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1.
Nat Commun ; 15(1): 6748, 2024 Aug 08.
Artículo en Inglés | MEDLINE | ID: mdl-39117606

RESUMEN

To survive extreme desiccation, seeds enter a period of quiescence that can last millennia. Seed quiescence involves the accumulation of protective storage proteins and lipids through unknown adjustments in protein homeostasis (proteostasis). Here, we show that mutation of all six type-II metacaspase (MCA-II) proteases in Arabidopsis thaliana disturbs proteostasis in seeds. MCA-II mutant seeds fail to restrict the AAA ATPase CELL DIVISION CYCLE 48 (CDC48) at the endoplasmic reticulum to discard misfolded proteins, compromising seed storability. Endoplasmic reticulum (ER) localization of CDC48 relies on the MCA-IIs-dependent cleavage of PUX10 (ubiquitination regulatory X domain-containing 10), the adaptor protein responsible for titrating CDC48 to lipid droplets. PUX10 cleavage enables the shuttling of CDC48 between lipid droplets and the ER, providing an important regulatory mechanism sustaining spatiotemporal proteolysis, lipid droplet dynamics, and protein homeostasis. In turn, the removal of the PUX10 adaptor in MCA-II mutant seeds partially restores proteostasis, CDC48 localization, and lipid droplet dynamics prolonging seed lifespan. Taken together, we uncover a proteolytic module conferring seed longevity.


Asunto(s)
Proteínas de Arabidopsis , Arabidopsis , Retículo Endoplásmico , Gotas Lipídicas , Mutación , Semillas , Proteína que Contiene Valosina , Arabidopsis/genética , Arabidopsis/metabolismo , Semillas/metabolismo , Proteínas de Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Retículo Endoplásmico/metabolismo , Proteína que Contiene Valosina/metabolismo , Proteína que Contiene Valosina/genética , Gotas Lipídicas/metabolismo , Proteostasis , Proteolisis , Regulación de la Expresión Génica de las Plantas , Longevidad/fisiología , Longevidad/genética
2.
Mol Plant ; 17(8): 1204-1220, 2024 Aug 05.
Artículo en Inglés | MEDLINE | ID: mdl-38894538

RESUMEN

Plants are sessile organisms that have acquired highly plastic developmental strategies to adapt to the environment. Among these processes, the floral transition is essential to ensure reproductive success and is finely regulated by several internal and external genetic networks. The photoperiodic pathway, which controls plant response to day length, is one of the most important pathways controlling flowering. In Arabidopsis photoperiodic flowering, CONSTANS (CO) is the central gene activating the expression of the florigen FLOWERING LOCUS T (FT) in the leaves at the end of a long day. The circadian clock strongly regulates CO expression. However, to date, no evidence has been reported regarding a feedback loop from the photoperiod pathway back to the circadian clock. Using transcriptional networks, we have identified relevant network motifs regulating the interplay between the circadian clock and the photoperiod pathway. Gene expression, chromatin immunoprecipitation experiments, and phenotypic analysis allowed us to elucidate the role of CO over the circadian clock. Plants with altered CO expression showed a different internal clock period, measured by daily leaf rhythmic movements. We showed that CO upregulates the expression of key genes related to the circadian clock, such as CCA1, LHY, PRR5, and GI, at the end of a long day by binding to specific sites on their promoters. Moreover, a high number of PRR5-repressed target genes are upregulated by CO, and this could explain the phase transition promoted by CO. The CO-PRR5 complex interacts with the bZIP transcription factor HY5 and helps to localize the complex in the promoters of clock genes. Taken together, our results indicate that there may be a feedback loop in which CO communicates back to the circadian clock, providing seasonal information to the circadian system.


Asunto(s)
Proteínas de Arabidopsis , Arabidopsis , Relojes Circadianos , Proteínas de Unión al ADN , Regulación de la Expresión Génica de las Plantas , Fotoperiodo , Factores de Transcripción , Arabidopsis/genética , Arabidopsis/fisiología , Arabidopsis/metabolismo , Proteínas de Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Relojes Circadianos/genética , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Flores/genética , Flores/fisiología
3.
J Sci Food Agric ; 104(10): 5789-5798, 2024 Aug 15.
Artículo en Inglés | MEDLINE | ID: mdl-38436436

RESUMEN

BACKGROUND: The steady world population growth and the current climate emergency crisis demand the development of sustainable methods to increase crop performance and resilience to the abiotic and biotic stresses produced by global warming. Microalgal extracts are being established as sustainable sources to produce compounds that improve agricultural yield, concurrently contributing during their production process to atmospheric CO2 abatement through the photosynthetic activity of microalgae. RESULTS: In the present study, we characterize the transcriptomic response in the model plant Arabidopsis thaliana and the plant of horticultural interest Solanum lycopersicum to the foliar application of a microalgae-based commercial preparation LRM™ (AlgaEnergy, Madrid, Spain). The foliar spray of LRM™ has a substantial effect over both transcriptomes potentially mediated by various compounds within LRM™, including its phytohormone content, activating systemic acquired resistance, possibly mediated by salicylic acid biosynthetic processes, and drought/heat acclimatization, induced by stomatal control and wax accumulation during cuticle development. Specifically, the agronomic improvements observed in treated S. lycopersicum (tomato) plants include an increase in the number of fruits, an acceleration in flowering time and the provision of higher drought resistance. The effect of LRM™ foliar spray in juvenile and adult plants was similar, producing a fast response detectable 2 h from its application that was also maintained 24 h later. CONCLUSION: The present study improves our knowledge on the transcriptomic effect of a novel microalgal extract on crops and provides the first step towards a full understanding of the yield and resistance improvement of crops. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.


Asunto(s)
Arabidopsis , Regulación de la Expresión Génica de las Plantas , Microalgas , Solanum lycopersicum , Transcriptoma , Arabidopsis/genética , Arabidopsis/metabolismo , Arabidopsis/crecimiento & desarrollo , Microalgas/metabolismo , Microalgas/genética , Microalgas/química , Solanum lycopersicum/genética , Solanum lycopersicum/metabolismo , Solanum lycopersicum/crecimiento & desarrollo , Solanum lycopersicum/química , Estrés Fisiológico , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Reguladores del Crecimiento de las Plantas/farmacología , Reguladores del Crecimiento de las Plantas/metabolismo , Fotosíntesis , Sequías
4.
Plant Cell ; 36(3): 559-584, 2024 Feb 26.
Artículo en Inglés | MEDLINE | ID: mdl-37971938

RESUMEN

Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because these subcellular structures lack a delineating membrane, determining their compositions is difficult. Here we describe a proximity-biotinylation approach for capturing the RNAs of the condensates known as processing bodies (PBs) in Arabidopsis (Arabidopsis thaliana). By combining this approach with RNA detection, in silico, and high-resolution imaging approaches, we studied PBs under normal conditions and heat stress. PBs showed a much more dynamic RNA composition than the total transcriptome. RNAs involved in cell wall development and regeneration, plant hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA-binding proteins and the liquidity of PBs modulated RNA recruitment, while RNAs were frequently recruited together with their encoded proteins. In PBs, RNAs follow distinct fates: in small liquid-like PBs, RNAs get degraded while in more solid-like larger ones, they are stored. PB properties can be regulated by the actin-polymerizing SCAR (suppressor of the cyclic AMP)-WAVE (WASP family verprolin homologous) complex. SCAR/WAVE modulates the shuttling of RNAs between PBs and the translational machinery, thereby adjusting ethylene signaling. In summary, we provide an approach to identify RNAs in condensates that allowed us to reveal a mechanism for regulating RNA fate.


Asunto(s)
Arabidopsis , ARN , Cuerpos de Procesamiento , Proteínas de Unión al ARN/genética , Proteínas de Unión al ARN/metabolismo , Respuesta al Choque Térmico , Arabidopsis/genética , Arabidopsis/metabolismo
5.
New Phytol ; 241(3): 1193-1209, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38009929

RESUMEN

The Arabidopsis thaliana transcription factor BRANCHED1 (BRC1) plays a pivotal role in the control of shoot branching as it integrates environmental and endogenous signals that influence axillary bud growth. Despite its remarkable activity as a growth inhibitor, the mechanisms by which BRC1 promotes bud dormancy are largely unknown. We determined the genome-wide BRC1 binding sites in vivo and combined these with transcriptomic data and gene co-expression analyses to identify bona fide BRC1 direct targets. Next, we integrated multi-omics data to infer the BRC1 gene regulatory network (GRN) and used graph theory techniques to find network motifs that control the GRN dynamics. We generated an open online tool to interrogate this network. A group of BRC1 target genes encoding transcription factors (BTFs) orchestrate this intricate transcriptional network enriched in abscisic acid-related components. Promoter::ß-GLUCURONIDASE transgenic lines confirmed that BTFs are expressed in axillary buds. Transient co-expression assays and studies in planta using mutant lines validated the role of BTFs in modulating the GRN and promoting bud dormancy. This knowledge provides access to the developmental mechanisms that regulate shoot branching and helps identify candidate genes to use as tools to adapt plant architecture and crop production to ever-changing environmental conditions.


Asunto(s)
Proteínas de Arabidopsis , Arabidopsis , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Redes Reguladoras de Genes , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Regiones Promotoras Genéticas , Regulación de la Expresión Génica de las Plantas , Brotes de la Planta/metabolismo
6.
Plant Cell ; 35(7): 2484-2503, 2023 06 26.
Artículo en Inglés | MEDLINE | ID: mdl-37070946

RESUMEN

Three-dimensional (3D) chromatin organization is highly dynamic during development and seems to play a crucial role in regulating gene expression. Self-interacting domains, commonly called topologically associating domains (TADs) or compartment domains (CDs), have been proposed as the basic structural units of chromatin organization. Surprisingly, although these units have been found in several plant species, they escaped detection in Arabidopsis (Arabidopsis thaliana). Here, we show that the Arabidopsis genome is partitioned into contiguous CDs with different epigenetic features, which are required to maintain appropriate intra-CD and long-range interactions. Consistent with this notion, the histone-modifying Polycomb group machinery is involved in 3D chromatin organization. Yet, while it is clear that Polycomb repressive complex 2 (PRC2)-mediated trimethylation of histone H3 on lysine 27 (H3K27me3) helps establish local and long-range chromatin interactions in plants, the implications of PRC1-mediated histone H2A monoubiquitination on lysine 121 (H2AK121ub) are unclear. We found that PRC1, together with PRC2, maintains intra-CD interactions, but it also hinders the formation of H3K4me3-enriched local chromatin loops when acting independently of PRC2. Moreover, the loss of PRC1 or PRC2 activity differentially affects long-range chromatin interactions, and these 3D changes differentially affect gene expression. Our results suggest that H2AK121ub helps prevent the formation of transposable element/H3K27me1-rich long loops and serves as a docking point for H3K27me3 incorporation.


Asunto(s)
Proteínas de Arabidopsis , Arabidopsis , Arabidopsis/genética , Arabidopsis/metabolismo , Histonas/genética , Histonas/metabolismo , Proteínas de Arabidopsis/metabolismo , Lisina/metabolismo , Proteínas del Grupo Polycomb/genética , Proteínas del Grupo Polycomb/metabolismo , Cromatina/genética , Cromatina/metabolismo , Complejo Represivo Polycomb 2/genética , Complejo Represivo Polycomb 2/metabolismo
7.
Front Plant Sci ; 13: 855243, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35599877

RESUMEN

The characterization of the molecular mechanisms, such as high light irradiance resistance, that allowed plant terrestralization is a cornerstone in evolutionary studies since the conquest of land by plants played a pivotal role in life evolution on Earth. Viridiplantae or the green lineage is divided into two clades, Chlorophyta and Streptophyta, that in turn splits into Embryophyta or land plants and Charophyta. Charophyta are used in evolutionary studies on plant terrestralization since they are generally accepted as the extant algal species most closely related to current land plants. In this study, we have chosen the facultative terrestrial early charophyte alga Klebsormidium nitens to perform an integrative transcriptomic and metabolomic analysis under high light in order to unveil key mechanisms involved in the early steps of plants terrestralization. We found a fast chloroplast retrograde signaling possibly mediated by reactive oxygen species and the inositol polyphosphate 1-phosphatase (SAL1) and 3'-phosphoadenosine-5'-phosphate (PAP) pathways inducing gene expression and accumulation of specific metabolites. Systems used by both Chlorophyta and Embryophyta were activated such as the xanthophyll cycle with an accumulation of zeaxanthin and protein folding and repair mechanisms constituted by NADPH-dependent thioredoxin reductases, thioredoxin-disulfide reductases, and peroxiredoxins. Similarly, cyclic electron flow, specifically the pathway dependent on proton gradient regulation 5, was strongly activated under high light. We detected a simultaneous co-activation of the non-photochemical quenching mechanisms based on LHC-like stress related (LHCSR) protein and the photosystem II subunit S that are specific to Chlorophyta and Embryophyta, respectively. Exclusive Embryophyta systems for the synthesis, sensing, and response to the phytohormone auxin were also activated under high light in K. nitens leading to an increase in auxin content with the concomitant accumulation of amino acids such as tryptophan, histidine, and phenylalanine.

8.
BMC Bioinformatics ; 23(1): 113, 2022 Mar 31.
Artículo en Inglés | MEDLINE | ID: mdl-35361110

RESUMEN

BACKGROUND: Microalgae are emerging as promising sustainable sources for biofuels, biostimulants in agriculture, soil bioremediation, feed and human nutrients. Nonetheless, the molecular mechanisms underpinning microalgae physiology and the biosynthesis of compounds of biotechnological interest are largely uncharacterized. This hinders the development of microalgae full potential as cell-factories. The recent application of omics technologies into microalgae research aims at unraveling these systems. Nevertheless, the lack of specific tools for analysing omics raw data generated from microalgae to provide biological meaningful information are hampering the impact of these technologies. The purpose of ALGAEFUN with MARACAS consists in providing researchers in microalgae with an enabling tool that will allow them to exploit transcriptomic and cistromic high-throughput sequencing data. RESULTS: ALGAEFUN with MARACAS consists of two different tools. First, MARACAS (MicroAlgae RnA-seq and Chip-seq AnalysiS) implements a fully automatic computational pipeline receiving as input RNA-seq (RNA sequencing) or ChIP-seq (chromatin immunoprecipitation sequencing) raw data from microalgae studies. MARACAS generates sets of differentially expressed genes or lists of genomic loci for RNA-seq and ChIP-seq analysis respectively. Second, ALGAEFUN (microALGAE FUNctional enrichment tool) is a web-based application where gene sets generated from RNA-seq analysis as well as lists of genomic loci from ChIP-seq analysis can be used as input. On the one hand, it can be used to perform Gene Ontology and biological pathways enrichment analysis over gene sets. On the other hand, using the results of ChIP-seq data analysis, it identifies a set of potential target genes and analyses the distribution of the loci over gene features. Graphical representation of the results as well as tables with gene annotations are generated and can be downloaded for further analysis. CONCLUSIONS: ALGAEFUN with MARACAS provides an integrated environment for the microalgae research community that facilitates the process of obtaining relevant biological information from raw RNA-seq and ChIP-seq data. These applications are designed to assist researchers in the interpretation of gene lists and genomic loci based on functional enrichment analysis. ALGAEFUN with MARACAS is publicly available on https://greennetwork.us.es/AlgaeFUN/ .


Asunto(s)
Secuenciación de Inmunoprecipitación de Cromatina , Microalgas , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos , Microalgas/genética , RNA-Seq , Análisis de Secuencia de ARN/métodos
9.
Plant Physiol ; 187(1): 88-102, 2021 09 04.
Artículo en Inglés | MEDLINE | ID: mdl-34618130

RESUMEN

In chloroplasts, thiol-dependent redox regulation is linked to light since the disulfide reductase activity of thioredoxins (Trxs) relies on photo-reduced ferredoxin (Fdx). Furthermore, chloroplasts harbor an NADPH-dependent Trx reductase (NTR) with a joint Trx domain, termed NTRC. The activity of these two redox systems is integrated by the redox balance of 2-Cys peroxiredoxin (Prx), which is controlled by NTRC. However, NTRC was proposed to participate in redox regulation of additional targets, prompting inquiry into whether the function of NTRC depends on its capacity to maintain the redox balance of 2-Cys Prxs or by direct redox interaction with chloroplast enzymes. To answer this, we studied the functional relationship of NTRC and 2-Cys Prxs by a comparative analysis of the triple Arabidopsis (Arabidopsis thaliana) mutant, ntrc-2cpab, which lacks NTRC and 2-Cys Prxs, and the double mutant 2cpab, which lacks 2-Cys Prxs. These mutants exhibit almost indistinguishable phenotypes: in growth rate, photosynthesis performance, and redox regulation of chloroplast enzymes in response to light and darkness. These results suggest that the most relevant function of NTRC is in controlling the redox balance of 2-Cys Prxs. A comparative transcriptomics analysis confirmed the phenotypic similarity of the two mutants and suggested that the NTRC-2-Cys Prxs system participates in cytosolic protein quality control. We propose that NTRC and 2-Cys Prxs constitute a redox relay, exclusive to photosynthetic organisms that fine-tunes the redox state of chloroplast enzymes in response to light and affects transduction pathways towards the cytosol.


Asunto(s)
Cloroplastos/metabolismo , Citoplasma/metabolismo , Luz , Arabidopsis , Proteínas de Arabidopsis , Cloroplastos/efectos de la radiación , Oscuridad , Oxidación-Reducción/efectos de la radiación
10.
Nucleic Acids Res ; 49(15): 8757-8776, 2021 09 07.
Artículo en Inglés | MEDLINE | ID: mdl-34379789

RESUMEN

As compared to eukaryotes, bacteria have a reduced tRNA gene set encoding between 30 and 220 tRNAs. Although in most bacterial phyla tRNA genes are dispersed in the genome, many species from distinct phyla also show genes forming arrays. Here, we show that two types of arrays with distinct evolutionary origins exist. This work focuses on long tRNA gene arrays (L-arrays) that encompass up to 43 genes, which disseminate by horizontal gene transfer and contribute supernumerary tRNA genes to the host. Although in the few cases previously studied these arrays were reported to be poorly transcribed, here we show that the L-array of the model cyanobacterium Anabaena sp. PCC 7120, encoding 23 functional tRNAs, is largely induced upon impairment of the translation machinery. The cellular response to this challenge involves a global reprogramming of the transcriptome in two phases. tRNAs encoded in the array are induced in the second phase of the response, directly contributing to cell survival. Results presented here show that in some bacteria the tRNA gene set may be partitioned between a housekeeping subset, which constantly sustains translation, and an inducible subset that is generally silent but can provide functionality under particular conditions.


Asunto(s)
Genes Bacterianos , Operón , Biosíntesis de Proteínas , ARN de Transferencia/genética , Estrés Fisiológico/genética , Anabaena/genética , Antibacterianos/farmacología , Regulación Bacteriana de la Expresión Génica , Genoma Bacteriano , Viabilidad Microbiana/genética , ARN de Transferencia/metabolismo , Secuencias Reguladoras de Ácidos Nucleicos
11.
Bioresour Technol ; 332: 125150, 2021 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-33878543

RESUMEN

Astaxanthin is a valuable and highly demanded ketocarotenoid pigment, for which the chlorophycean microalga Haematococcus pluvialis is an outstanding natural source. Although information on astaxanthin accumulation in H. pluvialis has substantially advanced in recent years, its underlying molecular bases remain elusive. An integrative metabolic and transcriptomic analysis has been performed for vegetative Haematococcus cells, grown both under N sufficiency (green palmelloid cells) and under moderate N limitation, allowing concurrent active cell growth and astaxanthin synthesis (reddish palmelloid cells). Transcriptional activation was noticeable in reddish cells of key enzymes participating in glycolysis, pentose phosphate cycle and pyruvate metabolism, determining the adequate provision of glyceraldehyde 3 phosphate and pyruvate, precursors of carotenoids and fatty acids. Moreover, for the first time, transcriptional regulators potentially involved in controlling astaxanthin accumulation have been identified, a knowledge enabling optimization of commercial astaxanthin production by Haematococcus through systems metabolic engineering.


Asunto(s)
Chlorophyceae , Chlorophyta , Chlorophyta/genética , Transcriptoma , Xantófilas
12.
Front Plant Sci ; 12: 633979, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33692818

RESUMEN

Anthocyanins are the primary pigments contributing to the variety of flower colors among angiosperms and are considered essential for survival and reproduction. Anthocyanins are members of the flavonoids, a broader class of secondary metabolites, of which there are numerous structural genes and regulators thereof. In western European populations of Lysimachia arvensis, there are blue- and orange-petaled individuals. The proportion of blue-flowered plants increases with temperature and daylength yet decreases with precipitation. Here, we performed a transcriptome analysis to characterize the coding sequences of a large group of flavonoid biosynthetic genes, examine their expression and compare our results to flavonoid biochemical analysis for blue and orange petals. Among a set of 140 structural and regulatory genes broadly representing the flavonoid biosynthetic pathway, we found 39 genes with significant differential expression including some that have previously been reported to be involved in similar flower color transitions. In particular, F3'5'H and DFR, two genes at a critical branchpoint in the ABP for determining flower color, showed differential expression. The expression results were complemented by careful examination of the SNPs that differentiate the two color types for these two critical genes. The decreased expression of F3'5'H in orange petals and differential expression of two distinct copies of DFR, which also exhibit amino acid changes in the color-determining substrate specificity region, strongly correlate with the blue to orange transition. Our biochemical analysis was consistent with the transcriptome data indicating that the shift from blue to orange petals is caused by a change from primarily malvidin to largely pelargonidin forms of anthocyanins. Overall, we have identified several flavonoid biosynthetic pathway loci likely involved in the shift in flower color in L. arvensis and even more loci that may represent the complex network of genetic and physiological consequences of this flower color polymorphism.

13.
Nat Commun ; 12(1): 315, 2021 01 12.
Artículo en Inglés | MEDLINE | ID: mdl-33436613

RESUMEN

Although it is well established that the Polycomb Group (PcG) complexes maintain gene repression through the incorporation of H2AK121ub and H3K27me3, little is known about the effect of these modifications on chromatin accessibility, which is fundamental to understand PcG function. Here, by integrating chromatin accessibility, histone marks and expression analyses in different Arabidopsis PcG mutants, we show that PcG function regulates chromatin accessibility. We find that H2AK121ub is associated with a less accessible but still permissive chromatin at transcriptional regulation hotspots. Accessibility is further reduced by EMF1 acting in collaboration with PRC2 activity. Consequently, H2AK121ub/H3K27me3 marks are linked to inaccessible although responsive chromatin. In contrast, only-H3K27me3-marked chromatin is less responsive, indicating that H2AK121ub-marked hotspots are required for transcriptional responses. Nevertheless, despite the loss of PcG activities leads to increased chromatin accessibility, this is not necessarily accompanied by transcriptional activation, indicating that accessible chromatin is not always predictive of gene expression.


Asunto(s)
Proteínas de Arabidopsis/metabolismo , Arabidopsis/genética , Cromatina/metabolismo , Regulación de la Expresión Génica de las Plantas , Transcripción Genética , Proteínas de Arabidopsis/genética , Modelos Genéticos , Mutación/genética , Proteínas del Grupo Polycomb/metabolismo , Análisis de Componente Principal , Plantones/metabolismo , Ubiquitina/metabolismo , Ubiquitinación
14.
BMC Genomics ; 20(1): 67, 2019 Jan 21.
Artículo en Inglés | MEDLINE | ID: mdl-30665350

RESUMEN

BACKGROUND: The orange pigmentation of the agar cultures of many Fusarium species is due to the production of carotenoids, terpenoid pigments whose synthesis is stimulated by light. The genes of the carotenoid pathway and their regulation have been investigated in detail in Fusarium fujikuroi. In this and other Fusarium species, such as F. oxysporum, deep-pigmented mutants affected in the gene carS, which encodes a protein of the RING-finger family, overproduce carotenoids irrespective of light. The induction of carotenogenesis by light and its deregulation in carS mutants are achieved on the transcription of the structural genes of the pathway. We have carried out global RNA-seq transcriptomics analyses to investigate the relationship between the regulatory role of CarS and the control by light in these fungi. RESULTS: The absence of a functional carS gene or the illumination exert wide effects on the transcriptome of F. fujikuroi, with predominance of genes activated over repressed and a greater functional diversity in the case of genes induced by light. The number of the latter decreases drastically in a carS mutant (1.1% vs. 4.8% in the wild-type), indicating that the deregulation produced by the carS mutation affects the light response of many genes. Moreover, approximately 27% of the genes activated at least 2-fold by light or by the carS mutation are coincident, raising to 40% for an 8-fold activation threshold. As expected, the genes with the highest changes under both regulatory conditions include those involved in carotenoid metabolism. In addition, light and CarS strongly influence the expression of some genes associated with stress responses, including three genes with catalase domains, consistent with roles in the control of oxidative stress. The effects of the CarS mutation or light in the transcriptome of F. oxysporum were partially coincident with those of F. fujikuroi, indicating the conservation of the objectives of their regulatory mechanisms. CONCLUSIONS: The CarS RING finger protein down-regulates many genes whose expression is up-regulated by light in wild strains of the two investigated Fusarium species, indicating a regulatory interplay between the mechanism of action of the CarS protein and the control by light.


Asunto(s)
Proteínas Fúngicas/fisiología , Fusarium/genética , Regulación Fúngica de la Expresión Génica/efectos de la radiación , Luz , Proteínas Fúngicas/genética , Fusarium/metabolismo , Fusarium/efectos de la radiación , Perfilación de la Expresión Génica , Mutación , Activación Transcripcional , Transcriptoma/efectos de la radiación
15.
Front Plant Sci ; 8: 1217, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28751903

RESUMEN

Daily rhythms play a key role in transcriptome regulation in plants and microalgae orchestrating responses that, among other processes, anticipate light transitions that are essential for their metabolism and development. The recent accumulation of genome-wide transcriptomic data generated under alternating light:dark periods from plants and microalgae has made possible integrative and comparative analysis that could contribute to shed light on the evolution of daily rhythms in the green lineage. In this work, RNA-seq and microarray data generated over 24 h periods in different light regimes from the eudicot Arabidopsis thaliana and the microalgae Chlamydomonas reinhardtii and Ostreococcus tauri have been integrated and analyzed using gene co-expression networks. This analysis revealed a reduction in the size of the daily rhythmic transcriptome from around 90% in Ostreococcus, being heavily influenced by light transitions, to around 40% in Arabidopsis, where a certain independence from light transitions can be observed. A novel Multiple Bidirectional Best Hit (MBBH) algorithm was applied to associate single genes with a family of potential orthologues from evolutionary distant species. Gene duplication, amplification and divergence of rhythmic expression profiles seems to have played a central role in the evolution of gene families in the green lineage such as Pseudo Response Regulators (PRRs), CONSTANS-Likes (COLs), and DNA-binding with One Finger (DOFs). Gene clustering and functional enrichment have been used to identify groups of genes with similar rhythmic gene expression patterns. The comparison of gene clusters between species based on potential orthologous relationships has unveiled a low to moderate level of conservation of daily rhythmic expression patterns. However, a strikingly high conservation was found for the gene clusters exhibiting their highest and/or lowest expression value during the light transitions.

16.
Front Plant Sci ; 8: 626, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28487716

RESUMEN

DELLA proteins are transcriptional regulators present in all land plants which have been shown to modulate the activity of over 100 transcription factors in Arabidopsis, involved in multiple physiological and developmental processes. It has been proposed that DELLAs transduce environmental information to pre-wired transcriptional circuits because their stability is regulated by gibberellins (GAs), whose homeostasis largely depends on environmental signals. The ability of GAs to promote DELLA degradation coincides with the origin of vascular plants, but the presence of DELLAs in other land plants poses at least two questions: what regulatory properties have DELLAs provided to the behavior of transcriptional networks in land plants, and how has the recruitment of DELLAs by GA signaling affected this regulation. To address these issues, we have constructed gene co-expression networks of four different organisms within the green lineage with different properties regarding DELLAs: Arabidopsis thaliana and Solanum lycopersicum (both with GA-regulated DELLA proteins), Physcomitrella patens (with GA-independent DELLA proteins) and Chlamydomonas reinhardtii (a green alga without DELLA), and we have examined the relative evolution of the subnetworks containing the potential DELLA-dependent transcriptomes. Network analysis indicates a relative increase in parameters associated with the degree of interconnectivity in the DELLA-associated subnetworks of land plants, with a stronger effect in species with GA-regulated DELLA proteins. These results suggest that DELLAs may have played a role in the coordination of multiple transcriptional programs along evolution, and the function of DELLAs as regulatory 'hubs' became further consolidated after their recruitment by GA signaling in higher plants.

17.
Genome Biol ; 18(1): 69, 2017 04 12.
Artículo en Inglés | MEDLINE | ID: mdl-28403905

RESUMEN

BACKGROUND: Polycomb group complexes PRC1 and PRC2 repress gene expression at the chromatin level in eukaryotes. The classic recruitment model of Polycomb group complexes in which PRC2-mediated H3K27 trimethylation recruits PRC1 for H2A monoubiquitination was recently challenged by data showing that PRC1 activity can also recruit PRC2. However, the prevalence of these two mechanisms is unknown, especially in plants as H2AK121ub marks were examined at only a handful of Polycomb group targets. RESULTS: By using genome-wide analyses, we show that H2AK121ub marks are surprisingly widespread in Arabidopsis thaliana, often co-localizing with H3K27me3 but also occupying a set of transcriptionally active genes devoid of H3K27me3. Furthermore, by profiling H2AK121ub and H3K27me3 marks in atbmi1a/b/c, clf/swn, and lhp1 mutants we found that PRC2 activity is not required for H2AK121ub marking at most genes. In contrast, loss of AtBMI1 function impacts the incorporation of H3K27me3 marks at most Polycomb group targets. CONCLUSIONS: Our findings show the relationship between H2AK121ub and H3K27me3 marks across the A. thaliana genome and unveil that ubiquitination by PRC1 is largely independent of PRC2 activity in plants, while the inverse is true for H3K27 trimethylation.


Asunto(s)
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Histonas/metabolismo , Proteínas Represoras/metabolismo , Factores de Transcripción/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Cromatina/metabolismo , Regulación de la Expresión Génica de las Plantas , Genes de Plantas , Glucosiltransferasas/genética , Glucosiltransferasas/metabolismo , Histonas/genética , Mutación , Complejo Represivo Polycomb 1/genética , Complejo Represivo Polycomb 2 , Proteínas del Grupo Polycomb/genética , Proteínas del Grupo Polycomb/metabolismo , Proteínas Represoras/genética , Factores de Transcripción/genética , Ubiquitinación
18.
Curr Opin Plant Biol ; 37: 10-17, 2017 06.
Artículo en Inglés | MEDLINE | ID: mdl-28391047

RESUMEN

Measuring day length confers a strong fitness improvement to photosynthetic organisms as it allows them to anticipate light phases and take the best decisions preceding diurnal transitions. In close association with signals from the circadian clock and the photoreceptors, photoperiodic sensing constitutes also a precise way to determine the passing of the seasons and to take annual decisions such as the best time to flower or the beginning of dormancy. Photoperiodic sensing in photosynthetic organisms is ancient and two major stages in its evolution could be identified, the cyanobacterial time sensing and the evolutionary tool kit that arose in green algae and developed into the photoperiodic system of modern plants. The most recent discoveries about the evolution of the perception of light, measurement of day length and relationship with the circadian clock along the evolution of the eukaryotic green lineage will be discussed in this review.


Asunto(s)
Cianobacterias/metabolismo , Fotoperiodo , Plantas/metabolismo , Chlorophyta/metabolismo , Chlorophyta/efectos de la radiación , Cianobacterias/efectos de la radiación , Luz , Plantas/efectos de la radiación
19.
Plant Physiol ; 173(1): 627-641, 2017 01.
Artículo en Inglés | MEDLINE | ID: mdl-27837089

RESUMEN

Polycomb Group regulation in Arabidopsis (Arabidopsis thaliana) is required to maintain cell differentiation and allow developmental phase transitions. This is achieved by the activity of three PcG repressive complex 2s (PRC2s) and the participation of a yet poorly defined PRC1. Previous results showed that apparent PRC1 components perform discrete roles during plant development, suggesting the existence of PRC1 variants; however, it is not clear in how many processes these components participate. We show that AtBMI1 proteins are required to promote all developmental phase transitions and to control cell proliferation during organ growth and development, expanding their proposed range of action. While AtBMI1 function during germination is closely linked to B3 domain transcription factors VAL1/2 possibly in combination with GT-box binding factors, other AtBMI1 regulatory networks require participation of different factor combinations. Conversely, EMF1 and LHP1 bind many H3K27me3 positive genes up-regulated in atbmi1a/b/c mutants; however, loss of their function affects expression of a different subset, suggesting that even if EMF1, LHP1, and AtBMI1 exist in a common PRC1 variant, their role in repression depends on the functional context.


Asunto(s)
Proteínas de Arabidopsis/genética , Arabidopsis/crecimiento & desarrollo , Arabidopsis/genética , Redes Reguladoras de Genes , Complejo Represivo Polycomb 1/genética , Proteínas de Arabidopsis/metabolismo , Proliferación Celular/genética , Endospermo/genética , Endospermo/crecimiento & desarrollo , Regulación de la Expresión Génica de las Plantas , Genoma de Planta , Glucosiltransferasas/genética , Glucosiltransferasas/metabolismo , Lisina/metabolismo , Meristema/genética , Complejos Multiproteicos , Mutación , Latencia en las Plantas/genética , Raíces de Plantas/genética , Raíces de Plantas/crecimiento & desarrollo , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
20.
Eur J Protistol ; 55(Pt A): 95-101, 2016 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-27062304

RESUMEN

Photosynthetic protists, also called microalgae, have been systematically studied for more than a century. However, only recently broad biotechnological applications have fostered a novel wave of research on their potentialities as sustainable resources of renewable energy as well as valuable industrial and agro-food products. At the recent VII European Congress of Protistology held in Seville, three outstanding examples of different research strategies on microalgae with biotechnological implications were presented, which suggested that integrative approaches will produce very significant advances in this field in the next future. In any case, intense research and the application of systems biology and genetic engineering techniques are absolutely essential to reach the full potential of microalgae as cell-factories of bio-based products and, therefore, could contribute significantly to solve the problems of biosustainability and energy shortage.


Asunto(s)
Biotecnología/tendencias , Microalgas/fisiología , Ingeniería Genética , Investigación/tendencias , Biología de Sistemas
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