Nuclear Transport of Yeast Proteasomes

Proteasomes are key proteases in regulating protein homeostasis. Their holo-enzymes are composed of 40 different subunits which are arranged in a proteolytic core (CP) flanked by one to two regulatory particles (RP). Proteasomal proteolysis is essential for the degradation of proteins which control time-sensitive processes like cell cycle progression and stress response. In dividing yeast and human cells, proteasomes are primarily nuclear suggesting that proteasomal proteolysis is mainly required in the nucleus during cell proliferation. In yeast, which have a closed mitosis, proteasomes are imported into the nucleus as immature precursors via the classical import pathway. During quiescence, the reversible absence of proliferation induced by nutrient depletion or growth factor deprivation, proteasomes move from the nucleus into the cytoplasm. In the cytoplasm of quiescent yeast, proteasomes are dissociated into CP and RP and stored in membrane-less cytoplasmic foci, named proteasome storage granules (PSGs). With the resumption of growth, PSGs clear and mature proteasomes are transported into the nucleus by Blm10, a conserved 240 kDa protein and proteasome-intrinsic import receptor. How proteasomes are exported from the nucleus into the cytoplasm is unknown

Structure of the VipA/B Type VI Secretion Complex Suggests a Contraction-State-Specific Recycling Mechanism

The bacterial type VI secretion system is a multicomponent molecular machine directed against eukaryotic host cells and competing bacteria. An intracellular contractile tubular structure that bears functional homology with bacteriophage tails is pivotal for ejection of pathogenic effectors. Here, we present the 6 A cryoelectron microscopy structure of the contracted Vibrio cholerae tubule consisting of the proteins VipA and VipB. We localized VipA and VipB in the protomer and identified structural homology between the C-terminal segment of VipB and the tail-sheath protein of T4 phages. We propose that homologous segments in VipB and T4 phages mediate tubule contraction. We show that in type VI secretion, contraction leads to exposure of the ClpV recognition motif, which is embedded in the type VI-specific four-helix-bundle N-domain of VipB. Disaggregation of the tubules by the AAA+ protein ClpV and recycling of the VipA/B subunits are thereby limited to the contracted state

Molecular snapshots of the Pex1/6 AAA + complex in action

The peroxisomal proteins Pex1 and Pex6 form a heterohexameric type II AAA+ ATPase complex, which fuels essential protein transport across peroxisomal membranes. Mutations in either ATPase in humans can lead to severe peroxisomal disorders and early death. We present an extensive structural and biochemical analysis of the yeast Pex1/6 complex. The heterohexamer forms a trimer of Pex1/6 dimers with a triangular geometry that is atypical for AAA+ complexes. While the C-terminal nucleotide-binding domains (D2) of Pex6 constitute the main ATPase activity of the complex, both D2 harbour essential sub-strate-binding motifs. ATP hydrolysis results in a pumping motion of the complex, suggesting that Pex1/6 function involves substrate translocation through its central channel. Mutation of the Walker B motif in one D2 domain leads to ATP hydrolysis in the neighbouring domain, giving structural insights into inter-domain communication of these unique heterohexameric AAA + assemblies

Proteasome assembly from 15S precursors involves major conformational changes and recycling of the Pba1-Pba2 chaperone

The chaperones Ump1 and Pba1-Pba2 promote efficient biogenesis of 20S proteasome core particles from its subunits via 15S intermediates containing alpha and beta subunits, except beta7. Here we elucidate the structural role of these chaperones in late steps of core particle biogenesis using biochemical, electron microscopy, cross-linking and mass spectrometry analyses. In 15S precursor complexes, Ump1 is largely unstructured, lining the inner cavity of the complex along the interface between alpha and beta subunits. The alpha and beta subunits form loosely packed rings with a wider alpha ring opening than in the 20S core particle, allowing for the Pba1-Pba2 heterodimer to be partially embedded in the central alpha ring cavity. During biogenesis, the heterodimer is expelled from the alpha ring by a restructuring event that organizes the beta ring and leads to tightening of the alpha ring opening. In this way, the Pba1-Pba2 chaperone is recycled for a new round of proteasome assembly

Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase

Metal-containing formate dehydrogenases (FDH) catalyse the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active site. They display a diverse subunit and cofactor composition, but structural information on these enzymes is limited. Here we report the cryo-electron microscopic structures of the soluble Rhodobacter capsulatus FDH (RcFDH) as isolated and in the presence of reduced nicotinamide adenine dinucleotide (NADH). RcFDH assembles into a 360 kDa dimer of heterotetramers revealing a putative interconnection of electron pathway chains. In the presence of NADH, the RcFDH structure shows charging of cofactors, indicative of an increased electron load

Nukleärer Import von 19S regulatorischen Komplexen in der Hefe Saccharomyces cerevisiae

Das 26S Proteasom führt die letzen Schritte des essentiellen, Ubiquitin abhängigen Proteinabbaus durch, indem es ubiquitinierte und fehlgefaltete Proteine erkennt und eliminiert. Da es in S. cerevisiae während allen Stadien der Zellteilung vornehmlich im Zellkern lokalisiert ist, ist der Importweg dieses 2,5 MDa umfassenden proteolytischen Komplexes in den Zellkern von besonderem Interesse. Das 26S Proteasom unterteilt sich in das katalytisch aktive 20S Proteasom sowie den 19S Regulatorkomplex. Für 20S Proteasomen konnten Lehmann und Mitarbeitende (2002, JMB, 317, 401) zeigen, dass Vorläuferkomplexe über den Karyopherin alpha/beta abhängigen Importweg in den Zellkern gelangen und dort zu 20S Proteasomen heranreifen. In dieser Arbeit wird gezeigt, dass die nukleäre Lokalisation der 19S Regulatorkomplexe ebenfalls von Karyopherin alpha/beta abhängt. Die Untersuchung der potentiellen klassischen Kernlokalisationssequenzen (cNLS) in den Untereinheiten des 19S Base Subkomplex ergab, dass Rpn2 und Rpt2, eine non-ATPase Untereinheit sowie eine ATPase Untereinheit des Base Komplex, funktionelle cNLS beherbergen. Die Deletion der Rpt2 NLS führte zur wt Lokalisation der proteasomalen Subkomplexe. Die Deletion der NLS in Rpn2 dagegen bewirkte eine verschlechterte proteasomale Funktion und eine Mislokalisation der Komplexe. Unsere Daten unterstützen ein Modell wonach die nukleären 26S Proteasomen aus Subkomplexen zusammengelagert werden, die durch Karyopherin alpha/beta in den Zellkern gelangen.26S proteasomes fulfil final steps in the ubiquitin-dependent degradation pathway by recognising and hydrolysing ubiquitylated proteins. As the 26S proteasome mainly localises to the nucleus in yeast, we addressed the question how this 2 MDa multisubunit complex is imported into the nucleus. 26S proteasomes consist of 20S proteolytically active core and 19S regulatory particles, the latter composed of two subcomplexes, namely the base and lid complexes. We have shown that 20S core particles are translocated into the nucleus as inactive precursor complexes via the classical karyopherin alpha/beta import pathway (Lehmann et al. 2002; JMB, 317, 401). Here, we provide evidence that nuclear import of base and lid complexes also depends on karyopherin alpha/beta. Potential classical nuclear localisation sequences (NLS) of base subunits were analysed. Rpn2 and Rpt2, a non-ATPase and an ATPase subunit of the base complex, harbour functional NLS. The Rpt2 NLS deletion yielded wild type localisation. However, the deletion of the Rpn2 NLS resulted in improper nuclear proteasome localisation and impaired proteasome function. Our data support the model by which nuclear 26S proteasomes are assembled from subcomplexes imported by karyopherin alpha/beta

Structural Mapping of Missense Mutations in the Pex1/Pex6 Complex

Peroxisome biogenesis disorders (PBDs) are nontreatable hereditary diseases with a broad range of severity. Approximately 65% of patients are affected by mutations in the peroxins Pex1 and Pex6. The proteins form the heteromeric Pex1/Pex6 complex, which is important for protein import into peroxisomes. To date, no structural data are available for this AAA+ ATPase complex. However, a wealth of information can be transferred from low-resolution structures of the yeast scPex1/scPex6 complex and homologous, well-characterized AAA+ ATPases. We review the abundant records of missense mutations described in PBD patients with the aim to classify and rationalize them by mapping them onto a homology model of the human Pex1/Pex6 complex. Several mutations concern functionally conserved residues that are implied in ATP hydrolysis and substrate processing. Contrary to fold destabilizing mutations, patients suffering from function-impairing mutations may not benefit from stabilizing agents, which have been reported as potential therapeutics for PBD patients

Cryo electron microscopy structures of Hsp100 proteins: crowbars in or out?

Independent cryo electron microscopy (cryo-EM) studies of the closely related protein disaggregases ClpB and Hsp104 have resulted in two different models of subunit arrangement in the active hexamer. We compare the EM maps and resulting atomic structure fits, discuss their differences, and relate them to published experimental information in an attempt to discriminate between models. In addition, we present some general assessment criteria for low-resolution cryo-EM maps to offer non-structural biologists tools to evaluate these structures

Structure and Function of p97 and Pex1/6 Type II AAA+ Complexes

Protein complexes of the Type II AAA+ (ATPases associated with diverse cellular activities) family are typically hexamers of 80–150 kDa protomers that harbor two AAA+ ATPase domains. They form double ring assemblies flanked by associated domains, which can be N-terminal, intercalated or C-terminal to the ATPase domains. Most prominent members of this family include NSF (N-ethyl-maleimide sensitive factor), p97/VCP (valosin-containing protein), the Pex1/Pex6 complex and Hsp104 in eukaryotes and ClpB in bacteria. Tremendous efforts have been undertaken to understand the conformational dynamics of protein remodeling type II AAA+ complexes. A uniform mode of action has not been derived from these works. This review focuses on p97/VCP and the Pex1/6 complex, which both structurally remodel ubiquitinated substrate proteins. P97/VCP plays a role in many processes, including ER- associated protein degradation, and the Pex1/Pex6 complex dislocates and recycles the transport receptor Pex5 from the peroxisomal membrane during peroxisomal protein import. We give an introduction into existing knowledge about the biochemical and cellular activities of the complexes before discussing structural information. We particularly emphasize recent electron microscopy structures of the two AAA+ complexes and summarize their structural differences