T-DNA fate, regulation and impact in Agrobacterium-Arabidopsis interaction – MOBIL_DNA

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.