Solution structure of yeast Rpn9: insights into proteasome lid assembly

Binary protein interactome mapping of the Giardia lamblia proteasome lid reveals extra proteasomal functions of GlRpn11

The assembly of the 26S proteasome, a multi-subunit complex for regulated protein turnover, proceeds via the formation of intermediates. Giardia lamblia does not encode proteasome regulatory subunit Rpn12 or proteasome complex subunit Sem1, two proteins crucial for assembling the proteasome lid. To understand how the interactions between the giardial proteasome lid subunits may have changed to compensate for their absence, we used yeast two-hybrid to generate a binary interactome map of Giardia's lid subunits. Most interactions within the Giardia lid are stronger than Saccharomyces cerevisiae lid, which may compensate for Rpn12 and Sem1 absence. A notable exception was the weaker interaction between the two non-ATPase lid subunits, GlRpn11 and GlRpn8, compared to the strong interaction between yeast orthologs Rpn11 and Rpn8. The Rpn11-Rpn8 dimer provides a platform for lid assembly. Their interaction involves the insertion of a methionine residue of Rpn11 into a hydrophobic pocket of Rpn8. Molecular modeling indicates that GlRpn8's pocket is wider, reconciling the experimental observation of its weak interaction with GlRpn11. This weaker interaction may have evolved to support proteasome-independent functions of GlRpn11, which localizes to multiple subcellular regions, including the mitosomes, where other proteasome subunits cannot be detected. Functional complementation in yeast shows that GlRpn11 can influence mitochondrial function and distribution. Together these observations show that GlRpn11 functions at the mitosome. Thus, this parasite's proteasome lid has a simpler subunit architecture than that of yeast with structural attributes to support dual functionalities for GlRpn11. Such parasite-specific proteasome features provide opportunities for controlling parasite transmission.

BAP1 Malignant Pleural Mesothelioma Mutations in Caenorhabditis elegans Reveal Synthetic Lethality between ubh-4/BAP1 and the Proteasome Subunit rpn-9/PSMD13

The deubiquitinase BAP1 (BRCA1-associated protein 1) is associated with BAP1 tumor predisposition syndrome (TPDS). BAP1 is a tumor suppressor gene whose alterations in cancer are commonly caused by gene mutations leading to protein loss of function. By CRISPR-Cas, we have generated mutations in ubh-4, the BAP1 ortholog in Caenorhabditis elegans, to model the functional impact of BAP1 mutations. We have found that a mimicked BAP1 cancer missense mutation (UBH-4 A87D; BAP1 A95D) resembles the phenotypes of ubh-4 deletion mutants. Despite ubh-4 being ubiquitously expressed, the gene is not essential for viability and its deletion causes only mild phenotypes without affecting 20S proteasome levels. Such viability facilitated an RNAi screen for ubh-4 genetic interactors that identified rpn-9, the ortholog of human PSMD13, a gene encoding subunit of the regulatory particle of the 26S proteasome. ubh-4[A87D], similarly to ubh-4 deletion, cause a synthetic genetic interaction with rpn-9 inactivation affecting body size, lifespan, and the development of germ cells. Finally, we show how ubh-4 inactivation sensitizes animals to the chemotherapeutic agent Bortezomib, which is a proteasome inhibitor. Thus, we have established a model to study BAP1 cancer-related mutations in C. elegans, and our data points toward vulnerabilities that should be studied to explore therapeutic opportunities within the complexity of BAP1 tumors.

Genetic determinants of micronutrient traits in graminaceous crops to combat hidden hunger

KEY MESSAGE

Improving the nutritional content of graminaceous crops is imperative to ensure nutritional security, wherein omics approaches play pivotal roles in dissecting this complex trait and contributing to trait improvement. Micronutrients regulate the metabolic processes to ensure the normal functioning of the biological system in all living organisms. Micronutrient deficiency, thereby, can be detrimental that can result in serious health issues. Grains of graminaceous crops serve as an important source of micronutrients to the human population; however, the rise in hidden hunger and malnutrition indicates an insufficiency in meeting the nutritional requirements. Improving the elemental composition and nutritional value of the graminaceous crops using conventional and biotechnological approaches is imperative to address this issue. Identifying the genetic determinants underlying the micronutrient biosynthesis and accumulation is the first step toward achieving this goal. Genetic and genomic dissection of this complex trait has been accomplished in major cereals, and several genes, alleles, and QTLs underlying grain micronutrient content were identified and characterized. However, no comprehensive study has been reported on minor cereals such as small millets, which are rich in micronutrients and other bioactive compounds. A comparative narrative on the reports available in major and minor Graminaceae species will illustrate the knowledge gained from studying the micronutrient traits in major cereals and provides a roadmap for dissecting this trait in other minor species, including millets. In this context, this review explains the progress made in studying micronutrient traits in major cereals and millets using omics approaches. Moreover, it provides insights into deploying integrated omics approaches and strategies for genetic improvement in micronutrient traits in graminaceous crops.

Backbone 1H, 13C and 15N resonance assignments of the proteasome lid subunit Rpn12 from Saccharomyces cerevisiae

The 26S proteasome degrades selected polyubiquitinated proteins in the ubiquitin-proteasome system, which is the major pathway for programmed protein degradation in eukaryotic cells. The Saccharomyces cerevisiae Rpn12 locates in the lid of the 19S regulatory particle within the 26S proteasome and plays a role in recruiting the extrinsic ubiquitin receptor Rpn10. Rpn12 contains a N-terminal TPR (tetratrico peptide repeat)-like domain and a C-terminal WH (winged helix) domain. Interaction of Rpn12 with several subunits of 19S has been observed and it may play an important role in the 19S regulatory particle rearrangement after ubiquitylated substrate binding to the proteasome. Herein, we report the resonance assignments of backbone ¹H, ¹³C and ¹⁵N atoms of the Saccharomyces cerevisiae Rpn12, which provide valuable information for further studies of the dynamics and interactions of the Rpn12 subunit using NMR techniques.

NMR 1H, 13C, 15N backbone and side chain resonance assignment of the N-terminal domain of yeast proteasome lid subunit Rpn5

The 26S proteasome is responsible for the selective, ATP-dependent degradation of polyubiquitinated proteins in eukaryotic cells. It consists of a 20S barrel-shaped core particle capped by two 19S regulatory particle at both ends. The Rpn5 subunit is a non-ATPase subunit located in the lid subcomplex of the 19S regulatory particle and is identified to inhibit the Rpn11 deubiquitinase activity in the isolated lid. The protein contains a C-terminal proteasome-CSN-eIF3 (PCI) domain and an N-terminal α-solenoid domain, the latter has been shown to be highly flexible in the isolated lid and may participate in interactions with different subunits of the proteasome. We herein report the ¹H, ¹³C and ¹⁵N atoms chemical shift assignments of the N-terminal domain (residues 1-136) of Saccharomyces cerevisiae Rpn5, which provide the basis for further studies of the structure, dynamics and interactions of the Rpn5 subunit by NMR technique.

Solution structure of the N-terminal domain of proteasome lid subunit Rpn5

The 26S proteasome is the major protein degradation machinery in living cells. The Rpn5 protein is one scaffolding subunit in the lid subcomplex of the 19S regulatory particle in the proteasome holoenzyme. Herein we report the solution structure of the N-terminal domain (NTD) of yeast Rpn5 at high resolution by NMR spectroscopy. The results show that Rpn5 NTD adopts α-solenoid-like fold in right-handed superhelical configuration formed by a number of α-helices. Structural comparisons with currently available cryo-EM structures reveal local structural differences in the first three helices between yeast and human Rpn5. The results further highlight the conformational flexibility in three possible protein interaction sites. Moreover, the structures of the NTD show large variations among different PCI-containing Rpn subunits. Our current results provide atomic-level structural basis for further investigations of protein-protein interactions and the proteasome assembly pathway.

Expression and Regulation of Deubiquitinase-Resistant, Unanchored Ubiquitin Chains in Drosophila

The modifier protein, ubiquitin (Ub) regulates various cellular pathways by controlling the fate of substrates to which it is conjugated. Ub moieties are also conjugated to each other, forming chains of various topologies. In cells, poly-Ub is attached to proteins and also exists in unanchored form. Accumulation of unanchored poly-Ub is thought to be harmful and quickly dispersed through dismantling by deubiquitinases (DUBs). We wondered whether disassembly by DUBs is necessary to control unanchored Ub chains in vivo. We generated Drosophila melanogaster lines that express Ub chains non-cleavable into mono-Ub by DUBs. These chains are rapidly modified with different linkages and represent various types of unanchored species. We found that unanchored poly-Ub is not devastating in Drosophila, under normal conditions or during stress. The DUB-resistant, free Ub chains are degraded by the proteasome, at least in part through the assistance of VCP and its cofactor, p47. Also, unanchored poly-Ub that cannot be cleaved by DUBs can be conjugated en bloc, in vivo. Our results indicate that unanchored poly-Ub species need not be intrinsically toxic; they can be controlled independently of DUB-based disassembly by being degraded, or through conjugation onto other proteins.

Precise assembly and regulation of 26S proteasome and correlation between proteasome dysfunction and neurodegenerative diseases

Neurodegenerative diseases (NDs) often involve the formation of abnormal and toxic protein aggregates, which are thought to be the primary factor in ND occurrence and progression. Aged neurons exhibit marked increases in aggregated protein levels, which can lead to increased cell death in specific brain regions. As no specific drugs/therapies for treating the symptoms or/and progression of NDs are available, obtaining a complete understanding of the mechanism underlying the formation of protein aggregates is needed for designing a novel and efficient removal strategy. Intracellular proteolysis generally involves either the lysosomal or ubiquitin-proteasome system. In this review, we focus on the structure and assembly of the proteasome, proteasome-mediated protein degradation, and the multiple dynamic regulatory mechanisms governing proteasome activity. We also discuss the plausibility of the correlation between changes in proteasome activity and the occurrence of NDs. [BMB Reports 2016; 49(9): 459-473]

Structure of ubiquitylated-Rpn10 provides insight into its autoregulation mechanism

Ubiquitin receptors decode ubiquitin signals into many cellular responses. Ubiquitin receptors also undergo coupled monoubiquitylation, and rapid deubiquitylation has hampered the characterization of the ubiquitylated state. Using bacteria that express a ubiquitylation apparatus, we purified and determined the crystal structure of the proteasomal ubiquitin-receptor Rpn10 in its ubiquitylated state. The structure shows a novel ubiquitin-binding patch that directs K84 ubiquitylation. Superimposition of ubiquitylated-Rpn10 onto electron-microscopy models of proteasomes indicates that the Rpn10-conjugated ubiquitin clashes with Rpn9, suggesting that ubiquitylation might be involved in releasing Rpn10 from the proteasome. Indeed, ubiquitylation on immobilized proteasomes dissociates the modified Rpn10 from the complex, while unmodified Rpn10 mainly remains associated. In vivo experiments indicate that contrary to wild type, Rpn10-K84R is stably associated with the proteasomal subunit Rpn9. Similarly Rpn10, but not ubiquitylated-Rpn10, binds Rpn9 in vitro. Thus we suggest that ubiquitylation functions to dissociate modified ubiquitin receptors from their targets, a function that promotes cyclic activity of ubiquitin receptors.

Ubiquitin (Ub) receptors are responsible for the recognition of ubiquitylated proteins. Here the authors describe the crystal structure of the ubiquitylated form of the Ub-receptor Rpn10, which suggest that ubiquitylation of Rpn10 promotes its dissociation from the proteasome.

Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition

The 26S proteasome is responsible for the selective, ATP-dependent degradation of polyubiquitinated cellular proteins. Removal of ubiquitin chains from targeted substrates at the proteasome is a prerequisite for substrate processing and is accomplished by Rpn11, a deubiquitinase within the 'lid' sub-complex. Prior to the lid's incorporation into the proteasome, Rpn11 deubiquitinase activity is inhibited to prevent unwarranted deubiquitination of polyubiquitinated proteins. Here we present the atomic model of the isolated lid sub-complex, as determined by cryo-electron microscopy at 3.5 Å resolution, revealing how Rpn11 is inhibited through its interaction with a neighboring lid subunit, Rpn5. Through mutagenesis of specific residues, we describe the network of interactions that are required to stabilize this inhibited state. These results provide significant insight into the intricate mechanisms of proteasome assembly, outlining the substantial conformational rearrangements that occur during incorporation of the lid into the 26S holoenzyme, which ultimately activates the deubiquitinase for substrate degradation.