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1.
Nature ; 546(7656): 148-152, 2017 06 01.
Artículo en Inglés | MEDLINE | ID: mdl-28538728

RESUMEN

The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences and required single-molecule real-time sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade and a sunflower-specific whole-genome duplication around 29 million years ago. An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs.


Asunto(s)
Evolución Molecular , Flores/genética , Flores/fisiología , Genoma de Planta/genética , Helianthus/genética , Helianthus/metabolismo , Aceites de Plantas/metabolismo , Aclimatación/genética , Duplicación de Gen/genética , Regulación de la Expresión Génica de las Plantas , Variación Genética , Genómica , Helianthus/clasificación , Análisis de Secuencia de ADN , Estrés Fisiológico/genética , Aceite de Girasol , Transcriptoma/genética
2.
Mol Plant Microbe Interact ; 29(3): 170-80, 2016 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-26894282

RESUMEN

Endosymbiosis interactions allow plants to grow in nutrient-deficient soil environments. The arbuscular mycorrhizal (AM) symbiosis is an ancestral interaction between land plants and fungi, whereas nitrogen-fixing symbioses are highly specific for certain plants, notably major crop legumes. The signaling pathways triggered by specific lipochitooligosaccharide molecules involved in these interactions have common components that also overlap with plant root development. These pathways include receptor-like kinases, transcription factors (TFs), and various intermediate signaling effectors, including noncoding (nc)RNAs. These latter molecules have emerged as major regulators of gene expression and small ncRNAs, composed of micro (mi)RNAs and small interfering (si)RNAs, are known to control gene expression at transcriptional (chromatin) or posttranscriptional levels. In this review, we describe exciting recent data connecting variants of conserved si/miRNAs with the regulation of TFs, such as NSP2, NFY-A1, auxin-response factors, and AP2-like proteins, known to be involved in symbiosis. The link between hormonal regulations and these si- and miRNA-TF nodes is proposed in a model in which different feedback loops or regulations controlling endosymbiosis signaling are integrated. The diversity and emerging regulatory networks of young legume miRNAs are also highlighted.


Asunto(s)
Micorrizas/fisiología , Raíces de Plantas/microbiología , ARN de Hongos/metabolismo , ARN no Traducido/metabolismo , Fijación del Nitrógeno/fisiología , ARN de Hongos/genética , ARN no Traducido/genética , Simbiosis
3.
Plant J ; 74(6): 920-34, 2013 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-23566016

RESUMEN

The root system is crucial for acquisition of resources from the soil. In legumes, the efficiency of mineral and water uptake by the roots may be reinforced due to establishment of symbiotic relationships with mycorrhizal fungi and interactions with soil rhizobia. Here, we investigated the role of miR396 in regulating the architecture of the root system and in symbiotic interactions in the model legume Medicago truncatula. Analyses with promoter-GUS fusions suggested that the mtr-miR396a and miR396b genes are highly expressed in root tips, preferentially in the transition zone, and display distinct expression profiles during lateral root and nodule development. Transgenic roots of composite plants that over-express the miR396b precursor showed lower expression of six growth-regulating factor genes (MtGRF) and two bHLH79-like target genes, as well as reduced growth and mycorrhizal associations. miR396 inactivation by mimicry caused contrasting tendencies, with increased target expression, higher root biomass and more efficient colonization by arbuscular mycorrhizal fungi. In contrast to MtbHLH79, repression of three GRF targets by RNA interference severely impaired root growth. Early activation of mtr-miR396b, concomitant with post-transcriptional repression of MtGRF5 expression, was also observed in response to exogenous brassinosteroids. Growth limitation in miR396 over-expressing roots correlated with a reduction in cell-cycle gene expression and the number of dividing cells in the root apical meristem. These results link the miR396 network to the regulation of root growth and mycorrhizal associations in plants.


Asunto(s)
Regulación de la Expresión Génica de las Plantas , Medicago truncatula/fisiología , MicroARNs/genética , Micorrizas/fisiología , Proteínas de Plantas/metabolismo , Biomasa , Proliferación Celular , Biología Computacional , Hongos/fisiología , Expresión Génica , Genes Reporteros , Medicago truncatula/citología , Medicago truncatula/genética , Medicago truncatula/crecimiento & desarrollo , Meristema/citología , Meristema/genética , Meristema/crecimiento & desarrollo , Meristema/fisiología , Micorrizas/citología , Micorrizas/genética , Micorrizas/crecimiento & desarrollo , Proteínas de Plantas/genética , Nodulación de la Raíz de la Planta , Raíces de Plantas/citología , Raíces de Plantas/genética , Raíces de Plantas/crecimiento & desarrollo , Raíces de Plantas/fisiología , Plantas Modificadas Genéticamente , Regiones Promotoras Genéticas/genética , Interferencia de ARN , Alineación de Secuencia , Sinorhizobium meliloti/fisiología , Simbiosis , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
4.
Plant Biotechnol J ; 12(9): 1308-18, 2014 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-25060922

RESUMEN

RNA-dependent RNA polymerase 6 (RDR6) and suppressor of gene silencing 3 (SGS3) act together in post-transcriptional transgene silencing mediated by small interfering RNAs (siRNAs) and in biogenesis of various endogenous siRNAs including the tasiARFs, known regulators of auxin responses and plant development. Legumes, the third major crop family worldwide, has been widely improved through transgenic approaches. Here, we isolated rdr6 and sgs3 mutants in the model legume Medicago truncatula. Two sgs3 and one rdr6 alleles led to strong developmental defects and impaired biogenesis of tasiARFs. In contrast, the rdr6.1 homozygous plants produced sufficient amounts of tasiARFs to ensure proper development. High throughput sequencing of small RNAs from this specific mutant identified 354 potential MtRDR6 substrates, for which siRNA production was significantly reduced in the mutant. Among them, we found a large variety of novel phased loci corresponding to protein-encoding genes or transposable elements. Interestingly, measurement of GFP expression revealed that post-transcriptional transgene silencing was reduced in rdr6.1 roots. Hence, this novel mis-sense mutation, affecting a highly conserved amino acid residue in plant RDR6s, may be an interesting tool both to analyse endogenous pha-siRNA functions and to improve transgene expression, at least in legume species.


Asunto(s)
Alelos , Silenciador del Gen , Medicago truncatula/genética , Desarrollo de la Planta/genética , ARN Interferente Pequeño/biosíntesis , ARN Polimerasa Dependiente del ARN/genética , Transgenes/genética , Sitios Genéticos , Medicago truncatula/crecimiento & desarrollo , Mutación/genética , Fenotipo , Proteínas de Plantas/genética , Transcripción Genética
5.
New Phytol ; 202(4): 1197-1211, 2014 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-24533947

RESUMEN

In plants, roots are essential for water and nutrient acquisition. MicroRNAs (miRNAs) regulate their target mRNAs by transcript cleavage and/or inhibition of protein translation and are known as major post-transcriptional regulators of various developmental pathways and stress responses. In Arabidopsis thaliana, four isoforms of miR169 are encoded by 14 different genes and target diverse mRNAs, encoding subunits A of the NF-Y transcription factor complex. These miRNA isoforms and their targets have previously been linked to nutrient signalling in plants. By using mimicry constructs against different isoforms of miR169 and miR-resistant versions of NF-YA genes we analysed the role of specific miR169 isoforms in root growth and branching. We identified a regulatory node involving the particular miR169defg isoform and NF-YA2 and NF-YA10 genes that acts in the control of primary root growth. The specific expression of MIM169defg constructs altered specific cell type numbers and dimensions in the root meristem. Preventing miR169defg-regulation of NF-YA2 indirectly affected laterial root initiation. We also showed that the miR169defg isoform affects NF-YA2 transcripts both at mRNA stability and translation levels. We propose that a specific miR169 isoform and the NF-YA2 target control root architecture in Arabidopsis.


Asunto(s)
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Factor de Unión a CCAAT/genética , Regulación de la Expresión Génica de las Plantas , MicroARNs/genética , Arabidopsis/citología , Arabidopsis/crecimiento & desarrollo , Proteínas de Arabidopsis/metabolismo , Factor de Unión a CCAAT/metabolismo , Expresión Génica , Genes Reporteros , Meristema/citología , Meristema/genética , Meristema/crecimiento & desarrollo , MicroARNs/metabolismo , Fenotipo , Raíces de Plantas/citología , Raíces de Plantas/genética , Raíces de Plantas/crecimiento & desarrollo , Plantas Modificadas Genéticamente , Isoformas de ARN , ARN de Planta/genética , ARN de Planta/metabolismo
6.
Plant J ; 72(3): 512-22, 2012 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-22775306

RESUMEN

Most land plants live symbiotically with arbuscular mycorrhizal fungi. Establishment of this symbiosis requires signals produced by both partners: strigolactones in root exudates stimulate pre-symbiotic growth of the fungus, which releases lipochito-oligosaccharides (Myc-LCOs) that prepare the plant for symbiosis. Here, we have investigated the events downstream of this early signaling in the roots. We report that expression of miR171h, a microRNA that targets NSP2, is up-regulated in the elongation zone of the root during colonization by Rhizophagus irregularis (formerly Glomus intraradices) and in response to Myc-LCOs. Fungal colonization was much reduced by over-expressing miR171h in roots, mimicking the phenotype of nsp2 mutants. Conversely, in plants expressing an NSP2 mRNA resistant to miR171h cleavage, fungal colonization was much increased and extended into the elongation zone of the roots. Finally, phylogenetic analyses revealed that miR171h regulation of NSP2 is probably conserved among mycotrophic plants. Our findings suggest a regulatory mechanism, triggered by Myc-LCOs, that prevents over-colonization of roots by arbuscular mycorrhizal fungi by a mechanism involving miRNA-mediated negative regulation of NSP2.


Asunto(s)
Glomeromycota/fisiología , Lipopolisacáridos/metabolismo , Medicago truncatula/genética , MicroARNs/genética , Micorrizas/fisiología , Factores de Transcripción/genética , Sitios de Unión , Expresión Génica , Regulación de la Expresión Génica de las Plantas , Glomeromycota/citología , Glomeromycota/genética , Glomeromycota/crecimiento & desarrollo , Lactonas/metabolismo , Medicago truncatula/citología , Medicago truncatula/microbiología , Medicago truncatula/fisiología , MicroARNs/metabolismo , Micorrizas/citología , Micorrizas/genética , Micorrizas/crecimiento & desarrollo , Fenotipo , Filogenia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Raíces de Plantas/genética , Raíces de Plantas/metabolismo , Raíces de Plantas/microbiología , ARN de Planta/genética , ARN de Planta/metabolismo , Transducción de Señal , Simbiosis , Factores de Transcripción/metabolismo , Regulación hacia Arriba
7.
Plant Cell ; 21(9): 2780-96, 2009 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-19767456

RESUMEN

Posttranscriptional regulation of a variety of mRNAs by small 21- to 24-nucleotide RNAs, notably the microRNAs (miRNAs), is emerging as a novel developmental mechanism. In legumes like the model Medicago truncatula, roots are able to develop a de novo meristem through the symbiotic interaction with nitrogen-fixing rhizobia. We used deep sequencing of small RNAs from root apexes and nodules of M. truncatula to identify 100 novel candidate miRNAs encoded by 265 hairpin precursors. New atypical precursor classes producing only specific 21- and 24-nucleotide small RNAs were found. Statistical analysis on sequencing reads abundance revealed specific miRNA isoforms in a same family showing contrasting expression patterns between nodules and root apexes. The differentially expressed conserved and nonconserved miRNAs may target a large variety of mRNAs. In root nodules, which show diverse cell types ranging from a persistent meristem to a fully differentiated central region, we discovered miRNAs spatially enriched in nodule meristematic tissues, vascular bundles, and bacterial infection zones using in situ hybridization. Spatial regulation of miRNAs may determine specialization of regulatory RNA networks in plant differentiation processes, such as root nodule formation.


Asunto(s)
Genoma de Planta , Medicago truncatula/genética , MicroARNs/genética , ARN de Planta/genética , Nódulos de las Raíces de las Plantas/genética , Mapeo Cromosómico , Hibridación Genómica Comparativa , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Meristema/genética , Raíces de Plantas/genética , Procesamiento Postranscripcional del ARN , Análisis de Secuencia de ARN
8.
Plant Mol Biol ; 77(1-2): 47-58, 2011 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-21607657

RESUMEN

MicroRNAs (miRNAs) are post-transcriptional regulators of growth and development in both plants and animals. In plants, roots play essential roles in their anchorage to the soil as well as in nutrient and water uptake. In this review, we present recent advances made in the identification of miRNAs involved in embryonic root development, radial patterning, vascular tissue differentiation and formation of lateral organs (i.e., lateral and adventitious roots and symbiotic nitrogen-fixing nodules in legumes). Certain mi/siRNAs target members of the Auxin Response Factors family involved in auxin homeostasis and signalling and participate in complex regulatory loops at several crucial stages of root development. Other miRNAs target and restrict the action of various transcription factors that control root-related processes in several species. Finally, because abiotic stresses, which include nutrient or water deficiencies, generally modulate root growth and branching, we summarise the action of certain miRNAs in response to these stresses that may be involved in the adaptation of the root system architecture to the soil environment.


Asunto(s)
MicroARNs/fisiología , Raíces de Plantas/genética , ARN de Planta/fisiología , Diferenciación Celular , Homeostasis , Ácidos Indolacéticos/metabolismo , Fijación del Nitrógeno , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Proteínas de Plantas/fisiología , Nodulación de la Raíz de la Planta/genética , Raíces de Plantas/crecimiento & desarrollo , Plantones/genética , Plantones/crecimiento & desarrollo , Transducción de Señal
9.
New Phytol ; 191(3): 647-661, 2011 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-21770944

RESUMEN

• Legume roots develop two types of lateral organs, lateral roots and nodules. Nodules develop as a result of a symbiotic interaction with rhizobia and provide a niche for the bacteria to fix atmospheric nitrogen for the plant. • The Arabidopsis NAC1 transcription factor is involved in lateral root formation, and is regulated post-transcriptionally by miRNA164 and by SINAT5-dependent ubiquitination. We analyzed in Medicago truncatula the role of the closest NAC1 homolog in lateral root formation and in nodulation. • MtNAC1 shows a different expression pattern in response to auxin than its Arabidopsis homolog and no changes in lateral root number or nodulation were observed in plants affected in MtNAC1 expression. In addition, no interaction was found with SINA E3 ligases, suggesting that post-translational regulation of MtNAC1 does not occur in M. truncatula. Similar to what was found in Arabidopsis, a conserved miR164 target site was retrieved in MtNAC1, which reduced protein accumulation of a GFP-miR164 sensor. Furthermore, miR164 and MtNAC1 show an overlapping expression pattern in symbiotic nodules, and overexpression of this miRNA led to a reduction in nodule number. • This work suggests that regulatory pathways controlling a conserved transcription factor are complex and divergent between M. truncatula and Arabidopsis.


Asunto(s)
Medicago truncatula/fisiología , Proteínas de Plantas/metabolismo , Sinorhizobium meliloti/fisiología , Factores de Transcripción/metabolismo , Secuencia de Aminoácidos , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Secuencia de Bases , Flores/efectos de los fármacos , Flores/genética , Flores/fisiología , Regulación de la Expresión Génica de las Plantas , Ácidos Indolacéticos/farmacología , Medicago truncatula/efectos de los fármacos , Medicago truncatula/genética , MicroARNs/genética , Datos de Secuencia Molecular , Mutación , Filogenia , Hojas de la Planta/efectos de los fármacos , Hojas de la Planta/genética , Hojas de la Planta/fisiología , Proteínas de Plantas/química , Proteínas de Plantas/genética , Nodulación de la Raíz de la Planta/genética , Raíces de Plantas/efectos de los fármacos , Raíces de Plantas/genética , Raíces de Plantas/fisiología , Brotes de la Planta/efectos de los fármacos , Brotes de la Planta/genética , Brotes de la Planta/fisiología , Plantas Modificadas Genéticamente/efectos de los fármacos , Plantas Modificadas Genéticamente/genética , Plantas Modificadas Genéticamente/fisiología , Estructura Terciaria de Proteína , ARN de Planta/genética , Proteínas Recombinantes de Fusión , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Nicotiana/genética , Nicotiana/metabolismo , Transactivadores/genética , Transactivadores/metabolismo , Factores de Transcripción/química , Factores de Transcripción/genética
10.
Methods Mol Biol ; 1822: 205-239, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-30043307

RESUMEN

This decade introduced "omics" approaches, such as genomics, transcriptomics, proteomics, and metabolomics in association with reverse and forward genetic approaches, developed earlier, to try to identify molecular pathways involved in the development or in the response to environmental conditions as well as in animals and plants. This review summarizes studies that utilized "omics" strategies to unravel the root development in the model legume Medicago truncatula and how external factors such as soil mineral status or the presence of bacteria and fungi affect root system architecture in this species. We also compare these "omics" data to the knowledges concerning the Arabidopsis thaliana root development, nowadays considered as the model of allorhiz root systems. However, unlike legumes, this species is unable to interact with soil nitrogen-fixing rhizobia and arbuscular-mycorrhizal (AM) fungi to develop novel root-derived symbiotic structures. Differences in root organization, development, and regulatory pathways between these two model species have been highlighted.


Asunto(s)
Medicago truncatula/genética , Desarrollo de la Planta/genética , Raíces de Plantas/genética , Ambiente , Regulación de la Expresión Génica de las Plantas , Genoma de Planta , Genómica/métodos , Medicago truncatula/crecimiento & desarrollo , Medicago truncatula/metabolismo , Reguladores del Crecimiento de las Plantas/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo
11.
Methods Mol Biol ; 1822: 123-132, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-30043301

RESUMEN

MicroRNAs are key regulators in the development processes or stress responses in plants. In the last decade, several conserved or non-conserved microRNAs have been identified in Medicago truncatula. Different strategies leading to the inactivation of microRNAs in plants have been described. Here, we propose a protocol for an effective inactivation of microRNAs using a STTM strategy in M. truncatula transgenic roots.


Asunto(s)
Regulación de la Expresión Génica de las Plantas , Silenciador del Gen , Medicago truncatula/genética , MicroARNs/genética , Raíces de Plantas/genética , Agrobacterium , Perfilación de la Expresión Génica , Medicago truncatula/microbiología , Interferencia de ARN , Transformación Genética
12.
Nat Plants ; 4(12): 1017-1025, 2018 12.
Artículo en Inglés | MEDLINE | ID: mdl-30397259

RESUMEN

Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacBio sequencing has led to a substantially improved genome assembly of Medicago truncatula A17, a legume model species notable for endosymbiosis studies1, and has enabled the identification of genome rearrangements between genotypes at a near-base-pair resolution. Annotation of the new M. truncatula genome sequence has allowed for a thorough analysis of transposable elements and their dynamics, as well as the identification of new players involved in symbiotic nodule development, in particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also discovered that a substantial proportion (~35% and 38%, respectively) of the genes upregulated in nodules or expressed in the nodule differentiation zone colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic islands. These islands contain numerous expressed lncRNA genes and display differentially both DNA methylation and histone marks. Epigenetic regulations and lncRNAs are therefore attractive candidate elements for the orchestration of symbiotic gene expression in the M. truncatula genome.


Asunto(s)
Epigénesis Genética , Genoma de Planta/genética , Medicago truncatula/genética , ARN no Traducido/genética , Simbiosis/genética , Metilación de ADN , Regulación de la Expresión Génica de las Plantas , Genómica , Familia de Multigenes , Proteínas de Plantas/genética , ARN de Planta/genética , Nódulos de las Raíces de las Plantas/genética
13.
Plant Sci ; 171(3): 300-7, 2006 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-22980199

RESUMEN

Drought is a major constraint for the production of common bean (Phaseolus vulgaris L.). To identify molecular responses to water deficit, we performed a differential display RT-PCR (DDRT) analysis using roots of bean plants grown aeroponically and submitted to dehydration. This allowed us to visualise 1200 DDRT bands, 8.7% of which showed a clear regulation by dehydration, and to clone 42 cDNAs, called PvD1 to PvD42. Among them, 20 early-dehydration-responsive cDNAs were selected by reverse northern that were induced or repressed before detectable water status changes and induction of ABA-regulated genes. Northern analysis for 16 PvD clones confirmed these early regulations and allowed us to identify four late dehydration-responsive genes. Their putative involvement in signalling, protein turn-over and translocation, chaperones as well as root growth modulations in response to water stress is discussed.

14.
BMC Syst Biol ; 10(Suppl 5): 126, 2016 Dec 05.
Artículo en Inglés | MEDLINE | ID: mdl-28105955

RESUMEN

BACKGROUND: Soybean (Glycine max) production is significantly hampered by frequent droughts in many regions of the world including the United States. Identifying microRNA (miRNA)-controlled posttranscriptional gene regulation under drought will enhance our understanding of molecular basis of drought tolerance in this important cash crop. Indeed, miRNA profiles in soybean exposed to drought were studied but not from the primary root tips, which is not only a main zone of water uptake but also critical for water stress sensing and signaling. METHODS: Here we report miRNA profiles specifically from well-watered and water-stressed primary root tips (0 to 8 mm from the root apex) of soybean. Small RNA sequencing confirmed the expression of vastly diverse miRNA (303 individual miRNAs) population, and, importantly several conserved miRNAs were abundantly expressed in primary root tips. RESULTS: Notably, 12 highly conserved miRNA families were differentially regulated in response to water-deficit; six were upregulated while six others were downregulated at least by one fold (log2) change. Differentially regulated soybean miRNAs are targeting genes include auxin response factors, Cu/Zn Superoxide dismutases, laccases and plantacyanin and several others. CONCLUSIONS: These results highlighted the importance of miRNAs in primary root tips both under control and water-deficit conditions; under control conditions, miRNAs could be important for cell division, cell elongation and maintenance of the root apical meristem activity including quiescent centre whereas under water stress differentially regulated miRNAs could decrease auxin signaling and oxidative stress as well as other metabolic processes that save energy and water.


Asunto(s)
Glycine max/efectos de los fármacos , Glycine max/genética , Meristema/efectos de los fármacos , Meristema/genética , MicroARNs/genética , Agua/farmacología , Secuencia de Bases , Sequías , Regulación de la Expresión Génica de las Plantas/efectos de los fármacos , Genotipo , Secuenciación de Nucleótidos de Alto Rendimiento , Análisis de Secuencia de ARN , Glycine max/fisiología , Estrés Fisiológico/efectos de los fármacos , Estrés Fisiológico/genética
15.
Med Sci (Paris) ; 20(10): 894-8, 2004 Oct.
Artículo en Francés | MEDLINE | ID: mdl-15461967

RESUMEN

MicroRNAs (miRs) are small non coding RNA, about 21-25 nucleotides in length, that direct post transcriptional regulation of gene expression through interaction with homologous mRNAs. Hundreds miR genes have been identified in animals and 40 in plants. Many of them are conserved between related species, and in some cases across phyla. Two mechanisms for regulation of gene expression by miRs have been reported. As described for lin-4 and let-7 miR of C.elegans, miRs can inhibit translation, which seems to represent the major mode of regulation in animals, or can direct cleavage of target mRNAs, which seems to represent the major mode of regulation in plants.


Asunto(s)
Regulación de la Expresión Génica , MicroARNs/genética , Animales , Diferenciación Celular/genética , Procesamiento Postranscripcional del ARN/genética
16.
Genome Biol ; 15(9): 457, 2014 Sep 24.
Artículo en Inglés | MEDLINE | ID: mdl-25248950

RESUMEN

BACKGROUND: Legume roots show a remarkable plasticity to adapt their architecture to biotic and abiotic constraints, including symbiotic interactions. However, global analysis of miRNA regulation in roots is limited, and a global view of the evolution of miRNA-mediated diversification in different ecotypes is lacking. RESULTS: In the model legume Medicago truncatula, we analyze the small RNA transcriptome of roots submitted to symbiotic and pathogenic interactions. Genome mapping and a computational pipeline identify 416 miRNA candidates, including known and novel variants of 78 miRNA families present in miRBase. Stringent criteria of pre-miRNA prediction yield 52 new mtr-miRNAs, including 27 miRtrons. Analyzing miRNA precursor polymorphisms in 26 M. truncatula ecotypes identifies higher sequence polymorphism in conserved rather than Medicago-specific miRNA precursors. An average of 19 targets, mainly involved in environmental responses and signalling, is predicted per novel miRNA. We identify miRNAs responsive to bacterial and fungal pathogens or symbionts as well as their related Nod and Myc-LCO symbiotic signals. Network analyses reveal modules of new and conserved co-expressed miRNAs that regulate distinct sets of targets, highlighting potential miRNA-regulated biological pathways relevant to pathogenic and symbiotic interactions. CONCLUSIONS: We identify 52 novel genuine miRNAs and large plasticity of the root miRNAome in response to the environment, and also in response to purified Myc/Nod signaling molecules. The new miRNAs identified and their sequence variation across M. truncatula ecotypes may be crucial to understand the adaptation of root growth to the soil environment, notably in the agriculturally important legume crops.


Asunto(s)
Medicago truncatula/genética , MicroARNs/genética , Raíces de Plantas/genética , ARN de Planta/genética , Secuencia Conservada , Regulación de la Expresión Génica de las Plantas , Interacción Gen-Ambiente , Genes de Plantas , Medicago truncatula/metabolismo , MicroARNs/metabolismo , Anotación de Secuencia Molecular , Raíces de Plantas/metabolismo , Polimorfismo de Nucleótido Simple , ARN de Planta/metabolismo , Transducción de Señal , Estrés Fisiológico , Transcriptoma
17.
Methods Mol Biol ; 959: 303-16, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-23299684

RESUMEN

In the past decade, hundreds of non-coding RNAs (small and long RNAs) have been identified as crucial elements in developmental processes and stress response in plants. Among small RNAs, the microRNAs or miRNAs control levels of specific mRNA by inhibiting translation or reducing the stability of their mRNA targets through integration into different ribonucleoproteins (RNP). Spatio-temporal expression of small and long RNAs, using reporter genes or in situ hybridization, is essential to understand their functions. We are interested in understanding the role of various non-coding RNAs (including miRNAs) in the regulation of root and nodule development in legumes, which are agriculturally important crops. Here, we present the protocol we are currently using for detection of small and long RNA in model legume plants and tissues, like nodules and roots. The probe selection, as well as the fixation and permeabilization steps allowing to preserve tissues and cell integrity and to increase accessibility to RNA targets, will be specifically discussed.


Asunto(s)
Hibridación in Situ/métodos , MicroARNs/genética , ARN de Planta/genética , Regulación de la Expresión Génica de las Plantas , ARN Mensajero/genética
18.
Methods Mol Biol ; 959: 317-22, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-23299685

RESUMEN

Proteins are distributed in different cellular compartments. Our group studies the role of non-coding RNAs and associated RNPs in the development and stress response in legumes. Ribonucleoproteins (RNPs) are RNA-protein complexes that play different roles in many cellular processes. Long and small non-coding RNAs determine the specificity of action of several RNPs as the RNA Induced Silencing Complex (RISC), or affect mRNA translation, splicing and stability by interacting with other RNPs such as P-bodies, spliceosome or polysomes. Together with small and long RNAs (Chapter 20), the precise localization of the associated RNPs or the translational products regulated by small RNAs (ie target proteins regulated by miRNAs, or translationally-regulated products) by immunocytochemistry could bring novel insights into these regulatory processes. The protocol described is currently used for detection of RNP associated proteins in nodules and roots of Medicago truncatula but could be extended to any other protein. The critical points, as the choice of the antibody and the fixation and permeabilization steps, that allow preservation of tissue and cell integrity and increase the accessibility to epitopes, will be discussed.


Asunto(s)
Proteínas de Plantas/metabolismo , Medicago truncatula/metabolismo , ARN no Traducido/metabolismo , Ribonucleoproteínas/metabolismo , Ribonucleoproteínas Nucleares Pequeñas/metabolismo , Empalmosomas/metabolismo
19.
Front Plant Sci ; 4: 236, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-23847640

RESUMEN

Small non-coding RNAs (smRNA) participate in the regulation of development, cell differentiation, adaptation to environmental constraints and defense responses in plants. They negatively regulate gene expression by degrading specific mRNA targets, repressing their translation or modifying chromatin conformation through homologous interaction with target loci. MicroRNAs (miRNA) and short-interfering RNAs (siRNA) are generated from long double stranded RNA (dsRNA) that are cleaved into 20-24-nucleotide dsRNAs by RNase III proteins called DICERs (DCL). One strand of the duplex is then loaded onto effective complexes containing different ARGONAUTE (AGO) proteins. In this review, we explored smRNA diversity in model legumes and compiled available data from miRBAse, the miRNA database, and from 22 reports of smRNA deep sequencing or miRNA identification genome-wide in three legumes: Medicago truncatula, soybean (Glycine max) and Lotus japonicus. In addition to conserved miRNAs present in other plant species, 229, 179, and 35 novel miRNA families were identified respectively in these 3 legumes, among which several seems legume-specific. New potential functions of several miRNAs in the legume-specific nodulation process are discussed. Furthermore, a new category of siRNA, the phased siRNAs, which seems to mainly regulate disease-resistance genes, was recently discovered in legumes. Despite that the genome sequence of model legumes are not yet fully completed, further analysis was performed by database mining of gene families and protein characteristics of DCLs and AGOs in these genomes. Although most components of the smRNA pathways are conserved, identifiable homologs of key smRNA players from non-legumes, like AGO10 or DCL4, could not yet be detected in M. truncatula available genomic and expressed sequence (EST) databases. In contrast to Arabidopsis, an important gene diversification was observed in the three legume models (for DCL2, AGO4, AGO2, and AGO10) or specifically in soybean for DCL1 and DCL4. Functional significance of these variant isoforms may reflect peculiarities of smRNA biogenesis and functions in legumes.

20.
Biol Aujourdhui ; 206(4): 313-22, 2012.
Artículo en Francés | MEDLINE | ID: mdl-23419258

RESUMEN

In recent years, in addition to mRNAs, the non-protein-coding RNAs (or ncRNAs) have emerged as a major part of the eukaryotic transcriptome. New genomic approaches allowed the discovery of many novel long and small ncRNAs that may be linked to the generation of evolutionary complexity in multicellular organisms. Many long ncRNAs are regulated by abiotic stresses although only very few long ncRNAs have been functionally analyzed. On the other hand, small RNAs act in the regulation of gene expression at transcriptional or post-transcriptional level and several among them have been linked to abiotic stress responses. Here we describe various ncRNAs associated with environmental stress responses such as to salt, cold or nutrient deprivation. The understanding of these RNA networks may reveal novel mechanisms involved in plant adaptation to changing environmental conditions.


Asunto(s)
Ambiente , Fenómenos Fisiológicos de las Plantas , Plantas/genética , ARN de Planta/fisiología , ARN no Traducido/fisiología , Estrés Fisiológico/genética , Regulación de la Expresión Génica de las Plantas , MicroARNs/genética , MicroARNs/fisiología , ARN Largo no Codificante/genética , ARN Largo no Codificante/fisiología , Estrés Fisiológico/fisiología
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