Beyond transcription: RNA-binding proteins as emerging regulators of plant response to environmental constraints

Ambrosone, Alfredo; Costa, Antonello; Leone, Antonella; Grillo, Stefania

doi:10.1016/j.plantsci.2011.02.004

Cited by 112 publications

(85 citation statements)

References 73 publications

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“…3), a small chloroplast protein increasingly recognized as master regulator of the Calvin cycle, complexes to downregulate GAPDH under oxidative conditions to form the binary complex A4-GAPDH/CP12, which strongly suppresses GAPDH activity (see GAPDH expression above; Wedel et al, 1997;Gontero and Maberly, 2012;Michelet et al, 2013;López-Calcagno et al, 2014) and is essential to the leaves' response to abiotic/oxidative stress (Yoo et al, 2011). The consistent up-regulation of universal stress protein and isoprene synthesis also agrees with the high abiotic stress conditions potentially produced by hydrocarbon contamination (Maqbool RNA biding proteins are emerging as regulators of plant responses to environmental stress (Ambrosone et al, 2012). RBM24 (Splicing factor 3b, subunit 4; high homologous to RNA chloroplast RNA binding protein CP29, also a subunit of the antenna complex) was shown to be up-regulated in response to abiotic stress, such as cold stress (Andersson et al, 2001;Yakushevska et al, 2003;Amme et al, 2006).…”

Section: Mapping Extracted Rna To Independently De Novo Assembled Tramentioning

confidence: 57%

Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants

et al. 2016

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Metatranscriptomic study of nonmodel organisms requires strategies that retain the highly resolved genetic information generated from model organisms while allowing for identification of the unexpected. A real-world biological application of phytoremediation, the field growth of 10 Salix cultivars on polluted soils, was used as an exemplar nonmodel and multifaceted crop response well-disposed to the study of gene expression. Sequence reads were assembled de novo to create 10 independent transcriptomes, a global transcriptome, and were mapped against the Salix purpurea 94006 reference genome. Annotation of assembled contigs was performed without a priori assumption of the originating organism. Global transcriptome construction from 3.03 billion paired-end reads revealed 606,880 unique contigs annotated from 1588 species, often common in all 10 cultivars. Comparisons between transcriptomic and metatranscriptomic methodologies provide clear evidence that nonnative RNA can mistakenly map to reference genomes, especially to conserved regions of common housekeeping genes, such as actin, a/b-tubulin, and elongation factor 1-a. In Salix, Rubisco activase transcripts were down-regulated in contaminated trees across all 10 cultivars, whereas thiamine thizole synthase and CP12, a Calvin Cycle master regulator, were uniformly up-regulated. De novo assembly approaches, with unconstrained annotation, can improve data quality; care should be taken when exploring such plant genetics to reduce de facto data exclusion by mapping to a single reference genome alone. Salix gene expression patterns strongly suggest cultivar-wide alteration of specific photosynthetic apparatus and protection of the antenna complexes from oxidation damage in contaminated trees, providing an insight into common stress tolerance strategies in a real-world phytoremediation system.Coppiced willows have the ability to produce high biomass yields in temperate regions under challenging conditions and have positive impacts on biodiversity (Labrecque et al

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Section: Mapping Extracted Rna To Independently De Novo Assembled Tramentioning

confidence: 57%

Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants

et al. 2016

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“…While outstanding progress has been made in the elucidation of perception and signaling cascades resulting in stress-induced modifications of gene expression and channel activation, RNA regulatory mechanisms such as synthesis, processing, transport, translation, storage, stability, and degradation of RNA molecules are emerging as key processes participating in the modulation of cellular responses to stress (Ambrosone et al, 2012;Nakaminami et al, 2012). The importance of mRNA stability mechanisms is known in the case of the Na + /H + antiporter SALT OVERLY SENSITIVE1 (SOS1) required for tolerance to salt stress.…”

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confidence: 99%

The Arabidopsis RNA-Binding Protein AtRGGA Regulates Tolerance to Salt and Drought Stress

et al. 2015

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Salt and drought stress severely reduce plant growth and crop productivity worldwide. The identification of genes underlying stress response and tolerance is the subject of intense research in plant biology. Through microarray analyses, we previously identified in potato (Solanum tuberosum) StRGGA, coding for an Arginine Glycine Glycine (RGG) box-containing RNA-binding protein, whose expression was specifically induced in potato cell cultures gradually exposed to osmotic stress. Here, we show that the Arabidopsis (Arabidopsis thaliana) ortholog, AtRGGA, is a functional RNA-binding protein required for a proper response to osmotic stress. AtRGGA gene expression was up-regulated in seedlings after long-term exposure to abscisic acid (ABA) and polyethylene glycol, while treatments with NaCl resulted in AtRGGA down-regulation. AtRGGA promoter analysis showed activity in several tissues, including stomata, the organs controlling transpiration. Fusion of AtRGGA with yellow fluorescent protein indicated that AtRGGA is localized in the cytoplasm and the cytoplasmic perinuclear region. In addition, the rgga knockout mutant was hypersensitive to ABA in root growth and survival tests and to salt stress during germination and at the vegetative stage. AtRGGA-overexpressing plants showed higher tolerance to ABA and salt stress on plates and in soil, accumulating lower levels of proline when exposed to drought stress. Finally, a global analysis of gene expression revealed extensive alterations in the transcriptome under salt stress, including several genes such as ASCORBATE PEROXIDASE2, GLUTATHIONE S-TRANSFERASE TAU9, and several SMALL AUXIN UPREGULATED RNA-like genes showing opposite expression behavior in transgenic and knockout plants. Taken together, our results reveal an important role of AtRGGA in the mechanisms of plant response and adaptation to stress.

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“…One of such genes codes RNA-binding proteins (RBPs) which play crucial roles in all aspects of post-transcriptional gene regulation. They are involved in developmental processes and in adaptation of plants to various environmental conditions (Lorkovic 2009;Ambrosone et al 2012).…”

Section: Discussionmentioning

confidence: 99%

Identification of proteins related to microspore embryogenesis responsiveness in anther cultures of winter triticale (×Triticosecale Wittm.)

et al. 2017

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For a better understanding of the physiological background of microspore embryogenesis (ME), the protein profile was analyzed in four winter triticale DH lines, which show extremely different embryogenic potential. The analysis were conducted with anthers at the phase of development optimal for ME induction and then after low temperature (LT, 3 weeks at 4°C) MEinducing tillers treatment. The sub-proteome of anthers was mapped by two-dimensional gel electrophoresis (2-DE). The protein species significantly more abundant (at least 2-fold) in responsive DH lines after LT treatment were chosen for identification by MALDI-TOF/TOF analysis. In total, 31 protein species were successfully identified as involved in the determination of microspore competence, stress response and in the regulation of ME induction. Microspore competence required sufficient energy supply and efficient system of cell protection that determine survival under prolonged LT stress treatment. LT stress was associated with increased accumulation of proteins typical for cell defence against oxidative stress (e.g., L-ascorbate peroxidase), chaperons (e.g., HSP70) and other enzymes/factors ensuring protein biosynthesis, stability and active cell divisions. Also here, effective cell defence required undisturbed energy supply. Among proteins that accumulated differentially in accordance with microspore embryogenic potential again the most important role seems to be played by the enzymes ensuring energy production and determining ability of plant stress adaptation. Two protein species (enolase, 12S storage protein), proposed earlier as candidates for markers of embryogenesis in other in vitro plant culture systems confirmed their utility for triticale anther cultures.

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Beyond transcription: RNA-binding proteins as emerging regulators of plant response to environmental constraints

Cited by 112 publications

References 73 publications

Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants

Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants

The Arabidopsis RNA-Binding Protein AtRGGA Regulates Tolerance to Salt and Drought Stress

Identification of proteins related to microspore embryogenesis responsiveness in anther cultures of winter triticale (×Triticosecale Wittm.)

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