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Alfaro GF, Palombo V, D’Andrea M, Cao W, Zhang Y, Beever JE, Muntifering RB, Pacheco WJ, Rodning SP, Wang X, Moisá SJ. Hepatic transcript profiling in beef cattle: Effects of feeding endophyte-infected tall fescue seeds. PLoS One 2024; 19:e0306431. [PMID: 39058685 PMCID: PMC11280227 DOI: 10.1371/journal.pone.0306431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/17/2024] [Indexed: 07/28/2024] Open
Abstract
The objective of our study was to evaluate the effect of endophyte-infected tall fescue (E+) seeds intake on liver tissue transcriptome in growing Angus × Simmental steers and heifers through RNA-seq analysis. Normal weaned calves (~8 months old) received either endophyte-free tall fescue (E-; n = 3) or infected tall fescue (E+; n = 6) seeds for a 30-d period. The diet offered was ad libitum bermudagrass (Cynodon dactylon) hay combined with a nutritional supplement of 1.61 kg (DM basis) of E+ or E- tall fescue seeds, and 1.61 kg (DM basis) of energy/protein supplement pellets for a 30-d period. Dietary E+ tall fescue seeds were included in a rate of 20 μg of ergovaline/kg BW/day. Liver tissue was individually obtained through biopsy at d 30. After preparation and processing of the liver samples for RNA sequencing, we detected that several metabolic pathways were activated (i.e., upregulated) by the consumption of E+ tall fescue. Among them, oxidative phosphorylation, ribosome biogenesis, protein processing in endoplasmic reticulum and apoptosis, suggesting an active mechanism to cope against impairment in normal liver function. Interestingly, hepatic protein synthesis might increase due to E+ consumption. In addition, there was upregulation of "thermogenesis" KEGG pathway, showing a possible increase in energy expenditure in liver tissue due to consumption of E+ diet. Therefore, results from our study expand the current knowledge related to liver metabolism of growing beef cattle under tall fescue toxicosis.
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Affiliation(s)
- Gastón F. Alfaro
- Department of Animal Sciences, Auburn University, Auburn, AL, United States of America
| | - Valentino Palombo
- Department of Agricultural, Environmental and Food Sciences, Università degli Studi del Molise, Campobasso, Italy
| | - MariaSilvia D’Andrea
- Department of Agricultural, Environmental and Food Sciences, Università degli Studi del Molise, Campobasso, Italy
| | - Wenqi Cao
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States of America
| | - Yue Zhang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States of America
| | - Jonathan E. Beever
- Department of Animal Sciences, University of Tennessee, Knoxville, TN, United States of America
| | | | - Wilmer J. Pacheco
- Department of Poultry Sciences, Auburn University, Auburn, AL, United States of America
| | - Soren P. Rodning
- Department of Animal Sciences, Auburn University, Auburn, AL, United States of America
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States of America
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Sonia J. Moisá
- Department of Animal Sciences, University of Tennessee, Knoxville, TN, United States of America
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2
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The RPN12a proteasome subunit is essential for the multiple hormonal homeostasis controlling the progression of leaf senescence. Commun Biol 2022; 5:1043. [PMID: 36180574 PMCID: PMC9525688 DOI: 10.1038/s42003-022-03998-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.
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3
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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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4
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The nuclear pore primes recombination-dependent DNA synthesis at arrested forks by promoting SUMO removal. Nat Commun 2020; 11:5643. [PMID: 33159083 PMCID: PMC7648084 DOI: 10.1038/s41467-020-19516-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 10/16/2020] [Indexed: 12/31/2022] Open
Abstract
Nuclear Pore complexes (NPCs) act as docking sites to anchor particular DNA lesions facilitating DNA repair by elusive mechanisms. Using replication fork barriers in fission yeast, we report that relocation of arrested forks to NPCs occurred after Rad51 loading and its enzymatic activity. The E3 SUMO ligase Pli1 acts at arrested forks to safeguard integrity of nascent strands and generates poly-SUMOylation which promote relocation to NPCs but impede the resumption of DNA synthesis by homologous recombination (HR). Anchorage to NPCs allows SUMO removal by the SENP SUMO protease Ulp1 and the proteasome, promoting timely resumption of DNA synthesis. Preventing Pli1-mediated SUMO chains was sufficient to bypass the need for anchorage to NPCs and the inhibitory effect of poly-SUMOylation on HR-mediated DNA synthesis. Our work establishes a novel spatial control of Recombination-Dependent Replication (RDR) at a unique sequence that is distinct from mechanisms engaged at collapsed-forks and breaks within repeated sequences. In yeast, collapsed forks shift to the nuclear periphery to associate with two distinct perinuclear anchorage sites such as the nuclear pore complex. Here, the authors reveal the mechanisms engaged at nuclear pore complex facilitating fork integrity and restart via SUMO regulation.
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5
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Fernando LM, Elliot J, Allen AK. The Caenorhabditis elegans proteasome subunit RPN-12 is required for hermaphrodite germline sex determination and oocyte quality. Dev Dyn 2020; 250:145-159. [PMID: 32767462 DOI: 10.1002/dvdy.235] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/16/2020] [Accepted: 07/31/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The proteasome is a multi-subunit complex and a major proteolytic machinery in cells. Most subunits are essential for proteasome function, and depletion of individual subunits normally results in lethality. RPN-12/Rpn12/PSMD8 is a lid subunit of the 19S regulatory particle (RP) of the 26S proteasome. Studies in Caenorhabditis elegans demonstrated that RNAi depletion of RPN-12 does not result in lethality. RPN-12 has not been well studied in higher eukaryotes. In this study, we investigate the biological significance of RPN-12 in C. elegans. RESULTS We found that the null mutant rpn-12(av93) did not cause major impairment of the proteolytic activity of the proteasome. Most rpn-12(av93) hermaphrodites lack sperm leading to feminization of the germ line that can be partially rescued by mating to males. The lack of sperm phenotype can be suppressed by downregulation of TRA-1, a player in the hermaphrodite germline sex determination pathway. Also, rpn-12(av93) animals show significant nuclear accumulation of the meiotic kinase WEE-1.3, a protein predominantly localized to the perinuclear region. Interestingly, chemical inhibition of the proteasome did not cause nuclear accumulation of WEE-1.3. CONCLUSIONS RPN-12 plays a previously unknown role in oogenesis and the germline sex determination pathway in C. elegans hermaphrodites.
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Affiliation(s)
- Lourds M Fernando
- Department of Biology, Howard University, Washington, District of Columbia, USA
| | - Jeandele Elliot
- Department of Biology, Howard University, Washington, District of Columbia, USA
| | - Anna K Allen
- Department of Biology, Howard University, Washington, District of Columbia, USA
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6
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Fernando L, Nguyen V, Hansen T, Golden A, Allen A. Loss of proteasome subunit RPN-12 causes an increased mean lifespan at a higher temperature in C. elegans. MICROPUBLICATION BIOLOGY 2020; 2020:10.17912/micropub.biology.000234. [PMID: 32550497 PMCID: PMC7252339 DOI: 10.17912/micropub.biology.000234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | - Tyler Hansen
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD,
Presently- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN
| | - Andy Golden
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Anna Allen
- Department of Biology, Howard University, Washington DC,
Correspondence to: Anna Allen ()
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7
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Niu X, Ma S, Hu Y, Jin C. Backbone 1H, 13C and 15N resonance assignments of the proteasome lid subunit Rpn12 from Saccharomyces cerevisiae. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:147-150. [PMID: 32072453 DOI: 10.1007/s12104-020-09935-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
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.
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Affiliation(s)
- Xiaogang Niu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China
| | - Shuaipeng Ma
- College of Life Sciences, Peking University, Beijing, 100871, China
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China
| | - Yunfei Hu
- Wuhan Institute of Physics and Mathematics, CAS, Wuhan, 430071, China
| | - Changwen Jin
- College of Life Sciences, Peking University, Beijing, 100871, China.
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China.
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China.
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8
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Zhang W, Zhao C, Hu Y, Jin C. Solution structure of the N-terminal domain of proteasome lid subunit Rpn5. Biochem Biophys Res Commun 2018; 504:225-230. [PMID: 30177392 DOI: 10.1016/j.bbrc.2018.08.159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 08/26/2018] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Wenbo Zhang
- College of Life Sciences, Peking University, Beijing 100871, China; Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
| | - Cong Zhao
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
| | - Yunfei Hu
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China.
| | - Changwen Jin
- College of Life Sciences, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China.
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9
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Zhu Y, Wang WL, Yu D, Ouyang Q, Lu Y, Mao Y. Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome. Nat Commun 2018; 9:1360. [PMID: 29636472 PMCID: PMC5893597 DOI: 10.1038/s41467-018-03785-w] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 03/12/2018] [Indexed: 01/08/2023] Open
Abstract
The proteasome is a sophisticated ATP-dependent molecular machine responsible for protein degradation in all known eukaryotic cells. It remains elusive how conformational changes of the AAA-ATPase unfoldase in the regulatory particle (RP) control the gating of the substrate–translocation channel leading to the proteolytic chamber of the core particle (CP). Here we report three alternative states of the ATP-γ-S-bound human proteasome, in which the CP gates are asymmetrically open, visualized by cryo-EM at near-atomic resolutions. At least four nucleotides are bound to the AAA-ATPase ring in these open-gate states. Variation in nucleotide binding gives rise to an axial movement of the pore loops narrowing the substrate-translation channel, which exhibit remarkable structural transitions between the spiral-staircase and saddle-shaped-circle topologies. Gate opening in the CP is thus regulated by nucleotide-driven conformational changes of the AAA-ATPase unfoldase. These findings demonstrate an elegant mechanism of allosteric coordination among sub-machines within the human proteasome holoenzyme. The 26S proteasome consists of a core particle that is capped at each side by a regulatory particle. Here the authors present cryo-EM structures of the activated human 26S proteasome holoenzyme in three alternative open-gate states, which provides mechanistic insights into gate opening and dynamic remodeling of the substrate–translocation pathway.
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Affiliation(s)
- Yanan Zhu
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.,State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter and Material Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Wei Li Wang
- Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Daqi Yu
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter and Material Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Qi Ouyang
- Center for Quantitative Biology, Peking University, Beijing, 100871, China.,State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter and Material Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Youdong Mao
- Center for Quantitative Biology, Peking University, Beijing, 100871, China. .,State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter and Material Physics, School of Physics, Peking University, Beijing, 100871, China. .,Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. .,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.
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10
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Küry S, Besnard T, Ebstein F, Khan TN, Gambin T, Douglas J, Bacino CA, Craigen WJ, Sanders SJ, Lehmann A, Latypova X, Khan K, Pacault M, Sacharow S, Glaser K, Bieth E, Perrin-Sabourin L, Jacquemont ML, Cho MT, Roeder E, Denommé-Pichon AS, Monaghan KG, Yuan B, Xia F, Simon S, Bonneau D, Parent P, Gilbert-Dussardier B, Odent S, Toutain A, Pasquier L, Barbouth D, Shaw CA, Patel A, Smith JL, Bi W, Schmitt S, Deb W, Nizon M, Mercier S, Vincent M, Rooryck C, Malan V, Briceño I, Gómez A, Nugent KM, Gibson JB, Cogné B, Lupski JR, Stessman HA, Eichler EE, Retterer K, Yang Y, Redon R, Katsanis N, Rosenfeld JA, Kloetzel PM, Golzio C, Bézieau S, Stankiewicz P, Isidor B. De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder. Am J Hum Genet 2017; 100:352-363. [PMID: 28132691 DOI: 10.1016/j.ajhg.2017.01.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/04/2017] [Indexed: 10/25/2022] Open
Abstract
Degradation of proteins by the ubiquitin-proteasome system (UPS) is an essential biological process in the development of eukaryotic organisms. Dysregulation of this mechanism leads to numerous human neurodegenerative or neurodevelopmental disorders. Through a multi-center collaboration, we identified six de novo genomic deletions and four de novo point mutations involving PSMD12, encoding the non-ATPase subunit PSMD12 (aka RPN5) of the 19S regulator of 26S proteasome complex, in unrelated individuals with intellectual disability, congenital malformations, ophthalmologic anomalies, feeding difficulties, deafness, and subtle dysmorphic facial features. We observed reduced PSMD12 levels and an accumulation of ubiquitinated proteins without any impairment of proteasome catalytic activity. Our PSMD12 loss-of-function zebrafish CRISPR/Cas9 model exhibited microcephaly, decreased convolution of the renal tubules, and abnormal craniofacial morphology. Our data support the biological importance of PSMD12 as a scaffolding subunit in proteasome function during development and neurogenesis in particular; they enable the definition of a neurodevelopmental disorder due to PSMD12 variants, expanding the phenotypic spectrum of UPS-dependent disorders.
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11
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Abstract
The proteasome is the major engine of protein degradation in all eukaryotic cells. At the heart of this machine is a heterohexameric ring of AAA (ATPases associated with diverse cellular activities) proteins that unfolds ubiquitylated target proteins that are concurrently translocated into a proteolytic chamber and degraded into peptides. Using cryoelectron microscopy, we determined a near-atomic-resolution structure of the 2.5-MDa human proteasome in its ground state, as well as subnanometer-resolution structures of the holoenzyme in three alternative conformational states. The substrate-unfolding AAA-ATPase channel is narrowed by 10 inward-facing pore loops arranged into two helices that run in parallel with each other, one hydrophobic in character and the other highly charged. The gate of the core particle was unexpectedly found closed in the ground state and open in only one of the alternative states. Coordinated, stepwise conformational changes of the regulatory particle couple ATP hydrolysis to substrate translocation and regulate gating of the core particle, leading to processive degradation.
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12
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Dambacher CM, Worden EJ, Herzik MA, Martin A, Lander GC. Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition. eLife 2016; 5:e13027. [PMID: 26744777 PMCID: PMC4749569 DOI: 10.7554/elife.13027] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 01/07/2016] [Indexed: 12/20/2022] Open
Abstract
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.
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Affiliation(s)
- Corey M Dambacher
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
| | - Evan J Worden
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,QB3 Institute, University of California, Berkeley, Berkeley, United States
| | - Mark A Herzik
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
| | - Andreas Martin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,QB3 Institute, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
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13
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An intrinsically disordered region of RPN10 plays a key role in restricting ubiquitin chain elongation in RPN10 monoubiquitination. Biochem J 2015. [DOI: 10.1042/bj20141571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The proteasomal ubiquitin receptor Rpn10 (regulatory particle non-ATPase 10) is monoubiquitinated by Rsp5 (reverses SPT-phenotype protein 5). We show that a disordered region flanking the ubiquitin-interacting motif of Rpn10 is required for restricting polyubiquitination in the process of Rpn10 monoubiquitination. A novel role of an unstructured protein domain in controlling ubiquitin chain elongation is proposed.
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14
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Hu Y, Wu Y, Li Q, Zhang W, Jin C. Solution structure of yeast Rpn9: insights into proteasome lid assembly. J Biol Chem 2015; 290:6878-89. [PMID: 25631053 DOI: 10.1074/jbc.m114.626762] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The regulatory particle (RP) of the 26 S proteasome functions in preparing polyubiquitinated substrates for degradation. The lid complex of the RP contains an Rpn8-Rpn11 heterodimer surrounded by a horseshoe-shaped scaffold formed by six proteasome-COP9/CSN-initiation factor (PCI)-containing subunits. The PCI domains are essential for lid assembly, whereas the detailed molecular mechanisms remain elusive. Recent cryo-EM studies at near-atomic resolution provided invaluable information on the RP architecture in different functional states. Nevertheless, atomic resolution structural information on the RP is still limited, and deeper understanding of RP assembly mechanism requires further studies on the structures and interactions of individual subunits or subcomplexes. Herein we report the high-resolution NMR structures of the PCI-containing subunit Rpn9 from Saccharomyces cerevisiae. The 45-kDa protein contains an all-helical N-terminal domain and a C-terminal PCI domain linked via a semiflexible hinge. The N-terminal domain mediates interaction with the ubiquitin receptor Rpn10, whereas the PCI domain mediates interaction with the neighboring PCI subunit Rpn5. The Rpn9-Rpn5 interface highlights two structural motifs on the winged helix module forming a hydrophobic center surrounded by ionic pairs, which is a common pattern for all PCI-PCI interactions in the lid. The results suggest that divergence in surface composition among different PCI pairs may contribute to the modulation of lid assembly.
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Affiliation(s)
- Yunfei Hu
- From the Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering
| | - Yujie Wu
- From the Beijing Nuclear Magnetic Resonance Center, College of Life Sciences, and
| | - Qianwen Li
- From the Beijing Nuclear Magnetic Resonance Center, College of Life Sciences, and
| | - Wenbo Zhang
- From the Beijing Nuclear Magnetic Resonance Center, College of Life Sciences, and
| | - Changwen Jin
- From the Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, College of Life Sciences, and Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
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15
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Crystal structure of the human COP9 signalosome. Nature 2014; 512:161-5. [PMID: 25043011 DOI: 10.1038/nature13566] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/06/2014] [Indexed: 12/26/2022]
Abstract
Ubiquitination is a crucial cellular signalling process, and is controlled on multiple levels. Cullin-RING E3 ubiquitin ligases (CRLs) are regulated by the eight-subunit COP9 signalosome (CSN). CSN inactivates CRLs by removing their covalently attached activator, NEDD8. NEDD8 cleavage by CSN is catalysed by CSN5, a Zn(2+)-dependent isopeptidase that is inactive in isolation. Here we present the crystal structure of the entire ∼350-kDa human CSN holoenzyme at 3.8 Å resolution, detailing the molecular architecture of the complex. CSN has two organizational centres: a horseshoe-shaped ring created by its six proteasome lid-CSN-initiation factor 3 (PCI) domain proteins, and a large bundle formed by the carboxy-terminal α-helices of every subunit. CSN5 and its dimerization partner, CSN6, are intricately embedded at the core of the helical bundle. In the substrate-free holoenzyme, CSN5 is autoinhibited, which precludes access to the active site. We find that neddylated CRL binding to CSN is sensed by CSN4, and communicated to CSN5 with the assistance of CSN6, resulting in activation of the deneddylase.
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16
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Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome. Proc Natl Acad Sci U S A 2014; 111:5544-9. [PMID: 24706844 DOI: 10.1073/pnas.1403409111] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The 26S proteasome is a 2.5 MDa molecular machine that executes the degradation of substrates of the ubiquitin-proteasome pathway. The molecular architecture of the 26S proteasome was recently established by cryo-EM approaches. For a detailed understanding of the sequence of events from the initial binding of polyubiquitylated substrates to the translocation into the proteolytic core complex, it is necessary to move beyond static structures and characterize the conformational landscape of the 26S proteasome. To this end we have subjected a large cryo-EM dataset acquired in the presence of ATP and ATP-γS to a deep classification procedure, which deconvolutes coexisting conformational states. Highly variable regions, such as the density assigned to the largest subunit, Rpn1, are now well resolved and rendered interpretable. Our analysis reveals the existence of three major conformations: in addition to the previously described ATP-hydrolyzing (ATPh) and ATP-γS conformations, an intermediate state has been found. Its AAA-ATPase module adopts essentially the same topology that is observed in the ATPh conformation, whereas the lid is more similar to the ATP-γS bound state. Based on the conformational ensemble of the 26S proteasome in solution, we propose a mechanistic model for substrate recognition, commitment, deubiquitylation, and translocation into the core particle.
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Sparks A, Dayal S, Das J, Robertson P, Menendez S, Saville MK. The degradation of p53 and its major E3 ligase Mdm2 is differentially dependent on the proteasomal ubiquitin receptor S5a. Oncogene 2013; 33:4685-96. [PMID: 24121268 PMCID: PMC4051618 DOI: 10.1038/onc.2013.413] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/10/2013] [Accepted: 08/09/2013] [Indexed: 01/24/2023]
Abstract
p53 and its major E3 ligase Mdm2 are both ubiquitinated and targeted to the proteasome for degradation. Despite the importance of this in regulating the p53 pathway, little is known about the mechanisms of proteasomal recognition of ubiquitinated p53 and Mdm2. In this study, we show that knockdown of the proteasomal ubiquitin receptor S5a/PSMD4/Rpn10 inhibits p53 protein degradation and results in the accumulation of ubiquitinated p53. Overexpression of a dominant-negative deletion of S5a lacking its ubiquitin-interacting motifs (UIM)s, but which can be incorporated into the proteasome, also causes the stabilization of p53. Furthermore, small-interferring RNA (siRNA) rescue experiments confirm that the UIMs of S5a are required for the maintenance of low p53 levels. These observations indicate that S5a participates in the recognition of ubiquitinated p53 by the proteasome. In contrast, targeting S5a has no effect on the rate of degradation of Mdm2, indicating that proteasomal recognition of Mdm2 can be mediated by an S5a-independent pathway. S5a knockdown results in an increase in the transcriptional activity of p53. The selective stabilization of p53 and not Mdm2 provides a mechanism for p53 activation. Depletion of S5a causes a p53-dependent decrease in cell proliferation, demonstrating that p53 can have a dominant role in the response to targeting S5a. This study provides evidence for alternative pathways of proteasomal recognition of p53 and Mdm2. Differences in recognition by the proteasome could provide a means to modulate the relative stability of p53 and Mdm2 in response to cellular signals. In addition, they could be exploited for p53-activating therapies. This work shows that the degradation of proteins by the proteasome can be selectively dependent on S5a in human cells, and that this selectivity can extend to an E3 ubiquitin ligase and its substrate.
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Affiliation(s)
- A Sparks
- Division of Cancer Research, Medical Research Institute, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - S Dayal
- Division of Cancer Research, Medical Research Institute, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - J Das
- Division of Cancer Research, Medical Research Institute, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - P Robertson
- Division of Molecular Medicine, College of Life Sciences, University of Dundee, Dundee, UK
| | - S Menendez
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - M K Saville
- Division of Cancer Research, Medical Research Institute, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
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Estrin E, Lopez-Blanco J, Chacón P, Martin A. Formation of an Intricate Helical Bundle Dictates the Assembly of the 26S Proteasome Lid. Structure 2013; 21:1624-35. [DOI: 10.1016/j.str.2013.06.023] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 06/15/2013] [Accepted: 06/17/2013] [Indexed: 12/18/2022]
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Lander GC, Martin A, Nogales E. The proteasome under the microscope: the regulatory particle in focus. Curr Opin Struct Biol 2013; 23:243-51. [PMID: 23498601 DOI: 10.1016/j.sbi.2013.02.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 02/13/2013] [Accepted: 02/13/2013] [Indexed: 10/27/2022]
Abstract
Since first imaged by electron microscopy, much effort has been placed into determining the structure and mechanism of the 26S proteasome. While the proteolytic core is understood in atomic detail, how substrates are engaged and transported to this core remains elusive. Substrate delivery is accomplished by a 19-subunit regulatory particle that binds to ubiquitinated substrates, detaches ubiquitin tags, unfolds the substrate, and translocates it into the peptidase in an ATP-dependent fashion. Recently, several labs have determined subnanometer cryoEM structures of the 26S proteasome, shedding light on the architecture of the regulatory complex. We discuss the biological insights into substrate processing provided by these structures, and the technical hurdles ahead to achieve an atomic resolution structure of the 26 proteasome.
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Affiliation(s)
- Gabriel C Lander
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Abstract
The proteasome refers to a collection of complexes centered on the 20S proteasome core particle (20S CP), a complex of 28 subunits that houses proteolytic sites in its hollow interior. Proteasomes are found in eukaryotes, archaea, and some eubacteria, and their activity is critical for many cellular pathways. Important recent advances include inhibitor binding studies and the structure of the immunoproteasome, whose specificity is altered by the incorporation of inducible catalytic subunits. The inherent repression of the 20S CP is relieved by the ATP-independent activators 11S and Blm10/PA200, whose structures reveal principles of proteasome mechanism. The structure of the ATP-dependent 19S regulatory particle, which mediates degradation of polyubiquitylated proteins, is being revealed by a combination of crystal or NMR structures of individual subunits and electron microscopy reconstruction of the intact complex. Other recent structural advances inform us about mechanisms of assembly and the role of conformational changes in the functional cycle.
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Affiliation(s)
- Erik Kish-Trier
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650, USA
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