Research

Research group: Plant-Microbe Interactions

Title: Searching the Sugar Beet Seed Microbiome for Cercosporin Resistant Traits.           
Abstract: Cercosporin is a phototoxic fungal secondary metabolite produced by members of the fungal genus Cercospora. One member of this genus, Cercospora beticola is the leading cause for sugar beet crop destruction. Recent studies have proven that C.beticola is able to remain dormant in the sugar beet seed coat until the plant is susceptible to colonization. It is perhaps possible that due to this, there are microbial members of the sugar beet seed microbiome that interact with cercosporin in an inhibitory or resistant manner. Currently little is known about C.beticola or cercosporin’s interaction with the seed microbiome. Here we explored the possibility that the seed microbiome contains genetic or physical resistance to cercosporin using the relatively new and evolving method of microbial GWAS (mGWAS).

What we found was a possible link between the microbial production of prephenate dehydrogenase and increased cercosporin inhibition. Additional research is recommended to confirm this link as well as study any other physical factors that could be contributing to the microbial relationship with cercosporin. As C.beticola is possibly able to utilize the product of prephenate dehydrogenase, L-tyrosine, it may also be reasonable to assume that it also exploits the production of L-tyrosine by arogenate dehydrogenase in plants 

Research group: Developmental Biology

Title: Bubl Trouble: BUBL-1 function in relation to intermediate filaments and V-ATPases.          
Abstract: The maintenance of tubular tissue structure and function is vital for homeostasis of an animal’s body, however many of the mechanisms regulating this remain elusive. The Caenorhabditis elegans intestine is an excellent model system to study and understand such integrity regulating mechanisms. BUBL-1 was previously identified as a regulator of lumen morphology and loss of bubl-1 leads to the formation of protrusions from the intestinal lumen. Interaction analyses showed that BUBL-1 interacts with intermediate filaments (IF) and V-ATPase proteins. We therefore aimed to understand the role of BUBL-1 in the maintenance of lumen morphology through its interactions with IFs and V-ATPases.

We show that the localization of BUBL-1 in the intestinal cells is dependent on the IF network structure, through direct interactions between BUBL-1 and the IFs. BUBL-1 is required for the maintenance of the IF network at all stages of C. elegans development, and loss the of bubl-1 greatly compromises the IF network structure. Additionally, V-ATPases and BUBL-1, which do not clearly co-localize at any major tissue, interact in the intestinal cells and are mutually dependent on their localization to the apical membrane of the intestinal cells. We propose a model in which BUBL-1, through its interaction with V-ATPases, regulates the structure of the IF network. The results of this study may have implications in understanding the mechanisms underpinning the maintenance of the lumen morphology.

Research group: Structural Biochemistry

Title: Catching targeting factors involved in co-translational import into mitochondria. 
Abstract: Nuclear-encoded genes encode 99 % of the mitochondrial proteome. Proteins translated from these genes are targeted to the mitochondria before they are imported into the organelle. This targeting and import can be post-translationally or co-translationally, of which the latter is not well described. In S.cerevisiae, there is evidence of proteins being co-translationally targeted through their N-terminal mitochondrial targeting sequence (MTS). Moreover, the nascent polypeptide-associated complex (NAC) has been shown to interact with ribosome nascent-chain complexes (RNCs). It has interaction partners on the mitochondrial membrane, suggesting it is an essential co-translational targeting chaperone. In mammalian systems, there is also evidence of MTS-based co-translational import. However, it is unknown which targeting factors are involved. The only structural data on co-translational targeting consist of a C.elegans 60s ribosome-NAC single particle analysis (SPA) reconstruction, showing that NAC probes the ribosomal exit tunnel. Therefore, this thesis aimed to find targeting factors like NAC in yeast and mammalian systems.

To find targeting factors in mammalian systems, OTC truncations containing a CMV stalling peptide and an S1 aptamer were successfully translated in a rabbit reticulocyte lysate (RRL) in vitro translation system to generate stalled RNC complexes. The RNCs and ribosomes were successfully isolated from the RRL reaction mixture and imaged using negative stain electron microscopy (EM) and Cryo-EM, revealing aggregation of the generated RNCs. Moreover, affinity purification of the RNCs, using the S1 aptamer was attempted, which resulted in unspecific binding of the RNCs to the beads. To study co-transitional import into the mitochondria in S.cerevisiae, an in vitro translation system was successfully established and optimized in the lab. Moreover, this system successfully translated truncated MDH1 RNCs also containing a CMV stalling peptide and an S1 aptamer. The RNCs and ribosomes were successfully isolated from the yeast lysate in vitro reaction mixture and imaged using negative stain EM, revealing non-aggregating 80s S.cerevisiae ribosomes. Moreover, affinity purification of the RNCs, using the S1 aptamer was attempted, which resulted in unspecific binding of the RNCs to the beads.

 Some of the track-affiliated research groups are:

• Cell Biology, Neurobiology and Biophysics
• Genome Biology and Epigenetics
• Developmental Biology
• Theoretical Biology & Bioinformatics
• Molecular Microbiology
• Plant Stress Resilience
• Translational Plant Biology
• Plant-Environment Signalling
• Plant-Microbe Interactions
• Fertility and Reproduction – Veterinary Medicine
• Cell Biology -UMCU
• Bacterial Infections and Immunity – UMCU
• Molecular Cancer Research – UMCU
• Several groups from the Hubrecht Institute and the Prinses Maxima Centrum

Some of the track-affiliated research groups are:

• Cell Biology, Neurobiology and Biophysics
• Developmental Biology
• Biomolecular Mass Spectrometry and Proteomics
• Cellular Protein Chemistry
• Membrane Biochemistry and Biophysics
• NMR Spectroscopy
• Structural Biochemistry
• Chemical Biology and Drug Discovery
• Virology – Veterinary Medicine
• Cell Biology, Metabolism & Cancer – Veterinary Medicine
• Infectious Diseases and Immunology – Veterinary Medicine
• Cell Biology – UMCU
• Clinical Chemistry – UMCU
• Bacterial Infections and Immunity – UMCU
• Molecular Cancer Research – UMCU
• Several groups from the Hubrecht Institute and the Prinses Maxima Centrum

Some of the track-affiliated research groups are:

• Cell Biology, Neurobiology and Biophysics
• Biomolecular Mass Spectrometry and Proteomics
• Membrane Biochemistry and Biophysics
• NMR Spectroscopy
• Structural Biochemistry
• Molecular Biophysics