Catálogo de publicaciones - revistas

<jats:title>SUMMARY</jats:title><jats:p>Circadian regulation produces a biological measure of time within cells. The daily cycle in the availability of light for photosynthesis causes dramatic changes in biochemical processes in photosynthetic organisms, with the circadian clock having crucial roles in adaptation to these fluctuating conditions. Correct alignment between the circadian clock and environmental day–night cycles maximizes plant productivity through its regulation of metabolism. Therefore, the processes that integrate circadian regulation with metabolism are key to understanding how the circadian clock contributes to plant productivity. This forms an important part of exploiting knowledge of circadian regulation to enhance sustainable crop production. Here, we examine the roles of circadian regulation in metabolic processes in source and sink organ structures of Arabidopsis. We also evaluate possible roles for circadian regulation in root exudation processes that deposit carbon into the soil, and the nature of the rhythmic interactions between plants and their associated microbial communities. Finally, we examine shared and differing aspects of the circadian regulation of metabolism between Arabidopsis and other model photosynthetic organisms, and between circadian control of metabolism in photosynthetic and non‐photosynthetic organisms. This synthesis identifies a variety of future research topics, including a focus on metabolic processes that underlie biotic interactions within ecosystems.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Although primary metabolism is well conserved across species, it is useful to explore the specificity of its network to assess the extent to which some pathways may contribute to particular outcomes. Constraint‐based metabolic modelling is an established framework for predicting metabolic fluxes and phenotypes and helps to explore how the plant metabolic network delivers specific outcomes from temporal series. After describing the main physiological traits during fruit development, we confirmed the correlations between fruit relative growth rate (RGR), protein content and time to maturity. Then a constraint‐based method is applied to a panel of eight fruit species with a knowledge‐based metabolic model of heterotrophic cells describing a generic metabolic network of primary metabolism. The metabolic fluxes are estimated by constraining the model using a large set of metabolites and compounds quantified throughout fruit development. Multivariate analyses showed a clear common pattern of flux distribution during fruit development with differences between fast‐ and slow‐growing fruits. Only the latter fruits mobilise the tricarboxylic acid cycle in addition to glycolysis, leading to a higher rate of respiration. More surprisingly, to balance nitrogen, the model suggests, on the one hand, nitrogen uptake by nitrate reductase to support a high RGR at early stages of cucumber and, on the other hand, the accumulation of alkaloids during ripening of pepper and eggplant. Finally, building virtual fruits by combining 12 biomass compounds shows that the growth‐defence trade‐off is supported mainly by cell wall synthesis for fast‐growing fruits and by total polyphenols accumulation for slow‐growing fruits.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Programmed cell death (PCD) facilitates selective, genetically controlled elimination of redundant, damaged, or infected cells. In plants, PCD is often an essential component of normal development and can mediate responses to abiotic and biotic stress stimuli. However, studying the transcriptional regulation of PCD is hindered by difficulties in sampling small groups of dying cells that are often buried within the bulk of living plant tissue. We addressed this challenge by using RNA sequencing and <jats:italic>Arabidopsis thaliana</jats:italic> suspension cells, a model system that allows precise monitoring of PCD rates. The use of three PCD‐inducing treatments (salicylic acid, heat, and critical dilution), in combination with three cell death modulators (3‐methyladenine, lanthanum chloride, and conditioned medium), enabled isolation of candidate core‐ and stimuli‐specific PCD genes, inference of underlying regulatory networks and identification of putative transcriptional regulators of PCD in plants. This analysis underscored a disturbance of the cell cycle and mitochondrial retrograde signaling, and repression of pro‐survival stress responses, as key elements of the PCD‐associated transcriptional signature. Further, phenotyping of Arabidopsis T‐DNA insertion mutants in selected candidate genes validated the potential of generated resources to identify novel genes involved in plant PCD pathways and/or stress tolerance.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Senescence is a highly regulated process driven by developmental age and environmental factors. Although leaf senescence is accelerated by nitrogen (N) deficiency, the underlying physiological and molecular mechanisms are largely unknown. Here, we reveal that BBX14, a previously uncharacterized BBX‐type transcription factor in Arabidopsis, is crucial for N starvation‐induced leaf senescence. We find that inhibiting <jats:italic>BBX14</jats:italic> by artificial miRNA (amiRNA) accelerates senescence during N starvation and in darkness, while <jats:italic>BBX14</jats:italic> overexpression (<jats:italic>BBX14‐OX</jats:italic>) delays it, identifying BBX14 as a negative regulator of N starvation‐ and dark‐induced senescence. During N starvation, nitrate and amino acids like glutamic acid, glutamine, aspartic acid, and asparagine were highly retained in <jats:italic>BBX14</jats:italic>‐OX leaves compared to the wild type. Transcriptome analysis showed a large number of senescence‐associated genes (SAGs) to be differentially expressed between <jats:italic>BBX14‐OX</jats:italic> and wild‐type plants, including <jats:italic>ETHYLENE INSENSITIVE3</jats:italic> (<jats:italic>EIN3</jats:italic>) which regulates N signaling and leaf senescence. Chromatin immunoprecipitation (ChIP) showed that BBX14 directly regulates <jats:italic>EIN3</jats:italic> transcription. Furthermore, we revealed the upstream transcriptional cascade of <jats:italic>BBX14</jats:italic>. By yeast one‐hybrid screen and ChIP, we found that MYB44, a stress‐responsive MYB transcription factor, directly binds to the promoter of <jats:italic>BBX14</jats:italic> and activates its expression. In addition, Phytochrome Interacting Factor 4 (PIF4) binds to the promoter of <jats:italic>BBX14</jats:italic> to repress <jats:italic>BBX14</jats:italic> transcription. Thus, BBX14 functions as a negative regulator of N starvation‐induced senescence through EIN3 and is directly regulated by PIF4 and MYB44.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Pear anthracnose caused by <jats:italic>Colletotrichum fructicola</jats:italic> is one of the main fungal diseases in all pear‐producing areas. The degradation of ubiquitinated proteins by the 26S proteasome is a regulatory mechanism of eukaryotes. E3 ubiquitin ligase is substrate specific and is one of the most diversified and abundant enzymes in the regulation mechanism of plant ubiquitination. Although numerous studies in other plants have shown that the degradation of ubiquitinated proteins by the 26S proteasome is closely related to plant immunity, there are limited studies on them in pear trees. Here, we found that an E3 ubiquitin ligase, PbATL18, interacts with and ubiquitinates the transcription factor PbbZIP4, and this process is enhanced by <jats:italic>C</jats:italic>. <jats:italic>fructicola</jats:italic> infection. PbATL18 overexpression in pear callus enhanced resistance to <jats:italic>C</jats:italic>. <jats:italic>fructicola</jats:italic> infection, whereas <jats:italic>PbbZIP4</jats:italic> overexpression increased sensitivity to <jats:italic>C</jats:italic>. <jats:italic>fructicola</jats:italic> infection. Silencing <jats:italic>PbATL18</jats:italic> and <jats:italic>PbbZIP4</jats:italic> in <jats:italic>Pyrus betulaefolia</jats:italic> seedlings resulted in opposite effects, with <jats:italic>PbbZIP4</jats:italic> silencing enhancing resistance to <jats:italic>C</jats:italic>. <jats:italic>fructicola</jats:italic> infection and <jats:italic>PbATL18</jats:italic> silencing increasing sensitivity to <jats:italic>C</jats:italic>. <jats:italic>fructicola</jats:italic> infection. Using yeast one‐hybrid screens, an electrophoretic mobility shift assay, and dual‐luciferase assays, we demonstrated that the transcription factor PbbZIP4 upregulated the expression of <jats:italic>PbNPR3</jats:italic> by directly binding to its promoter. <jats:italic>PbNPR3</jats:italic> is one of the key genes in the salicylic acid (SA) signal transduction pathway that can inhibit SA signal transduction. Here, we proposed a PbATL18‐PbbZIP4‐PbNPR3‐SA model for plant response to <jats:italic>C</jats:italic>. <jats:italic>fructicola</jats:italic> infection. PbbZIP4 was ubiquitinated by PbATL18 and degraded by the 26S proteasome, which decreased the expression of <jats:italic>PbNPR3</jats:italic> and promoted SA signal transduction, thereby enhancing plant <jats:italic>C</jats:italic>. <jats:italic>fructicola</jats:italic> resistance. Our study provides new insights into the molecular mechanism of pear response to <jats:italic>C</jats:italic>. <jats:italic>fructicola</jats:italic> infection, which can serve as a theoretical basis for breeding superior disease‐resistant pear varieties.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Plant cells and organs grow into a remarkable diversity of shapes, as directed by cell walls composed primarily of polysaccharides such as cellulose and multiple structurally distinct pectins. The properties of the cell wall that allow for precise control of morphogenesis are distinct from those of the individual polysaccharide components. For example, cellulose, the primary determinant of cell morphology, is a chiral macromolecule that can self‐assemble <jats:italic>in vitro</jats:italic> into larger‐scale structures of consistent chirality, and yet most plant cells do not display consistent chirality in their growth. One interesting exception is the <jats:italic>Arabidopsis thaliana rhm1</jats:italic> mutant, which has decreased levels of the pectin rhamnogalacturonan‐I and causes conical petal epidermal cells to grow with a left‐handed helical twist. Here, we show that in <jats:italic>rhm1</jats:italic> the cellulose is bundled into large macrofibrils, unlike the evenly distributed microfibrils of the wild type. This cellulose bundling becomes increasingly severe over time, consistent with cellulose being synthesized normally and then self‐associating into macrofibrils. We also show that in the wild type, cellulose is oriented transversely, whereas in <jats:italic>rhm1</jats:italic> mutants, the cellulose forms right‐handed helices that can account for the helical morphology of the petal cells. Our results indicate that when the composition of pectin is altered, cellulose can form cellular‐scale chiral structures <jats:italic>in vivo</jats:italic>, analogous to the helicoids formed <jats:italic>in vitro</jats:italic> by cellulose nano‐crystals. We propose that an important emergent property of the interplay between rhamnogalacturonan‐I and cellulose is to permit the assembly of nonbundled cellulose structures, providing plants flexibility to orient cellulose and direct morphogenesis.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Floral morphology varies considerably between dicots and monocots. The ABCDE model explaining how floral organ development is controlled was formulated using core eudicots and applied to grass crops. Barley (<jats:italic>Hordeum. vulgare</jats:italic>) has unique floral morphogenesis. Wild barley (<jats:italic>H</jats:italic>. vulgare ssp. <jats:italic>spontaneum</jats:italic>), which is the immediate ancestor of cultivated barley (<jats:italic>H</jats:italic>. <jats:italic>vulgare</jats:italic> ssp. <jats:italic>vulgare</jats:italic>), contains a rich reservoir of genetic diversity. However, the wild barley genes involved in floral organ development are still relatively uncharacterized. In this study, we generated an organ‐specific transcriptome atlas for wild barley floral organs. Genome‐wide transcription profiles indicated that 22 838 protein‐coding genes were expressed in at least one organ. These genes were grouped into seven clusters according to the similarities in their expression patterns. Moreover, 5619 genes exhibited organ‐enriched expression, 677 of which were members of 47 transcription factor families. Gene ontology analyses suggested that the functions of the genes with organ‐enriched expression influence the biological processes in floral organs. The co‐expression regulatory network showed that the expression of 690 genes targeted by MADS‐box proteins was highly positively correlated with the expression of ABCDE model genes during floral morphogenesis. Furthermore, the expression of 138 genes was specific to the wild barley OUH602 genome and not the Morex genome; most of these genes were highly expressed in the glume, awn, lemma, and palea. This study revealed the global gene expression patterns underlying floral morphogenesis in wild barley. On the basis of the study findings, a molecular mechanism controlling floral morphology in barley was proposed.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Dehydration response element binding (DREB) proteins are vital for plant abiotic stress responses, but the understanding of <jats:italic>DREBs</jats:italic> in bamboo, an important sustainable non‐timber forest product, is limited. Here we conducted a comprehensive genome‐wide analysis of the <jats:italic>DREB</jats:italic> gene family in Moso bamboo, representing the most important running bamboo species in Asia. In total, 44 <jats:italic>PeDREBs</jats:italic> were identified, and information on their gene structures, protein motifs, phylogenetic relationships, and stress‐related <jats:italic>cis</jats:italic>‐regulatory elements (CREs) was provided. Based on the bioinformatical analysis, we further analyzed <jats:italic>PeDREBs</jats:italic> from the A5 group and found that four of five <jats:italic>PeDREB</jats:italic> transcripts were induced by salt, drought, and cold stresses, and their proteins could bind to stress‐related CREs. Among these, <jats:italic>PeDREB28</jats:italic> was selected as a promising candidate for further functional characterization. PeDREB28 is localized in nucleus, has transcriptional activation activity, and could bind to the DRE‐ and coupling element 1‐ (CE1) CREs. Overexpression of <jats:italic>PeDREB28</jats:italic> in Arabidopsis and bamboo improved plant abiotic stress tolerance. Transcriptomic analysis showed that broad changes due to the overexpression of <jats:italic>PeDREB28</jats:italic>. Furthermore, 628 genes that may act as the direct <jats:italic>PeDREB28</jats:italic> downstream genes were identified by combining DAP‐seq and RNA‐seq analysis. Moreover, we confirmed that PeDREB28 could bind to the promoter of pyrabactin‐resistance‐like gene (<jats:italic>DlaPYL3</jats:italic>), which is a homolog of abscisic acid receptor in Arabidopsis, and activates its expression. In summary, our study provides important insights into the <jats:italic>DREB</jats:italic> gene family in Moso bamboo, and contributes to their functional verification and genetic engineering applications in the future.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>The protein factors for the specific C‐to‐U RNA editing events in plant mitochondria and chloroplasts possess unique arrays of RNA‐binding pentatricopeptide repeats (PPRs) linked to carboxy‐terminal cytidine deaminase DYW domains via the extension motifs E1 and E2. The E1 and E2 motifs have distant similarities to tetratricopeptide repeats known to mediate protein–protein interactions but their precise function is unclear. Here, we investigate the tolerance of PPR56 and PPR65, two functionally characterized RNA editing factors of the moss <jats:italic>Physcomitrium patens</jats:italic>, for the creation of chimeras by variably replacing their C‐terminal protein regions. Making use of a heterologous RNA editing assay system in <jats:italic>Escherichia coli</jats:italic> we find that heterologous DYW domains can strongly restrict or widen the spectrum of off‐targets in the bacterial transcriptome for PPR56. Surprisingly, our data suggest that these changes are not only caused by the preference of a given heterologous DYW domain for the immediate sequence environment of the cytidine to be edited but also by a long‐range impact on the nucleotide selectivity of the upstream PPRs.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Success in plant reproduction is highly dependent on the correct timing of the floral transition, which is tightly regulated by the flowering pathways. In the model plant <jats:italic>Arabidopsis thaliana</jats:italic>, the central flowering repressor <jats:italic>FLOWERING LOCUS C</jats:italic> (<jats:italic>FLC</jats:italic>) is precisely regulated by multiple flowering time regulators in the vernalization pathway and autonomous pathway, including FPA. Here we report that Arabidopsis MEDIATOR SUBUNIT 8 (MED8) promotes floral transition in Arabidopsis by recruiting FPA to the <jats:italic>FLC</jats:italic> locus to repress <jats:italic>FLC</jats:italic> expression. Loss of MED8 function leads to a significant late‐flowering phenotype due to increased <jats:italic>FLC</jats:italic> expression. We further show that MED8 directly interacts with FPA in the nucleus and recruits FPA to the <jats:italic>FLC</jats:italic> locus. Moreover, MED8 is indispensable for FPA's function in controlling flowering time and regulating <jats:italic>FLC</jats:italic> expression. Our study thus reveals a flowering mechanism by which the Mediator subunit MED8 represses <jats:italic>FLC</jats:italic> expression by facilitating the binding of FPA to the <jats:italic>FLC</jats:italic> locus to ensure appropriate timing of flowering for reproductive success.</jats:p>