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Biology subjects

Schubert, H. L.

Publications and source records attributed to Schubert, H. L..

4 recordsLinked to original sources

Mutations that prevent phosphorylation of the BMP4 prodomain impair proteolytic maturation of homodimers leading to early lethality in mice

Bone morphogenetic protein4 (BMP4) plays numerous roles during embryogenesis and can signal either alone as a homodimer, or together with BMP7 as a more active heterodimer. BMPs are generated as inactive precursor proteins that dimerize and are cleaved to generate the bioactive ligand and inactive prodomain fragments. In humans, heterozygous mutations within the prodomain of BMP4 are associated with birth defects. We studied the effect of two of these mutations (p.S91C and p.E93G), which disrupt a conserved FAM20C phosphorylation motif, on ligand activity. We compared the activity of ligands generated from BMP4, BMP4S91C or BMP4E93G in Xenopus embryos and found that these mutations reduce the activity of BMP4 homodimers but not BMP4/7 heterodimers. We generated Bmp4S91C and Bmp4E93Gknock-in mice and found that Bmp4S91C/S91C mice die by E11.5 and display reduced BMP activity in multiple tissues including the heart. Most Bmp4E93G/E93G mice die before weaning and Bmp4-/E93Gmutants die prenatally with reduced or absent eyes, heart and ventral body wall closure defects. Mouse embryonic fibroblasts (MEFs) isolated from Bmp4S91C and Bmp4E93G embryos show accumulation of BMP4 precursor protein, reduced levels of cleaved BMP ligand and reduced BMP activity relative to MEFs from wild type littermates. Because Bmp7 is not expressed in MEFs, the accumulation of unprocessed BMP4 precursor protein in mice carrying these mutations most likely reflects an inability to cleave BMP4 homodimers, leading to reduced levels of ligand and BMP activity in vivo. Our results suggest that phosphorylation of the BMP4 prodomain is required for proteolytic activation of BMP4 homodimers, but not heterodimers. Summary StatementMutations associated with birth defects in humans that prevent phosphorylation of the BMP4 prodomain preclude proteolytic activation of the precursor protein

cell biology↗

Tom1p ubiquitin ligase structure, interaction with Spt6p, and function in maintaining normal transcript levels and the stability of chromatin in promoters

Phosphorylation-dependent binding of the S. cerevisiae Spt6p tSH2 domain (Spt6ptSH2) to the Rbp1p subunit of RNA polymerase II supports efficient transcription. Here, we report that Spt6ptSH2 also binds the HECT-family E3 ubiquitin ligase Tom1p, a homolog of human HUWE1. Tom1p/HUWE1 have been implicated in targeting many small basic proteins for degradation, including excess ribosomal subunits and histones, although the mechanism of substrate recognition is not known. Our cryo-EM data revealed that Tom1p can adopt a compact -solenoidal "basket" similar to the previously described structure of HUWE1, with the central cavity partially occupied by a disordered acidic domain. Sub-regions of this acidic domain supported binding to Spt6p or histones/nucleosomes in vitro, and the histone-binding region was important for Tom1p function in vivo. We also visualized Tom1p in more extended forms, and speculate that transitions among these forms could be important for substrate selection and ubiquitylation. Genomic analyses provided additional support for the previously observed role for Tom1p in maintaining ribosomal protein pools, and also demonstrated a role in maintaining chromatin structure near genes. This suggests that the interaction with Spt6ptSH2 affects substrate specificity by anchoring Tom1p to localized environments where histone ubiquitylation alters chromatin architecture.

molecular biology↗

Visualization of the Cdc48 AAA+ ATPase protein unfolding pathway

The Cdc48 AAA+ ATPase is an abundant and essential enzyme that unfolds substrates in multiple protein quality control pathways. The enzyme includes two conserved AAA+ ATPase cassettes, D1 and D2, that assemble as hexameric rings with D1 stacked above D2. Here, we report an ensemble of structures of Cdc48 affinity purified from lysate in complex with the adaptor Shp1 in the act of unfolding substrate. Our analysis reveals a continuum of structural snapshots that spans the entire translocation cycle. These data reveal new elements of Shp1-Cdc48 binding and support a "hand-over-hand" mechanism in which the sequential movement of individual subunits is closely coordinated. D1 hydrolyzes ATP and disengages from substrate prior to D2, while D2 rebinds ATP and re-engages with substrate prior to D1, thereby explaining the dominant role played by D2 in substrate translocation/unfolding.

biochemistry↗

Protein-Metabolite Interactomics Reveals Novel Regulation of Carbohydrate Metabolism

Metabolism is highly interconnected and also has profound effects on other cellular processes. However, the interactions between metabolites and proteins that mediate this connectivity are frequently low affinity and difficult to discover, hampering our understanding of this important area of cellular biochemistry. Therefore, we developed the MIDAS platform, which can identify protein-metabolite interactions with great sensitivity. We analyzed 33 enzymes from central carbon metabolism and identified 830 protein-metabolite interactions that were mostly novel, but also included known regulators, substrates, products and their analogs. We validated previously unknown interactions, including two atomic-resolution structures of novel protein-metabolite complexes. We also found that both ATP and long-chain fatty acyl-CoAs inhibit lactate dehydrogenase A (LDHA), but not LDHB, at physiological concentrations in vitro. Treating cells with long-chain fatty acids caused a loss of pyruvate/lactate interconversion, but only in cells reliant on LDHA. We propose that these regulatory mechanisms are part of the metabolic connectivity that enables survival in an ever-changing nutrient environment, and that MIDAS enables a broader and deeper understanding of that network.

biochemistry↗