Project


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Projects

DFG Emmy Noether Project: Proteolytic degradation pathways and their role in plant immunity (2018-2024)

The interplay between endomembranes and autophagy

Proteomic analysis of possible targets of pathogen-induced autophagy led to the discovery that in addition to the proteasome, other pathways such as RNA metabolism, protein translation and vesicle trafficking might be autophagy targets or regulators. Based on this preliminary data we have identified a vesicle trafficking component as a novel modulator of autophagy (Gouguet et al., unpublished). It appears that the loss of this and other trafficking components and interference with protein secretion at ER exit sites modulates autophagy responses revealing a novel layer of crosstalk between the endomembrane system and autophagy mechanism. 

Bacterial effector proteins as probes to dissect cellular degradation pathways

Using Pseudomonas and Xanthomonas effectors we have systematically screened them for their ability to interfere with proteasome function and autophagy. IP-MS experiments with candidate effector proteins revealed a subset of effectors interacting with autophagy components. So far, we have identified a Xanthomonas effector that is able to target an autophagy component to modulate autophagic turnover (Leong et al., in preparation), which we will further characterize using cell biological and biochemical approaches. We will extend our studies to other effector proteins and are  currently using the CRISPR/Cas9 technology to engineer tomato plants with altered proteolytic profiles.

SFB1101 : Molecular Enoding of Specificity in Plant Processes (since 2019)

Specificity of proteasome regulation during plant immunity

Regulatory fine-tuning of the proteasome is central to the outcome of plant-microbe interactions and seems to be a sensitive combination between down- and up-regulation of its activity. Therefore, we are currently analysing the mechanistic insights of how the proteasome is regulated on the transcriptional and post-translational level during plant immunity in a project funded through the CRC1101. Within this project we have identified two transcription factors that regulate proteasome gene expression during bacterial infection (Langin et al., unpublished). Interaction studies with both transcription factors revealed various proteins implicated in their degradation via the ERAD system and trafficking to the nucleus from the ER. Currently, we are looking into additional target genes of these transcription factors as they seem to mediate the trade-off between proteasome activation, growth and defence.

 

Manipulation of protein translation as a virulence strategy of pathogenic bacteria (Boehringer Ingelheim Foundation/Rise Up!)

Protein homeostasis is epitomized by a tight equilibrium of protein biosynthesis and degradation; the ‘life and death’ of proteins. Approximately one-third of newly synthesized proteins are degraded. As such, regulated protein translation and turnover are tightly regulated to maintain cellular integrity and survival. Thus, the control of protein homeostasis in response to environmental stimuli has emerged as a strategy to respond to perturbations ranging from ageing to pathological diseases in animals, and plants. Recent evidence suggests that protein degradation pathways are required to maintain immune responses and hence it is also targeted by pathogens. In addition, there is mounting evidence that translational reprogramming occurs upon various stresses in different systems. To allow rapid, versatile, and cost-efficient responses to sudden environmental changes, eukaryotes utilize reversible translational arrest caused by compartmentalization of transcripts in cytosolic membraneless aggregates formed by phase separation. One such type of aggregates are processing bodies (PBs), dynamic ribonucleoprotein aggregates conserved among eukaryotes. PBs are involved in translational arrest, mRNA decay and both RNA and protein quality control and regulate several developmental processes and responses to abiotic stresses. However, our knowledge of how and under which conditions PBs are formed as well as if PBs are hijacked by pathogens to manipulate protein translation is unknown. Based on our previous work on PBs and their involvement in host-bacteria interactions we propose to study how bacteria utilize PBs to repress translation for their own benefit. We aim to use our model system to understand the composition and formation of PBs during stress conditions. With this, we expect to uncover the holistic picture of how proteostasis on the level of protein translation controls immune responses and hence is exploited by pathogenic bacteria. Understanding the fundamental molecular mechanisms of how translation is modulated during disease will contribute towards developing novel strategies to combat diseases and environmental challenges.

 

ERC Starting Grant: DIVERSIPHAGY (since 2021)

In a more complete scenario, plants are constantly exposed to different pathogenic and beneficial microbes and hence it is crucial to include the bacteriome (microbiome) into this equation to obtain a holistic picture of the role of autophagy in plant-microbe interactions. The picture is getting even more complex if we look at cell-type specific autophagy response on the plant side. By studying how the microbiome and how different cell-types might shape autophagy and vice versa, we will get a deeper understanding of the role of autophagy in plant-microbe interactions. Thus, we will study in the ERC Starting Grant funded project DIVERSIPHAGY following questions and objectives:

  • How does the bacteriome impact autophagy and vice versa?
  • Can we use the bacteriome to identify the autophagy degradome and novel autophagy factors?
  • Do bacteria shape tissue and cell-type specific modulation of autophagy?

In DIVERSIPHAGY, we will use a combination of state-of-the-art biochemical, proteomic, single-cell transcriptomics and cell-type specific reverse genetic approaches to decipher the role of autophagy in plant-microbe interactions. We aim to obtain a holistic view of how autophagy plays a role in plant-microbe interactions utilizing bacterial, genetic and cellular diversity with an emphasis on cell-type and organ-specific autophagy responses.