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Addressing the role of microRNAs in reprogramming leaf growth during drought stress in Brachypodium distachyon.

ABSTRACT: Plant responses to drought are regulated by complex genetic and epigenetic networks leading to rapid reprogramming of plant growth. miRNAs have been widely indicated as key players in the regulation of growth and development. The role of miRNAs in drought response was investigated in young leaves of Brachypodium distachyon, a drought-tolerant monocot model species. Adopting an in vivo drought assay, shown to cause a dramatic reduction in leaf size, mostly due to reduced cell expansion, small RNA libraries were produced from proliferating and expanding leaf cells. Next-generation sequencing data were analyzed using an in-house bioinformatics pipeline allowing the identification of 66 annotated miRNA genes and 122 new high confidence predictions greatly expanding the number of known Brachypodium miRNAs. In addition, we identified four TAS3 loci and a large number of siRNA-producing loci that show characteristics suggesting that they may represent young miRNA genes. Most miRNAs showed a high expression level, consistent with their involvement in early leaf development and cell identity. Proliferating and expanding leaf cells respond differently to drought treatment and differential expression analyses suggest novel evidence for an miRNA regulatory network controlling cell division in both normal and stressed conditions and demonstrate that drought triggers a genetic reprogramming of leaf growth in which miRNAs are deeply involved.

SUBMITTER: Bertolini E

PROVIDER: S-EPMC3603004 | biostudies-literature | 2013 Mar

REPOSITORIES: biostudies-literature

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Addressing the role of microRNAs in reprogramming leaf growth during drought stress in Brachypodium distachyon.

Bertolini Edoardo E Verelst Wim W Horner David Stephen DS Gianfranceschi Luca L Piccolo Viviana V Inzé Dirk D Pè Mario Enrico ME Mica Erica E

Molecular plant 20121221 2

Plant responses to drought are regulated by complex genetic and epigenetic networks leading to rapid reprogramming of plant growth. miRNAs have been widely indicated as key players in the regulation of growth and development. The role of miRNAs in drought response was investigated in young leaves of Brachypodium distachyon, a drought-tolerant monocot model species. Adopting an in vivo drought assay, shown to cause a dramatic reduction in leaf size, mostly due to reduced cell expansion, small RNA ...[more]

PMID: 23264558

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Project description:Plant growth-promoting bacteria (PGB) induce positive effects in plants, for instance, increased growth and reduced abiotic stresses susceptibility. The mechanisms by which these bacteria impact the host plant are numerous, diverse and often specific. Here, we studied the agronomical, molecular and biochemical effects of the endophytic PGB Bacillus subtilis B26 on the full life cycle of Brachypodium distachyon Bd21, an established model species for functional genomics in cereal crops and temperate grasses. Inoculation of Brachypodium with B. subtilis strain B26 increased root and shoot weights, accelerated growth rate and seed yield as compared to control plants. B. subtilis strain B26 efficiently colonized the plant and was recovered from roots, stems and blades as well as seeds of Brachypodium, indicating that the bacterium is able to migrate, spread systemically inside the plant, establish itself in the aerial plant tissues and organs, and is vertically transmitted to seeds. The presence of B. subtilis strain B26 in the seed led to systemic colonization of the next generation of Brachypodium plants. Inoculated Brachypodium seedlings and mature plants exposed to acute and chronic drought stress minimized the phenotypic effect of drought compared to plants not harbouring the bacterium. Protection from the inhibitory effects of drought by the bacterium was linked to upregulation of the drought-response genes, DREB2B-like, DHN3-like and LEA-14-A-like and modulation of the DNA methylation genes, MET1B-like, CMT3-like and DRM2-like, that regulate the process. Additionally, total soluble sugars and starch contents increased in stressed inoculated plants, a biochemical indication of drought tolerance. In conclusion, we show a single inoculation of Brachypodium with a PGB affected the whole growth cycle of the plant, accelerating its growth rates, shortening its vegetative period, and alleviating drought stress effects. These effects are relevant to grasses and cereal crops.

Project description:Brachypodium distachyon (Brachypodium) is a non-domesticated model grass that has been used to assess population level genomic variation. We have previously established a collection of 55 Brachypodium accessions that were sampled to reflect five different climatic regions of Turkey; designated 1a, 1c, 2, 3 and 4. Genomic and methylomic variation differentiated the collection into two subpopulations designated as coastal and central (respectively from regions 1a, 1c and the other from 2, 3 and 4) which were linked to environmental variables such as relative precipitation. Here, we assessed how far genomic variation would be reflected in the metabolomes and if this could be linked to an adaptive trait. Metabolites were extracted from eight-week-old seedlings from each accession and assessed using flow infusion high-resolution mass spectrometry (FIE-HRMS). Principal Component Analysis (PCA) of the derived metabolomes differentiated between samples from coastal and central subpopulations. The major sources of variation between seedling from the coastal and central subpopulations were identified. The central subpopulation was typified by significant increases in alanine, aspartate and glutamate metabolism and the tricarboxylic acid (TCA) cycle. Coastal subpopulation exhibited elevated levels of the auxin, indolacetic acid and rhamnose. The metabolomes of the seedling were also determined following the imposition of drought stress for seven days. The central subpopulation exhibited a metabolomic shift in response to drought, but no significant changes were seen in the coastal one. The drought responses in the central subpopulation were typified by changes in amino acids, increasing the glutamine that could be functioning as a stress signal. There were also changes in sugars that were likely to be an osmotic counter to drought, and changes in bioenergetic metabolism. These data indicate that genomic variation in our Turkish Brachypodium collection is largely reflected as distinctive metabolomes ("metabolotypes") through which drought tolerance might be mediated.

Project description:Brachypodium distachyon is a new model plant for wheat, barley and several potential biofuel grasses. The Bd21 leaf was initially treated with salt concentrations ranging from 80 to 320 mM followed by a recovery process prior to proteome analysis. Leaf total protein was extracted according to the method of Wang et al. with minor modifications, followed by 2D DIGE separation as recommended by the manufacturer (GE Healthcare). The differentially expressed proteins spots were identified using ImageMaster 2D Platinum Software Version 5.0 (Amersham Biosciences). Protein identification was carried out by the ABI 4800 Proteomics Analyzer MALDI-TOF/TOF (Applied Biosystems, Foster City) operating in a result-dependent acquisition mode. Peptide mass maps were acquired in positive ion reflector mode (20 kV accelerating voltage) with 1000 laser shots per spectrum. Monoisotopic peak masses were automatically determined within the mass range 800-4000 Da with a signal to noise ratio minimum set to 10 and a local noise window width of m/z 250. Up to five of the most intense ions with minimum signal to noise ratio 50 were selected as precursors for MS/MS acquisition, excluding common trypsin autolysis peaks and matrix ion signals. In MS/MS-positive ion mode, spectra were averaged, collision energy was 2 kV, and default calibration was set. Monoisotopic peak masses were automatically determined with a signal to noise ratio minimum set to 5 and a local noise window width of m/z 250. The MS together with MS/MS spectra were searched against NCBI Brachypodium protein database (26035 entries in total, downloaded on July 16, 2011) using the software MASCOT version 2.1 (Matrix Science) with the following parameter settings: trypsin cleavage, one missed cleavage allowed, carbamidomethylation set as fixed modification, oxidation of methionines and phosphorylation of serine, threonine, and tyrosine allowed as variable modification, peptide mass tolerance set to 100 ppm and fragment tolerance set to ± 0.3 Da. All searches were evaluated based on the significant scores obtained from MASCOT. The results were creditable with Protein Score C. I. % and Total Ion Score C. I. % both above 95% and significance threshold p < 0.05 for the MS/MS.

Dataset Information

Addressing the role of microRNAs in reprogramming leaf growth during drought stress in Brachypodium distachyon.

Publications

Addressing the role of microRNAs in reprogramming leaf growth during drought stress in Brachypodium distachyon.

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