Small angle X-ray scattering study of the yeast prion Ure2p

Structural stability of E. coli trigger factor studied by synchrotron small-angle X-ray scattering

Solution small-angle X-ray scattering (SAXS) is an effective technique for quantitatively measuring the compactness and shape of proteins. We use SAXS to study the structural characteristics and unfolding transitions induced by urea for full length Escherichia coli trigger factor (TF) and a series of truncation mutants, obtaining and comparing the radiuses of gyration (Rg), the distance-distribution function (P(r) function) and integrated intensity of TF variants in native and unfolding states. The C-terminal 72-residue truncated mutant TF360 exhibited dramatic structural differences and reduced stability compared with the whole TF molecule, while the N-domain truncated mutant MC maintained its compact structure with reduced stability. These results indicate that the C-terminal region of TF plays an important role in the structural and conformational stabilities of the TF molecule, while the N-domain is relatively independent.

Deletion of a Ure2 C-terminal prion-inhibiting region promotes the rate of fibril seed formation and alters interaction with Hsp40

Prions are proteins that can undergo a heritable conformational change to an aggregated amyloid-like state, which is then transmitted to other similar molecules. Ure2, the nitrogen metabolism regulation factor of Saccharomyces cerevisiae, shows prion properties in vivo and forms amyloid fibrils in vitro. Ure2 consists of an N-terminal prion-inducing domain and a C-terminal functional domain. Previous studies have shown that mutations affecting the prion properties of Ure2 are not restricted to the N-terminal prion domain: the deletion of residues 151-158 in the C-domain increases the in vivo prion-inducing propensity of Ure2. Here, we characterized this mutant in vitro and found that the 151-158 deletion has minimal effect on the thermodynamic stability or folding properties of the protein. However, deletion of residues 151-158 accelerates the nucleation, growth and fragmentation of amyloid-like aggregates in vitro, and the aggregates formed are able to seed formation of fibrils of the wild-type protein. In addition, the absence of 151-158 was found to disrupt the inhibitory effect of the Hsp40 chaperone Ydj1 on Ure2 fibril formation. These results suggest that the enhanced in vivo prion-inducing ability of the 151-158 deletion mutant is due to its enhanced ability to generate prion seeds.

The yeast prion protein Ure2: Structure, function and folding

The Saccharomyces cerevisiae protein Ure2 functions as a regulator of nitrogen metabolism and as a glutathione-dependent peroxidase. Ure2 also has the characteristics of a prion, in that it can undergo a heritable conformational change to an aggregated state; the prion form of Ure2 loses the regulatory function, but the enzymatic function appears to be maintained. A number of factors are found to affect the prion properties of Ure2, including mutation and expression levels of molecular chaperones, and the effect of these factors on structure and stability are being investigated. The relationship between structure, function and folding for the yeast prion Ure2 are discussed.

The Yeast Prion Protein Ure2 Shows Glutathione Peroxidase Activity in Both Native and Fibrillar Forms

Ure2p is the precursor protein of the Saccharomyces cerevisiae prion [URE3]. Ure2p shows homology to glutathione transferases but lacks typical glutathione transferase activity. A recent study found that deletion of the Ure2 gene causes increased sensitivity to heavy metal ions and oxidants, whereas prion strains show normal sensitivity. To demonstrate that protection against oxidant toxicity is an inherent property of native and prion Ure2p requires biochemical characterization of the purified protein. Here we use steady-state kinetic methods to characterize the multisubstrate peroxidase activity of Ure2p using GSH with cumene hydroperoxide, hydrogen peroxide, or tert-butyl hydroperoxide as substrates. Glutathione-dependent peroxidase activity was proportional to the Ure2p concentration and showed optima at pH 8 and 40 degrees C. Michaelis-Menten behavior with convergent straight lines in double reciprocal plots was observed. This excludes a ping-pong mechanism and implies either a rapid-equilibrium random or a steady-state ordered sequential mechanism for Ure2p, consistent with its classification as a glutathione transferase. The mutant 90Ure2, which lacks the unstructured N-terminal prion domain, showed kinetic parameters identical to wild type. Fibrillar aggregates showed the same level of activity as native protein. Demonstration of peroxidase activity for Ure2 represents important progress in elucidation of its role in vivo. Further, establishment of an in vitro activity assay provides a valuable tool for the study of structure-function relationships of the Ure2 protein as both a prion and an enzyme.

Amyloid nucleation and hierarchical assembly of Ure2p fibrils. Role of asparagine/glutamine repeat and nonrepeat regions of the prion domains

The yeast prion protein Ure2 forms amyloid-like filaments in vivo and in vitro. This ability depends on the N-terminal prion domain, which contains Asn/Gln repeats, a motif thought to cause human disease by forming stable protein aggregates. The Asn/Gln region of the Ure2p prion domain extends to residue 89, but residues 15-42 represent an island of "normal" random sequence, which is highly conserved in related species and is relatively hydrophobic. We compare the time course of structural changes monitored by thioflavin T (ThT) binding fluorescence and atomic force microscopy for Ure2 and a series of prion domain mutants under a range of conditions. Atomic force microscopy height images at successive time points during a single growth experiment showed the sequential appearance of at least four fibril types that could be readily differentiated by height (5, 8, 12, or 9 nm), morphology (twisted or smooth), and/or time of appearance (early or late in the plateau phase of ThT binding). The Ure2 dimer (h = 2.6 +/- 0.5 nm) and granular particles corresponding to higher order oligomers (h = 4-12 nm) could also be detected. The mutants 15Ure2 and Delta 15-42Ure2 showed the same time-dependent variation in fibril types but with an increased lag time detected by ThT binding compared with wild-type Ure2. In addition, Delta 15-42Ure2 showed reduced binding to ThT. The results imply a role of the conserved region in both amyloid nucleation and formation of the binding surface recognized by ThT. Further, Ure2 amyloid formation is a multistep process via a series of fibrillar intermediates.