LTR-STRESS

Upon insertion in or next to coding regions, Transposable Elements (TEs) can impact gene expression and function in various ways, from contributing to proteic sequences to changing gene regulatory patterns. TE-generated variations significantly expand the functional potentialities of host genomes, bearing important consequences for the generation of phenotypic diversity. TEs themselves are subject to transcriptional and epigenetic regulations in response to developmental cues and external stimuli. As a consequence, host genes adjacent to TE insertions can be placed under the control of these TE responses, leading to reprogramming of batteries of genes as part of the organism's response to specific stimuli, hence a recent definition of TEs as "distributed genomic control modules". This is particularly true for LTR-retrotransposons, whose Long Terminal Repeats (LTRs) represent small autonomous promoter/regulatory capsules that can be functional at different genomic positions. In the last few years, a wealth of data from human and animal studies showed that LTRs mediate the coordinated regulation of numerous adjacent genes in response to developmental cues, via the production of LTR/gene chimeric co-transcripts driven from the LTR and extending into flanking sequences. LTRs may thus represent intermediates or "sensors" of specific stimuli, able to translate and redirect these messages towards adjacent cellular functions. This new and open field of research is still largely unchartered in plants, although large plant genomes are highly enriched in TEs (up to 80%), with LTR-retrotransposons being by far the predominant type. The objectives of this proposal aim at evaluating the functional and evolutionary importance of LTR-mediated reprogramming of plant gene expression in response to stress. The proposal builds up on very recent preliminary bioinformatic data reporting an abundance of LTR/gene co-transcripts produced by tobacco in stress conditions, and notably from the LTR of the best known plant retrotransposon, the stress-activated tobacco Tnt1 element, previously isolated and characterized by one partner of this project. These preliminary data provide a very strong base to support the hypothesis that activation of the Tnt1 LTR by stress, in addition to driving Tnt1 amplification, may also be involved in modulating the expression of several tobacco genes in stress conditions. In this project, we will evaluate the impact of LTR-driven co-transcripts on adjacent genes expression changes, and the precise correlation of these changes with the tobacco stress responses. We will notably evaluate the quantitative importance of LTR/gene co-transcripts produced in tobacco in various developmental and stress conditions and their molecular impact targeted genes, as well as their evolutionary importance. These studies will allow a global insight on the modifications of gene expression and/or function generated in tobacco by transcriptional activation of retrotransposon LTRs in response to stress. In addition, we will expand the significance of our studies by monitoring changes in the production (and possibly the impact) of LTR/gene co-transcripts in conditions where the retrotransposon transcriptional activation is affected, firstly by artificially altering the tobacco defense response, and secondly by artificially altering Tnt1 transcripts levels. To this aim, we will use transgenic tobacco lines in which the early signal transduction pathways elicited by microbial stress (such as fungal elicitins also known to activate Tnt1 expression) are defective, and transgenic tobacco lines expressing double-stranded and antisense Tnt1 transcripts designed to silence Tnt1 expression via the RNAi pathways. These complementary analyses will confirm that LTR-mediated changes in adjacent gene expression are directly correlated to the retrotransposon transcriptional activation and to the host stress response. The project represents a direct, original and timely valorization of previous competences established in the proposed partnership in the field of plant stress response and its fine interplay with retrotransposon activity. We expect that it will rapidly generate a wealth of experimental data from which will emerge, for the first time, a large-scale picture of the co-optation of retrotransposon LTR promoters by plant host genomes. This will allow a major breakthrough on the understanding of the biological impact of retrotransposons on plant host genomes, which may be of key significance for plant adaptability to environmental changes, as plants can not move to avoid these changes and have thus evolved complex and highly coordinated responses to biotic and abiotic challenges.