The Help2Lib project aims to better understand the impacts of the multiple crises in Lebanon (COVID-19, economic, explosion of the port of Beirut, oil spill) on Lebanese coastal fisheries and marine habitats through an inventory and the implementation of 'actions to restore essential habitats such as nurseries. This will notably involve better understanding the changes in the behavior of Lebanese artisanal fishermen in connection with the crises and helping to improve their income in the long term and make their activity more sustainable by reducing environmental impacts. This work should help prioritize environmental needs, as well as improve the development of indicators for assessing the ecological state of coastal systems. It could also help to better apply and coordinate management measures at an appropriate scale for ecosystem conservation.

Inter-species transfer of mobile elements is now recognized as an important factor in eukaryotic genome evolution. Yet the dynamics, control and short-term impacts of this process are poorly known because difficult to study. A major limitation to investigate these is the low frequency at which transfer presumably occurs and the need of a tractable system to study the different steps involved and their control. The T-DNA is a mobile element that is transferred from Agrobacterium tumefaciens bacteria to many dicot plants, including Arabidopsis thaliana. Interestingly, many wild and domesticated dicots contain relics of T-DNA in their genome indicating that the T-DNA transfer can modify the genome permanently. Hence, the interaction between A. tumefaciens, T-DNA and A. thaliana offers a unique opportunity to study, under controlled conditions, a natural process of DNA transfer since its arrival into the cell, in real-time, the control of its expression, as well as its impact on host-pathogen interaction and genome rearrangements. The MOBIL_DNA project will investigate the fate and regulation of wild T-DNA in the host plant and its impact on host cells as well as on pathogen cells and lifestyle. By accessing single-cell and single-molecule resolution, the MOBIL_DNA project proposes to unravel novel plant molecular processes to cope with T-DNAs (and more generally foreign DNA) upon arrival in the cell. This project, at the interface of plant-pathogen interactions, and foreign DNA regulation is possible because of complementary expertise of the 3 partners, their published data and preliminary data they acquired. The MOBIL_DNA consortium combines expertise in A. tumefaciens lifestyle (Partner1 Faure team at I2BC, Gif-sur-Yvette), DNA and RNA real-time imaging in plants (Partner2 Pontvianne team at LGDP, Perpignan) and regulation of mobile elements in plants (Partner3 Déléris team at I2BC, Gif-sur-Yvette). This project will also benefit of infrastructure and expertise of I2BC and LGDP sequencing, microscopy and bioinformatics platforms. Mobil_DNA is organized in 3 work packages (WPs). In WP1, we will determine the co-transcriptomic landscape of the A. thaliana-A. tumefaciens interaction at two key stages of infection, with a focus on processes involved in T-DNA transfer, host response to foreign DNA, control of genomic variability and pathogen lifestyle on roots and tumors. Single cell transcriptomics will further resolve the heterogeneity of the plant cell populations in the tumor to reveal genome responses and regulatory pathways associated with T-DNA expression or lack thereof, at the cellular level. In WP2, we will use pioneering live-imaging of DNA and RNA to characterize the localization and fate of pathogenic T-DNA in the plant cells, with sub-tissular and sub-cellular resolution, and relate this information to T-DNA transcriptional status and Single Cell transcriptomics. In WP3, we aim to understand the mechanisms controlling T-DNA expression (post-transcriptional / transcriptional silencing), as these are likely to be critical for plant defense, and how they could be dampened by bacteria. In this somatic context of insertion, we aim to reveal the regulation of armed T-DNA, global changes of epigenomic landscape in the plant tumor, and crosstalks between regulations of T-DNA and host transposable elements (TE). Somatic transpositions and other genome rearrangements in the plant and bacterial genome will be assessed. The contribution of the proliferative tumor state to mobile element activation and to bacterial abundance /gene expression patterns will be tested using appropriate mutants and tools. Overall, this work will lead to major discoveries on the spatial-temporal dynamics of T-DNA horizontal transfer with unprecedented resolution and on T-DNA control and impacts, providing valuable information for genome evolution studies, and for improving efficiency of T-DNA-based genome engineering and plant protection.

The stability and translational activity of messenger RNAs (mRNAs) are important checkpoints in the regulation of gene expression. These processes are massively reprogrammed during development and in response to stress. In the last couple of years, several studies have shown that stability and translation of mRNAs are intertwined through a mRNA degradation pathway, called 5'-3’ co-translational decay (CoTD). Our knowledge of this interconnection is still limited with the actors, mechanisms and functions remain to be discovered. The objective of the MATILDA project is to understand the role and physiological importance of this degradation pathway in the plant model Arabidopsis thaliana. We have already demonstrated the importance of this degradation pathway during development and in response to heat stress. However, the importance of this pathway in the general mechanism of mRNA decay has never been assessed in any model organism. For this project, we have set up a transgenic line allowing the discrimination between the co-translational degradation pathway and the classical cytosolic degradation pathway. In the project, we will determine the general stability of transcripts using an in vivo RNA labeling approach using this transgenic line in order to determine the importance of co-translational decay in the general mRNA stability (WP1). We will then determine the cis-elements triggering this pathway. Our preliminary data suggest the importance of codon optimality in the regulation of this mechanism (WP2). We will try to identify the signaling pathway that modulates the co-translational decay activity within the plant (WP3). Finally, we will determine the physiological conditions where the co-translational decay plays an important role (WP4). In conclusion, the MATILDA project will produce crucial knowledge on the function of the co-translational decay in plants and more generally on the role of post-transcriptional regulation of mRNAs in development and stress response in eukaryotes.