Eukaryotic cells maintain proteostasis by quality control (QC) degradation. These pathways can specifically target a wide variety of distinct misfolded proteins, and so are important for management of cellular stress. Although a number of conserved QC pathways have been described in yeast, the E3 ligases responsible for cytoplasmic QC are unknown. We now show that Ubr1 and San1 mediate chaperone-dependent ubiquitination of numerous misfolded cytoplasmic proteins. This action of Ubr1 is distinct from its role in the "N-end rule." In this capacity, Ubr1 functions to protect cells from proteotoxic stresses. Our phenotypic and biochemical studies of Ubr1 and San1 indicate that two strategies are employed for cytoplasmic QC: chaperone-assisted ubiquitination by Ubr1 and chaperone-dependent delivery to nuclear San1. The broad conservation of Ubr ligases and the relevant chaperones indicates that these mechanisms will be important in understanding both basic and biomedical aspects of cellular proteostasis.chaperone | proteostasis | misfolding P rotein quality control (QC) functions to ensure that damaged and misfolded proteins are maintained at acceptable levels to limit their stress-causing, or proteotoxic, effects. One strategy of protein QC is the selective degradation of misfolded proteins. For degradative QC pathways to be effective, they must be specific for aberrant proteins; sufficiently general to recognize selectively common structural hallmarks shared by numerous unrelated proteins; and physiologically important, better allowing the cell to survive proteotoxic stress. Because protein QC underlies many pressing maladies, such as parkinsonism, cystic fibrosis, and aging, discovery of the rules of substrate selectivity and destruction is a key step in understanding these conditions and designing appropriate therapeutical interventions to combat them.In eukaryotes, the ubiquitin proteasome system is employed in the selective degradation of many proteins (1). A substrate protein is marked for degradation by assembly of a polyubiquitin chain, initiated by covalent addition of the small (7.6 kDa) protein ubiquitin to a lysine in an isopeptide bond, followed by iterative addition of the next ubiquitin to the previously added one to create a polyubiquitin chain that is uniquely recognized by the 26S proteasome. Protein ubiquitination is catalyzed by a three-enzyme cascade. The single E1 ubiquitin-activating enzyme hydrolyzes ATP to acquire ubiquitin in labile thioester linkage, which is then transferred in thioester linkage to one of a small group of E2s or ubiquitin-conjugating enzymes (UBCs). E2-bound ubiquitin is finally transferred to an isopeptide linkage on the target protein or the growing polyubiquitin chain by the action of the E3 ubiquitin ligase. It is the E3 ubiquitin ligase that determines the specificity of a given ubiquitination process; identifying and understanding the E3s involved in a degradative pathway are thus key parts of understanding the mechanisms of substrate selection and modification.E3s ...

Pyruvate, orthophosphate dikinase (PPDK; E.C.2.7.9.1) is most well known as a photosynthetic enzyme in C4 plants. The enzyme is also ubiquitous in C3 plant tissues, although a precise non-photosynthetic C3 function(s) is yet to be validated, owing largely to its low abundance in most C3 organs. The single C3 organ type where PPDK is in high abundance, and, therefore, where its function is most amenable to elucidation, are the developing seeds of graminaceous cereals. In this report, we suggest a non-photosynthetic function for C3 PPDK by characterizing its abundance and posttranslational regulation in developing Oryza sativa (rice) seeds. Using primarily an immunoblot-based approach, we show that PPDK is a massively expressed protein during the early syncitial-endosperm/-cellularization stage of seed development. As seed development progresses from this early stage, the enzyme undergoes a rapid, posttranslational down-regulation in activity and amount via regulatory threonyl-phosphorylation (PPDK inactivation) and protein degradation. Immunoblot analysis of separated seed tissue fractions (pericarp, embryo + aleurone, seed embryo) revealed that regulatory phosphorylation of PPDK occurs in the non-green seed embryo and green outer pericarp layer, but not in the endosperm + aleurone layer. The modestly abundant pool of inactive PPDK (phosphorylated + dephosphorylated) that was found to persist in mature rice seeds was shown to remain largely unchanged (inactive) upon seed germination, suggesting that PPDK in rice seeds function in developmental rather than in post-developmental processes. These and related observations lead us to postulate a putative function for the enzyme that aligns its PEP to pyruvate-forming reaction with biosynthetic processes that are specific to early cereal seed development.

In a mixed-race population of over 20,000 U.S. patients, CYP gene polymorphisms associated with DDIs and other interaction threats were prevalent, and most individuals were not categorized as normal metabolizers of all five CYP isozymes of interest.

Chaperones can mediate both protein folding and degradation. This process is referred to as protein triage, which demands study to reveal mechanisms of quality control for both basic scientific and translational purposes. In yeast, many misfolded proteins undergo chaperone dependent ubiquitination by the action of E3 ligases Ubr1 and San1, allowing detailed study of protein triage. In cells, both HSP70 and HSP90 mediated substrate ubiquitination, and the canonical ATP cycle was required for HSP70’s role: we have found that ATP hydrolysis by HSP70, the nucleotide exchange activity of SSE1, and the action of J proteins are all needed for Ubr1 mediated quality control. To discern if chaperones were directly involved in Ubr1-mediated ubiquitination, we developed a bead-based assay with covalently immobilized but releasable misfolded protein to obviate possible chaperone effects on substrate physical state or transport. In this in vitro assay, only HSP70 was required, along with its ATPase cycle and relevant cochaperones, for Ubr1-mediated ubiquitination. The requirement for the HSP70 ATP cycle in ubiquitination suggests a possible model of triage, in which efficiently folded proteins are spared, while slow- or non-folding proteins are iteratively tagged with ubiquitin for subsequent degradation.