RESUMEN
Hydrogen peroxide (H2O2) is a common signal molecule initiating transcriptional responses to all the known biotic and abiotic stresses of land plants. However, the degree of involvement of H2O2 in these stress responses has not yet been well studied. Here we identify time-dependent transcriptome profiles stimulated by H2O2 application in Arabidopsis (Arabidopsis thaliana) seedlings. Promoter prediction based on transcriptome data suggests strong crosstalk among high light, heat, and wounding stress responses in terms of environmental stresses and between the abscisic acid (ABA) and salicylic acid (SA) responses in terms of phytohormone signaling. Quantitative analysis revealed that ABA accumulation is induced by H2O2 but SA is not, suggesting that the implied crosstalk with ABA is achieved through ABA accumulation while the crosstalk with SA is different. We identified potential direct regulatory pairs between regulator transcription factor (TF) proteins and their regulated TF genes based on the time-course transcriptome analysis for the H2O2 response, in vivo regulation of the regulated TF by the regulator TF identified by expression analysis of mutants and overexpressors, and in vitro binding of the regulator TF protein to the target TF promoter. These analyses enabled the establishment of part of the transcriptional regulatory network for the H2O2 response composed of 15 regulatory pairs of TFs, including five pairs previously reported. This regulatory network is suggested to be involved in a wide range of biotic and abiotic stress responses in Arabidopsis.
Asunto(s)
Arabidopsis/genética , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas/efectos de los fármacos , Redes Reguladoras de Genes , Peróxido de Hidrógeno/farmacología , Plantones/genética , Ácido Abscísico/metabolismo , Ácido Abscísico/farmacología , Proteínas de Arabidopsis/genética , Peróxido de Hidrógeno/metabolismo , Oxidantes/metabolismo , Oxidantes/farmacología , Reguladores del Crecimiento de las Plantas/metabolismo , Reguladores del Crecimiento de las Plantas/farmacología , Regiones Promotoras Genéticas/genética , Ácido Salicílico/metabolismo , Ácido Salicílico/farmacología , Transducción de Señal/efectos de los fármacos , Transducción de Señal/genética , Factores de Transcripción/genéticaRESUMEN
An improvement in plant production is increasingly important for a sustainable human society. For this purpose, understanding the mechanism of plant production, that is, the plant metabolic system, is an immediate necessity. After the sequencing of the Arabidopsis genome, it has become possible to obtain a bird's eye view of its metabolism by means of omics such as transcriptomics and proteomics. Availability of thousands of transcriptome data points in the public domain has resulted in great advances in the methodology of functional genomics. Metabolome data can be a "gold mine" of biological findings. However, as the total throughput of metabolomics is far lower than that of transcriptomics due to technical difficulties, there is currently no publicly available large-scale metabolome dataset that is comparable in size to the transcriptome dataset. Recently, we established a novel methodology, termed widely targeted metabolomics, which can generate thousands of metabolome data points in a high-throughput manner. We previously conducted a targeted metabolite analysis of large-scale Arabidopsis bioresources, namely transposon-tagged mutants and accessions, to make a smaller dataset of metabolite accumulation. In this paper, we release approximately 3,000 metabolic profiles obtained by targeted analysis for 36 metabolites and discuss the possible regulation of amino acid accumulation.
Asunto(s)
Arabidopsis/genética , Arabidopsis/metabolismo , Genoma de Planta , Metaboloma , Metabolómica/métodos , Aminoácidos de Cadena Ramificada/metabolismo , Elementos Transponibles de ADN/genética , Glucosinolatos/metabolismo , Mutagénesis/genética , Mutación/genética , Semillas/metabolismoRESUMEN
Molecular breeding of crops is an efficient way to upgrade plant functions useful to mankind. A key step is forward genetics or positional cloning to identify the genes that confer useful functions. In order to accelerate the whole research process, we have developed an integrated database system powered by an intelligent data-retrieval engine termed PosMed-plus (Positional Medline for plant upgrading science), allowing us to prioritize highly promising candidate genes in a given chromosomal interval(s) of Arabidopsis thaliana and rice, Oryza sativa. By inferentially integrating cross-species information resources including genomes, transcriptomes, proteomes, localizomes, phenomes and literature, the system compares a user's query, such as phenotypic or functional keywords, with the literature associated with the relevant genes located within the interval. By utilizing orthologous and paralogous correspondences, PosMed-plus efficiently integrates cross-species information to facilitate the ranking of rice candidate genes based on evidence from other model species such as Arabidopsis. PosMed-plus is a plant science version of the PosMed system widely used by mammalian researchers, and provides both a powerful integrative search function and a rich integrative display of the integrated databases. PosMed-plus is the first cross-species integrated database that inferentially prioritizes candidate genes for forward genetics approaches in plant science, and will be expanded for wider use in plant upgrading in many species.