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Maitland MER, Lajoie GA, Shaw GS, Schild-Poulter C. Structural and Functional Insights into GID/CTLH E3 Ligase Complexes. Int J Mol Sci 2022; 23:5863. [PMID: 35682545 PMCID: PMC9180843 DOI: 10.3390/ijms23115863] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 11/29/2022] Open
Abstract
Multi-subunit E3 ligases facilitate ubiquitin transfer by coordinating various substrate receptor subunits with a single catalytic center. Small molecules inducing targeted protein degradation have exploited such complexes, proving successful as therapeutics against previously undruggable targets. The C-terminal to LisH (CTLH) complex, also called the glucose-induced degradation deficient (GID) complex, is a multi-subunit E3 ligase complex highly conserved from Saccharomyces cerevisiae to humans, with roles in fundamental pathways controlling homeostasis and development in several species. However, we are only beginning to understand its mechanistic basis. Here, we review the literature of the CTLH complex from all organisms and place previous findings on individual subunits into context with recent breakthroughs on its structure and function.
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Affiliation(s)
- Matthew E. R. Maitland
- Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 5B7, Canada;
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON N6G 2V4, Canada; (G.A.L.); (G.S.S.)
| | - Gilles A. Lajoie
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON N6G 2V4, Canada; (G.A.L.); (G.S.S.)
| | - Gary S. Shaw
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON N6G 2V4, Canada; (G.A.L.); (G.S.S.)
| | - Caroline Schild-Poulter
- Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 5B7, Canada;
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON N6G 2V4, Canada; (G.A.L.); (G.S.S.)
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Kabani M, Pilard M, Melki R. Glucose availability dictates the export of the soluble and prion forms of Sup35p via periplasmic or extracellular vesicles. Mol Microbiol 2020; 114:322-332. [PMID: 32339313 DOI: 10.1111/mmi.14515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/25/2020] [Accepted: 04/06/2020] [Indexed: 11/28/2022]
Abstract
The yeast [PSI+ ] prion originates from the self-perpetuating transmissible aggregates of the translation termination factor Sup35p. We previously showed that infectious Sup35p particles are exported outside the cells via extracellular vesicles (EV). This finding suggested a function for EV in the vertical and horizontal transmission of yeast prions. Here we report a significant export of Sup35p within periplasmic vesicles (PV) upon glucose starvation. We show that PV are up to three orders of magnitude more abundant than EV. However, PV and EV are different in terms of size and protein content, and their export is oppositely regulated by glucose availability in the growth medium. Overall, our work suggests that the export of prion particles to both the periplasm and the extracellular space needs to be considered to address the physiological consequences of vesicle-mediated yeast prions trafficking.
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Affiliation(s)
- Mehdi Kabani
- Institut de Biologie François Jacob, Molecular Imaging Research Center (MIRCen), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Direction de la Recherche Fondamentale (DRF), Laboratoire des Maladies Neurodégénératives, Centre National de la Recherche Scientifique (CNRS), Fontenay-aux-Roses, France
| | - Marion Pilard
- Institut de Biologie François Jacob, Molecular Imaging Research Center (MIRCen), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Direction de la Recherche Fondamentale (DRF), Laboratoire des Maladies Neurodégénératives, Centre National de la Recherche Scientifique (CNRS), Fontenay-aux-Roses, France
| | - Ronald Melki
- Institut de Biologie François Jacob, Molecular Imaging Research Center (MIRCen), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Direction de la Recherche Fondamentale (DRF), Laboratoire des Maladies Neurodégénératives, Centre National de la Recherche Scientifique (CNRS), Fontenay-aux-Roses, France
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Salemi LM, Maitland MER, McTavish CJ, Schild-Poulter C. Cell signalling pathway regulation by RanBPM: molecular insights and disease implications. Open Biol 2018; 7:rsob.170081. [PMID: 28659384 PMCID: PMC5493780 DOI: 10.1098/rsob.170081] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 06/01/2017] [Indexed: 12/25/2022] Open
Abstract
RanBPM (Ran-binding protein M, also called RanBP9) is an evolutionarily conserved, ubiquitous protein which localizes to both nucleus and cytoplasm. RanBPM has been implicated in the regulation of a number of signalling pathways to regulate several cellular processes such as apoptosis, cell adhesion, migration as well as transcription, and plays a critical role during development. In addition, RanBPM has been shown to regulate pathways implicated in cancer and Alzheimer's disease, implying that RanBPM has important functions in both normal and pathological development. While its functions in these processes are still poorly understood, RanBPM has been identified as a component of a large complex, termed the CTLH (C-terminal to LisH) complex. The yeast homologue of this complex functions as an E3 ubiquitin ligase that targets enzymes of the gluconeogenesis pathway. While the CTLH complex E3 ubiquitin ligase activity and substrates still remain to be characterized, the high level of conservation between the complexes in yeast and mammals infers that the CTLH complex could also serve to promote the degradation of specific substrates through ubiquitination, therefore suggesting the possibility that RanBPM's various functions may be mediated through the activity of the CTLH complex.
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Affiliation(s)
- Louisa M Salemi
- Robarts Research Institute, Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, 1151 Richmond Street North, London, Ontario, Canada N6A 5B7
| | - Matthew E R Maitland
- Robarts Research Institute, Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, 1151 Richmond Street North, London, Ontario, Canada N6A 5B7
| | - Christina J McTavish
- Robarts Research Institute, Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, 1151 Richmond Street North, London, Ontario, Canada N6A 5B7
| | - Caroline Schild-Poulter
- Robarts Research Institute, Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, 1151 Richmond Street North, London, Ontario, Canada N6A 5B7
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Lipids and lipid domains of the yeast vacuole. Biochem Soc Trans 2018; 46:1047-1054. [PMID: 30242116 DOI: 10.1042/bst20180120] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 07/30/2018] [Accepted: 08/01/2018] [Indexed: 11/17/2022]
Abstract
The membrane raft has been a focus of intensive research for the past two decades. Liquid-ordered domains form in artificial liposomes containing sterol and saturated lipids, but their presence in living cell membranes has been controversial. The yeast vacuole is exceptional in that micron-sized raft-like domains form in the stationary phase and under several other conditions. The sterol content of the vacuole in the log phase is much lower than that of liposomes showing liquid-ordered domains, suggesting that sterols may need to be supplied to the vacuole for the raft-like domain formation. We will discuss how lipids and lipid domains are organized in the vacuolar membrane and examine whether evidence is strong enough to conclude that the observed micron-sized domains are rafts.
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Artier J, da Silva Zandonadi F, de Souza Carvalho FM, Pauletti BA, Leme AFP, Carnielli CM, Selistre‐de‐Araujo HS, Bertolini MC, Ferro JA, Belasque Júnior J, de Oliveira JCF, Novo‐Mansur MTM. Comparative proteomic analysis of Xanthomonas citri ssp. citri periplasmic proteins reveals changes in cellular envelope metabolism during in vitro pathogenicity induction. MOLECULAR PLANT PATHOLOGY 2018; 19:143-157. [PMID: 27798950 PMCID: PMC6638008 DOI: 10.1111/mpp.12507] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Citrus canker is a plant disease caused by Gram-negative bacteria from the genus Xanthomonas. The most virulent species is Xanthomonas citri ssp. citri (XAC), which attacks a wide range of citrus hosts. Differential proteomic analysis of the periplasm-enriched fraction was performed for XAC cells grown in pathogenicity-inducing (XAM-M) and pathogenicity-non-inducing (nutrient broth) media using two-dimensional electrophoresis combined with liquid chromatography-tandem mass spectrometry. Amongst the 40 proteins identified, transglycosylase was detected in a highly abundant spot in XAC cells grown under inducing condition. Additional up-regulated proteins related to cellular envelope metabolism included glucose-1-phosphate thymidylyltransferase, dTDP-4-dehydrorhamnose-3,5-epimerase and peptidyl-prolyl cis-trans-isomerase. Phosphoglucomutase and superoxide dismutase proteins, known to be involved in pathogenicity in other Xanthomonas species or organisms, were also detected. Western blot and quantitative real-time polymerase chain reaction analyses for transglycosylase and superoxide dismutase confirmed that these proteins were up-regulated under inducing condition, consistent with the proteomic results. Multiple spots for the 60-kDa chaperonin and glyceraldehyde-3-phosphate dehydrogenase were identified, suggesting the presence of post-translational modifications. We propose that substantial alterations in cellular envelope metabolism occur during the XAC infectious process, which are related to several aspects, from defence against reactive oxygen species to exopolysaccharide synthesis. Our results provide new candidates for virulence-related proteins, whose abundance correlates with the induction of pathogenicity and virulence genes, such as hrpD6, hrpG, hrpB7, hpa1 and hrpX. The results present new potential targets against XAC to be investigated in further functional studies.
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Affiliation(s)
- Juliana Artier
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e EvoluçãoUniversidade Federal de São Carlos, UFSCarSão CarlosSP13565‐905Brazil
| | - Flávia da Silva Zandonadi
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e EvoluçãoUniversidade Federal de São Carlos, UFSCarSão CarlosSP13565‐905Brazil
| | - Flávia Maria de Souza Carvalho
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESPUniversidade Estadual PaulistaJaboticabalSP14884‐900Brazil
| | - Bianca Alves Pauletti
- LNBio, CNPEMLaboratório de Espectrometria de Massas, Laboratório Nacional de BiociênciasCampinasSP13083‐970Brazil
| | - Adriana Franco Paes Leme
- LNBio, CNPEMLaboratório de Espectrometria de Massas, Laboratório Nacional de BiociênciasCampinasSP13083‐970Brazil
| | - Carolina Moretto Carnielli
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e EvoluçãoUniversidade Federal de São Carlos, UFSCarSão CarlosSP13565‐905Brazil
| | | | - Maria Célia Bertolini
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESPUniversidade Estadual PaulistaAraraquaraSP14800‐060Brazil
| | - Jesus Aparecido Ferro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESPUniversidade Estadual PaulistaJaboticabalSP14884‐900Brazil
| | - José Belasque Júnior
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura ‘Luiz de Queiroz’Universidade de São PauloPiracicabaSP13418‐900Brazil
| | - Julio Cezar Franco de Oliveira
- Laboratório de Interações Microbianas, Departamento de Ciências BiológicasUniversidade Federal de São Paulo, UNIFESPDiademaSP09913‐030Brazil
| | - Maria Teresa Marques Novo‐Mansur
- Laboratório de Bioquímica e Biologia Molecular Aplicada, Departamento de Genética e EvoluçãoUniversidade Federal de São Carlos, UFSCarSão CarlosSP13565‐905Brazil
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Analysis of the Proteins Secreted from the Oryza meyeriana Suspension-Cultured Cells Induced by Xanthomonas oryzae pv. oryzae. PLoS One 2016; 11:e0154793. [PMID: 27196123 PMCID: PMC4873123 DOI: 10.1371/journal.pone.0154793] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/19/2016] [Indexed: 01/18/2023] Open
Abstract
Oryza meyeriana, a wild species of rice from China, shows high resistance to Xanthomonas oryzae pv. oryzae (Xoo), the cause of rice bacterial blight, one of the most serious rice pathogens. To better understand the resistance mechanism, a proteomic study was conducted to identify changes in the proteins secreted in embryo cell suspension cultures in response to Xoo. After two-dimensional difference gel electrophoresis (2D-DIGE), 72 differentially expressed protein spots corresponding to 34 proteins were identified by Matrix-Assisted Laser Desorption/ Ionization Time of Flight Mass Spectrometry. Of the 34 proteins, 10 were up regulated and 24 down regulated. The secreted proteins identified were predicted to be involved in various biological processes, including signal transduction, defense, ROS and cell wall modification. 77% of the 34 proteins were predicted to have a signal peptide by Signal P. Quantitative Real-Time PCR showed that transcript levels of 14 secreted proteins were not well correlated with secreted protein levels. Peroxidase activity was up regulated in both O. meyriana and susceptible rice but was about three times higher in O. meyeriana. This suggests that peroxidases may play an important role in the early response to Xoo in O. meyeriana. These results not only provide a better understanding of the resistance mechanism of O. meyeriana, but have implications for studies of the interactions between other plants and their pathogens.
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Nakatsukasa K, Okumura F, Kamura T. Proteolytic regulation of metabolic enzymes by E3 ubiquitin ligase complexes: lessons from yeast. Crit Rev Biochem Mol Biol 2015; 50:489-502. [PMID: 26362128 DOI: 10.3109/10409238.2015.1081869] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Eukaryotic organisms use diverse mechanisms to control metabolic rates in response to changes in the internal and/or external environment. Fine metabolic control is a highly responsive, energy-saving process that is mediated by allosteric inhibition/activation and/or reversible modification of preexisting metabolic enzymes. In contrast, coarse metabolic control is a relatively long-term and expensive process that involves modulating the level of metabolic enzymes. Coarse metabolic control can be achieved through the degradation of metabolic enzymes by the ubiquitin-proteasome system (UPS), in which substrates are specifically ubiquitinated by an E3 ubiquitin ligase and targeted for proteasomal degradation. Here, we review select multi-protein E3 ligase complexes that directly regulate metabolic enzymes in Saccharomyces cerevisiae. The first part of the review focuses on the endoplasmic reticulum (ER) membrane-associated Hrd1 and Doa10 E3 ligase complexes. In addition to their primary roles in the ER-associated degradation pathway that eliminates misfolded proteins, recent quantitative proteomic analyses identified native substrates of Hrd1 and Doa10 in the sterol synthesis pathway. The second part focuses on the SCF (Skp1-Cul1-F-box protein) complex, an abundant prototypical multi-protein E3 ligase complex. While the best-known roles of the SCF complex are in the regulation of the cell cycle and transcription, accumulating evidence indicates that the SCF complex also modulates carbon metabolism pathways. The increasing number of metabolic enzymes whose stability is directly regulated by the UPS underscores the importance of the proteolytic regulation of metabolic processes for the acclimation of cells to environmental changes.
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Affiliation(s)
- Kunio Nakatsukasa
- a Division of Biological Sciences , Graduate School of Science, Nagoya University , Nagoya , Aichi , Japan
| | - Fumihiko Okumura
- a Division of Biological Sciences , Graduate School of Science, Nagoya University , Nagoya , Aichi , Japan
| | - Takumi Kamura
- a Division of Biological Sciences , Graduate School of Science, Nagoya University , Nagoya , Aichi , Japan
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Stein K, Chiang HL. Exocytosis and Endocytosis of Small Vesicles across the Plasma Membrane in Saccharomyces cerevisiae. MEMBRANES 2014; 4:608-29. [PMID: 25192542 PMCID: PMC4194051 DOI: 10.3390/membranes4030608] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 08/02/2014] [Accepted: 08/18/2014] [Indexed: 12/14/2022]
Abstract
When Saccharomyces cerevisiae is starved of glucose, the gluconeogenic enzymes fructose-1,6-bisphosphatase (FBPase), phosphoenolpyruvate carboxykinase, isocitrate lyase, and malate dehydrogenase, as well as the non-gluconeogenic enzymes glyceraldehyde-3-phosphate dehydrogenase and cyclophilin A, are secreted into the periplasm. In the extracellular fraction, these secreted proteins are associated with small vesicles that account for more than 90% of the total number of extracellular structures observed. When glucose is added to glucose-starved cells, FBPase is internalized and associated with clusters of small vesicles in the cytoplasm. Specifically, the internalization of FBPase results in the decline of FBPase and vesicles in the extracellular fraction and their appearance in the cytoplasm. The clearance of extracellular vesicles and vesicle-associated proteins from the extracellular fraction is dependent on the endocytosis gene END3. This internalization is regulated when cells are transferred from low to high glucose. It is rapidly occurring and is a high capacity process, as clusters of vesicles occupy 10%–20% of the total volume in the cytoplasm in glucose re-fed cells. FBPase internalization also requires the VPS34 gene encoding PI3K. Following internalization, FBPase is delivered to the vacuole for degradation, whereas proteins that are not degraded may be recycled.
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Affiliation(s)
- Kathryn Stein
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
| | - Hui-Ling Chiang
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
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Giardina BJ, Stein K, Chiang HL. The endocytosis gene END3 is essential for the glucose-induced rapid decline of small vesicles in the extracellular fraction in Saccharomyces cerevisiae. J Extracell Vesicles 2014; 3:23497. [PMID: 24665361 PMCID: PMC3963178 DOI: 10.3402/jev.v3.23497] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 01/28/2014] [Accepted: 02/17/2014] [Indexed: 12/21/2022] Open
Abstract
Background Protein secretion is a fundamental process in all living cells. Gluconeogenic enzymes are secreted when Saccharomyces cerevisiae are grown in media containing low glucose. However, when cells are transferred to media containing high glucose, they are internalized. We investigated whether or not gluconeogenic enzymes were associated with extracellular vesicles in glucose-starved cells. We also examined the role that the endocytosis gene END3 plays in the internalization of extracellular proteins/vesicles in response to glucose addition. Methods Transmission electron microscopy was performed to determine the presence of extracellular vesicles in glucose-starved wild-type cells and the dynamics of vesicle transport in cells lacking the END3 gene. Proteomics was used to identify extracellular proteins that associated with these vesicles. Results Total extracts prepared from glucose-starved cells consisted of about 95% small vesicles (30–50 nm) and 5% large structures (100–300 nm). The addition of glucose caused a rapid decline in small extracellular vesicles in wild-type cells. However, most of the extracellular vesicles were still observed in cells lacking the END3 gene following glucose replenishment. Proteomics was used to identify 72 extracellular proteins that may be associated with these vesicles. Gluconeogenic enzymes fructose-1,6-bisphosphatase, malate dehydrogenase, isocitrate lyase, and phosphoenolpyruvate carboxykinase, as well as non-gluconeogenic enzymes glyceraldehyde-3-phosphate dehydrogenase and cyclophilin A, were distributed in the vesicle-enriched fraction in total extracts prepared from cells grown in low glucose. Distribution of these proteins in the vesicle-enriched fraction required the integrity of the membranes. When glucose was added to glucose-starved wild-type cells, levels of extracellular fructose-1,6-bisphosphatase, malate dehydrogenase, isocitrate lyase, phosphoenolpyruvate carboxykinase, glyceraldehyde-3-phosphate dehydrogenase, and cyclophilin A were reduced. In contrast, in cells lacking the END3 gene, levels of these proteins in the extracellular fraction remained high. Conclusion The END3 gene is required for the rapid decline of extracellular proteins and vesicles in response to glucose addition.
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Affiliation(s)
- Bennett J Giardina
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA, USA
| | - Kathryn Stein
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA, USA
| | - Hui-Ling Chiang
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA, USA
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Giardina BJ, Chiang HL. Fructose-1,6-bisphosphatase, Malate Dehydrogenase, Isocitrate Lyase, Phosphoenolpyruvate Carboxykinase, Glyceraldehyde-3-phosphate Dehydrogenase, and Cyclophilin A are secreted in Saccharomyces cerevisiae grown in low glucose. Commun Integr Biol 2013; 6:e27216. [PMID: 24563717 DOI: 10.4161/cib.27216] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 11/14/2013] [Accepted: 11/15/2013] [Indexed: 12/31/2022] Open
Abstract
Our previous studies demonstrated that the key gluconeogenic enzyme fructose-1,6-bisphosphatase is secreted when Saccharomyces cerevisiae are starved of glucose for a prolonged period of time. In this study, we showed that malate dehydrogenase, isocitrate lyase, phosphoenolpyruvate carboxykinase, glyceraldehyde-3-phosphate dehydrogenase, and cyclophilin A are also secreted in glucose-starved cells. Thus, both gluconeogenic and non-gluconeogenic enzymes are secreted via the non-classical pathway.
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Affiliation(s)
- Bennett J Giardina
- Department of Cellular and Molecular Physiology; Penn State University College of Medicine; Hershey, PA USA
| | - Hui-Ling Chiang
- Department of Cellular and Molecular Physiology; Penn State University College of Medicine; Hershey, PA USA
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