Examinando por Autor "Quintana, Julia"

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A cerato-platanin-like protein HaCPL2 from Heterobasidion annosum sensu stricto induces cell death in Nicotiana tabacum and Pinus sylvestris.
(Elsevier, 2015-09-15) Chen, Hongxin; Quintana, Julia; Kovalchuk, Andriy; Ubhayasekera, Wimal; Asiegbu, Fred O
The cerato-platanin family is a group of small secreted cysteine-rich proteins exclusive for filamentous fungi. They have been shown to be involved in the interactions between fungi and plants. Functional characterization of members from this family has been performed mainly in Ascomycota, except Moniliophthora perniciosa. Our previous phylogenetic analysis revealed that recent gene duplication of cerato-platanins has occurred in Basidiomycota but not in Ascomycota, suggesting higher functional diversification of this protein family in Basidiomycota than in Ascomycota. In this study, we identified three cerato-platanin homologues from the basidiomycete conifer pathogen Heterobasidion annosum sensu stricto. Expression of the homologues under various conditions as well as their roles in the H. annosum s.s.-Pinus sylvestris (Scots pine) pathosystem was investigated. Results showed that HaCPL2 (cerato-platanin-like protein 2) had the highest sequence similarity to cerato-platanin from Ceratocystis platani and hacpl2 was significantly induced during nutrient starvation and necrotrophic growth. The treatment with recombinant HaCPL2 induced cell death, phytoalexin production and defense gene expression in Nicotiana tabacum. Eliciting and cell death-inducing ability accompanied by retardation of apical root growth was also demonstrated in Scots pine seedlings. Our results suggest that HaCPL2 might contribute to the virulence of H. annosum s.s. by promoting plant cell death.
An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study.
(Wiley, 2018-07-26) Parmar, Jignesh H; Quintana, Julia; Ramírez, David; Laubenbacher, Reinhard; Argüello, José; Mendes, Pedro
Biological systems require precise copper homeostasis enabling metallation of cuproproteins while preventing metal toxicity. In bacteria, sensing, transport, and storage molecules act in coordination to fulfill these roles. However, there is not yet a kinetic schema explaining the system integration. Here, we report a model emerging from experimental and computational approaches that describes the dynamics of copper distribution in Pseudomonas aeruginosa. Based on copper uptake experiments, a minimal kinetic model describes well the copper distribution in the wild-type bacteria but is unable to explain the behavior of the mutant strain lacking CopA1, a key Cu+ efflux ATPase. The model was expanded through an iterative hypothesis-driven approach, arriving to a mechanism that considers the induction of compartmental pools and the parallel function of CopA and Cus efflux systems. Model simulations support the presence of a periplasmic copper storage with a crucial role under dyshomeostasis conditions in P. aeruginosa. Importantly, the model predicts not only the interplay of periplasmic and cytoplasmic pools but also the existence of a threshold in the concentration of external copper beyond which cells lose their ability to control copper levels.
Bacterial Cu(+)-ATPases: models for molecular structure-function studies.
(Oxford University Press, 2016-07-22) Argüello, José; Patel, Sarju; Quintana, Julia
The early discovery of the human Cu(+)-ATPases and their link to Menkes and Wilson's diseases brought attention to the unique role of these transporters in copper homeostasis. The characterization of bacterial Cu(+)-ATPases has significantly furthered our understanding of the structure, selectivity and transport mechanism of these enzymes, as well as their interplay with other elements of Cu(+) distribution networks. This review focuses on the structural-functional insights that have emerged from studies of bacterial Cu(+)-ATPases at the molecular level and how these observations have contributed to drawing up a comprehensive picture of cellular copper homeostasis.
Copper homeostasis networks in the bacterium Pseudomonas aeruginosa.
(Elsevier, 2017-07-31) Quintana, Julia; Novoa-Aponte, Lorena; Argüello, José
Bacterial copper (Cu⁺) homeostasis enables both precise metallation of diverse cuproproteins and control of variable metal levels. To this end, protein networks mobilize Cu⁺ to cellular targets with remarkable specificity. However, the understanding of these processes is rather fragmented. Here, we use genome-wide transcriptomic analysis by RNA-Seq to characterize the response of Pseudomonas aeruginosa to external 0.5 mm CuSO₄, a condition that did not generate pleiotropic effects. Pre-steady-state (5-min) and steady-state (2-h) Cu⁺ fluxes resulted in distinct transcriptome landscapes. Cells quickly responded to Cu²⁺ stress by slowing down metabolism. This was restored once steady state was reached. Specific Cu⁺ homeostasis genes were strongly regulated in both conditions. Our system-wide analysis revealed induction of three Cu⁺ efflux systems (a P_1B-ATPase, a porin, and a resistance-nodulation-division (RND) system) and of a putative Cu⁺-binding periplasmic chaperone and the unusual presence of two cytoplasmic CopZ proteins. Both CopZ chaperones could bind Cu⁺ with high affinity. Importantly, novel transmembrane transporters probably mediating Cu⁺ influx were among those largely repressed upon Cu⁺ stress. Compartmental Cu⁺ levels appear independently controlled; the cytoplasmic Cu⁺ sensor CueR controls cytoplasmic chaperones and plasma membrane transporters, whereas CopR/S responds to periplasmic Cu⁺ Analysis of ΔcopR and ΔcueR mutant strains revealed a CopR regulon composed of genes involved in periplasmic Cu⁺ homeostasis and its putative DNA recognition sequence. In conclusion, our study establishes a system-wide model of a network of sensors/regulators, soluble chaperones, and influx/efflux transporters that control the Cu⁺ levels in P. aeruginosa compartments.
Differential expression of zinc transporters accompanies the differentiation of C2C12 myoblasts.
(Elsevier, 2018-04-20) Paskavitz, Amanda L; Quintana, Julia; Cangussu, Daniella; Tavera-Montañez, Cristina; Xiao, Yao; Ortiz-Miranda, Sonia; Navea, Juan G; Padilla-Benavides, Teresita
Zinc transporters facilitate metal mobilization and compartmentalization, playing a key role in cellular development. Little is known about the mechanisms and pathways of Zn movement between Zn transporters and metalloproteins during myoblast differentiation. We analyzed the differential expression of ZIP and ZnT transporters during C2C12 myoblast differentiation. Zn transporters account for a transient decrease of intracellular Zn upon myogenesis induction followed by a gradual increase of Zn in myotubes. Considering the subcellular localization and function of each of the Zn transporters, our findings indicate that a fine regulation is necessary to maintain correct metal concentrations in the cytosol and subcellular compartments to avoid toxicity, maintain homeostasis, and for loading metalloproteins needed during myogenesis. This study advances our basic understanding of the complex Zn transport network during muscle differentiation.
Energy status-promoted growth and development of Arabidopsis require copper deficiency response transcriptional regulator SPL7
(Oxford University Press, 2022-07-22) Schulten, Anna; Pietzenuk, Bjoern; Quintana, Julia; Scholle, Marleen; Feil, Regina; Krause, Markus; Romera-Branchat, Maida; Wahl, Vanessa; Severing, Edouard; Coupland, George; Kraemer, Ute
Copper (Cu) is a cofactor of around 300 Arabidopsis proteins, including photosynthetic and mitochondrial electron transfer chain enzymes critical for adenosine triphosphate (ATP) production and carbon fixation. Plant acclimation to Cu deficiency requires the transcription factor SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE7 (SPL7). We report that in the wild type (WT) and in the spl7-1 mutant, respiratory electron flux via Cu-dependent cytochrome c oxidase is unaffected under both normal and low-Cu cultivation conditions. Supplementing Cu-deficient medium with exogenous sugar stimulated growth of the WT, but not of spl7 mutants. Instead, these mutants accumulated carbohydrates, including the signaling sugar trehalose 6-phosphate, as well as ATP and NADH, even under normal Cu supply and without sugar supplementation. Delayed spl7-1 development was in agreement with its attenuated sugar responsiveness. Functional TARGET OF RAPAMYCIN and SNF1-RELATED KINASE1 signaling in spl7-1 argued against fundamental defects in these energy-signaling hubs. Sequencing of chromatin immunoprecipitates combined with transcriptome profiling identified direct targets of SPL7-mediated positive regulation, including Fe SUPEROXIDE DISMUTASE1 (FSD1), COPPER-DEFICIENCY-INDUCED TRANSCRIPTION FACTOR1 (CITF1), and the uncharacterized bHLH23 (CITF2), as well as an enriched upstream GTACTRC motif. In summary, transducing energy availability into growth and reproductive development requires the function of SPL7. Our results could help increase crop yields, especially on Cu-deficient soils.
Genetic characterization of chestnut (Castanea sativa Mill.) orchards and traditional nut varieties in El Bierzo, a glacial refuge and major cultivation site in northwestern Spain
(SpringerLink, 2015-02) Quintana, Julia; Contreras, Angela; Merino, Irene; Vimnuesa, Álvaro; Orozco, Gabriela; Ovalle, Felipe; Gomez, Luis
This paper presents a detailed genetic study of Castanea sativa in El Bierzo, a major nut production region with interesting features. It is located within a glacial refuge at one extreme of the distribution area (northwest Spain); it has a centenary tradition of chestnut management; and more importantly, it shows an unusual degree of genetic isolation. Seven nuclear microsatellite markers were selected to analyze the genetic variability and structure of 169 local trees grafted for nut production. We analyzed in the same manner 62 local nuts. The selected loci were highly discriminant for the genotypes studied, giving a combined probability of identity of 6.1 × 10−6. An unprecedented density of trees was sampled for this project over the entire region, and nuts were collected representing 18 cultivars marketed by local producers. Several instances of misclassification by local growers were detected. Fixation index estimates and analysis of molecular variance (AMOVA) data are supportive of an unexpectedly high level of genetic differentiation in El Bierzo, larger than that estimated in a previous study with broader geographical scope but based on limited local sampling (Pereira-Lorenzo et al., Tree Genet Genomes 6: 701–715, 2010a). Likewise, we have determined that clonality due to grafting had been previously overestimated. In line with these observations, no significant spatial structure was found using both a model-based Bayesian procedure and Mantel’s tests. Taken together, our results evidence the need for more fine-scale genetic studies if conservation strategies are to be efficiently improved.
Obtaining the Most Accurate de novo Transcriptomes for Non-model Organisms: The Case of Castanea sativa
(SpringerLink, 2017) Espigares, Marina; Seoane, Pedro; Bautista, Rocío; Quintana, Julia; Claros, Gonzalo; Gomez, Luis
Gene expression analyses of non-model organisms must start with the construction of a high accurate de novo transcriptome as a reference. The best way to determine the suitability of any de novo transcriptome assembling is its comparison with other well-known “reference” transcriptomes. In this study, we took six complete plant transcriptomes (Arabidopsis thaliana, Vitis vinifera, Zea mays, Populus trichocarpa, Triticum aestivum and Oryza sativa) and compared all of them using a series of metrics system for a principal component analysis, resulting that A. thaliana and P. trichocarpa were the best references. This has been automated using AutoFlow. A primary assembly of short reads from Illumina Platform (50 nt, single reads) and long reads from Roche-454 technology from Castanea sativa was performed individually using k-mers from 25 to 35 and different assemblers (Oases v2, SOAPdenovoTrans, RAY, MIRA4 and MINIMUS). The resulting contigs were then reconciled with the aim of obtaining the best transcriptome. Oases and SOAP were used for the assembling of short reads, MIRA and MINIMUS for the assembling of long reads or the reconciliations, and RAY, that can compute de novo transcript assembling from heterogeneous (long and short reads) next-generation sequencing data, was included to avoid the reconciliation step. A total of 90 different assemblies were generated in a single run of the pipeline. A hierarchical clustering on the PCA components (HCPC) was implemented to automatically identify the best assembling strategies based on the shortest distance in HCPC to the two plant reference transcriptomes is selected. In this approach, reconciliation of Roche/454 long reads with Illumina contigs produce more complete and accurate gene reconstructions than other combinations. Surprisingly, reconstructions based only on Illumina and the ones creates with RAY seem to be less accurate. For this specific study, the most complete and accurate transcriptome corresponds to the Illumina contigs obtained with SOAPdenovoTrans and reassembled with 454 long reads using MIRA4. This is only a one example of a transcriptome building. Many other assembling can be performed just changing parameters, k-mers, sequencing technology, assemblers, reference organisms, etc. The pipeline in AutoFlow is easily customizable for those purposes.
Root‐to‐shoot iron partitioning in Arabidopsis requires IRON‐REGULATED TRANSPORTER1 (IRT1) protein but not its iron(II) transport function
(Wiley, 2022) Quintana, Julia; Bernal, María; Scholle Marleen; Holländer‐Czytko, Heike; Nga, Nguyen T.; Piotrowski, Markus; Mendoza‐Cózatl, David G.; Haydon, Michael J.; Kraemer, Ute
IRON‐REGULATED TRANSPORTER1 (IRT1) is the root high‐affinity ferrous iron uptake system and indispensable for the completion of the life cycle of Arabidopsis thaliana without vigorous iron (Fe) supplementation. Here we provide evidence supporting a second role of IRT1 in root‐to‐shoot partitioning of Fe. We show that irt1 mutants over‐accumulate Fe in roots, most prominently in the cortex of the differentiation zone in irt1‐2, compared to the wild type. Shoots of irt1‐2 are severely Fe‐deficient according to Fe content and marker transcripts, as expected. We generated irt1‐2 lines producing IRT1 mutant variants carrying single amino‐acid substitutions of key residues in transmembrane helices IV and V, Ser206 and His232, which are required for transport activity in yeast. Root short‐term 55Fe uptake rates were uninformative concerning IRT1‐mediated transport. Overall irt1‐like concentrations of the secondary substrate Mn suggested that the transgenic Arabidopsis lines also remain incapable of IRT1‐mediated root Fe uptake. Yet, IRT1S206A partially complements rosette dwarfing and leaf chlorosis, as well as root‐to‐shoot Fe partitioning and gene expression defects of irt1‐2, all of which are fully complemented by wild‐type IRT1. Taken together, these results suggest a function for IRT1 in root‐to‐shoot Fe partitioning that does not require Fe transport activity of IRT1. Among the genes of which transcript levels are partially dependent on IRT1, we identify MYB DOMAIN PROTEIN10, MYB DOMAIN PROTEIN72 and NICOTIANAMINE SYNTHASE4 as candidates for effecting IRT1‐dependent Fe mobilization in roots. Understanding the biological functions of IRT1 will help to improve iron nutrition and the nutritional quality of agricultural crops.
Tema 10. Procesamiento de RNA
(2024-12) Quintana, Julia
TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms
(BMC, 2018) Seoane, Pedro; Espigares, Marina; Carmona, Rosario; Polonio, Alvaro; Quintana, Julia; Cretazzo, Enrico; Bota, Josefina; Perez-Garcia, Alejandro; de Dios Alche, Juan; Gomez, Luis; Claros, Gonzalo
Background The advances in high-throughput sequencing technologies are allowing more and more de novo assembling of transcriptomes from many new organisms. Some degree of automation and evaluation is required to warrant reproducibility, repetitivity and the selection of the best possible transcriptome. Workflows and pipelines are becoming an absolute requirement for such a purpose, but the issue of assembling evaluation for de novo transcriptomes in organisms lacking a sequenced genome remains unsolved. An automated, reproducible and flexible framework called TransFlow to accomplish this task is described. Results TransFlow with its five independent modules was designed to build different workflows depending on the nature of the original reads. This architecture enables different combinations of Illumina and Roche/454 sequencing data, and can be extended to other sequencing platforms. Its capabilities are illustrated with the selection of reliable plant reference transcriptomes and the assembling six transcriptomes (three case studies for grapevine leaves, olive tree pollen, and chestnut stem, and other three for haustorium, epiphytic structures and their combination for the phytopathogenic fungus Podosphaera xanthii). Arabidopsis and poplar transcriptomes revealed to be the best references. A common result regarding de novo assemblies is that Illumina paired-end reads of 100 nt in length assembled with OASES can provide reliable transcriptomes, while the contribution of longer reads is noticeable only when they complement a set of short, single-reads. Conclusions TransFlow can handle up to 181 different assembling strategies. Evaluation based on principal component analyses allows its self-adaptation to different sets of reads to provide a suitable transcriptome for each combination of reads and assemblers. As a result, each case study has its own behaviour, prioritises evaluation parameters, and gives an objective and automated way for detecting the best transcriptome within a pool of them. Sequencing data type and quantity (preferably several hundred millions of 2×100 nt or longer), assemblers (OASES for Illumina, MIRA4 and EULER-SR reconciled with CAP3 for Roche/454) and strategy (preferably scaffolding with OASES, and probably merging with Roche/454 when available) arise as the most impacting factors.
TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms
(BMC, 2018-11-20) Seoane, Pedro; Espigares, Marina; Carmona, Rosario; Polonio, Álvaro; Quintana, Julia; Cretazzo, Enrico; Bota, Josefina; Pérez-García, Alejandro; Alché, Juan de Dios; Gómez, Luis; Claros, M Gonzalo
The advances in high-throughput sequencing technologies are allowing more and more de novo assembling of transcriptomes from many new organisms. Some degree of automation and evaluation is required to warrant reproducibility, repetitivity and the selection of the best possible transcriptome. Workflows and pipelines are becoming an absolute requirement for such a purpose, but the issue of assembling evaluation for de novo transcriptomes in organisms lacking a sequenced genome remains unsolved. An automated, reproducible and flexible framework called TransFlow to accomplish this task is described.
Translational fidelity and growth of Arabidopsis require stress-sensitive diphthamide biosynthesis
(Springer Nature, 2022) Zhang, Hongliang; Quintana, Julia; Ütkür, Koray; Adrian, Lorenz; Hawer, Harmen; Mayer, Klaus; Gong, Xiaodi; Castanedo, Leonardo; Schulten, Anna; Janina, Nadežda; Peters, Marcus; Wirtz, Markus; Brinkmann, Ulrich; Schaffrath, Raffael; Kraemer, Ute
Diphthamide, a post-translationally modified histidine residue of eukaryotic TRANSLATION ELONGATION FACTOR2 (eEF2), is the human host cell-sensitizing target of diphtheria toxin. Diphthamide biosynthesis depends on the 4Fe-4S-cluster protein Dph1 catalyzing the first committed step, as well as Dph2 to Dph7, in yeast and mammals. Here we show that diphthamide modification of eEF2 is conserved in Arabidopsis thaliana and requires AtDPH1. Ribosomal −1 frameshifting-error rates are increased in Arabidopsis dph1 mutants, similar to yeast and mice. Compared to the wild type, shorter roots and smaller rosettes of dph1 mutants result from fewer formed cells. TARGET OF RAPAMYCIN (TOR) kinase activity is attenuated, and autophagy is activated, in dph1 mutants. Under abiotic stress diphthamide-unmodified eEF2 accumulates in wild-type seedlings, most strongly upon heavy metal excess, which is conserved in human cells. In summary, our results suggest that diphthamide contributes to the functionality of the translational machinery monitored by plants to regulate growth. Diphthamide is a post-translationally modified histidine residue present in animal and yeast TRANSLATION ELONGATION FACTOR2. Here the authors show that diphthamide modification of eEF2 is conserved in Arabidopsis thaliana and contributes to translational fidelity and growth via cell proliferation.