DSpace Angular :: Browsing by Author "Gutierrez, Rodrigo A."

Browsing by Author "Gutierrez, Rodrigo A."

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A Deficiency in the Flavoprotein of Arabidopsis Mitochondrial Complex II Results in Elevated Photosynthesis and Better Growth in Nitrogen-Limiting Conditions
(AMER SOC PLANT BIOLOGISTS, 2011) Fuentes, Daniela; Meneses, Marco; Nunes Nesi, Adriano; Araujo, Wagner L.; Tapia, Rodrigo; Gomez, Isabel; Holuigue, Loreto; Gutierrez, Rodrigo A.; Fernie, Alisdair R.; Jordana, Xavier
Mitochondrial complex II (succinate dehydrogenase [SDH]) plays roles both in the tricarboxylic acid cycle and the respiratory electron transport chain. In Arabidopsis (Arabidopsis thaliana), its flavoprotein subunit is encoded by two nuclear genes, SDH1-1 and SDH1-2. Here, we characterize heterozygous SDH1-1/sdh1-1 mutant plants displaying a 30% reduction in SDH activity as well as partially silenced plants obtained by RNA interference. We found that these plants displayed significantly higher CO2 assimilation rates and enhanced growth than wild-type plants. There was a strong correlation between CO2 assimilation and stomatal conductance, and both mutant and silenced plants displayed increased stomatal aperture and density. By contrast, no significant differences were found for dark respiration, chloroplastic electron transport rate, CO2 uptake at saturating concentrations of CO2, or biochemical parameters such as the maximum rates of carboxylation by Rubisco and of photosynthetic electron transport. Thus, photosynthesis is enhanced in SDH-deficient plants by a mechanism involving a specific effect on stomatal function that results in improved CO2 uptake. Metabolic and transcript profiling revealed that mild deficiency in SDH results in limited effects on metabolism and gene expression, and data suggest that decreases observed in the levels of some amino acids were due to a higher flux to proteins and other nitrogen-containing compounds to support increased growth. Strikingly, SDH1-1/sdh1-1 seedlings grew considerably better in nitrogen-limiting conditions. Thus, a subtle metabolic alteration may lead to changes in important functions such as stomatal function and nitrogen assimilation.
An Open One-Step RT-qPCR for SARS-CoV-2 detection
(2024) Cerda, Ariel; Rivera, Maira; Armijo, Grace; Ibarra-Henriquez, Catalina; Reyes, Javiera; Blazquez-Sanchez, Paula; Aviles, Javiera; Arce, Anibal; Seguel, Aldo; Brown, Alexander J.; Vasquez, Yesseny; Cortez-San Martin, Marcelo; Cubillos, Francisco A.; Garcia, Patricia; Ferres, Marcela; Ramirez-Sarmiento, Cesar A.; Federici, Fernan; Gutierrez, Rodrigo A.
The COVID-19 pandemic has resulted in millions of deaths globally, and while several diagnostic systems were proposed, real-time reverse transcription polymerase chain reaction (RT-PCR) remains the gold standard. However, diagnostic reagents, including enzymes used in RT-PCR, are subject to centralized production models and intellectual property restrictions, which present a challenge for less developed countries. With the aim of generating a standardized One-Step open RT-qPCR protocol to detect SARS-CoV-2 RNA in clinical samples, we purified and tested recombinant enzymes and a non-proprietary buffer. The protocol utilized M-MLV RT and Taq DNA pol enzymes to perform a Taqman probe-based assay. Synthetic RNA samples were used to validate the One-Step RT-qPCR components, demonstrating sensitivity comparable to a commercial kit routinely employed in clinical settings for patient diagnosis. Further evaluation on 40 clinical samples (20 positive and 20 negative) confirmed its comparable diagnostic accuracy. This study represents a proof of concept for an open approach to developing diagnostic kits for viral infections and diseases, which could provide a cost-effective and accessible solution for less developed countries.
ANOTHER TALE FROM THE HARSH WORLD: HOW PLANTS ADAPT TO EXTREME ENVIRONMENTS
(2021) Dussarrat, Thomas; Decros, Guillaume; Diaz, Francisca P.; Gibon, Yves; Latorre, Claudio; Rolin, Dominique; Gutierrez, Rodrigo A.; Petriacq, Pierre
The environmental fluctuations of a constantly evolving world can mould a changing context, often unfavourable to sessile organisms that must adjust their resource allocation between both resistance or tolerance mechanisms and growth. Plants bear the fascinating ability to survive and thrive under extreme conditions, a capacity that has always attracted the curiosity of humans, who have discovered and improved species capable of meeting our physiological needs. In this context, plant research has produced a great wealth of knowledge on the responses of plants to a range of abiotic stresses, mostly considering model species and/or controlled conditions. However, there is still minimal comprehension of plant adaptations and acclimations to extreme environments, which cries out for future investigations. In this article, we examined the main advances in understanding the adapted traits fixed through evolution that allowed for plant resistance against abiotic stress in extreme natural ecosystems. Spatio-temporal adaptations from extremophile plant species are described from morpho-anatomical features to physiological function and metabolic pathways adjustments. Considering that metabolism is at the heart of plant adaptations, a focus is given to the study of primary and secondary metabolic adjustments as well as redox metabolism under extreme conditions. This article further casts a critical glance at the main successes in studying extreme environments and examines some of the challenges and opportunities this research offers, especially considering the possible interaction with ecology and metaphenomics.
Cell surface receptor kinase FERONIA linked to nutrient sensor TORC signaling controls root hair growth at low temperature linked to low nitrate in Arabidopsis thaliana
(2023) Martinez Pacheco, Javier; Song, Limei; Kubenova, Lenka; Ovecka, Miroslav; Berdion Gabarain, Victoria; Manuel Peralta, Juan; Urzua Lehuede, Tomas; Angel Ibeas, Miguel; Ricardi, Martiniano M.; Zhu, Sirui; Shen, Yanan; Schepetilnikov, Mikhail; Ryabova, Lyubov A.; Alvarez, Jose M.; Gutierrez, Rodrigo A.; Grossmann, Guido; Samaj, Jozef; Yu, Feng; Estevez, Jose M.
Root hairs (RH) are excellent model systems for studying cell size and polarity since they elongate several hundred-fold their original size. Their tip growth is determined both by intrinsic and environmental signals. Although nutrient availability and temperature are key factors for a sustained plant growth, the molecular mechanisms underlying their sensing and downstream signaling pathways remain unclear. We use genetics to address the roles of the cell surface receptor kinase FERONIA (FER) and the nutrient sensing TOR Complex 1 (TORC) in RH growth. We identified that low temperature (10 degrees C) triggers a strong RH elongation response in Arabidopsis thaliana involving FER and TORC. We found that FER is required to perceive limited nutrient availability caused by low temperature. FERONIA interacts with and activates TORC-downstream components to trigger RH growth. In addition, the small GTPase Rho of plants 2 (ROP2) is also involved in this RH growth response linking FER and TOR. We also found that limited nitrogen nutrient availability can mimic the RH growth response at 10 degrees C in a NRT1.1-dependent manner. These results uncover a molecular mechanism by which a central hub composed by FER-ROP2-TORC is involved in the control of RH elongation under low temperature and nitrogen deficiency.
Dynamic changes in mRNA nucleocytoplasmic localization in the nitrate response of Arabidopsis roots
(2024) Fonseca, Alejandro; Riveras, Eleodoro; Moyano, Tomas C.; Alvarez, Jose M.; Rosa, Stefanie; Gutierrez, Rodrigo A.
Nitrate is a nutrient and signal that regulates gene expression. The nitrate response has been extensively characterized at the organism, organ, and cell-type-specific levels, but intracellular mRNA dynamics remain unexplored. To characterize nuclear and cytoplasmic transcriptome dynamics in response to nitrate, we performed a time-course expression analysis after nitrate treatment in isolated nuclei, cytoplasm, and whole roots. We identified 402 differentially localized transcripts (DLTs) in response to nitrate treatment. Induced DLT genes showed rapid and transient recruitment of the RNA polymerase II, together with an increase in the mRNA turnover rates. DLTs code for genes involved in metabolic processes, localization, and response to stimulus indicating DLTs include genes with relevant functions for the nitrate response that have not been previously identified. Using single-molecule RNA FISH, we observed early nuclear accumulation of the NITRATE REDUCTASE 1 (NIA1) transcripts in their transcription sites. We found that transcription of NIA1, a gene showing delayed cytoplasmic accumulation, is rapidly and transiently activated; however, its transcripts become unstable when they reach the cytoplasm. Our study reveals the dynamic localization of mRNAs between the nucleus and cytoplasm as an emerging feature in the temporal control of gene expression in response to nitrate treatment in Arabidopsis roots.
Ecological and metabolic implications of the nurse effect of Maihueniopsis camachoi in the Atacama Desert
(2024) Diaz, Francisca P.; Dussarrat, Thomas; Carrasco-Puga, Gabriela; Colombie, Sophie; Prigent, Sylvain; Decros, Guillaume; Bernillon, Stephane; Cassan, Cedric; Flandin, Amelie; Guerrero, Pablo C.; Gibon, Yves; Rolin, Dominique; Cavieres, Lohengrin A.; Petriacq, Pierre; Latorre, Claudio; Gutierrez, Rodrigo A.
Plant-plant positive interactions are key drivers of community structure. Yet, the underlying molecular mechanisms of facilitation processes remain unexplored. We investigated the 'nursing' effect of Maihueniopsis camachoi, a cactus that thrives in the Atacama Desert between c. 2800 and 3800 m above sea level. We hypothesised that an important protective factor is thermal amelioration of less cold-tolerant species with a corresponding impact on molecular phenotypes.To test this hypothesis, we compared plant cover and temperatures within the cactus foliage with open areas and modelled the effect of temperatures on plant distribution. We combined eco-metabolomics and machine learning to test the molecular consequences of this association.Multiple species benefited from the interaction with M. camachoi. A conspicuous example was the extended distribution of Atriplex imbricata to colder elevations in association with M. camachoi (400 m higher as compared to plants in open areas). Metabolomics identified 93 biochemical markers predicting the interaction status of A. imbricata with 79% accuracy, independently of year.These findings place M. camachoi as a key species in Atacama plant communities, driving local biodiversity with an impact on molecular phenotypes of nursed species. Our results support the stress-gradient hypothesis and provide pioneer insights into the metabolic consequences of facilitation.
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
Genome sequencing and transcriptomic analysis of the Andean killifish Orestias ascotanensis reveals adaptation to high-altitude aquatic life
(2022) Di Genova, Alex; Nardocci, Gino; Maldonado-Agurto, Rodrigo; Hodar, Christian; Valdivieso, Camilo; Morales, Pamela; Gajardo, Felipe; Marina, Raquel; Gutierrez, Rodrigo A.; Orellana, Ariel; Cambiazo, Veronica; Gonzalez, Mauricio; Glavic, Alvaro; Mendez, Marco A.; Maass, Alejandro; Allende, Miguel L.; Montecino, Martin A.
Orestias ascotanensis (Cyprinodontidae) is a teleost pupfish endemic to springs feeding into the Ascotan saltpan in the Chilean Altiplano (3,700 m.a.s.l.) and represents an opportunity to study adaptations to high-altitude aquatic environments. We have de novo assembled the genome of O. ascotanensis at high coverage. Comparative analysis of the O. ascotanensis genome showed an overall process of contraction, including loss of genes related to Gprotein signaling, chemotaxis and signal transduction, while there was expansion of gene families associated with microtubule-based movement and protein ubiquitination. We identified 818 genes under positive selection, many of which are involved in DNA repair. Additionally, we identified novel and conserved microRNAs expressed in O. ascotanensis and its closely-related species, Orestias gloriae. Our analysis suggests that positive selection and expansion of genes that preserve genome stability are a potential adaptive mechanism to cope with the increased solar UV radiation to which high-altitude animals are exposed to.
Genomes of the Orestias pupfish from the Andean Altiplano shed light on their evolutionary history and phylogenetic relationships within Cyprinodontiformes
(2024) Morales, Pamela; Gajardo, Felipe; Valdivieso, Camilo; Valladares, Moises A.; Di Genova, Alex; Orellana, Ariel; Gutierrez, Rodrigo A.; Gonzalez, Mauricio; Montecino, Martin; Maass, Alejandro; Mendez, Marco A.; Allende, Miguel L.
Background To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated partly on unavailable or incomplete information. As a consequence, it was assigned to the family Cyprindontidae, relating this Andean fish to other geographically distant genera distributed in the Mediterranean, Middle East and North and Central America. In this study, using complete genome sequencing, we aim to clarify the phylogenetic position of Orestias within the Cyprinodontiformes order.
Genomic Footprinting Analyses from DNase-seq Data to Construct Gene Regulatory Networks
(HUMANA PRESS INC, 2021) Moyano, Tomas C.; Gutierrez, Rodrigo A.; Alvarez, Jose M.; Mukhtar, S
Chromatin accessibility is directly linked with transcription in eukaryotes. Accessible regions associated with regulatory proteins are highly sensitive to DNase I digestion and are termed DNase I hypersensitive sites (DHSs). DHSs can be identified by DNase I digestion, followed by high-throughput DNA sequencing (DNase-seq). The single-base-pair resolution digestion patterns from DNase-seq allows identifying transcription factor (TF) footprints of local DNA protection that predict TF-DNA binding. The identification of differential footprinting between two conditions allows mapping relevant TF regulatory interactions. Here, we provide step-by-step instructions to build gene regulatory networks from DNase-seq data. Our pipeline includes steps for DHSs calling, identification of differential TF footprints between treatment and control conditions, and construction of gene regulatory networks. Even though the data we used in this example was obtained from Arabidopsis thaliana, the workflow developed in this guide can be adapted to work with DNase-seq data from any organism with a sequenced genome.
Nakazawaea atacamensis f.a., sp. nov. a novel nonconventional fermentative ascomycetous yeast species from the Atacama Desert
(2024) Araya, Macarena; Villarreal, Pablo; Moyano, Tomas; Santos, Ana R. O.; Diaz, Francisca P.; Bustos-Jarufe, Andrea; Urbina, Kamila; del Pino, Javier E.; Groenewald, Marizeth; Gutierrez, Rodrigo A.; Rosa, Carlos A.; Cubillos, Francisco A.
In this study, we describe Nakazawaea atacamensis f. a., sp. nov., a novel species obtained from Neltuma chilensis plant samples in Chile's hyperarid Atacama Desert. In total, three strains of N. atacamensis were obtained from independent N. chilensis samples (synonym Prosopis chilensis, Algarrobo). Two strains were obtained from bark samples, while the third strain was obtained from bark-exuded gum from another tree. The novel species was defined using molecular characteristics and subsequently characterized with respect to morphological, physiological, and biochemical properties. A neighbor-joining analysis using the sequences of the D1/D2 domains of the large subunit ribosomal RNA gene revealed that N. atacamensis clustered with Nakazawaea pomicola. The sequence of N. atacamensis differed from closely related species by 1.3%-5.2% in the D1/D2 domains. A phylogenomic analysis based on single-nucleotide polymorphism's data confirms that the novel species belongs to the genus Nakazawaea, where N. atacamensis clustered with N. peltata. Phenotypic comparisons demonstrated that N. atacamensis exhibited distinct carbon assimilation patterns compared to its related species. Genome sequencing of the strain ATA-11A-BT revealed a genome size of approximately 12.4 Mbp, similar to other Nakazawaea species, with 5116 protein-coding genes annotated using InterProScan. In addition, N. atacamensis exhibited the capacity to ferment synthetic wine must, representing a potential new yeast for mono or co-culture wine fermentations. This comprehensive study expands our understanding of the genus Nakazawaea and highlights the ecological and industrial potential of N. atacamensis in fermentation processes. The holotype of N. atacamensis sp. nov. is CBS 18375T. The Mycobank number is MB 849680.
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.
Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport
(2021) Otvos, Krisztina; Marconi, Marco; Vega, Andrea; O'Brien, Jose; Johnson, Alexander; Abualia, Rashed; Antonielli, Livio; Montesinos, Juan Carlos; Zhang, Yuzhou; Tan, Shutang; Cuesta, Candela; Artner, Christina; Bouguyon, Eleonore; Gojon, Alain; Friml, Jiri; Gutierrez, Rodrigo A.; Wabnik, Krzysztof; Benkova, Eva
Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate-dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments.
Molecular mechanisms underlying nitrate responses in plants
(2022) Lamig, Liliana; Moreno, Sebastian; Alvarez, Jose M.; Gutierrez, Rodrigo A.
Nitrate is an important source of inorganic nitrogen. Nitrate modulates many plant metabolic, physiological, and developmental processes. This minireview highlights recent findings on the intricate molecular wiring that allows plants to adapt to environmental nitrate conditions. We focus on the role of regulatory pathways and their components - transporters, receptors, second messengers, kinases, and transcription factors - in mediating plant metabolic and developmental responses to nitrate. Work is still needed to identify missing components of the nitrate signaling pathway and their interplay with known and well-characterized master regulators and to validate their molecular interactions to explain the complexity of phenotypical responses to nitrate. Understanding how plants perceive nitrate and transduce it into responses at the molecular level is crucial to optimize nitrogen-use efficiency, improve crop yield and mitigate the adverse environmental impacts of fertilizer overuse in a changing world.
Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture
(2021) Vega, Andrea; Fredes, Isabel; O'Brien, Jose; Shen, Zhouxin; otvos, Krisztina; Abualia, Rashed; Benkova, Eva; Briggs, Steven P.; Gutierrez, Rodrigo A.
Nitrate commands genome-wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild-type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post-translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate.
Plant ecological genomics at the limits of life in the Atacama Desert
(2021) Eshel, Gil; Araus, Viviana; Undurraga, Soledad; Soto, Daniela C.; Moraga, Carol; Montecinos, Alejandro; Moyano, Tomas; Maldonado, Jonathan; Diaz, Francisca P.; Varala, Kranthi; Nelson, Chase W.; Contreras-Lopez, Orlando; Pal-Gabor, Henrietta; Kraiser, Tatiana; Carrasco-Puga, Gabriela; Nilo-Poyanco, Ricardo; Zegar, Charles M.; Orellana, Ariel; Montecino, Martin; Maass, Alejandro; Allende, Miguel L.; DeSalle, Robert; Stevenson, Dennis W.; Gonzalez, Mauricio; Latorre, Claudio; Coruzzi, Gloria M.; Gutierrez, Rodrigo A.
The Atacama Desert in Chile-hyperarid and with high-ultraviolet irradiance levels-is one of the harshest environments on Earth. Yet, dozens of species grow there, including Atacama-endemic plants. Herein, we establish the Talabre-Leji = a transect (TLT) in the Atacama as an unparalleled natural laboratory to study plant adaptation to extreme environmental conditions. We characterized climate, soil, plant, and soil-microbe diversity at 22 sites (every 100 m of altitude) along the TLT over a 10-y period. We quantified drought, nutrient deficiencies, large diurnal temperature oscillations, and pH gradients that define three distinct vegetational belts along the altitudinal cline. We deep-sequenced transcriptomes of 32 dominant plant species spanning the major plant clades, and assessed soil microbes by metabarcoding sequencing. The top-expressed genes in the 32 Atacama species are enriched in stress responses, metabolism, and energy production. Moreover, their root-associated soils are enriched in growthpromoting bacteria, including nitrogen fixers. To identify genes associated with plant adaptation to harsh environments, we compared 32 Atacama species with the 32 closest sequenced species, comprising 70 taxa and 1,686,950 proteins. To perform phylogenomic reconstruction, we concatenated 15,972 ortholog groups into a supermatrix of 8,599,764 amino acids. Using two codonbased methods, we identified 265 candidate positively selected genes (PSGs) in the Atacama plants, 64% of which are located in Pfam domains, supporting their functional relevance. For 59/184 PSGs with an Arabidopsis ortholog, we uncovered functional evidence linking them to plant resilience. As some Atacama plants are closely related to staple crops, these candidate PSGs are a "genetic goldmine" to engineer crop resilience to face climate change.
Predictive metabolomics of multiple Atacama plant species unveils a core set of generic metabolites for extreme climate resilience
(2022) Dussarrat, Thomas; Prigent, Sylvain; Latorre, Claudio; Bernillon, Stephane; Flandin, Amelie; Diaz, Francisca P.; Cassan, Cedric; Van Delft, Pierre; Jacob, Daniel; Varala, Kranthi; Joubes, Jerome; Gibon, Yves; Rolin, Dominique; Gutierrez, Rodrigo A.; Petriacq, Pierre
Current crop yield of the best ideotypes is stagnating and threatened by climate change. In this scenario, understanding wild plant adaptations in extreme ecosystems offers an opportunity to learn about new mechanisms for resilience. Previous studies have shown species specificity for metabolites involved in plant adaptation to harsh environments. Here, we combined multispecies ecological metabolomics and machine learning-based generalized linear model predictions to link the metabolome to the plant environment in a set of 24 species belonging to 14 families growing along an altitudinal gradient in the Atacama Desert. Thirty-nine common compounds predicted the plant environment with 79% accuracy, thus establishing the plant metabolome as an excellent integrative predictor of environmental fluctuations. These metabolites were independent of the species and validated both statistically and biologically using an independent dataset from a different sampling year. Thereafter, using multiblock predictive regressions, metabolites were linked to climatic and edaphic stressors such as freezing temperature, water deficit and high solar irradiance. These findings indicate that plants from different evolutionary trajectories use a generic metabolic toolkit to face extreme environments. These core metabolites, also present in agronomic species, provide a unique metabolic goldmine for improving crop performances under abiotic pressure.
Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis
(2007) Gutierrez, Rodrigo A.; Lejay, Laurence V.; Dean, Alexis; Chiaromonte, Francesca; Shasha, Dennis E.; Coruzzi, Gloria M.
Background: Carbon (C) and nitrogen (N) metabolites can regulate gene expression in Arabidopsis thaliana. Here, we use multinetwork analysis of microarray data to identify molecular networks regulated by C and N in the Arabidopsis root system.
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.
Sungear
(2007) Poultney, Christopher S.; Gutierrez, Rodrigo A.; Katari, Manpreet S.; Gifford, Miriam L.; Paley, W. Bradford; Coruzzi, Gloria M.; Shasha, Dennis E.
Sungear is a software system that supports a rapid, visually interactive and biologist-driven comparison of large datasets. The datasets can come from microarray experiments (e.g. genes induced in each experiment), from comparative genomics (e.g. genes present in each genome) or even from non-biological applications (e.g. demographics or baseball statistics). Sungear represents multiple datasets as vertices in a polygon. Each possible intersection among the sets is represented as a circle inside the polygon. The position of the circle is determined by the position of the vertices represented in the intersection and the area of the circle is determined by the number of elements in the intersection. Sungear shows which Gene Ontology terms are over-represented in a subset of circles or anchors. The intuitive Sungear interface has enabled biologists to determine quickly which dataset or groups of datasets play a role in a biological function of interest.

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