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Journal of Molecular Biology Jul 2024The Hsp70 chaperone system is a central component of cellular protein quality control (PQC) by acting in a multitude of protein folding processes ranging from the... (Review)
Review
The Hsp70 chaperone system is a central component of cellular protein quality control (PQC) by acting in a multitude of protein folding processes ranging from the folding of newly synthesized proteins to the disassembly and refolding of protein aggregates. This multifunctionality of Hsp70 is governed by J-domain proteins (JDPs), which act as indispensable co-chaperones that target specific substrates to Hsp70. The number of distinct JDPs present in a species always outnumbers Hsp70, documenting JDP function in functional diversification of Hsp70. In this review, we describe the physiological roles of JDPs in the Saccharomyces cerevisiae PQC system, with a focus on the abundant JDP generalists, Zuo1, Ydj1 and Sis1, which function in fundamental cellular processes. Ribosome-bound Zuo1 cooperates with the Hsp70 chaperones Ssb1/2 in folding and assembly of nascent polypeptides. Ydj1 and Sis1 cooperate with the Hsp70 members Ssa1 to Ssa4 to exert overlapping functions in protein folding and targeting of newly synthesized proteins to organelles including mitochondria and facilitating the degradation of aberrant proteins by E3 ligases. Furthermore, they act in protein disaggregation reactions, though Ydj1 and Sis1 differ in their modes of Hsp70 cooperation and substrate specificities. This results in functional specialization as seen in prion propagation and the underlying dominant role of Sis1 in targeting Hsp70 for shearing of prion amyloid fibrils.
Topics: Saccharomyces cerevisiae Proteins; Saccharomyces cerevisiae; HSP70 Heat-Shock Proteins; Protein Folding; HSP40 Heat-Shock Proteins; Molecular Chaperones; Protein Domains; Heat-Shock Proteins
PubMed: 38331212
DOI: 10.1016/j.jmb.2024.168484 -
Cell Reports Nov 2023The molecular mechanisms that trigger Tau aggregation in Alzheimer's disease (AD) remain elusive. Fungi, especially Saccharomyces cerevisiae (S. cerevisiae), can be...
The molecular mechanisms that trigger Tau aggregation in Alzheimer's disease (AD) remain elusive. Fungi, especially Saccharomyces cerevisiae (S. cerevisiae), can be found in brain samples from patients with AD. Here, we show that the yeast protein Ure2p from S. cerevisiae interacts with Tau and facilitates its aggregation. The Ure2p-seeded Tau fibrils are more potent in seeding Tau and causing neurotoxicity in vitro. When injected into the hippocampus of Tau P301S transgenic mice, the Ure2p-seeded Tau fibrils show enhanced seeding activity compared with pure Tau fibrils. Strikingly, intracranial injection of Ure2p fibrils promotes the aggregation of Tau and cognitive impairment in Tau P301S mice. Furthermore, intranasal infection of S. cerevisiae in the nasal cavity of Tau P301S mice accelerates the aggregation of Tau. Together, these observations indicate that the yeast protein Ure2p initiates Tau pathology. Our results provide a conceptual advance that non-mammalian prions may cross-seed mammalian prion-like proteins.
Topics: Animals; Mice; Disease Models, Animal; Mice, Transgenic; Prions; Saccharomyces cerevisiae; tau Proteins; Tauopathies; Saccharomyces cerevisiae Proteins; Glutathione Peroxidase
PubMed: 37897723
DOI: 10.1016/j.celrep.2023.113342 -
Thrombosis Research Mar 2024Underlying mechanisms for bleeding and impaired thrombin generation (TG) and plasma clot formation (PCF) in patients with mild to moderate bleeding disorders (MBDs) are...
BACKGROUND
Underlying mechanisms for bleeding and impaired thrombin generation (TG) and plasma clot formation (PCF) in patients with mild to moderate bleeding disorders (MBDs) are still to be elucidated, especially in bleeding disorder of unknown cause (BDUC). The role of the natural anticoagulants activated protein C (APC) and free protein S (PS) has not yet been investigated in this patient population.
AIMS
To analyze antigen levels of APC and PS in patients with MBDs and BDUC and investigate associations to clinical bleeding phenotype and severity as well as and hemostatic capacity.
METHODS
Antigen levels of APC and free PS were measured in 262 patients from the Vienna Bleeding Biobank (VIBB), a single-center cohort study, by ELISA and compared to 61 healthy controls (HC).
RESULTS
Antigen levels of APC were higher in MBD patients than in HC when adjusted for age, sex and BMI (median (IQR) 33.1 (20.6-52.6) and 28.6 (16.4-47.2) ng/mL). This was most pronounced in patients with BDUC (35.3 (21.7-54.3) ng/mL). No differences in PS antigen levels between patients and HC were seen overall, or according to specific diagnoses. Further, no association between APC or PS and bleeding severity or global tests of hemostasis or TG were identified, while paradoxically APC weakly correlated with shorter lag time and time to peak of PCF in BDUC.
CONCLUSION
Our data demonstrate increased antigen levels of APC in BDUC, which might contribute to the bleeding tendency in some patients and could be a future therapeutic target in BDUC.
Topics: Humans; Protein C; Cohort Studies; Blood Coagulation Disorders; Anticoagulants; Enzyme-Linked Immunosorbent Assay
PubMed: 38324941
DOI: 10.1016/j.thromres.2024.01.018 -
Molecules (Basel, Switzerland) Oct 2023In 2012, Kim and Hirata derived two generalized Langevin equations (GLEs) for a biomolecule in water, one for the structural fluctuation of the biomolecule and the other... (Review)
Review
In 2012, Kim and Hirata derived two generalized Langevin equations (GLEs) for a biomolecule in water, one for the structural fluctuation of the biomolecule and the other for the density fluctuation of water, by projecting all the mechanical variables in phase space onto the two dynamic variables: the structural fluctuation defined by the displacement of atoms from their equilibrium positions, and the solvent density fluctuation. The equation has an expression similar to the classical Langevin equation (CLE) for a harmonic oscillator, possessing terms corresponding to the restoring force proportional to the structural fluctuation, as well as the frictional and random forces. However, there is a distinct difference between the two expressions that touches on the essential physics of the structural fluctuation, that is, the in the restoring force. In the CLE, this is given by the second derivative of the potential energy among atoms in a protein. So, the quadratic nature or the harmonicity is only valid at the of the potential surface. On the contrary, the linearity of the restoring force in the GLE originates from the . Taking this into consideration, Kim and Hirata proposed an for the . The ansatz is used to equate the Hessian matrix with the second derivative of the free-energy surface or the potential of the mean force of a protein in water, defined by the sum of the potential energy among atoms in a protein and the solvation free energy. Since the free energy can be calculated from the molecular mechanics and the RISM/3D-RISM theory, one can perform an analysis similar to the normal mode analysis (NMA) just by diagonalizing the Hessian matrix of the free energy. This method is referred to as the Generalized Langevin Mode Analysis (GLMA). This theory may be realized to explore a variety of biophysical processes, including protein folding, spectroscopy, and chemical reactions. The present article is devoted to reviewing the development of this theory, and to providing perspective in exploring life phenomena.
Topics: Thermodynamics; Proteins; Solvents; Water; Molecular Dynamics Simulation
PubMed: 37959769
DOI: 10.3390/molecules28217351 -
Protein Science : a Publication of the... Nov 2023Predicting the effects of mutations on protein function and stability is an outstanding challenge. Here, we assess the performance of a variant of RoseTTAFold jointly...
Predicting the effects of mutations on protein function and stability is an outstanding challenge. Here, we assess the performance of a variant of RoseTTAFold jointly trained for sequence and structure recovery, RF , for mutation effect prediction. Without any further training, we achieve comparable accuracy in predicting mutation effects for a diverse set of protein families using RF to both another zero-shot model (MSA Transformer) and a model that requires specific training on a particular protein family for mutation effect prediction (DeepSequence). Thus, although the architecture of RF was developed to address the protein design problem of scaffolding functional motifs, RF acquired an understanding of the mutational landscapes of proteins during model training that is equivalent to that of recently developed large protein language models. The ability to simultaneously reason over protein structure and sequence could enable even more precise mutation effect predictions following supervised training on the task. These results suggest that RF has a quite broad understanding of protein sequence-structure landscapes, and can be viewed as a joint model for protein sequence and structure which could be broadly useful for protein modeling.
Topics: Proteins; Mutation; Amino Acid Sequence; Protein Stability
PubMed: 37695922
DOI: 10.1002/pro.4780 -
PLoS Biology May 2024The relationship between genetic code robustness and protein evolvability is unknown. A new study in PLOS Biology using in silico rewiring of genetic codes and...
The relationship between genetic code robustness and protein evolvability is unknown. A new study in PLOS Biology using in silico rewiring of genetic codes and functional protein data identified a positive correlation between code robustness and protein evolvability that is protein-specific.
Topics: Genetic Code; Evolution, Molecular; Proteins; Models, Genetic
PubMed: 38758732
DOI: 10.1371/journal.pbio.3002627 -
The Journal of Cell Biology Oct 2023Mitochondria are highly dynamic double membrane-bound organelles that maintain their shape in part through fission and fusion. Mitochondrial fission is performed by a...
Mitochondria are highly dynamic double membrane-bound organelles that maintain their shape in part through fission and fusion. Mitochondrial fission is performed by a dynamin-related protein, Dnm1 (Drp1 in humans), that constricts and divides the mitochondria in a GTP hydrolysis-dependent manner. However, it is unclear whether factors inside mitochondria help coordinate the process and if Dnm1/Drp1 activity is sufficient to complete the fission of both mitochondrial membranes. Here, we identify an intermembrane space protein required for mitochondrial fission in yeast, which we propose to name Mdi1 (also named Atg44). Loss of Mdi1 causes mitochondrial hyperfusion due to defects in fission, but not the lack of Dnm1 recruitment to mitochondria. Mdi1 is conserved in fungal species, and its homologs contain an amphipathic α-helix, mutations of which disrupt mitochondrial morphology. One model is that Mdi1 distorts mitochondrial membranes to enable Dnm1 to robustly complete fission. Our work reveals that Dnm1 cannot efficiently divide mitochondria without the coordinated function of Mdi1 inside mitochondria.
Topics: Dynamins; Mitochondria; Mitochondrial Dynamics; Mitochondrial Membranes; Mitochondrial Proteins; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; GTP Phosphohydrolases
PubMed: 37540145
DOI: 10.1083/jcb.202303147 -
The Journal of Cell Biology Aug 2023In macroautophagy, cellular components are sequestered within autophagosomes and transported to lysosomes/vacuoles for degradation. Although phosphatidylinositol...
In macroautophagy, cellular components are sequestered within autophagosomes and transported to lysosomes/vacuoles for degradation. Although phosphatidylinositol 3-kinase complex I (PI3KCI) plays a pivotal role in the regulation of autophagosome biogenesis, little is known about how this complex localizes to the pre-autophagosomal structure (PAS). In Saccharomyces cerevisiae, PI3KCI is composed of PI3K Vps34 and conserved subunits Vps15, Vps30, Atg14, and Atg38. In this study, we discover that PI3KCI interacts with the vacuolar membrane anchor Vac8, the PAS scaffold Atg1 complex, and the pre-autophagosomal vesicle component Atg9 via the Atg14 C-terminal region, the Atg38 C-terminal region, and the Vps30 BARA domain, respectively. While the Atg14-Vac8 interaction is constitutive, the Atg38-Atg1 complex interaction and the Vps30-Atg9 interaction are enhanced upon macroautophagy induction depending on Atg1 kinase activity. These interactions cooperate to target PI3KCI to the PAS. These findings provide a molecular basis for PAS targeting of PI3KCI during autophagosome biogenesis.
Topics: Autophagosomes; Autophagy; Autophagy-Related Proteins; Membrane Proteins; Phosphatidylinositol 3-Kinases; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Vesicular Transport Proteins
PubMed: 37436710
DOI: 10.1083/jcb.202210017 -
Nature Communications Jan 2024The resilience of cellular proteostasis declines with age, which drives protein aggregation and compromises viability. The nucleus has emerged as a key quality control...
The resilience of cellular proteostasis declines with age, which drives protein aggregation and compromises viability. The nucleus has emerged as a key quality control compartment that handles misfolded proteins produced by the cytosolic protein biosynthesis system. Here, we find that age-associated metabolic cues target the yeast protein disaggregase Hsp104 to the nucleus to maintain a functional nuclear proteome during quiescence. The switch to respiratory metabolism and the accompanying decrease in translation rates direct cytosolic Hsp104 to the nucleus to interact with latent translation initiation factor eIF2 and to suppress protein aggregation. Hindering Hsp104 from entering the nucleus in quiescent cells results in delayed re-entry into the cell cycle due to compromised resumption of protein synthesis. In sum, we report that cytosolic-nuclear partitioning of the Hsp104 disaggregase is a critical mechanism to protect the latent protein synthesis machinery during quiescence in yeast, ensuring the rapid restart of translation once nutrients are replenished.
Topics: Cell Cycle; Cell Division; Cytosol; Protein Aggregates; Saccharomyces cerevisiae; Heat-Shock Proteins; Protein Biosynthesis; Saccharomyces cerevisiae Proteins
PubMed: 38182580
DOI: 10.1038/s41467-023-44538-8 -
The Journal of Cell Biology Aug 2023As eukaryotic cells progress through cell division, the nuclear envelope (NE) membrane must expand to accommodate the formation of progeny nuclei. In Saccharomyces...
As eukaryotic cells progress through cell division, the nuclear envelope (NE) membrane must expand to accommodate the formation of progeny nuclei. In Saccharomyces cerevisiae, closed mitosis allows visualization of NE biogenesis during mitosis. During this period, the SUMO E3 ligase Siz2 binds the inner nuclear membrane (INM) and initiates a wave of INM protein SUMOylation. Here, we show these events increase INM levels of phosphatidic acid (PA), an intermediate of phospholipid biogenesis, and are necessary for normal mitotic NE membrane expansion. The increase in INM PA is driven by the Siz2-mediated inhibition of the PA phosphatase Pah1. During mitosis, this results from the binding of Siz2 to the INM and dissociation of Spo7 and Nem1, a complex required for the activation of Pah1. As cells enter interphase, the process is then reversed by the deSUMOylase Ulp1. This work further establishes a central role for temporally controlled INM SUMOylation in coordinating processes, including membrane expansion, that regulate NE biogenesis during mitosis.
Topics: Cell Nucleus; Mitosis; Nuclear Envelope; Nuclear Proteins; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Sumoylation; Organelle Biogenesis
PubMed: 37398994
DOI: 10.1083/jcb.202208137