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Unraveling the regulatory network of developmental programmed cell death in plants

Periodic Reporting for period 4 - PROCELLDEATH (Unraveling the regulatory network of developmental programmed cell death in plants)

Reporting period: 2019-10-01 to 2020-03-31

Programmed cell death (PCD) is a fundamental biological process that actively terminates a cell’s vital functions by a well-ordered sequence of cellular events. In animals and plants, various types of PCD are crucial for development, immunity to pathogens, and the responses to environmental stresses.
In the context of plant development, PCD is an inherent part of many vital processes including reproduction, seed development, or the formation of plant vessels. Despite their importance, only little is known about developmental PCD (dPCD) processes and their molecular control in plants. We hypothesize that an intricate regulatory network exists that renders specific plant cell types competent to initiate and execute dPCD and subsequent partial or complete cell-autonomous corpse clearance as final step of their developmental differentiation.
PROCELLDEATH exploited a new powerful dPCD model system, the PCD process occurring during root cap differentiation in Arabidopsis thaliana. Exploiting the unique accessibility of the root cap system enables us to tackle fundamental questions about the molecular regulation of dPCD in plants. We revealed that the control of gene expression is an important element coordinating cellular differentiation with PCD as the ultimate differentiation step. We identified a commonly regulated core of PCD-associated genes that are expressed prior to PCD not only in the root cap, but also in other dPCD contexts. These genes are controlled by transcription factors as part of a complex gene regulatory network orchestrating cellular differentiation and PCD in various plant organs.
Detailed knowledge on plant PCD will generate new leads to apply the unexploited potential of PCD in plant breeding and weed control. Our research can provide leads to develop crop varieties that autonomously delete organ primordia by targeted PCD, which can result in plant architectures optimally adapted to different cultivation methods. Furthermore, stress resilient crop varieties could be developed, as environmental stresses often lead to accelerated senescence and cell death in reproductive tissues. Interfering with these processes, crops could be rendered more resistant to stresses, stabilizing and intensifying crop yield under suboptimal environmental conditions. Finally, our findings can be a basis to develop novel next-generation agrochemicals or biologicals that induce systemic PCD processes in weeds.
In the course of PROCELLDEATH, we made decisive progress in our understanding of dPCD and its roles in plant development. By means of bioinformatics analyses we identified a conserved core of transcriptionally regulated genes that can be used as landmark genes to diagnose dPCD processes and distinguish them from environmentally induced cell death events (Olvera-Carrillo Y, et al., Plant Physiology 2015 Dec;169(4):2684-2699). We further discovered that two related NAC transcription factors, ANAC087 and ANAC046, control different aspects of root cap PCD. While ANAC087 controls post-mortem corpse clearance upstream of the nuclease BFN1, ANAC046 restricts the life span of columella root cap cells after their shedding into the rhizosphere. These results uncovered a previously unrecognized cell death process in the columella root cap (Huysmans M, et al., Plant Cell 2018 Sep;30(9):2197-2213). Furthermore, a collaboration with the lab of Prof. Tom Beeckman (VIB-UGent Center for Plant Systems Biology) has revealed that root cap PCD contributes to the patterning of lateral root primordia via the release of auxin to surrounding root tissues (Xuan W, et al., Science 2016 Jan 22;351(6271):384-387). Thanks to our expertise on the root cap, we also contributed to a publication of Christiane Nawrath’s lab (Université de Lausanne, Switzerland) showing the existence of a previously unknown extracellular cuticular structure on the root cap important for seedling stress resilience and emerging of lateral roots (Berhin A, et al., Cell. 2019 Mar 7;176(6):1367-1378).
Together with the lab of Dr. Thomas Jacobs (VIB-UGent Center for Plant Systems Biology) we developed CRISPR-TSKO, a novel technology to target CRISPR/Cas genome editing to specific plant cell types, tissues, or organs. This technological breakthrough will enable us to restrict mutagenesis to the root cap, circumventing potentially lethal effects of PCD manipulation in essential vegetative or reproductive tissues (Decaestecker W, et al., Plant Cell. 2019 Dec;31(12):2868-2887).
In addition to discoveries in the Arabidopsis root cap, PROCELLDEATH has also spurred discoveries in other plant organs. We revealed that an age-induced PCD process in the floral stigma terminates flower receptivity in Arabidopsis, and identified a transcription factor, KIRA1, that controls this process (Gao Z, et al., Nature Plants. 2018 Jun;4(6):365-375.) In a collaboration with Arp Schnittger (University of Hamburg, Germany), we discovered a cell-cycle module that controls timely entry into the meiosis, prior to cell death of the non-functional megaspores (Zhao X, et al., Science. 2017 Apr 28;356(6336):eaaf6532).
In addition to these publications, PROCELLDEATH funding also contributed decisively to the consolidation of the plant protease and programmed cell death community. These developments are showcased by the organization of the 4th Plant Programmed Cell Death and Protease Symposium in Gent (2018), and the publication of a number of review articles on plant programmed cell death over the last five years (Buono RA, et al., J Exp Bot. 2019 Apr 12;70(7):2097-2112; Huysmans M, et al., Curr Opin Plant Biol. 2017 Feb;35:37-44; Daneva A, et al., Annu Rev Cell Dev Biol. 2016 Oct 6;32:441-468; Van Durme M, et al., Curr Opin Plant Biol. 2016 Feb;29:29-37; Kumpf RP, et al., J Exp Bot. 2015 Sep;66(19):5651-62).
Finally, PROCELLDEATH also laid the foundation for a collaboration with a major agricultural chemical and seed company. The aims of this alliance are to exploit the fundamental knowledge on plant PCD as a basis to improve the stress resilience and yield stability of crop plants.
A major innovative aspect of PROCELLDEATH has been the combination of developmental genetics and advanced imaging techniques in the context of PCD. PCD is a fast process followed by rapid clearance of the cellular contents, making it difficult to detect or visualize. We have countered these challenges with the development of tools that enable cutting-edge live-cell imaging approaches. Furthermore, by CRISPR-TSKO we are able produce root-cap specific mutant phenotypes, enabling us to overcome both genetic redundancy and mutant lethality in the future investigation of plant PCD processes. Finally, we applied computational modelling approaches to describe the intricate four-dimensional pattern of root cap differentiation and PCD in the context of the growing root tip. This challenging approach will provide important information for root cap development and root growth at large.
With the knowledge and the tools that we developed in the course of PROCELLDEATH, we are now in the pole position to further dissect the PCD gene regulatory network, as well as to tackle the most challenging aspect of cell death research – to identify the actual mechanisms are employed to actively terminate the vital functions of a cell in a controlled fashion during plant PCD.