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Hagiwara T, Minami R, Ushio C, Yokota N, Kawahara H. Proteotoxic stresses stimulate dissociation of UBL4A from the tail-anchored protein recognition complex. Biochem J 2023; 480:1583-1598. [PMID: 37747814 PMCID: PMC10586765 DOI: 10.1042/bcj20230267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 09/27/2023]
Abstract
Inclusion body formation is associated with cytotoxicity in a number of neurodegenerative diseases. However, the molecular basis of the toxicity caused by the accumulation of aggregation-prone proteins remains controversial. In this study, we found that disease-associated inclusions induced by elongated polyglutamine chains disrupt the complex formation of BAG6 with UBL4A, a mammalian homologue of yeast Get5. UBL4A also dissociated from BAG6 in response to proteotoxic stresses such as proteasomal inhibition and mitochondrial depolarization. These findings imply that the cytotoxicity of pathological protein aggregates might be attributed in part to disruption of the BAG6-UBL4A complex that is required for the biogenesis of tail-anchored proteins.
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Affiliation(s)
- Takumi Hagiwara
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Ryosuke Minami
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Chizuru Ushio
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Naoto Yokota
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Hiroyuki Kawahara
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
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Jung M, Zimmermann R. Quantitative Mass Spectrometry Characterizes Client Spectra of Components for Targeting of Membrane Proteins to and Their Insertion into the Membrane of the Human ER. Int J Mol Sci 2023; 24:14166. [PMID: 37762469 PMCID: PMC10532041 DOI: 10.3390/ijms241814166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
To elucidate the redundancy in the components for the targeting of membrane proteins to the endoplasmic reticulum (ER) and/or their insertion into the ER membrane under physiological conditions, we previously analyzed different human cells by label-free quantitative mass spectrometry. The HeLa and HEK293 cells had been depleted of a certain component by siRNA or CRISPR/Cas9 treatment or were deficient patient fibroblasts and compared to the respective control cells by differential protein abundance analysis. In addition to clients of the SRP and Sec61 complex, we identified membrane protein clients of components of the TRC/GET, SND, and PEX3 pathways for ER targeting, and Sec62, Sec63, TRAM1, and TRAP as putative auxiliary components of the Sec61 complex. Here, a comprehensive evaluation of these previously described differential protein abundance analyses, as well as similar analyses on the Sec61-co-operating EMC and the characteristics of the topogenic sequences of the various membrane protein clients, i.e., the client spectra of the components, are reported. As expected, the analysis characterized membrane protein precursors with cleavable amino-terminal signal peptides or amino-terminal transmembrane helices as predominant clients of SRP, as well as the Sec61 complex, while precursors with more central or even carboxy-terminal ones were found to dominate the client spectra of the SND and TRC/GET pathways for membrane targeting. For membrane protein insertion, the auxiliary Sec61 channel components indeed share the client spectra of the Sec61 complex to a large extent. However, we also detected some unexpected differences, particularly related to EMC, TRAP, and TRAM1. The possible mechanistic implications for membrane protein biogenesis at the human ER are discussed and can be expected to eventually advance our understanding of the mechanisms that are involved in the so-called Sec61-channelopathies, resulting from deficient ER protein import.
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Affiliation(s)
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany;
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Llido JP, Fioriti E, Pascut D, Giuffrè M, Bottin C, Zanconati F, Tiribelli C, Gazzin S. Bilirubin-Induced Transcriptomic Imprinting in Neonatal Hyperbilirubinemia. BIOLOGY 2023; 12:834. [PMID: 37372119 DOI: 10.3390/biology12060834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023]
Abstract
Recent findings indicated aberrant epigenetic control of the central nervous system (CNS) development in hyperbilirubinemic Gunn rats as an additional cause of cerebellar hypoplasia, the landmark of bilirubin neurotoxicity in rodents. Because the symptoms in severely hyperbilirubinemic human neonates suggest other regions as privileged targets of bilirubin neurotoxicity, we expanded the study of the potential impact of bilirubin on the control of postnatal brain development to regions correlating with human symptoms. Histology, transcriptomic, gene correlation, and behavioral studies were performed. The histology revealed widespread perturbation 9 days after birth, restoring in adulthood. At the genetic level, regional differences were noticed. Bilirubin affected synaptogenesis, repair, differentiation, energy, extracellular matrix development, etc., with transient alterations in the hippocampus (memory, learning, and cognition) and inferior colliculi (auditory functions) but permanent changes in the parietal cortex. Behavioral tests confirmed the presence of a permanent motor disability. The data correlate well both with the clinic description of neonatal bilirubin-induced neurotoxicity, as well as with the neurologic syndromes reported in adults that suffered neonatal hyperbilirubinemia. The results pave the way for better deciphering the neurotoxic features of bilirubin and evaluating deeply the efficacy of new therapeutic approaches against the acute and long-lasting sequels of bilirubin neurotoxicity.
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Affiliation(s)
- John Paul Llido
- Liver Brain Unit "Rita Moretti", Fondazione Italiana Fegato-Onlus, Bldg. Q, AREA Science Park, 34149 Basovizza, Italy
- Department of Science and Technology, Philippine Council for Health Research and Development, Bicutan, Taguig City 1631, Philippines
- Department of Life Sciences, University of Trieste, 34139 Trieste, Italy
| | - Emanuela Fioriti
- Liver Brain Unit "Rita Moretti", Fondazione Italiana Fegato-Onlus, Bldg. Q, AREA Science Park, 34149 Basovizza, Italy
| | - Devis Pascut
- Liver Cancer Unit, Fondazione Italiana Fegato-Onlus, Bldg. Q, AREA Science Park, 34149 Basovizza, Italy
| | - Mauro Giuffrè
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy
- Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Cristina Bottin
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Fabrizio Zanconati
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Claudio Tiribelli
- Liver Brain Unit "Rita Moretti", Fondazione Italiana Fegato-Onlus, Bldg. Q, AREA Science Park, 34149 Basovizza, Italy
| | - Silvia Gazzin
- Liver Brain Unit "Rita Moretti", Fondazione Italiana Fegato-Onlus, Bldg. Q, AREA Science Park, 34149 Basovizza, Italy
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Tirincsi A, O’Keefe S, Nguyen D, Sicking M, Dudek J, Förster F, Jung M, Hadzibeganovic D, Helms V, High S, Zimmermann R, Lang S. Proteomics Identifies Substrates and a Novel Component in hSnd2-Dependent ER Protein Targeting. Cells 2022; 11:cells11182925. [PMID: 36139500 PMCID: PMC9496750 DOI: 10.3390/cells11182925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Importing proteins into the endoplasmic reticulum (ER) is essential for about 30% of the human proteome. It involves the targeting of precursor proteins to the ER and their insertion into or translocation across the ER membrane. Furthermore, it relies on signals in the precursor polypeptides and components, which read the signals and facilitate their targeting to a protein-conducting channel in the ER membrane, the Sec61 complex. Compared to the SRP- and TRC-dependent pathways, little is known about the SRP-independent/SND pathway. Our aim was to identify additional components and characterize the client spectrum of the human SND pathway. The established strategy of combining the depletion of the central hSnd2 component from HeLa cells with proteomic and differential protein abundance analysis was used. The SRP and TRC targeting pathways were analyzed in comparison. TMEM109 was characterized as hSnd3. Unlike SRP but similar to TRC, the SND clients are predominantly membrane proteins with N-terminal, central, or C-terminal targeting signals.
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Affiliation(s)
- Andrea Tirincsi
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany
| | - Sarah O’Keefe
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Duy Nguyen
- Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Germany
| | - Mark Sicking
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany
| | - Johanna Dudek
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Martin Jung
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany
| | | | - Volkhard Helms
- Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Germany
| | - Stephen High
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany
- Correspondence: (R.Z.); (S.L.)
| | - Sven Lang
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany
- Correspondence: (R.Z.); (S.L.)
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Lang S, Nguyen D, Bhadra P, Jung M, Helms V, Zimmermann R. Signal Peptide Features Determining the Substrate Specificities of Targeting and Translocation Components in Human ER Protein Import. Front Physiol 2022; 13:833540. [PMID: 35899032 PMCID: PMC9309488 DOI: 10.3389/fphys.2022.833540] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 05/17/2022] [Indexed: 12/11/2022] Open
Abstract
In human cells, approximately 30% of all polypeptides enter the secretory pathway at the level of the endoplasmic reticulum (ER). This process involves cleavable amino-terminal signal peptides (SPs) or more or less amino-terminal transmembrane helices (TMHs), which serve as targeting determinants, at the level of the precursor polypeptides and a multitude of cytosolic and ER proteins, which facilitate their ER import. Alone or in combination SPs and TMHs guarantee the initial ER targeting as well as the subsequent membrane integration or translocation. Cytosolic SRP and SR, its receptor in the ER membrane, mediate cotranslational targeting of most nascent precursor polypeptide chains to the polypeptide-conducting Sec61 complex in the ER membrane. Alternatively, fully-synthesized precursor polypeptides and certain nascent precursor polypeptides are targeted to the ER membrane by either the PEX-, SND-, or TRC-pathway. Although these targeting pathways may have overlapping functions, the question arises how relevant this is under cellular conditions and which features of SPs and precursor polypeptides determine preference for a certain pathway. Irrespective of their targeting pathway(s), most precursor polypeptides are integrated into or translocated across the ER membrane via the Sec61 channel. For some precursor polypeptides specific Sec61 interaction partners have to support the gating of the channel to the open state, again raising the question why and when this is the case. Recent progress shed light on the client spectrum and specificities of some auxiliary components, including Sec62/Sec63, TRAM1 protein, and TRAP. To address the question which precursors use a certain pathway or component in intact human cells, i.e., under conditions of fast translation rates and molecular crowding, in the presence of competing precursors, different targeting organelles, and relevant stoichiometries of the involved components, siRNA-mediated depletion of single targeting or transport components in HeLa cells was combined with label-free quantitative proteomics and differential protein abundance analysis. Here, we present a summary of the experimental approach as well as the resulting differential protein abundance analyses and discuss their mechanistic implications in light of the available structural data.
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Affiliation(s)
- Sven Lang
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
- *Correspondence: Sven Lang, ; Richard Zimmermann,
| | - Duy Nguyen
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Pratiti Bhadra
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Martin Jung
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
- *Correspondence: Sven Lang, ; Richard Zimmermann,
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