-B stress in Arabidopsis. First, tga256 mutant plants showed reduced capacity to scavenge H2O2 and restrict oxidative damage in response to UV-B, and also to methylviologen-induced photooxidative stress. The TGA2 transgene (tga256/TGA2 plants) complemented these phenotypes. Second, RNAseq followed by clustering and Gene Ontology term analyses indicate that TGA2/5/6 positively control the UV-B-induced expression of a group of genes with oxidoreductase, glutathione transferase, and glucosyltransferase activities, such as members of the glutathione S-transferase Tau subfamily (GSTU), which encodes peroxide-scavenging enzymes. Accordingly, increased glutathione peroxidase activity triggered by UV-B was impaired in tga256 mutants. Third, the function of TGA2/5/6 as transcriptional activators of GSTU genes in the UV-B response was confirmed for GSTU7, GSTU8, and GSTU25, using quantitative reverse transcription–PCR and ChIP analyses. Fourth, expression of the GSTU7 transgene complemented the UV-B-susceptible phenotype of tga256 mutant plants. Together, this evidence indicates that TGA2/5/6 factors are key regulators of the antioxidant/detoxifying response to an abiotic stress such as UV-B light overexposure.
The Calcium Ion Is a Second Messenger in the Nitrate Signaling Pathway of Arabidopsis thaliana
(2015) Riveras Hernández, Eleodoro Javier; Álvarez, José M.; Vidal, Elena A.; Oses, Carolina; Vega, Andrea; Gutiérrez Ilabaca, Rodrigo Antonio
Transcription factor TGA2 is essential for UV-B stress tolerance controlling oxidative stress in Arabidopsis
(2020) Herrera Vásquez, Ariel Esteban; Fonseca Cárdenas, Alejandro Alfredo; Ugalde Valdivia, José Manuel; Lamig Giannini, Liliana Andrea; Seguel Avello, Aldo Luis; Moyano Yugovic, Tomás Custodio; Gutiérrez Ilabaca, Rodrigo Antonio; Salinas, Paula; Vidal, Elena A.; Holuigue Barros, Loreto
Plants possess a diversity of Reactive Oxygen Species (ROS)-processing enzymes involved in sensing and controlling ROS levels under basal and stressful conditions. There is little information on the transcriptional regulators that control the expression of these ROS-processing enzymes, particularly at the onset of the defense response to abiotic stress. Filling this gap, this paper reports a critical role for Arabidopsis TGA class II factors (TGA2, TGA5, and TGA6) in the tolerance response to UV-B light and photooxidative stress, by activating the expression of genes with antioxidative roles. We identified two clusters of genes responsive to UV-B and activated by TGA2/5/6 were identified using RNAseq and clustering analysis. The GSTU gene family, which encodes glutathione transferase enzymes from the Tau subclass, was overrepresented in these clusters. We corroborated the TGA2-mediated activation in response to UV-B for three model genes (GSTU7, GSTU8, and GSTU25) using RT-qPCR and ChIP analyses. Interestingly, using tga256 mutant and TGA2- and GSTU7-complemented mutant plants, we demonstrated that TGA2-mediated induction of GSTU genes is essential to control ROS levels and oxidative damage after UV-B and MeV treatments. This evidence positions TGA class II factors, particularly TGA2, as a key players in the redox signaling network of Arabidopsis plants.
Transcriptional networks in the nitrate response of Arabidopsis thaliana
(2015) Vidal, Elena A.; Álvarez, José M.; Moyano, Tomás C.; Gutiérrez Ilabaca, Rodrigo Antonio
Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans
(2019) Vidal, Elena A.; Moyano, Tomas C.; Bustos, Bernabe, I; Perez-Palma, Eduardo; Moraga, Carol; Riveras Hernández, Eleodoro Javier; Pérez-Palma E.; Moraga, C.; Montecinos, A.; Azócar, L.; Soto, D. C.; Di Genova, A.; Puschel Illanes, Klaus; Nürnberg, P.; Buch, S.; Hampe, J; Allende, M. L.; Cambiazo, V.; González, M.; Hodar, C.; Montecino, M.; Muñoz-Espinoza, C.; Orellana, A.; Reyes-Jara, A.; Travisany, D.; Vizoso, P.; Moraga, M.; Eyheramendy Duerr, Susana; Maass, A.; Ferrari, G. V. de; Miquel P., Juan Francisco; Gutiérrez Ilabaca, Rodrigo Antonio

Browsing by Author "Vidal, Elena A."

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