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TRANSPHO Report Summary

Project ID: 327954
Funded under: FP7-PEOPLE
Country: France

Final Report Summary - TRANSPHO (Roles of non-coding RNAs in translational regulation during root developmental adaptation to phosphate starvation)

Abiotic stresses are increasingly affecting agricultural yield as a result of global climate change and scarcity of water and nutrients. One way to minimize the negative impact of these factors on yield is to manipulate root system architecture (RSA) towards a distribution of roots in the soil that optimizes water and nutrient uptake. Thus, a greater understanding of root growth processes may enable improvement of crop plants through more environmentally friendly agricultural practices. One of the basic response mechanisms to abiotic stress is the alteration of gene expression. Gene expression can be regulated at multiple levels, including transcription, processing, translation, and post-translational modification. Among these steps, translational control provides cells a mechanism to rapidly control gene expression in a reversible manner, in response to environmental and developmental cues.
Long non Coding RNAs (lncRNA) are RNA molecules that do not encode for proteins but are though to possess a regulatory function on the expression of protein coding genes. lncRNA are emerging as important actors in the adaptation of plants to environmental constraints though their regulation of gene expression. They have been shown to regulate a myriad a biological processes such as cell differentiation, genomic imprinting and response to stress. Most studies so far have focused on their role in the regulation of transcription but several recent lines of evidences suggest they may also controls the regulation of translation. However, little is known about global impact of lncRNA on translational regulation in plants

In the frame of this project, we have adapted to plant biology advanced technologies, which allow to isolated ribosomes with a high purity from virtually any cell-type and to sequence mRNA fragments protected by the two subunits (ie fragment of mRNA being translated). Therefore, this technology allows mapping very precisely the position and number of ribosomes on RNAs at a genome-wide level.

We have applied this approach to monitor ribosome position and number across RNA transcripts in roots of Arabidopsis undergoing phosphate (Pi) deprivation. Comparison of translational and transcriptional activities in genic regions revealed that transcription and translation are correlated under Pi deficiency but illuminated some gene-specific translational regulation that may play a role in physiological responses to low Pi. Strikingly, we also observed the association of hundreds of known and putative novel long non-coding RNAs (lncRNA) with ribosomes. This result was unanticipated because ribosomes are thought to bind only to mRNA (ie coding RNAs). A deeper analysis of ribosome distribution on lncRNA revealed that lncRNAs actually represent a reservoir of new small peptides, a number of which are evolutionarily conserved. Indeed, our work has identified potential translation of several hundreds of new small peptides in the genome for which 70 of them the corresponding peptides were subsequently detected using mass spectroscopy. This result opens a new area of research in plant biology to determine their biological functions, particularly during the responses environmental stresses. Functional characterization of these small peptides in the response to stresses may also represent new agricultural products to enhance crops stress tolerance in the field.

One other outcome of this project was the discovery that ribosome binding to small ORF embedded in a precursor of small regulatory RNA (siRNA), an extensively studied plant non-coding RNA family. Taking one member of this family (TAS3) as an example, our work has shown that translation of small Open Reading Frame on TAS3 seems to be necessary for its non-coding function. As many we identify many non-coding RNAs sharing similar ribosome binding features, this phenomenon may represent a more general mechanism linking ribosomes with the function of many cytoplasmic non coding RNAs.

Long noncoding antisense RNAs (NATs) are RNA molecules complementary to endogenous mRNAs. NATs are emerging as regulators of the adaptation to a wide range of environments in eukaryotes. Our work has revealed the association of hundreds of NATs with Arabidopsis ribosomes. Moreover, the induction of a small group of these molecules by low phosphate (Pi) availability coincides with increased translation of their target mRNA, including genes which are important for root adaptations to nutrient deficiency. Functional analysis at currently being preformed to determine the role and the mode of action of this new class of molecule, in translational regulations and root adaptations to nutrient deficiency in the soil. Potential outcomes of this work may lead to the development of new tools to modulate gene expression in plants.

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Life Sciences
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