Biology subjects

van Wijlick, L.

Publications and source records attributed to van Wijlick, L..

4 recordsLinked to original sources

bioRxiv2026

Ubp3 mediates dynamic deubiquitination of mitochondria upon induction of mitophagy

Ensuring quality and maintenance of mitochondria within eukaryotic cells is important for cellular fitness. One critical pathway that needs to be tightly controlled to achieve this is mitophagy, which is negatively regulated by the deubiquitinase Ubp3 in Saccharomyces cerevisiae. Here we show that beyond this established role of Ubp3, it is critical to mediate substantial temporal changes of the mitochondrial ubiquitin landscape during mitophagy. Isolated mitochondria displayed extensive ubiquitination under steady-state conditions, whereas rapamycin-mediated induction of mitophagy/autophagy led to a progressive elimination of mitochondrial ubiquitination. A systematic screening analysis revealed that Ubp3 and Ubp4 are crucial regulators of rapamycin-induced mitochondrial deubiquitination. Deletion of Bre5, a cofactor of Ubp3, or of the UBI4 gene, encoding Ubi4 required for mitophagy, did not impair deubiquitination of mitochondria during mitophagy, indicating that Ubp3 has additional functions. We further showed that Ubi4 acts epistatic to Ubp3 for regulating mitophagy, supporting that mitophagy does not simply depend on the extent of mitochondrial ubiquitination, but rather on specific ubiquitinated substrates. Consistent with the role of Ubp3 in vivo, purified Ubp3 or its catalytic domain alone were sufficient to efficiently deubiquitinate isolated mitochondria in vitro in a Bre5-independent manner. Together, these findings highlight Ubp3 as a prominent rheostat of mitochondrial ubiquitin remodelling, revealing mitochondrial ubiquitin storage and its dynamic release as another layer of stress regulation by ubiquitin-dependent quality control pathways.

cell biology↗

bioRxiv2026

Species Context Reverses PPIP5K Control of Fungal Morphogenesis and Actin Organization

Inositol pyrophosphates are conserved signaling molecules synthesized by the bifunctional PPIP5K enzymes, but how their cellular functions diversify across species remains poorly understood. Here, we compared the PPIP5K enzyme Asp1 in the fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus and in the distantly related fungus Ustilago maydis. All three homologs retained a conserved kinase-phosphatase architecture and catalytic activity. However, whereas Asp1 produced broadly similar effects on actin organization and morphogenesis in S. pombe and U. maydis, its regulatory output was reversed in S. japonicus. In S. pombe and U. maydis, Asp1 positively supported Arp2/3-dependent actin functions, as loss of Asp1 increased sensitivity to the Arp2/3 inhibitor CK666. In contrast, deletion of asp1 in S. japonicus conferred strong CK666 resistance and caused excessive, spatially deregulated actin-patch organization. This opposing cytoskeletal phenotype was mirrored at the level of morphogenesis: Asp1 restricted the yeast-to-hypha transition in S. japonicus, whereas Asp1 was required for pseudohyphal growth in S. pombe and for filamentous development in U. maydis. However, the negative regulatory activity observed in S. japonicus was not an intrinsic property of the SjAsp1 protein. When expressed in S. pombe, SjAsp1 promoted invasive pseudohyphal growth, reproducing the regulatory output of the S. pombe Asp1 morphogenesis pathway rather than that of its native species. Similarly, SjAsp1 supported Arp2/3 functions when expressed in S. pombe. Thus, SjAsp1 adopted the functional behavior imposed by the host cellular environment. S. pombe Asp1 was originally identified as a suppressor of Arp2/3-complex mutant phenotypes, establishing a genetic connection between Asp1 and the actin nucleator. Extending this link, affinity enrichment with inositol pyrophosphates reagents recovered all seven subunits of the S. pombe Arp2/3 complex, providing biochemical support for a potential association between inositol pyrophosphate and Arp2/3. Together, these findings identify S. japonicus as a functional outlier in which a conserved PPIP5K pathway produces an opposing biological output. They further demonstrate that this divergence is determined primarily by species-specific cellular networks rather than by intrinsic differences in the Asp1 protein.

cell biology↗

bioRxiv2026

LUstiGE, Light responsive Ustilago maydis Gene Expression: Optogenetic control of morphogenesis and pathogenesis in the corn fungal pathogen Ustilago maydis

The basidiomycete Ustilago maydis is a well-characterized model organism for studying pathogen-host interactions and of great interest for a broad spectrum of biotechnological applications. We set here to develop light inducible molecular tools to enable dynamic studies on signaling networks and fungi-host communication, and for metabolic engineering approaches. In particular, light-controlled, optogenetic switches provide quantitative, spatio-temporal control capabilities, are minimal invasive and reversible. We engineered two blue light-inducible LOV-domain-based gene expression switches, to up- (Blue-ON) and down-regulate (Blue-OFF) gene expression, and performed a functional characterization in sporidia and hyphae of U. maydis. Profiting from the dynamic control ranges and rapid kinetics, we implemented the optoswitches to control cell morphology by initiating the transition from a haploid sporidial cellular morphotype to filaments upon regulation of the levels of the polarity factor Rac1 and its constitutive active mutant Q61L. In addition to showing how expression level of effectors can be precisely regulated as an approach to understand fungi-plants interaction, we show in two proof-of-principle applications targeted control over U. maydis filamentous fungal invasion of plant tissue and the mechanisms of tumor formation. For this we placed under Blue-ON and Blue-OFF control two U. maydis effectors, See1 (Seedling efficient effector 1) and TIN2 (Tumor inducing 2), and tumor formation was assayed on maize leaves. Taken together, this study established blue-light switches as effective tools to control morphogenesis and pathogenesis in U. maydis.

synthetic biology↗

bioRxiv2023

Metabolic reprogramming during Candida albicans planktonic-biofilm transition is modulated by the ZCF15 and ZCF26 paralogs

Candida albicans is a commensal of the human microbiota that can form biofilms on implanted medical devices. These biofilms are tolerant to antifungals and to the host immune system. To identify novel genes modulating C. albicans biofilm formation, we performed a large-scale screen with 2454 C. albicans doxycycline-dependent overexpression strains and identified 16 genes whose overexpression significantly hampered biofilm formation. Among those, overexpression of the ZCF15 and ZCF26 paralogs that encode transcription factors and have orthologs only in biofilm-forming species of the Candida clade, caused impaired biofilm formation both in vitro and in vivo. Interestingly, overexpression of ZCF15 specifically impeded biofilm formation without any defect in hyphal growth. Transcript profiling, transcription factor binding, and phenotypic microarray analyses conducted upon overexpression of ZCF15 and ZCF26 demonstrated their direct role in reprogramming cellular metabolism by regulating glycolytic cycle and tricarboxylic acid cycle genes. Taken together, this study has identified a new set of biofilm regulators, including ZCF15 and ZCF26, that appear to control biofilm development through their specific role in metabolic remodeling.

microbiology↗