Project description:RNF213 is novel transthiolating E3 ligase that is activated by ATP. To determine whether cellular RNF213 is activated by elevated ATP levels, we electroplated an E3 activity-based probe into HEK293 cells stably expressing RNF213 in a knockout background. DIA analysis was performed in cells that were coelectroporated with the poorly hydrolysable ATP analog, ATPgS, or buffer control.
Project description:Homeostatic control of intracellular ionic strength is essential for protein, organelle and genome function, yet mechanisms that sense and enable adaptation to ionic stress remain poorly understood in animals. We find that the transcription factor NFAT5 directly senses solution ionic strength using a C-terminal intrinsically disordered region. Both in intact cells and in a purified system, NFAT5 forms dynamic, reversible biomolecular condensates in response to increasing ionic strength. This self-associative property, conserved from insects to mammals, allows NFAT5 to accumulate in the nucleus and activate genes that restore cellular ion content. Mutations that reduce condensation or those that promote aggregation both reduce NFAT5 activity, highlighting the importance of optimally tuned associative interactions. To investigate the composition of NFAT5 condensates in response to hypertonic stress, proteins in close proximity of NFAT5 were identified using a variant of NFAT5 fused to TurboID as bait. Hypertonic stress increases NFAT5 proximity to protein complexes belonging to the GO gene sets of “transcription coactivator activity” and “positive regulation of DNA templated transcription initiation.” Closer inspection revealed that the association between NFAT5 and two transcriptional co-activators (the mediator complex and BRD4) and RNAPII itself increased in response to hypertonic stress.
Project description:SDE2, a highly conserved and essential gene required for genome maintenance, coordinates essential processes ranging from pre-mRNA splicing and ribosome biogenesis to DNA repair and replication stress response. It is expressed as a full-length precursor (SDE2FL,) bearing an N-terminal ULD, which is proteolytically cleaved to generate two protein fragments, SDE2UBL and the larger C-terminal domain (SDE2CT). In this study we report the identification of the protease responsible for SDE2 processing, resolving a previously uncharacterized mechanism of post-translational regulation.
Project description:SDE2, a highly conserved and essential gene required for genome maintenance, coordinates essential processes ranging from pre-mRNA splicing and ribosome biogenesis to DNA repair and replication stress response. It is expressed as a full-length precursor (SDE2FL,) bearing an N-terminal ULD, which is proteolytically cleaved to generate two protein fragments, SDE2UBL and the larger C-terminal domain (SDE2CT). Here we report the use of activity-based probe to aid the identification of the protease responsible for SDE2 processing, resolving a previously uncharacterized mechanism of post-translational regulation.
Project description:Methods to affinity purify proteins are widely used in protein research. One important application is to identify interacting proteins of an affinity-purified protein of interest (POI) by mass spectrometry. Here, we developed an optogenetics-derived and light-controlled affinity purification method based on the light-regulated reversible protein interaction between phytochrome B (PhyB) and its phytochrome interacting factor 6 (PIF6). We engineered a truncated variant of PIF6 comprising only 22 amino acids that can be genetically fused to the POI as an affinity tag. Thereby the POI can be purified with PhyB-functionalized resin material using 660 nm light for binding and washing and 740 nm light for elution. As proof-of-concept, we expressed PIF-tagged variants of the tyrosine kinase ZAP70 in ZAP70-deficient Jurkat T cells, purified ZAP70 and associating proteins using our light-controlled system and identified the interaction partners by mass spectrometry
Project description:Differential proteome composition of wild-type yeast cells (S. cerevisiae BY4741) grown at 30 ºC or 37 ºC was studied using SILAC based quantitative proteomics.