101
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Jiang Y, Lee J, Lee JH, Lee JW, Kim JH, Choi WH, Yoo YD, Cha-Molstad H, Kim BY, Kwon YT, Noh SA, Kim KP, Lee MJ. The arginylation branch of the N-end rule pathway positively regulates cellular autophagic flux and clearance of proteotoxic proteins. Autophagy 2016; 12:2197-2212. [PMID: 27560450 DOI: 10.1080/15548627.2016.1222991] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The N-terminal amino acid of a protein is an essential determinant of ubiquitination and subsequent proteasomal degradation in the N-end rule pathway. Using para-chloroamphetamine (PCA), a specific inhibitor of the arginylation branch of the pathway (Arg/N-end rule pathway), we identified that blocking the Arg/N-end rule pathway significantly impaired the fusion of autophagosomes with lysosomes. Under ER stress, ATE1-encoded Arg-tRNA-protein transferases carry out the N-terminal arginylation of the ER heat shock protein HSPA5 that initially targets cargo proteins, along with SQSTM1, to the autophagosome. At the late stage of autophagy, however, proteasomal degradation of arginylated HSPA5 might function as a critical checkpoint for the proper progression of autophagic flux in the cells. Consistently, the inhibition of the Arg/N-end rule pathway with PCA significantly elevated levels of MAPT and huntingtin aggregates, accompanied by increased numbers of LC3 and SQSTM1 puncta. Cells treated with the Arg/N-end rule inhibitor became more sensitized to proteotoxic stress-induced cytotoxicity. SILAC-based quantitative proteomics also revealed that PCA significantly alters various biological pathways, including cellular responses to stress, nutrient, and DNA damage, which are also closely involved in modulation of autophagic responses. Thus, our results indicate that the Arg/N-end rule pathway may function to actively protect cells from detrimental effects of cellular stresses, including proteotoxic protein accumulation, by positively regulating autophagic flux.
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Affiliation(s)
- Yanxialei Jiang
- a Department of Biochemistry and Molecular Biology , Seoul National University College of Medicine , Seoul , Korea
| | - Jeeyoung Lee
- a Department of Biochemistry and Molecular Biology , Seoul National University College of Medicine , Seoul , Korea.,b Department of Biomedical Sciences , Seoul National University Graduate School , Seoul , Korea
| | - Jung Hoon Lee
- a Department of Biochemistry and Molecular Biology , Seoul National University College of Medicine , Seoul , Korea.,b Department of Biomedical Sciences , Seoul National University Graduate School , Seoul , Korea
| | - Joon Won Lee
- d Department of Applied Chemistry , College of Applied Sciences, Kyung Hee University , Yongin , Korea
| | - Ji Hyeon Kim
- a Department of Biochemistry and Molecular Biology , Seoul National University College of Medicine , Seoul , Korea.,b Department of Biomedical Sciences , Seoul National University Graduate School , Seoul , Korea
| | - Won Hoon Choi
- a Department of Biochemistry and Molecular Biology , Seoul National University College of Medicine , Seoul , Korea.,b Department of Biomedical Sciences , Seoul National University Graduate School , Seoul , Korea
| | - Young Dong Yoo
- b Department of Biomedical Sciences , Seoul National University Graduate School , Seoul , Korea
| | - Hyunjoo Cha-Molstad
- c World Class Institute, Korea Research Institute of Bioscience and Biotechnology , Ochang, Cheongwon , Korea
| | - Bo Yeon Kim
- c World Class Institute, Korea Research Institute of Bioscience and Biotechnology , Ochang, Cheongwon , Korea
| | - Yong Tae Kwon
- b Department of Biomedical Sciences , Seoul National University Graduate School , Seoul , Korea
| | - Sue Ah Noh
- d Department of Applied Chemistry , College of Applied Sciences, Kyung Hee University , Yongin , Korea
| | - Kwang Pyo Kim
- d Department of Applied Chemistry , College of Applied Sciences, Kyung Hee University , Yongin , Korea
| | - Min Jae Lee
- a Department of Biochemistry and Molecular Biology , Seoul National University College of Medicine , Seoul , Korea.,b Department of Biomedical Sciences , Seoul National University Graduate School , Seoul , Korea
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102
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Dimerization of Arginyl-tRNA Synthetase by Free Heme Drives Its Inactivation in Plasmodium falciparum. Structure 2016; 24:1476-87. [PMID: 27502052 DOI: 10.1016/j.str.2016.06.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/15/2016] [Accepted: 06/20/2016] [Indexed: 11/23/2022]
Abstract
Excess cellular heme is toxic, and malaria parasites regulate its levels during hemoglobin digestion. Aminoacyl-tRNA synthetases are ubiquitous enzymes, and of these, arginyl-tRNA synthetase (RRS) is unique as its enzymatic product of charged tRNA is required for protein synthesis and degradation. We show that Plasmodium falciparum arginyl-tRNA synthetase (PfRRS) is an active, cytosolic, and monomeric enzyme. Its high-resolution crystal structure highlights critical structural differences with the human enzyme. We further show that hemin binds to and inhibits the aminoacylation activity of PfRRS. Hemin induces a dimeric form of PfRRS that is thus rendered enzymatically dead as it is unable to recognize its cognate tRNA(arg). Excessive hemin in chloroquine-treated malaria parasites results in significantly reduced charged tRNA(arg) levels, thus suggesting deceleration of protein synthesis. These data together suggest that the inhibition of Plasmodium falciparum arginyl-tRNA synthetase can now be synergized with existing antimalarials for more potent drug cocktails against malaria parasites.
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103
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Lehmann G, Ziv T, Braten O, Admon A, Udasin RG, Ciechanover A. Ubiquitination of specific mitochondrial matrix proteins. Biochem Biophys Res Commun 2016; 475:13-8. [DOI: 10.1016/j.bbrc.2016.04.150] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/28/2016] [Indexed: 12/01/2022]
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104
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Li Y, Xiong W, Zhang EE. The ratio of intracellular CRY proteins determines the clock period length. Biochem Biophys Res Commun 2016; 472:531-8. [PMID: 26966073 DOI: 10.1016/j.bbrc.2016.03.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/05/2016] [Indexed: 10/22/2022]
Abstract
Although a deficiency in CRY1 or CRY2 correlates with a shorter or longer circadian period, the regulation of CRY proteins in the circadian period has not been well studied. In this study, we found that both CRY1 and CRY2 were able to rescue oscillation in CRY null cells and that they displayed different periods. Furthermore, we demonstrated that protein nuclear import rates, not protein stability, regulate the period-length at the cellular level. Co-transfection of CRY1 and CRY2 in various ratios in the same cells gives rise to the predicted period length in a dose-dependent manner. Given the distinct characteristics of the C-terminal tails of the CRY1 and CRY2 proteins, our study addresses a long-standing hypothesis that the ratio of these two CRY molecules affects the clock period.
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Affiliation(s)
- Yang Li
- College of Biological Sciences, China Agricultural University, Beijing 100083, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Wei Xiong
- National Institute of Biological Sciences, Beijing 102206, China; School of Life Sciences, Peking University, Beijing 100871, China
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105
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Lee KE, Heo JE, Kim JM, Hwang CS. N-Terminal Acetylation-Targeted N-End Rule Proteolytic System: The Ac/N-End Rule Pathway. Mol Cells 2016; 39:169-78. [PMID: 26883906 PMCID: PMC4794598 DOI: 10.14348/molcells.2016.2329] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/11/2016] [Accepted: 01/14/2016] [Indexed: 12/12/2022] Open
Abstract
Although Nα-terminal acetylation (Nt-acetylation) is a pervasive protein modification in eukaryotes, its general functions in a majority of proteins are poorly understood. In 2010, it was discovered that Nt-acetylation creates a specific protein degradation signal that is targeted by a new class of the N-end rule proteolytic system, called the Ac/N-end rule pathway. Here, we review recent advances in our understanding of the mechanism and biological functions of the Ac/N-end rule pathway, and its crosstalk with the Arg/N-end rule pathway (the classical N-end rule pathway).
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Affiliation(s)
- Kang-Eun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790–784,
Korea
| | - Ji-Eun Heo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790–784,
Korea
| | - Jeong-Mok Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790–784,
Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790–784,
Korea
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106
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Takahashi Y, Shinoda A, Kamada H, Shimizu M, Inoue J, Sato R. Perilipin2 plays a positive role in adipocytes during lipolysis by escaping proteasomal degradation. Sci Rep 2016; 6:20975. [PMID: 26876687 PMCID: PMC4753471 DOI: 10.1038/srep20975] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/14/2016] [Indexed: 12/18/2022] Open
Abstract
Perilipin2 (Plin2), also known as adipose differentiation-related protein (ADRP), or adipophilin, is a member of the PAT family involved in lipid droplet (LD) formation in the liver and peripheral tissues. Although Plin2 was originally identified as a highly expressed gene in adipocytes, its physiological role in mature adipocytes is largely unknown. In this report, we investigated the regulation of Plin2 expression and its function in differentiated adipocytes of mouse embryonic fibroblasts (MEFs). Plin2 mRNA levels increased during adipocyte differentiation whereas protein levels did not. Plin2 was degraded through the ubiquitin-proteasome pathway but was inhibited by lipolytic inducers. Furthermore, lentiviral-mediated Plin2 knockdown attenuated lipolysis in differentiated MEFs in a time-dependent manner. Oleic acid-induced LD formation enhanced Plin2 protein stability when it was localized to LDs. Furthermore, a mutational analysis revealed that the ubiquitination and degradation of Plin2 required both the second and third alanine in the N-terminal region. These results suggest that Plin2 is degraded in the cytosol in its N-terminal amino acid sequence-dependent manner and instead becomes stable when localized on LDs. Our findings highlight the relationship between protein stability and a previously unnoticed function of Plin2 during lipolysis in adipocytes.
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Affiliation(s)
- Yu Takahashi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Akihiro Shinoda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Haruhiko Kamada
- Laboratory of Biopharmaceutical Research, National Institute of Biomedical Innovation, Osaka, Japan.,The Center for Advanced Medical Engineering and Informatics, Osaka University, Osaka, Japan
| | - Makoto Shimizu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Jun Inoue
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ryuichiro Sato
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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107
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Burkhart JM, Taskin AA, Zahedi RP, Vögtle FN. Quantitative Profiling for Substrates of the Mitochondrial Presequence Processing Protease Reveals a Set of Nonsubstrate Proteins Increased upon Proteotoxic Stress. J Proteome Res 2015; 14:4550-63. [PMID: 26446170 DOI: 10.1021/acs.jproteome.5b00327] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The majority of mitochondrial preproteins are targeted via N-terminal presequences that are cleaved upon import into the organelle. The essential mitochondrial processing protease (MPP) is assumed to cleave the majority of incoming precursors; however, only a small fraction of mitochondrial precursors have been experimentally analyzed limiting the information on MPP recognition and substrate specificity. Here we present the first systematic approach for identification of authentic MPP substrate proteins using a temperature-sensitive mutant of the MPP subunit Mas1. Inactivation of MPP at nonpermissive temperature leads to accumulation of immature precursors in mitochondria, which were measured by quantitative N-terminal ChaFRADIC. This led to the identification of 66 novel MPP substrates. Deduction of the cleaved presequences determines arginine in position -2 of the cleavage site as a main factor for MPP recognition. Interestingly, a set of nonprocessed proteins was also increased in mas1 mutant mitochondria. Additionally, mas1 mitochondria respond to temperature elevation with an increase in membrane potential and oxygen consumption. These changes might indicate that mas1 cells exert a response to balance the proteotoxic stress induced by MPP dysfunction.
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Affiliation(s)
- Julia M Burkhart
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Asli A Taskin
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg , Stefan-Meier-Str. 17, 79104 Freiburg, Germany
- Faculty of Biology, Universität Freiburg , Schänzlestrasse 1, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg , Albertstrasse 19A, 79104 Freiburg, Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - F-Nora Vögtle
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg , Stefan-Meier-Str. 17, 79104 Freiburg, Germany
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108
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Devrekanli A, Kanemaki MT. Conditional Budding Yeast Mutants with Temperature-Sensitive and Auxin-Inducible Degrons for Screening of Suppressor Genes. Methods Mol Biol 2015; 1369:257-78. [PMID: 26519318 DOI: 10.1007/978-1-4939-3145-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The conditional control of protein expression is useful to characterize the function of proteins, especially of those that are essential for cell viability. Two degron-based systems, temperature-sensitive and auxin-inducible degrons, can be used to generate conditional mutants of budding yeast, simply by transforming appropriate cells with PCR-amplified DNA. We describe a protocol for the generation of temperature-sensitive and auxin-inducible degron mutants. We also show that a conditional mutant with few spontaneous revertants was generated by combining two degron systems for the Inn1 protein. Finally, we describe a suppressor screening method that uses the dual degron-Inn1 mutant to identify mutant proteins that suppress Inn1-K31A, which has a defect in cytokinesis.
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Affiliation(s)
- Asli Devrekanli
- Department of Molecular Biology and Genetics, Canik Basari University, Gürgenyatak Köyü, Samsun, 55080, Turkey.
| | - Masato T Kanemaki
- Center of Frontier Research, National Institute of Genetics, Research Organization of Information and Systems, SOKENDAI, Yata 1111, Mishima, Shizuoka, 411-8540, Japan. .,Department of Genetics, SOKENDAI, Mishima, Shizuoka, Japan. .,JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
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109
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Lee JH, Jiang Y, Kwon YT, Lee MJ. Pharmacological Modulation of the N-End Rule Pathway and Its Therapeutic Implications. Trends Pharmacol Sci 2015; 36:782-797. [PMID: 26434644 DOI: 10.1016/j.tips.2015.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/13/2015] [Accepted: 07/16/2015] [Indexed: 11/26/2022]
Abstract
The N-end rule pathway is a proteolytic system in which single N-terminal amino acids of short-lived substrates determine their metabolic half-lives. Substrates of this pathway have been implicated in the pathogenesis of many diseases, including malignancies, neurodegeneration, and cardiovascular disorders. This review provides a comprehensive overview of current knowledge about the mechanism and functions of the N-end rule pathway. Pharmacological strategies for the modulation of target substrate degradation are also reviewed, with emphasis on their in vivo implications. Given the rapid advances in structural and biochemical understanding of the recognition components (N-recognins) of the N-end rule pathway, small-molecule inhibitors and activating ligands of N-recognins emerge as therapeutic agents with novel mechanisms of action.
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Affiliation(s)
- Jung Hoon Lee
- Department of Biochemistry and Molecular Biology, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Yanxialei Jiang
- Department of Biochemistry and Molecular Biology, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Yong Tae Kwon
- Protein Metabolism Medical Research Center, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea.
| | - Min Jae Lee
- Department of Biochemistry and Molecular Biology, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea; Protein Metabolism Medical Research Center, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea; Neuroscience Research Institute, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea.
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110
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Kitamura K. Inhibition of the Arg/N-end rule pathway-mediated proteolysis by dipeptide-mimetic molecules. Amino Acids 2015; 48:235-43. [PMID: 26334349 DOI: 10.1007/s00726-015-2083-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/21/2015] [Indexed: 11/30/2022]
Abstract
Ubr11 in the fission yeast Schizosaccharomyces pombe is an evolutionarily conserved ubiquitin ligase functioning in the Arg/N-end rule pathway, which promotes degradation of substrate proteins via the proteasome. Ubr11 recognizes the N-degron sequence in substrates. The primary N-degron contains a destabilization-inducing N-terminal amino acid, which is either a basic (type 1) or bulky hydrophobic (type 2) residue. Dipeptides are known to inhibit proteolytic degradation via the Arg/N-end rule pathway. Here, I examined the potency of some amino acid- or dipeptide-related molecules in their inhibition of Ubr11/N-end rule-mediated degradation. An amide form of L-arginine and L-tryptophan had weak inhibitory activity for type 1 and type 2 substrates, respectively, although the unmodified amino acid monomer and its carboxymethylated ester were ineffective. Among the naturally occurring dipeptides tested, Lys-Leu and Tyr-Leu showed potent inhibitory activity, but their effect was transient, especially at submillimolar concentrations. L-arginine-β-naphthylamide (Arg-βNA) showed stronger activity than several dipeptides for type 1 substrates, but all Lys-Leu, Tyr-Leu, and Arg-βNA caused growth retardation. The inhibitory activity of the L-phenylalanine carbobenzoxy-hydrazide for type 2 substrates was not very strong, but it prolonged the action of Tyr-Leu at low concentrations and, importantly, did not interfere with cell growth. Apart from their utility, these dipeptidomimetics provide a clue for understanding the determinants of recognition by Ubr ubiquitin ligase and further designing novel inhibitors of the Arg/N-end rule pathway.
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Affiliation(s)
- Kenji Kitamura
- Center for Gene Science, Hiroshima University, 1-4-2 Kagamiyama, Higashi-Hiroshima, 739-8527, Japan.
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111
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Moncrieff S, Moncan M, Scialpi F, Ditzel M. Regulation of hedgehog Ligand Expression by the N-End Rule Ubiquitin-Protein Ligase Hyperplastic Discs and the Drosophila GSK3β Homologue, Shaggy. PLoS One 2015; 10:e0136760. [PMID: 26334301 PMCID: PMC4559392 DOI: 10.1371/journal.pone.0136760] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 08/07/2015] [Indexed: 12/11/2022] Open
Abstract
Hedgehog (Hh) morphogen signalling plays an essential role in tissue development and homeostasis. While much is known about the Hh signal transduction pathway, far less is known about the molecules that regulate the expression of the hedgehog (hh) ligand itself. Here we reveal that Shaggy (Sgg), the Drosophila melanogaster orthologue of GSK3β, and the N-end Rule Ubiquitin-protein ligase Hyperplastic Discs (Hyd) act together to co-ordinate Hedgehog signalling through regulating hh ligand expression and Cubitus interruptus (Ci) expression. Increased hh and Ci expression within hyd mutant clones was effectively suppressed by sgg RNAi, placing sgg downstream of hyd. Functionally, sgg RNAi also rescued the adult hyd mutant head phenotype. Consistent with the genetic interactions, we found Hyd to physically interact with Sgg and Ci. Taken together we propose that Hyd and Sgg function to co-ordinate hh ligand and Ci expression, which in turn influences important developmental signalling pathways during imaginal disc development. These findings are important as tight temporal/spatial regulation of hh ligand expression underlies its important roles in animal development and tissue homeostasis. When deregulated, hh ligand family misexpression underlies numerous human diseases (e.g., colorectal, lung, pancreatic and haematological cancers) and developmental defects (e.g., cyclopia and polydactyly). In summary, our Drosophila-based findings highlight an apical role for Hyd and Sgg in initiating Hedgehog signalling, which could also be evolutionarily conserved in mammals.
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Affiliation(s)
- Sophie Moncrieff
- MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh CRUK Cancer Research Centre, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, United Kingdom
| | - Matthieu Moncan
- MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh CRUK Cancer Research Centre, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, United Kingdom
| | - Flavia Scialpi
- MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh CRUK Cancer Research Centre, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, United Kingdom
| | - Mark Ditzel
- MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh CRUK Cancer Research Centre, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, United Kingdom
- * E-mail:
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112
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Kaur G, Subramanian S. The UBR-box and its relationship to binuclear RING-like treble clef zinc fingers. Biol Direct 2015; 10:36. [PMID: 26185100 PMCID: PMC4506424 DOI: 10.1186/s13062-015-0066-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/02/2015] [Indexed: 11/30/2022] Open
Abstract
Background The N-end rule pathway is a part of the ubiquitin–dependent proteolytic system wherein N-recognin proteins recognize the amino terminal degradation signals (N-degrons) of the substrate. The type 1 N-degron recognizing UBR-box domain of the eukaryotic Arg/N-end rule pathway is known to possess a novel three-zinc-stabilized heart-shaped fold. Results Using sequence and structure analysis we argue that the UBR-box fold emerged from a binuclear RING-like treble clef zinc finger. The RING-like core is preserved in the UBR-box and the metal-chelating motifs display significant sequence and structural similarity to B-box and ZZ domains. UBR-box domains retrieved in our analysis co-occur with a variety of other protein domains, suggestive of its involvement in diverse biological roles. The UBR-box is a unique family of RING-like treble clefs as it displays a distinct circular permutation at the zinc-knuckle of the first zinc-binding site unlike other documented permutations of the RING-like domains which occur at the second zinc-binding site. The circular permutation of the RING-like treble clef scaffold has possibly aided the gain of a novel and relatively deep cleft suited for binding N-degrons. The N- and C-terminal extensions to the circularly permuted RING-like region bind a third zinc ion, which likely provides additional stability to the domain by keeping the two halves of the permuted zinc-knuckle together. Conclusions Structural modifications and extensions to the RING-like core have resulted in a novel UBR-box fold, which can recognize and target the type 1 N-degron containing proteins for ubiquitin-mediated proteolysis. The UBR-box appears to have emerged during the expansion of ubiquitin system pathway-related functions in eukaryotes, but is also likely to have other non-N-recognin functions as well. Reviewers This article was reviewed by Eugene Koonin, Balaji Santhanam, Kira S. Makarova. Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0066-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gurmeet Kaur
- CSIR-Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh, 160036, India.
| | - Srikrishna Subramanian
- CSIR-Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh, 160036, India.
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113
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Bittner LM, Westphal K, Narberhaus F. Conditional Proteolysis of the Membrane Protein YfgM by the FtsH Protease Depends on a Novel N-terminal Degron. J Biol Chem 2015; 290:19367-78. [PMID: 26092727 DOI: 10.1074/jbc.m115.648550] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Indexed: 01/16/2023] Open
Abstract
Regulated proteolysis efficiently and rapidly adapts the bacterial proteome to changing environmental conditions. Many protease substrates contain recognition motifs, so-called degrons, that direct them to the appropriate protease. Here we describe an entirely new degron identified in the cytoplasmic N-terminal end of the membrane-anchored protein YfgM of Escherichia coli. YfgM is stable during exponential growth and degraded in stationary phase by the essential FtsH protease. The alarmone (p)ppGpp, but not the previously described YfgM interactors RcsB and PpiD, influence YfgM degradation. By scanning mutagenesis, we define individual amino acids responsible for turnover of YfgM and find that the degron does not at all comply with the known N-end rule pathway. The YfgM degron is a distinct module that facilitates FtsH-mediated degradation when fused to the N terminus of another monotopic membrane protein but not to that of a cytoplasmic protein. Several lines of evidence suggest that stress-induced degradation of YfgM relieves the response regulator RcsB and thereby permits cellular protection by the Rcs phosphorelay system. On the basis of these and other results in the literature, we propose a model for how the membrane-spanning YfgM protein serves as connector between the stress responses in the periplasm and cytoplasm.
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Affiliation(s)
| | - Kai Westphal
- From Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Franz Narberhaus
- From Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany
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114
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Amino-terminal arginylation targets endoplasmic reticulum chaperone BiP for autophagy through p62 binding. Nat Cell Biol 2015; 17:917-29. [PMID: 26075355 PMCID: PMC4490096 DOI: 10.1038/ncb3177] [Citation(s) in RCA: 178] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/20/2015] [Indexed: 02/07/2023]
Abstract
We show that ATE1-encoded Arg-transfer RNA transferase (R-transferase) of the N-end rule pathway mediates N-terminal arginylation of multiple endoplasmic reticulum (ER)-residing chaperones, leading to their cytosolic relocalization and turnover. N-terminal arginylation of BiP (also known as GRP78), protein disulphide isomerase and calreticulin is co-induced with autophagy during innate immune responses to cytosolic foreign DNA or proteasomal inhibition, associated with increased ubiquitylation. Arginylated BiP (R-BiP) is induced by and associated with cytosolic misfolded proteins destined for p62 (also known as sequestosome 1, SQSTM1) bodies. R-BiP binds the autophagic adaptor p62 through the interaction of its N-terminal arginine with the p62 ZZ domain. This allosterically induces self-oligomerization and aggregation of p62 and increases p62 interaction with LC3, leading to p62 targeting to autophagosomes and selective lysosomal co-degradation of R-BiP and p62 together with associated cargoes. In this autophagic mechanism, Nt-arginine functions as a delivery determinant, a degron and an activating ligand. Bioinformatics analysis predicts that many ER residents use arginylation to regulate non-ER processes.
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115
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Van Damme P, Hole K, Gevaert K, Arnesen T. N-terminal acetylome analysis reveals the specificity of Naa50 (Nat5) and suggests a kinetic competition between N-terminal acetyltransferases and methionine aminopeptidases. Proteomics 2015; 15:2436-46. [PMID: 25886145 DOI: 10.1002/pmic.201400575] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/04/2015] [Accepted: 04/14/2015] [Indexed: 11/08/2022]
Abstract
Cotranslational N-terminal (Nt-) acetylation of nascent polypeptides is mediated by N-terminal acetyltransferases (NATs). The very N-terminal amino acid sequence largely determines whether or not a given protein is Nt-acetylated. Currently, there are six distinct NATs characterized, NatA-NatF, in humans of which the in vivo substrate specificity of Naa50 (Nat5)/NatE, an alternative catalytic subunit of the human NatA, so far remained elusive. In this study, we quantitatively compared the Nt-acetylomes of wild-type yeast S. cerevisiae expressing the endogenous yeast Naa50 (yNaa50), the congenic strain lacking yNaa50, and an otherwise identical strain expressing human Naa50 (hNaa50). Six canonical yeast NatA substrates were Nt-acetylated less in yeast lacking yNaa50 than in wild-type yeast. In contrast, the ectopically expressed hNaa50 resulted, predominantly, in the Nt-acetylation of N-terminal Met (iMet) starting N-termini, including iMet-Lys, iMet-Val, iMet-Ala, iMet-Tyr, iMet-Phe, iMet-Leu, iMet-Ser, and iMet-Thr N-termini. This identified hNaa50 as being similar, in its substrate specificity, to the previously characterized hNaa60/NatF. In addition, the identification, in yNaa50-lacking yeast expressing hNaa50, of Nt-acetylated iMet followed by a small residue such as Ser, Thr, Ala, or Val, revealed a kinetic competition between Naa50 and Met-aminopeptidases (MetAPs), and implied that Nt-acetylated iMet followed by a small residue cannot be removed by MetAPs, a deduction supported by our in vitro data. As such, Naa50-mediated Nt-acetylation may act to retain the iMet of proteins of otherwise MetAP susceptible N-termini and the fraction of retained and Nt-acetylated iMet (followed by a small residue) in such a setting would be expected to depend on the relative levels of ribosome-associated Naa50/NatA and MetAPs.
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Affiliation(s)
- Petra Van Damme
- Department of Medical Protein Research, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Kristine Hole
- Department of Molecular Biology, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Bergen, Norway
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116
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The biological functions of Naa10 - From amino-terminal acetylation to human disease. Gene 2015; 567:103-31. [PMID: 25987439 DOI: 10.1016/j.gene.2015.04.085] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/20/2015] [Accepted: 04/27/2015] [Indexed: 01/07/2023]
Abstract
N-terminal acetylation (NTA) is one of the most abundant protein modifications known, and the N-terminal acetyltransferase (NAT) machinery is conserved throughout all Eukarya. Over the past 50 years, the function of NTA has begun to be slowly elucidated, and this includes the modulation of protein-protein interaction, protein-stability, protein function, and protein targeting to specific cellular compartments. Many of these functions have been studied in the context of Naa10/NatA; however, we are only starting to really understand the full complexity of this picture. Roughly, about 40% of all human proteins are substrates of Naa10 and the impact of this modification has only been studied for a few of them. Besides acting as a NAT in the NatA complex, recently other functions have been linked to Naa10, including post-translational NTA, lysine acetylation, and NAT/KAT-independent functions. Also, recent publications have linked mutations in Naa10 to various diseases, emphasizing the importance of Naa10 research in humans. The recent design and synthesis of the first bisubstrate inhibitors that potently and selectively inhibit the NatA/Naa10 complex, monomeric Naa10, and hNaa50 further increases the toolset to analyze Naa10 function.
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117
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Scialpi F, Mellis D, Ditzel M. EDD, a ubiquitin-protein ligase of the N-end rule pathway, associates with spindle assembly checkpoint components and regulates the mitotic response to nocodazole. J Biol Chem 2015; 290:12585-94. [PMID: 25833949 PMCID: PMC4432279 DOI: 10.1074/jbc.m114.625673] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 04/01/2015] [Indexed: 01/09/2023] Open
Abstract
In this work, we identify physical and genetic interactions that implicate E3 identified by differential display (EDD) in promoting spindle assembly checkpoint (SAC) function. During mitosis, the SAC initiates a mitotic checkpoint in response to chromosomes with kinetochores unattached to spindle pole microtubules. Similar to Budding uninhibited by benzimidazoles-related 1 (BUBR1) siRNA, a bona fide SAC component, EDD siRNA abrogated G2/M accumulation in response to the mitotic destabilizing agent nocodazole. Furthermore, EDD siRNA reduced mitotic cell viability and, in nocodazole-treated cells, increased expression of the promitotic progression protein cell division cycle 20 (CDC20). Copurification studies also identified physical interactions with CDC20, BUBR1, and other components of the SAC. Taken together, these observations highlight the potential role of EDD in regulating mitotic progression and the cellular response to perturbed mitosis.
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Affiliation(s)
- Flavia Scialpi
- From the MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, Scotland, United Kingdom
| | - David Mellis
- From the MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, Scotland, United Kingdom
| | - Mark Ditzel
- From the MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, Scotland, United Kingdom
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118
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Goitea VE, Hallak ME. Calreticulin and Arginylated Calreticulin Have Different Susceptibilities to Proteasomal Degradation. J Biol Chem 2015; 290:16403-14. [PMID: 25969538 DOI: 10.1074/jbc.m114.626127] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Indexed: 12/31/2022] Open
Abstract
Post-translational arginylation has been suggested to target proteins for proteasomal degradation. The degradation mechanism for arginylated calreticulin (R-CRT) localized in the cytoplasm is unknown. To evaluate the effect of arginylation on CRT stability, we examined the metabolic fates and degradation mechanisms of cytoplasmic CRT and R-CRT in NIH 3T3 and CHO cells. Both CRT isoforms were found to be proteasomal substrates, but the half-life of R-CRT (2 h) was longer than that of cytoplasmic CRT (0.7 h). Arginylation was not required for proteasomal degradation of CRT, although R-CRT displays ubiquitin modification. A CRT mutant incapable of dimerization showed reduced metabolic stability of R-CRT, indicating that R-CRT dimerization may protect it from proteasomal degradation. Our findings, taken together, demonstrate a novel function of arginylation: increasing the half-life of CRT in cytoplasm.
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Affiliation(s)
- Victor E Goitea
- From the Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Consejo Nacional de Investigaciones Científicas y Técnicas, and Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
| | - Marta E Hallak
- From the Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Consejo Nacional de Investigaciones Científicas y Técnicas, and Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
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119
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Degradation of misfolded proteins in neurodegenerative diseases: therapeutic targets and strategies. Exp Mol Med 2015; 47:e147. [PMID: 25766616 PMCID: PMC4351408 DOI: 10.1038/emm.2014.117] [Citation(s) in RCA: 567] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 11/19/2014] [Indexed: 12/13/2022] Open
Abstract
Mammalian cells remove misfolded proteins using various proteolytic systems, including the ubiquitin (Ub)-proteasome system (UPS), chaperone mediated autophagy (CMA) and macroautophagy. The majority of misfolded proteins are degraded by the UPS, in which Ub-conjugated substrates are deubiquitinated, unfolded and cleaved into small peptides when passing through the narrow chamber of the proteasome. The substrates that expose a specific degradation signal, the KFERQ sequence motif, can be delivered to and degraded in lysosomes via the CMA. Aggregation-prone substrates resistant to both the UPS and the CMA can be degraded by macroautophagy, in which cargoes are segregated into autophagosomes before degradation by lysosomal hydrolases. Although most misfolded and aggregated proteins in the human proteome can be degraded by cellular protein quality control, some native and mutant proteins prone to aggregation into β-sheet-enriched oligomers are resistant to all known proteolytic pathways and can thus grow into inclusion bodies or extracellular plaques. The accumulation of protease-resistant misfolded and aggregated proteins is a common mechanism underlying protein misfolding disorders, including neurodegenerative diseases such as Huntington's disease (HD), Alzheimer's disease (AD), Parkinson's disease (PD), prion diseases and Amyotrophic Lateral Sclerosis (ALS). In this review, we provide an overview of the proteolytic pathways in neurons, with an emphasis on the UPS, CMA and macroautophagy, and discuss the role of protein quality control in the degradation of pathogenic proteins in neurodegenerative diseases. Additionally, we examine existing putative therapeutic strategies to efficiently remove cytotoxic proteins from degenerating neurons.
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120
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Parsons K, Nakatani Y, Nguyen MD. p600/UBR4 in the central nervous system. Cell Mol Life Sci 2015; 72:1149-60. [PMID: 25424645 PMCID: PMC11113099 DOI: 10.1007/s00018-014-1788-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 11/06/2014] [Accepted: 11/17/2014] [Indexed: 10/24/2022]
Abstract
A decade ago, the large 600 kDa mammalian protein p600 (also known as UBR4) was discovered as a multifunctional protein with roles in anoikis, viral transformation and protein degradation. Recently, p600 has emerged as a critical protein in the mammalian brain with roles in neurogenesis, neuronal migration, neuronal signaling and survival. How p600 integrates these apparently unrelated functions to maintain tissue homeostasis and murine survival remains unclear. The common molecular basis underlying many of the actions of p600 suggests, however, certain conservation and transposition of these functions across systems. In this review, we summarize the central nervous system functions of p600 and propose new perspectives on its biological complexity in neuronal physiology and neurological diseases.
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Affiliation(s)
- Kari Parsons
- Department of Clinical Neurosciences, University of Calgary, Hotchkiss Brain Institute, 3330 Hospital Drive NW, Calgary, T2N 4N1, Canada,
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121
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Weaver BP, Zabinsky R, Weaver YM, Lee ES, Xue D, Han M. CED-3 caspase acts with miRNAs to regulate non-apoptotic gene expression dynamics for robust development in C. elegans. eLife 2014; 3:e04265. [PMID: 25432023 PMCID: PMC4279084 DOI: 10.7554/elife.04265] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/26/2014] [Indexed: 12/29/2022] Open
Abstract
Genetic redundancy and pleiotropism have limited the discovery of functions associated with miRNAs and other regulatory mechanisms. To overcome this, we performed an enhancer screen for developmental defects caused by compromising both global miRISC function and individual genes in Caenorhabditis elegans. Among 126 interactors with miRNAs, we surprisingly found the CED-3 caspase that has only been well studied for its role in promoting apoptosis, mostly through protein activation. We provide evidence for a non-apoptotic function of CED-3 caspase that regulates multiple developmental events through proteolytic inactivation. Specifically, LIN-14, LIN-28, and DISL-2 proteins are known miRNA targets, key regulators of developmental timing, and/or stem cell pluripotency factors involved in miRNA processing. We show CED-3 cleaves these proteins in vitro. We also show CED-3 down-regulates LIN-28 in vivo, possibly rendering it more susceptible to proteasomal degradation. This mechanism may critically contribute to the robustness of gene expression dynamics governing proper developmental control. DOI:http://dx.doi.org/10.7554/eLife.04265.001 For an organism to develop from a single cell into a collection of many different, specialized cells, different genes must be switched on or off at particular times. However, some of these genes involved in development are ‘redundant’ and carry out the same or similar tasks. This acts like a backup system, so if one of the genes is unable to complete a task, the others can compensate and the organism will still develop correctly. To produce a protein from a gene, the DNA sequence that makes up the gene is used as a template to create another molecule called messenger RNA. Genes can also be ‘silenced’—prevented from making proteins—by small molecules called microRNAs, which bind to messenger RNA molecules and mark them for destruction. MicroRNA molecules therefore play an important role in controlling development. However, as many microRNA molecules often work together, and as many genes are redundant, it can be difficult to discover the effects of specific microRNAs. It is also difficult to discover whether any other mechanisms work alongside the microRNAs to control development. Weaver, Zabinsky et al. used mutant forms of the nematode worm Caenorhabditis elegans, in which microRNA gene regulation did not work correctly, to investigate the mechanisms that work alongside microRNAs to control development. Genes in these worms were silenced; those silenced genes that caused additional developmental defects were considered likely to work ‘redundantly’ in the same role as a microRNA molecule. This revealed over one hundred genes that were previously unknown to work with microRNA molecules. Weaver, Zabinsky et al. focused on one of these genes, called ced-3. The CED-3 protein produced from this gene is known to execute programmed cell death, a carefully controlled process also known as apoptosis, but was not known to have other developmental functions. However, the worms with mutant forms of the ced-3 gene already have problems performing apoptosis but are otherwise relatively normal, so Weaver, Zabinsky et al. reasoned that the CED-3 protein must also have another role in development. Further investigation revealed that ced-3 mutations most severely disrupt development when they are combined with mutations in one particular family of microRNAs. These microRNAs are particularly important for controlling both when cells specialize into a particular type of cell, and the timing of when certain stages of development happen. Experiments using purified proteins showed that CED-3 breaks down three proteins that are produced from genes controlled by this family of microRNA molecules, and one of these proteins was also broken down by CED-3 in experiments with mutant worms. Weaver, Zabinsky et al. therefore propose that CED-3 is part of a semi-redundant system that ensures the proteins are produced at the right level and at the right time even if the microRNAs insufficiently regulate them. This finding demonstrated both a specific role and specific targets for the CED-3 protein during development, entirely distinct from its role in apoptosis. Although Weaver, Zabinsky et al. have identified a large number of genes that work alongside microRNAs to control development, these are only the genes that cause obvious developmental defects in healthy worms. Further experiments using similar techniques performed on worms under stress may reveal yet more such genes. DOI:http://dx.doi.org/10.7554/eLife.04265.002
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Affiliation(s)
- Benjamin P Weaver
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Rebecca Zabinsky
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Yi M Weaver
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, United States
| | - Eui Seung Lee
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Ding Xue
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Min Han
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, United States
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122
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Greer MS, Truksa M, Deng W, Lung SC, Chen G, Weselake RJ. Engineering increased triacylglycerol accumulation in Saccharomyces cerevisiae using a modified type 1 plant diacylglycerol acyltransferase. Appl Microbiol Biotechnol 2014; 99:2243-53. [DOI: 10.1007/s00253-014-6284-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 11/14/2014] [Accepted: 11/29/2014] [Indexed: 10/24/2022]
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123
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Gibbs DJ, Bacardit J, Bachmair A, Holdsworth MJ. The eukaryotic N-end rule pathway: conserved mechanisms and diverse functions. Trends Cell Biol 2014; 24:603-11. [DOI: 10.1016/j.tcb.2014.05.001] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 04/30/2014] [Accepted: 05/01/2014] [Indexed: 12/30/2022]
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124
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A neurostimulant para-chloroamphetamine inhibits the arginylation branch of the N-end rule pathway. Sci Rep 2014; 4:6344. [PMID: 25212999 PMCID: PMC4161967 DOI: 10.1038/srep06344] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/12/2014] [Indexed: 11/08/2022] Open
Abstract
In the arginylation branch of the N-end rule pathway, unacetylated N-terminal destabilizing residues function as essential determinants of protein degradation signals (N-degron). Here, we show that a neurostimulant, para-chloroamphetamine (PCA), specifically inhibits the Arg/N-end rule pathway, delaying the degradation of its artificial and physiological substrates, including regulators of G protein signaling 4 (RGS4), in vitro and in cultured cells. In silico computational analysis indicated that PCA strongly interacts with both UBR box and ClpS box, which bind to type 1 and type 2 N-degrons, respectively. Moreover, intraperitoneal injection of PCA significantly stabilized endogenous RGS4 proteins in the whole mouse brain and, particularly, in the frontal cortex and hippocampus. Consistent with the role of RGS4 in G protein signaling, treatment with PCA impaired the activations of GPCR downstream effectors in N2A cells, phenocopying ATE1-null mutants. In addition, levels of pathological C-terminal fragments of TDP43 bearing N-degrons (Arg208-TDP25) were significantly elevated in the presence of PCA. Thus, our study identifies PCA as a potential tool to understand and modulate various pathological processes regulated by the Arg/N-end rule pathway, including neurodegenerative processes in FTLD-U and ALS.
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125
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Ubr3 E3 ligase regulates apoptosis by controlling the activity of DIAP1 in Drosophila. Cell Death Differ 2014; 21:1961-70. [PMID: 25146930 DOI: 10.1038/cdd.2014.115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 07/15/2014] [Accepted: 07/15/2014] [Indexed: 12/31/2022] Open
Abstract
Apoptosis has essential roles in a variety of cellular and developmental processes. Although the pathway is well studied, how the activities of individual components in the pathway are regulated is less understood. In Drosophila, a key component in apoptosis is Drosophila inhibitor of apoptosis protein 1 (DIAP1), which is required to prevent caspase activation. Here, we demonstrate that Drosophila CG42593 (ubr3), encoding the homolog of mammalian UBR3, has an essential role in regulating the apoptosis pathway. We show that loss of ubr3 activity causes caspase-dependent apoptosis in Drosophila eye and wing discs. Our genetic epistasis analyses show that the apoptosis induced by loss of ubr3 can be suppressed by loss of initiator caspase Drosophila Nedd2-like caspase (Dronc), or by ectopic expression of the apoptosis inhibitor p35, but cannot be rescued by overexpression of DIAP1. Importantly, we show that the activity of Ubr3 in the apoptosis pathway is not dependent on its Ring-domain, which is required for its E3 ligase activity. Furthermore, we find that through the UBR-box domain, Ubr3 physically interacts with the neo-epitope of DIAP1 that is exposed after caspase-mediated cleavage. This interaction promotes the recruitment and ubiquitination of substrate caspases by DIAP1. Together, our data indicate that Ubr3 interacts with DIAP1 and positively regulates DIAP1 activity, possibly by maintaining its active conformation in the apoptosis pathway.
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126
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Ling HH, Beaulé C, Chiang CK, Tian R, Figeys D, Cheng HYM. Time-of-day- and light-dependent expression of ubiquitin protein ligase E3 component N-recognin 4 (UBR4) in the suprachiasmatic nucleus circadian clock. PLoS One 2014; 9:e103103. [PMID: 25084275 PMCID: PMC4118842 DOI: 10.1371/journal.pone.0103103] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 06/25/2014] [Indexed: 12/20/2022] Open
Abstract
Circadian rhythms of behavior and physiology are driven by the biological clock that operates endogenously but can also be entrained to the light-dark cycle of the environment. In mammals, the master circadian pacemaker is located in the suprachiasmatic nucleus (SCN), which is composed of individual cellular oscillators that are driven by a set of core clock genes interacting in transcriptional/translational feedback loops. Light signals can trigger molecular events in the SCN that ultimately impact on the phase of expression of core clock genes to reset the master pacemaker. While transcriptional regulation has received much attention in the field of circadian biology in the past, other mechanisms including targeted protein degradation likely contribute to the clock timing and entrainment process. In the present study, proteome-wide screens of the murine SCN led to the identification of ubiquitin protein ligase E3 component N-recognin 4 (UBR4), a novel E3 ubiquitin ligase component of the N-end rule pathway, as a time-of-day-dependent and light-inducible protein. The spatial and temporal expression pattern of UBR4 in the SCN was subsequently characterized by immunofluorescence microscopy. UBR4 is expressed across the entire rostrocaudal extent of the SCN in a time-of-day-dependent fashion. UBR4 is localized exclusively to arginine vasopressin (AVP)-expressing neurons of the SCN shell. Upon photic stimulation in the early subjective night, the number of UBR4-expressing cells within the SCN increases. This study is the first to identify a novel E3 ubiquitin ligase component, UBR4, in the murine SCN and to implicate the N-end rule degradation pathway as a potential player in regulating core clock mechanisms and photic entrainment.
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Affiliation(s)
- Harrod H. Ling
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Christian Beaulé
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Cheng-Kang Chiang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Ruijun Tian
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Hai-Ying M. Cheng
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- * E-mail:
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127
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Van Roey K, Uyar B, Weatheritt RJ, Dinkel H, Seiler M, Budd A, Gibson TJ, Davey NE. Short Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell Regulation. Chem Rev 2014; 114:6733-78. [DOI: 10.1021/cr400585q] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Kim Van Roey
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Bora Uyar
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Robert J. Weatheritt
- MRC
Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Holger Dinkel
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Markus Seiler
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Aidan Budd
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Toby J. Gibson
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Norman E. Davey
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department
of Physiology, University of California, San Francisco, San Francisco, California 94143, United States
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128
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Sun M, Liu J, Qi J, Tefsen B, Shi Y, Yan J, Gao GF. Nα-terminal acetylation for T cell recognition: molecular basis of MHC class I-restricted nα-acetylpeptide presentation. THE JOURNAL OF IMMUNOLOGY 2014; 192:5509-19. [PMID: 24829406 DOI: 10.4049/jimmunol.1400199] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
As one of the most common posttranslational modifications (PTMs) of eukaryotic proteins, N(α)-terminal acetylation (Nt-acetylation) generates a class of N(α)-acetylpeptides that are known to be presented by MHC class I at the cell surface. Although such PTM plays a pivotal role in adjusting proteolysis, the molecular basis for the presentation and T cell recognition of N(α)-acetylpeptides remains largely unknown. In this study, we determined a high-resolution crystallographic structure of HLA (HLA)-B*3901 complexed with an N(α)-acetylpeptide derived from natural cellular processing, also in comparison with the unmodified-peptide complex. Unlike the α-amino-free P1 residues of unmodified peptide, of which the α-amino group inserts into pocket A of the Ag-binding groove, the N(α)-linked acetyl of the acetylated P1-Ser protrudes out of the groove for T cell recognition. Moreover, the Nt-acetylation not only alters the conformation of the peptide but also switches the residues in the α1-helix of HLA-B*3901, which may impact the T cell engagement. The thermostability measurements of complexes between N(α)-acetylpeptides and a series of MHC class I molecules derived from different species reveal reduced stability. Our findings provide the insight into the mode of N(α)-acetylpeptide-specific presentation by classical MHC class I molecules and shed light on the potential of acetylepitope-based immune intervene and vaccine development.
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Affiliation(s)
- Mingwei Sun
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; and
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Boris Tefsen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinghua Yan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - George F Gao
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; and Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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129
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Hamilton EM, Polder E, Vanderver A, Naidu S, Schiffmann R, Fisher K, Raguž AB, Blumkin L, van Berkel CGM, Waisfisz Q, Simons C, Taft RJ, Abbink TEM, Wolf NI, van der Knaap MS. Hypomyelination with atrophy of the basal ganglia and cerebellum: further delineation of the phenotype and genotype-phenotype correlation. ACTA ACUST UNITED AC 2014; 137:1921-30. [PMID: 24785942 DOI: 10.1093/brain/awu110] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Hypomyelination with atrophy of the basal ganglia and cerebellum is a rare leukoencephalopathy that was identified using magnetic resonance imaging in 2002. In 2013, whole exome sequencing of 11 patients with the disease revealed that they all had the same de novo mutation in TUBB4A, which encodes tubulin β-4A. We investigated the mutation spectrum in a cohort of 42 patients and the relationship between genotype and phenotype. Patients were selected on the basis of clinical and magnetic resonance imaging abnormalities that are indicative of hypomyelination with atrophy of the basal ganglia and cerebellum. Genetic testing and a clinical inventory were performed, and sequential magnetic resonance images were evaluated using a standard protocol. The heterozygous TUBB4A mutation observed in the first 11 patients was the most common (25 patients). Additionally, 13 other heterozygous mutations were identified, located in different structural domains of tubulin β-4A. We confirmed that the mutations were de novo in all but three patients. In two of these three cases we lacked parental DNA and in one the mutation was also found in the mother, most likely due to mosaicism. Patients showed a phenotypic continuum ranging from neonatal to childhood disease onset, normal to delayed early development and slow to more rapid neurological deterioration. Neurological symptomatology consisted of extrapyramidal movement abnormalities, spasticity, ataxia, cognitive deficit and sometimes epilepsy. Three patients died and the oldest living patient was 29 years of age. The patients' magnetic resonance images showed an absent or disappearing putamen, variable cerebellar atrophy and highly variable cerebral atrophy. Apart from hypomyelination, myelin loss was evident in several cases. Three severely affected patients had similar, somewhat atypical magnetic resonance image abnormalities. The study results were strongly suggestive of a genotype-phenotype correlation. The 25 patients with the common c.745G>A mutation generally had a less rapidly progressive disease course than the 17 cases with other TUBB4A mutations. Overall, this work demonstrates that the distinctive magnetic resonance imaging pattern for hypomyelination with atrophy of the basal ganglia and cerebellum defines a homogeneous clinical phenotype of variable severity. Patients almost invariably have prominent extrapyramidal movement abnormalities, which are rarely seen in patients with hypomyelination of different origin. A dominant TUBB4A mutation is also associated with dystonia type 4, in which magnetic resonance images of the brain seem normal. It is highly likely that there is a disease continuum associated with TUBB4A mutations, of which hypomyelination with atrophy of the basal ganglia and cerebellum and dystonia type 4 are the extremes. This would indicate that extrapyramidal movement abnormalities constitute the core feature of the disease spectrum related to dominant TUBB4A mutations and that all other features are variable.
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Affiliation(s)
- Eline M Hamilton
- 1 Department of Child Neurology, VU University Medical Centre, Neuroscience Campus Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Emiel Polder
- 1 Department of Child Neurology, VU University Medical Centre, Neuroscience Campus Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Adeline Vanderver
- 2 Centre for Genetic Medicine Research, Children's National Medical Centre, 111 Michigan Avenue, DC 20010 Washington, USA
| | - Sakkubai Naidu
- 3 Johns Hopkins University School of Medicine, Hugo Moser Research Institute, Kennedy Krieger Institute, 707, N. Broadway, Baltimore, USA
| | - Raphael Schiffmann
- 4 Institute of Metabolic Disease, Baylor Research Institute, 3812 Elm Street, TX 75226 Dallas, USA
| | - Kate Fisher
- 5 Department of Paediatrics, Western Sussex Hospitals NHS Foundation Trust, Worthing Hospital, Lyndhurst Road, Worthing, West Sussex, BN11 2DH, UK
| | - Ana Boban Raguž
- 6 Department of Child Neurology, Clinical Hospital Mostar, Bijeli Brijeg, 88 000 Mostar, Bosnia and Herzegovina
| | - Luba Blumkin
- 7 Paediatric Neurology Unit, Metabolic-Neurogenetic Clinic, The E. Wolfson Medical Centre, P.O. Box 5, Holon 58100, Israel
| | | | - Carola G M van Berkel
- 1 Department of Child Neurology, VU University Medical Centre, Neuroscience Campus Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Quinten Waisfisz
- 8 Department of Clinical Genetics, VU University Medical Centre, 1081 BT Amsterdam, The Netherlands
| | - Cas Simons
- 9 Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Ryan J Taft
- 9 Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Truus E M Abbink
- 1 Department of Child Neurology, VU University Medical Centre, Neuroscience Campus Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Nicole I Wolf
- 1 Department of Child Neurology, VU University Medical Centre, Neuroscience Campus Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Marjo S van der Knaap
- 1 Department of Child Neurology, VU University Medical Centre, Neuroscience Campus Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands10 Department of Functional Genomics, Centre for Neurogenomics and Cognitive Research, VU University, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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130
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Affiliation(s)
- Jeong-Mok Kim
- Department of Life Sciences; Pohang University of Science and Technology; Pohang, Gyeongbuk, South Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences; Pohang University of Science and Technology; Pohang, Gyeongbuk, South Korea
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131
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Zimmerman SW, Yi YJ, Sutovsky M, van Leeuwen FW, Conant G, Sutovsky P. Identification and characterization of RING-finger ubiquitin ligase UBR7 in mammalian spermatozoa. Cell Tissue Res 2014; 356:261-78. [PMID: 24664117 DOI: 10.1007/s00441-014-1808-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 01/13/2014] [Indexed: 01/03/2023]
Abstract
The ubiquitin-proteasome system (UPS) controls intracellular protein turnover in a substrate-specific manner via E3-type ubiquitin ligases. Mammalian fertilization and particularly sperm penetration through the oocyte vitelline coat, the zona pellucida (ZP), is regulated by UPS. We use an extrinsic substrate of the proteasome-dependent ubiquitin-fusion degradation pathway, the mutant ubiquitin UBB(+1), to provide evidence that an E3-type ligase activity exists in sperm-acrosomal fractions. Protein electrophoresis gels from such de novo ubiquitination experiments contained a unique protein band identified by tandem mass spectrometry as being similar to ubiquitin ligase UBR7 (alternative name: C14ORF130). Corresponding mRNA was amplified from boar testis and several variants of the UBR7 protein were detected in boar, mouse and human sperm extracts by Western blotting. Genomic analysis indicated a high degree of evolutionary conservation, remarkably constant purifying selection and conserved testis expression of the UBR7 gene. By immunofluorescence, UBR7 was localized to the spermatid acrosomal cap and sperm acrosome, in addition to hotspots of proteasomal activity in spermatids, such as the cytoplasmic lobe, caudal manchette, nucleus and centrosome. During fertilization, UBR7 remained with the ZP-bound acrosomal shroud following acrosomal exocytosis. Thus, UBR7 is present in the acrosomal cap of round spermatids and within the acrosomal matrix of mature boar spermatozoa. These data provide the first evidence of ubiquitin ligase activity in mammalian spermatozoa and indicate UBR7 involvement in spermiogenesis.
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Affiliation(s)
- Shawn W Zimmerman
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211-5300, USA
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132
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Measuring activity in the ubiquitin-proteasome system: from large scale discoveries to single cells analysis. Cell Biochem Biophys 2014; 67:75-89. [PMID: 23686610 DOI: 10.1007/s12013-013-9621-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The ubiquitin-proteasome system (UPS) is the primary pathway responsible for the recognition and degradation of misfolded, damaged, or tightly regulated proteins in addition to performing essential roles in DNA repair, cell cycle regulation, cell migration, and the immune response. While traditional biochemical techniques have proven useful in the identification of key proteins involved in this pathway, the implementation of novel reporters responsible for measuring enzymatic activity of the UPS has provided valuable insight into the effectiveness of therapeutics and role of the UPS in various human diseases such as multiple myeloma and Huntington's disease. These reporters, usually consisting of a recognition sequence fused to an analytical handle, are designed to specifically evaluate enzymatic activity of certain members of the UPS including the proteasome, E3 ubiquitin ligases, and deubiquitinating enzymes. This review highlights the more commonly used reporters employed in a variety of scenarios ranging from high-throughput screening of novel inhibitors to single cell microscopy techniques measuring E3 ligase or proteasome activity. Finally, a recent study is presented highlighting the development of a novel degron-based substrate designed to overcome the limitations of current reporting techniques in measuring E3 ligase and proteasome activity in patient samples.
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133
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Gibbs DJ, Md Isa N, Movahedi M, Lozano-Juste J, Mendiondo GM, Berckhan S, Marín-de la Rosa N, Vicente Conde J, Sousa Correia C, Pearce SP, Bassel GW, Hamali B, Talloji P, Tomé DFA, Coego A, Beynon J, Alabadí D, Bachmair A, León J, Gray JE, Theodoulou FL, Holdsworth MJ. Nitric oxide sensing in plants is mediated by proteolytic control of group VII ERF transcription factors. Mol Cell 2014; 53:369-79. [PMID: 24462115 PMCID: PMC3969242 DOI: 10.1016/j.molcel.2013.12.020] [Citation(s) in RCA: 251] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 11/14/2013] [Accepted: 12/13/2013] [Indexed: 11/28/2022]
Abstract
Nitric oxide (NO) is an important signaling compound in prokaryotes and eukaryotes. In plants, NO regulates critical developmental transitions and stress responses. Here, we identify a mechanism for NO sensing that coordinates responses throughout development based on targeted degradation of plant-specific transcriptional regulators, the group VII ethylene response factors (ERFs). We show that the N-end rule pathway of targeted proteolysis targets these proteins for destruction in the presence of NO, and we establish them as critical regulators of diverse NO-regulated processes, including seed germination, stomatal closure, and hypocotyl elongation. Furthermore, we define the molecular mechanism for NO control of germination and crosstalk with abscisic acid (ABA) signaling through ERF-regulated expression of ABSCISIC ACID INSENSITIVE5 (ABI5). Our work demonstrates how NO sensing is integrated across multiple physiological processes by direct modulation of transcription factor stability and identifies group VII ERFs as central hubs for the perception of gaseous signals in plants.
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Affiliation(s)
- Daniel J Gibbs
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Nurulhikma Md Isa
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Mahsa Movahedi
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ciudad Politécnica de la Innovación, 46022 Valencia, Spain
| | - Guillermina M Mendiondo
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Sophie Berckhan
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Nora Marín-de la Rosa
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ciudad Politécnica de la Innovación, 46022 Valencia, Spain
| | - Jorge Vicente Conde
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Cristina Sousa Correia
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Simon P Pearce
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - George W Bassel
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Bulut Hamali
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9, Vienna 1030, Austria
| | - Prabhavathi Talloji
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9, Vienna 1030, Austria
| | - Daniel F A Tomé
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Alberto Coego
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ciudad Politécnica de la Innovación, 46022 Valencia, Spain
| | - Jim Beynon
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - David Alabadí
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ciudad Politécnica de la Innovación, 46022 Valencia, Spain
| | - Andreas Bachmair
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9, Vienna 1030, Austria
| | - José León
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ciudad Politécnica de la Innovación, 46022 Valencia, Spain
| | - Julie E Gray
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Frederica L Theodoulou
- Biological Chemistry and Crop Protection Department, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Michael J Holdsworth
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK.
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134
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A comparative analysis of the ubiquitination kinetics of multiple degrons to identify an ideal targeting sequence for a proteasome reporter. PLoS One 2013; 8:e78082. [PMID: 24205101 PMCID: PMC3812159 DOI: 10.1371/journal.pone.0078082] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 09/09/2013] [Indexed: 01/03/2023] Open
Abstract
The ubiquitin proteasome system (UPS) is the primary pathway responsible for the recognition and degradation of misfolded, damaged, or tightly regulated proteins. The conjugation of a polyubiquitin chain, or polyubiquitination, to a target protein requires an increasingly diverse cascade of enzymes culminating with the E3 ubiquitin ligases. Protein recognition by an E3 ligase occurs through a specific sequence of amino acids, termed a degradation sequence or degron. Recently, degrons have been incorporated into novel reporters to monitor proteasome activity; however only a limited few degrons have successfully been incorporated into such reporters. The goal of this work was to evaluate the ubiquitination kinetics of a small library of portable degrons that could eventually be incorporated into novel single cell reporters to assess proteasome activity. After an intensive literary search, eight degrons were identified from proteins recognized by a variety of E3 ubiquitin ligases and incorporated into a four component degron-based substrate to comparatively calculate ubiquitination kinetics. The mechanism of placement of multiple ubiquitins on the different degron-based substrates was assessed by comparing the data to computational models incorporating first order reaction kinetics using either multi-monoubiquitination or polyubiquitination of the degron-based substrates. A subset of three degrons was further characterized to determine the importance of the location and proximity of the ubiquitination site lysine with respect to the degron. Ultimately, this work identified three candidate portable degrons that exhibit a higher rate of ubiquitination compared to peptidase-dependent degradation, a desired trait for a proteasomal targeting motif.
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135
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Nakamura T, Tu S, Akhtar MW, Sunico CR, Okamoto SI, Lipton SA. Aberrant protein s-nitrosylation in neurodegenerative diseases. Neuron 2013; 78:596-614. [PMID: 23719160 DOI: 10.1016/j.neuron.2013.05.005] [Citation(s) in RCA: 277] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2013] [Indexed: 12/14/2022]
Abstract
S-Nitrosylation is a redox-mediated posttranslational modification that regulates protein function via covalent reaction of nitric oxide (NO)-related species with a cysteine thiol group on the target protein. Under physiological conditions, S-nitrosylation can be an important modulator of signal transduction pathways, akin to phosphorylation. However, with aging or environmental toxins that generate excessive NO, aberrant S-nitrosylation reactions can occur and affect protein misfolding, mitochondrial fragmentation, synaptic function, apoptosis or autophagy. Here, we discuss how aberrantly S-nitrosylated proteins (SNO-proteins) play a crucial role in the pathogenesis of neurodegenerative diseases, including Alzheimer's and Parkinson's diseases. Insight into the pathophysiological role of aberrant S-nitrosylation pathways will enhance our understanding of molecular mechanisms leading to neurodegenerative diseases and point to potential therapeutic interventions.
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Affiliation(s)
- Tomohiro Nakamura
- Del E. Web Center for Neuroscience, Aging, and Stem Cell Research, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
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136
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Posttranslational modifications of HIV-1 integrase by various cellular proteins during viral replication. Viruses 2013; 5:1787-801. [PMID: 23863879 PMCID: PMC3738961 DOI: 10.3390/v5071787] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/08/2013] [Accepted: 07/09/2013] [Indexed: 12/21/2022] Open
Abstract
HIV-1 integrase (IN) is a key viral enzyme during HIV-1 replication that catalyzes the insertion of viral DNA into the host genome. Recent studies have provided important insights into the multiple posttranslational modifications (PTMs) of IN (e.g., ubiquitination, SUMOylation, acetylation and phosphorylation), which regulate its multifaceted functions. A number of host cellular proteins, including Lens Epithelium‑derived Growth factor (LEDGF/p75), p300 and Ku70 have been shown to interact with IN and be involved in the PTM process of IN, either facilitating or counteracting the IN PTMs. Although previous studies have revealed much about the important roles of IN PTMs, how IN functions are fine-tuned by these PTMs under the physiological setting still needs to be determined. Here, we review the advances in the understanding of the mechanisms and roles of multiple IN PTMs.
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137
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Nakaya T, Ishiguro KI, Belzil C, Rietsch AM, Yu Q, Mizuno SI, Bronson RT, Geng Y, Nguyen MD, Akashi K, Sicinski P, Nakatani Y. p600 Plays Essential Roles in Fetal Development. PLoS One 2013; 8:e66269. [PMID: 23824717 PMCID: PMC3688873 DOI: 10.1371/journal.pone.0066269] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 05/03/2013] [Indexed: 11/19/2022] Open
Abstract
p600 is a multifunctional protein implicated in cytoskeletal organization, integrin-mediated survival signaling, calcium-calmodulin signaling and the N-end rule pathway of ubiquitin-proteasome-mediated proteolysis. While push, the Drosophila counterpart of p600, is dispensable for development up to adult stage, the role of p600 has not been studied during mouse development. Here we generated p600 knockout mice to investigate the in vivo functions of p600. Interestingly, we found that homozygous deletion of p600 results in lethality between embryonic days 11.5 and 13.5 with severe defects in both embryo and placenta. Since p600 is required for placental development, we performed conditional disruption of p600, which deletes selectively p600 in the embryo but not in the placenta. The conditional mutant embryos survive longer than knockout embryos but ultimately die before embryonic day 14.5. The mutant embryos display severe cardiac problems characterized by ventricular septal defects and thin ventricular walls. These anomalies are associated with reduced activation of FAK and decreased expression of MEF2, which is regulated by FAK and plays a crucial role in cardiac development. Moreover, we observed pleiotropic defects in the liver and brain. In sum, our study sheds light on the essential roles of p600 in fetal development.
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Affiliation(s)
- Takeo Nakaya
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Translational Research Unit and Department of Molecular Pathology, Tokyo Medical University, Shinjuku, Tokyo, Japan
| | - Kei-ichiro Ishiguro
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Bunkyo, Tokyo, Japan
| | - Camille Belzil
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Anna M. Rietsch
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Qunyan Yu
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shin-ichi Mizuno
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Roderick T. Bronson
- Dana-Farber/Harvard Cancer Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yan Geng
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Minh Dang Nguyen
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Koichi Akashi
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yoshihiro Nakatani
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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138
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Zhang F, Bhat S, Gabelli SB, Chen X, Miller MS, Nacev BA, Cheng YL, Meyers DJ, Tenney K, Shim JS, Crews P, Amzel LM, Ma D, Liu JO. Pyridinylquinazolines selectively inhibit human methionine aminopeptidase-1 in cells. J Med Chem 2013; 56:3996-4016. [PMID: 23634668 DOI: 10.1021/jm400227z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Methionine aminopeptidases (MetAPs), which remove the initiator methionine from nascent peptides, are essential in all organisms. While MetAP2 has been demonstrated to be a therapeutic target for inhibiting angiogenesis in mammals, MetAP1 seems to be vital for cell proliferation. Our earlier efforts identified two structural classes of human MetAP1 (HsMetAP1)-selective inhibitors (1-4), but all of them failed to inhibit cellular HsMetAP1. Using Mn(II) or Zn(II) to activate HsMetAP1, we found that 1-4 could only effectively inhibit purified HsMetAP1 in the presence of physiologically unachievable concentrations of Co(II). In an effort to seek Co(II)-independent inhibitors, a novel structural class containing a 2-(pyridin-2-yl)quinazoline core has been discovered. Many compounds in this class potently and selectively inhibited HsMetAP1 without Co(II). Subsequently, we demonstrated that 11j, an auxiliary metal-dependent inhibitor, effectively inhibited HsMetAP1 in primary cells. This is the first report that an HsMetAP1-selective inhibitor is effective against its target in cells.
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Affiliation(s)
- Feiran Zhang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, USA
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139
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Sriram S, Lee JH, Mai BK, Jiang Y, Kim Y, Yoo YD, Banerjee R, Lee SH, Lee MJ. Development and Characterization of Monomeric N-End Rule Inhibitors through In Vitro Model Substrates. J Med Chem 2013; 56:2540-6. [DOI: 10.1021/jm400046q] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Shashi Sriram
- Department
of Pharmaceutical
Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Jung Hoon Lee
- Department of Applied Chemistry,
College of Applied Sciences, Kyung Hee University, Yongin 446-701, Korea
| | - Binh Khanh Mai
- Department of Applied Chemistry,
College of Applied Sciences, Kyung Hee University, Yongin 446-701, Korea
| | - Yanxialei Jiang
- Department of Applied Chemistry,
College of Applied Sciences, Kyung Hee University, Yongin 446-701, Korea
| | - Yongho Kim
- Department of Applied Chemistry,
College of Applied Sciences, Kyung Hee University, Yongin 446-701, Korea
| | - Young Dong Yoo
- World Class University (WCU) Program,
Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate
School of Convergence Science and Technology and College of Medicine, Seoul National University, Seoul 110-799, Korea
| | - Rajkumar Banerjee
- Division of Lipid Science and
Technology, CSIR-Indian Institute of Chemical Technology, Hyderabad, Andhra Pradesh 500007, India
| | - Seung-Han Lee
- Department of Applied Chemistry,
College of Applied Sciences, Kyung Hee University, Yongin 446-701, Korea
| | - Min Jae Lee
- Department of Applied Chemistry,
College of Applied Sciences, Kyung Hee University, Yongin 446-701, Korea
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140
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UBR box N-recognin-4 (UBR4), an N-recognin of the N-end rule pathway, and its role in yolk sac vascular development and autophagy. Proc Natl Acad Sci U S A 2013; 110:3800-5. [PMID: 23431188 DOI: 10.1073/pnas.1217358110] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The N-end rule pathway is a proteolytic system in which destabilizing N-terminal residues of short-lived proteins act as degradation determinants (N-degrons). Substrates carrying N-degrons are recognized by N-recognins that mediate ubiquitylation-dependent selective proteolysis through the proteasome. Our previous studies identified the mammalian N-recognin family consisting of UBR1/E3α, UBR2, UBR4/p600, and UBR5, which recognize destabilizing N-terminal residues through the UBR box. In the current study, we addressed the physiological function of a poorly characterized N-recognin, 570-kDa UBR4, in mammalian development. UBR4-deficient mice die during embryogenesis and exhibit pleiotropic abnormalities, including impaired vascular development in the yolk sac (YS). Vascular development in UBR4-deficient YS normally advances through vasculogenesis but is arrested during angiogenic remodeling of primary capillary plexus associated with accumulation of autophagic vacuoles. In the YS, UBR4 marks endoderm-derived, autophagy-enriched cells that coordinate differentiation of mesoderm-derived vascular cells and supply autophagy-generated amino acids during early embryogenesis. UBR4 of the YS endoderm is associated with a tissue-specific autophagic pathway that mediates bulk lysosomal proteolysis of endocytosed maternal proteins into amino acids. In cultured cells, UBR4 subpopulation is degraded by autophagy through its starvation-induced association with cellular cargoes destined to autophagic double membrane structures. UBR4 loss results in multiple misregulations in autophagic induction and flux, including synthesis and lipidation/activation of the ubiquitin-like protein LC3 and formation of autophagic double membrane structures. Our results suggest that UBR4 plays an important role in mammalian development, such as angiogenesis in the YS, in part through regulation of bulk degradation by lysosomal hydrolases.
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141
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Lange PF, Overall CM. Protein TAILS: when termini tell tales of proteolysis and function. Curr Opin Chem Biol 2013; 17:73-82. [DOI: 10.1016/j.cbpa.2012.11.025] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 11/17/2012] [Accepted: 11/27/2012] [Indexed: 10/27/2022]
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142
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Voos W, Ward LA, Truscott KN. The role of AAA+ proteases in mitochondrial protein biogenesis, homeostasis and activity control. Subcell Biochem 2013; 66:223-263. [PMID: 23479443 DOI: 10.1007/978-94-007-5940-4_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Mitochondria are specialised organelles that are structurally and functionally integrated into cells in the vast majority of eukaryotes. They are the site of numerous enzymatic reactions, some of which are essential for life. The double lipid membrane of the mitochondrion, that spatially defines the organelle and is necessary for some functions, also creates a physical but semi-permeable barrier to the rest of the cell. Thus to ensure the biogenesis, regulation and maintenance of a functional population of proteins, an autonomous protein handling network within mitochondria is required. This includes resident mitochondrial protein translocation machinery, processing peptidases, molecular chaperones and proteases. This review highlights the contribution of proteases of the AAA+ superfamily to protein quality and activity control within the mitochondrion. Here they are responsible for the degradation of unfolded, unassembled and oxidatively damaged proteins as well as the activity control of some enzymes. Since most knowledge about these proteases has been gained from studies in the eukaryotic microorganism Saccharomyces cerevisiae, much of the discussion here centres on their role in this organism. However, reference is made to mitochondrial AAA+ proteases in other organisms, particularly in cases where they play a unique role such as the mitochondrial unfolded protein response. As these proteases influence mitochondrial function in both health and disease in humans, an understanding of their regulation and diverse activities is necessary.
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Affiliation(s)
- Wolfgang Voos
- Institut für Biochemie und Molekularbiologie (IBMB), Universität Bonn, Nussallee 11, 53115, Bonn, Germany,
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143
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Jiang Y, Pore SK, Lee JH, Sriram S, Mai BK, Han DH, Agarwalla P, Zakrzewska A, Kim Y, Banerjee R, Lee SH, Lee MJ. Characterization of mammalian N-degrons and development of heterovalent inhibitors of the N-end rule pathway. Chem Sci 2013. [DOI: 10.1039/c3sc51059j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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144
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Kanemaki MT. Frontiers of protein expression control with conditional degrons. Pflugers Arch 2012; 465:419-25. [DOI: 10.1007/s00424-012-1203-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 12/06/2012] [Indexed: 12/21/2022]
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145
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Gao T, Liu Z, Wang Y, Cheng H, Yang Q, Guo A, Ren J, Xue Y. UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation. Nucleic Acids Res 2012; 41:D445-51. [PMID: 23172288 PMCID: PMC3531133 DOI: 10.1093/nar/gks1103] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In this work, we developed a family-based database of UUCD (http://uucd.biocuckoo.org) for ubiquitin and ubiquitin-like conjugation, which is one of the most important post-translational modifications responsible for regulating a variety of cellular processes, through a similar E1 (ubiquitin-activating enzyme)-E2 (ubiquitin-conjugating enzyme)-E3 (ubiquitin-protein ligase) enzyme thioester cascade. Although extensive experimental efforts have been taken, an integrative data resource is still not available. From the scientific literature, 26 E1s, 105 E2s, 1003 E3s and 148 deubiquitination enzymes (DUBs) were collected and classified into 1, 3, 19 and 7 families, respectively. To computationally characterize potential enzymes in eukaryotes, we constructed 1, 1, 15 and 6 hidden Markov model (HMM) profiles for E1s, E2s, E3s and DUBs at the family level, separately. Moreover, the ortholog searches were conducted for E3 and DUB families without HMM profiles. Then the UUCD database was developed with 738 E1s, 2937 E2s, 46 631 E3s and 6647 DUBs of 70 eukaryotic species. The detailed annotations and classifications were also provided. The online service of UUCD was implemented in PHP + MySQL + JavaScript + Perl.
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Affiliation(s)
- Tianshun Gao
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan, Hubei 430074, China
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146
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Lee K, Rhee K. Separase-dependent cleavage of pericentrin B is necessary and sufficient for centriole disengagement during mitosis. Cell Cycle 2012; 11:2476-85. [PMID: 22722493 DOI: 10.4161/cc.20878] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Centriole disengagement is considered an essential step for licensing a new round of centriole duplication in the next cell cycle. Separase is critical for centriole disengagement. Here, we showed that pericentrin B (PCNTB) is specifically cleaved by separase at the exit of mitosis. The cleavage-resistant PCNTB mutant blocks the centriole disengagement and duplication. We also observed that an artificial cleavage of PCNTB during M phase induced premature disengagement of centrioles. Based on these results, we concluded that the separase-dependent cleavage of PCNTB is necessary and sufficient for centriole disengagement during mitosis.
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Affiliation(s)
- Kwanwoo Lee
- Department of Biological Sciences, Seoul National University, Korea
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147
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Anand R, Langer T, Baker MJ. Proteolytic control of mitochondrial function and morphogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:195-204. [PMID: 22749882 DOI: 10.1016/j.bbamcr.2012.06.025] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Revised: 06/08/2012] [Accepted: 06/15/2012] [Indexed: 12/18/2022]
Abstract
Mitochondrial proteostasis depends on a hierarchical system of tightly controlled quality surveillance mechanisms. Proteases within mitochondria take center stage in this network. They eliminate misfolded and damaged proteins and ensure the biogenesis and morphogenesis of mitochondria by processing or degrading short-lived regulatory proteins. Mitochondrial gene expression, the mitochondrial phospholipid metabolism and the fusion of mitochondrial membranes are under proteolytic control. Furthermore, in response to stress and mitochondrial dysfunction, proteolysis inhibits fusion and facilitates mitophagy and apoptosis. Defining these versatile activities of mitochondrial proteases will be pivotal for understanding the pathogenesis of various neurodegenerative disorders associated with defective mitochondria-associated proteolysis. This article is part of a Special Issue entitled: Mitochondrial dynamics and physiology.
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148
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Bogan JS, Rubin BR, Yu C, Löffler MG, Orme CM, Belman JP, McNally LJ, Hao M, Cresswell JA. Endoproteolytic cleavage of TUG protein regulates GLUT4 glucose transporter translocation. J Biol Chem 2012; 287:23932-47. [PMID: 22610098 DOI: 10.1074/jbc.m112.339457] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To promote glucose uptake into fat and muscle cells, insulin causes the translocation of GLUT4 glucose transporters from intracellular vesicles to the cell surface. Previous data support a model in which TUG traps GLUT4-containing vesicles and tethers them intracellularly in unstimulated cells and in which insulin mobilizes this pool of vesicles by releasing this tether. Here we show that TUG undergoes site-specific endoproteolytic cleavage, which separates a GLUT4-binding, N-terminal region of TUG from a C-terminal region previously suggested to bind an intracellular anchor. Cleavage is accelerated by insulin stimulation in 3T3-L1 adipocytes and is highly dependent upon adipocyte differentiation. The N-terminal TUG cleavage product has properties of a novel 18-kDa ubiquitin-like modifier, which we call TUGUL. The C-terminal product is observed at the expected size of 42 kDa and also as a 54-kDa form that is released from membranes into the cytosol. In transfected cells, intact TUG links GLUT4 to PIST and also binds Golgin-160 through its C-terminal region. PIST is an effector of TC10α, a GTPase previously shown to transmit an insulin signal required for GLUT4 translocation, and we show using RNAi that TC10α is required for TUG proteolytic processing. Finally, we demonstrate that a cleavage-resistant form of TUG does not support highly insulin-responsive GLUT4 translocation or glucose uptake in 3T3-L1 adipocytes. Together with previous results, these data support a model whereby insulin stimulates TUG cleavage to liberate GLUT4 storage vesicles from the Golgi matrix, which promotes GLUT4 translocation to the cell surface and enhances glucose uptake.
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Affiliation(s)
- Jonathan S Bogan
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520-8020, USA.
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149
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UBR2 of the N-end rule pathway is required for chromosome stability via histone ubiquitylation in spermatocytes and somatic cells. PLoS One 2012; 7:e37414. [PMID: 22616001 PMCID: PMC3355131 DOI: 10.1371/journal.pone.0037414] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Accepted: 04/19/2012] [Indexed: 11/20/2022] Open
Abstract
The N-end rule pathway is a proteolytic system in which its recognition components (N-recognins) recognize destabilizing N-terminal residues of short-lived proteins as an essential element of specific degrons, called N-degrons. The RING E3 ligases UBR2 and UBR1 are major N-recognins that share size (200 kDa), conserved domains and substrate specificities to N-degrons. Despite the known function of the N-end rule pathway in degradation of cytosolic proteins, the major phenotype of UBR2-deficient male mice is infertility caused by arrest of spermatocytes at meiotic prophase I. UBR2-deficient spermatocytes are impaired in transcriptional silencing of sex chromosome-linked genes and ubiquitylation of histone H2A. In this study we show that the recruitment of UBR2 to meiotic chromosomes spatiotemporally correlates to the induction of chromatin-associated ubiquitylation, which is significantly impaired in UBR2-deficient spermatocytes. UBR2 functions as a scaffold E3 that promotes HR6B/UbcH2-dependent ubiquitylation of H2A and H2B but not H3 and H4, through a mechanism distinct from typical polyubiquitylation. The E3 activity of UBR2 in histone ubiquitylation is allosterically activated by dipeptides bearing destabilizing N-terminal residues. Insufficient monoubiquitylation and polyubiquitylation on UBR2-deficient meiotic chromosomes correlate to defects in double strand break (DSB) repair and other meiotic processes, resulting in pachytene arrest at stage IV and apoptosis. Some of these functions of UBR2 are observed in somatic cells, in which UBR2 is a chromatin-binding protein involved in chromatin-associated ubiquitylation upon DNA damage. UBR2-deficient somatic cells show an array of chromosomal abnormalities, including hyperproliferation, chromosome instability, and hypersensitivity to DNA damage-inducing reagents. UBR2-deficient mice enriched in C57 background die upon birth with defects in lung expansion and neural development. Thus, UBR2, known as the recognition component of a major cellular proteolytic system, is associated with chromatin and controls chromatin dynamics and gene expression in both germ cells and somatic cells.
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150
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Greene W, Zhang W, He M, Witt C, Ye F, Gao SJ. The ubiquitin/proteasome system mediates entry and endosomal trafficking of Kaposi's sarcoma-associated herpesvirus in endothelial cells. PLoS Pathog 2012; 8:e1002703. [PMID: 22615563 PMCID: PMC3355089 DOI: 10.1371/journal.ppat.1002703] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 03/30/2012] [Indexed: 01/12/2023] Open
Abstract
Ubiquitination, a post-translational modification, mediates diverse cellular functions including endocytic transport of molecules. Kaposi's sarcoma-associated herpesvirus (KSHV), an enveloped herpesvirus, enters endothelial cells primarily through clathrin-mediated endocytosis. Whether ubiquitination and proteasome activity regulates KSHV entry and endocytosis remains unknown. We showed that inhibition of proteasome activity reduced KSHV entry into endothelial cells and intracellular trafficking to nuclei, thus preventing KSHV infection of the cells. Three-dimensional (3-D) analyses revealed accumulation of KSHV particles in a cytoplasmic compartment identified as EEA1+ endosomal vesicles upon proteasome inhibition. KSHV particles are colocalized with ubiquitin-binding proteins epsin and eps15. Furthermore, ubiquitination mediates internalization of both KSHV and one of its receptors integrin β1. KSHV particles are colocalized with activated forms of the E3 ligase c-Cbl. Knock-down of c-Cbl or inhibition of its phosphorylation reduced viral entry and intracellular trafficking, resulting in decreased KSHV infectivity. These results demonstrate that ubiquitination mediates internalization of both KSHV and one of its cognate receptors integrin β1, and identify c-Cbl as a potential E3 ligase that facilitates this process. Ubiquitination, a post-translational modification, mediates important cellular functions including endocytic transport of molecules. Kaposi's sarcoma-associated herpesvirus (KSHV) is a gammaherpesvirus linked to the development of Kaposi's sarcoma, an endothelial malignancy commonly found in AIDS patients, and several other malignancies. KSHV enters endothelial cells primarily through clathrin-mediated endocytosis. In this study, we show that the proteasome activity is required for KSHV entry into endothelial cells and intracellular trafficking to nuclei. Inhibition of proteasome activity reduced KSHV infectivity and led to the accumulation of KSHV particles in EEA1+ early endosomal vesicles. Furthermore, we show that ubiquitination mediates the internalization of both KSHV and one of its receptors integrin β1. KSHV particles are colocalized with ubiquitin-binding proteins epsin and eps15, as well as activated forms of the E3 ligase c-Cbl. Knock-down of c-Cbl or inhibition of its phosphorylation blocked KSHV entry and trafficking, thus preventing KSHV infection of endothelial cells. Together, these results illustrate the essential role of ubiquitination during the internalization of KSHV and its cognate receptor integrin β1. The identification of an E3 ligase that mediates the ubiquitination of KSHV and its cognate receptor integrin β1 leading to viral entry provide a potential therapeutic target for this oncogenic virus.
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Affiliation(s)
- Whitney Greene
- Tumor Virology Program, Greehey Children's Cancer Research Institute, and Department of Pediatrics, University of Texas Health Science Center San Antonio, San Antonio, Texas, United States of America
| | - Wei Zhang
- Tumor Virology Program, Greehey Children's Cancer Research Institute, and Department of Pediatrics, University of Texas Health Science Center San Antonio, San Antonio, Texas, United States of America
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Meilan He
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Colleen Witt
- Department of Biology, College of Sciences, University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Fengchun Ye
- Tumor Virology Program, Greehey Children's Cancer Research Institute, and Department of Pediatrics, University of Texas Health Science Center San Antonio, San Antonio, Texas, United States of America
| | - Shou-Jiang Gao
- Tumor Virology Program, Greehey Children's Cancer Research Institute, and Department of Pediatrics, University of Texas Health Science Center San Antonio, San Antonio, Texas, United States of America
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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