1
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Zheng X, Li A, Qiu J, Yan G, Ji Y, Wang G. β-N-methylamino-L-alanine production, photosynthesis and transcriptional expression in a possible mutation strain and a wild strain of Thalassiosira minima. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135301. [PMID: 39053058 DOI: 10.1016/j.jhazmat.2024.135301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/02/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
The neurotoxin β-N-methylamino-L-alanine (BMAA) produced by marine diatoms has been implicated as an important environmental trigger of neurodegenerative diseases in humans. However, the biosynthesis mechanism of BMAA in marine diatoms is still unknown. In the present study, the strain of diatom Thalassiosira minima almost lost the biosynthesis ability for BMAA after a long-term subculture in our laboratory. The production of BMAA-containing proteins in the mutant strain of T. minima reduced to 18.2 % of that in the wild strain, meanwhile the cell size decreased but pigment content increased in the mutant strain. Take consideration of our previous transcriptional data on the mixed diatom and cyanobacterium cultures, the current transcriptome analysis showed four identical and highly correlated KEGG pathways associated with the accumulation of misfolded proteins in diatom, including ribosome, proteasome, SNARE interactions in vesicle transport, and protein processing in the endoplasmic reticulum. Analysis of amino acids and transcriptional information suggested that amino acid synthesis and degradation are associated with the biosynthesis of BMAA-containing proteins. In addition, a reduction in the precision of ubiquitination-mediated protein hydrolysis and vesicular transport by the COPII system will exacerbate the accumulation of BMAA-containing proteins in diatoms.
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Affiliation(s)
- Xianyao Zheng
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Aifeng Li
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China.
| | - Jiangbing Qiu
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China
| | - Guowang Yan
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Ying Ji
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Guixiang Wang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
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2
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Yao Z, Ramachandran S, Huang S, Kim E, Jami-Alahmadi Y, Kaushal P, Bouhaddou M, Wohlschlegel JA, Li MM. Interaction of chikungunya virus glycoproteins with macrophage factors controls virion production. EMBO J 2024:10.1038/s44318-024-00193-3. [PMID: 39261662 DOI: 10.1038/s44318-024-00193-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 09/13/2024] Open
Abstract
Despite their role as innate sentinels, macrophages can serve as cellular reservoirs of chikungunya virus (CHIKV), a highly-pathogenic arthropod-borne alphavirus that has caused large outbreaks among human populations. Here, with the use of viral chimeras and evolutionary selection analysis, we define CHIKV glycoproteins E1 and E2 as critical for virion production in THP-1 derived human macrophages. Through proteomic analysis and functional validation, we further identify signal peptidase complex subunit 3 (SPCS3) and eukaryotic translation initiation factor 3 subunit K (eIF3k) as E1-binding host proteins with anti-CHIKV activities. We find that E1 residue V220, which has undergone positive selection, is indispensable for CHIKV production in macrophages, as its mutation attenuates E1 interaction with the host restriction factors SPCS3 and eIF3k. Finally, we show that the antiviral activity of eIF3k is translation-independent, and that CHIKV infection promotes eIF3k translocation from the nucleus to the cytoplasm, where it associates with SPCS3. These functions of CHIKV glycoproteins late in the viral life cycle provide a new example of an intracellular evolutionary arms race with host restriction factors, as well as potential targets for therapeutic intervention.
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Affiliation(s)
- Zhenlan Yao
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sangeetha Ramachandran
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Serina Huang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Erin Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Prashant Kaushal
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Mehdi Bouhaddou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Melody Mh Li
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA.
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3
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Bian C, Marchetti A, Dias M, Perrin J, Cosson P. Short transmembrane domains target type II proteins to the Golgi apparatus and type I proteins to the endoplasmic reticulum. J Cell Sci 2024; 137:jcs261738. [PMID: 38973735 DOI: 10.1242/jcs.261738] [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: 10/20/2023] [Accepted: 06/18/2024] [Indexed: 07/09/2024] Open
Abstract
Transmembrane domains (TMDs) contain information targeting membrane proteins to various compartments of the secretory pathway. In previous studies, short or hydrophilic TMDs have been shown to target membrane proteins either to the endoplasmic reticulum (ER) or to the Golgi apparatus. However, the basis for differential sorting to the ER and to the Golgi apparatus remained unclear. To clarify this point, we quantitatively analyzed the intracellular targeting of a collection of proteins exhibiting a single TMD. Our results reveal that membrane topology is a major targeting element in the early secretory pathway: type I proteins with a short TMD are targeted to the ER, and type II proteins to the Golgi apparatus. A combination of three features accounts for the sorting of simple membrane proteins in the secretory pathway: membrane topology, length and hydrophilicity of the TMD, and size of the cytosolic domain. By clarifying the rules governing sorting to the ER and to the Golgi apparatus, our study could revive the search for sorting mechanisms in the early secretory pathway.
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Affiliation(s)
- Claudie Bian
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
- Manufacturing Science and Technologies, Biotech Department, Merck, Z.I. de l'Ouriettaz 150, 1170 Aubonne, Switzerland
| | - Anna Marchetti
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Marco Dias
- Manufacturing Science and Technologies, Biotech Department, Merck, Z.I. de l'Ouriettaz 150, 1170 Aubonne, Switzerland
| | - Jackie Perrin
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Pierre Cosson
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
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4
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Gemmer M, Chaillet ML, Förster F. Exploring the molecular composition of the multipass translocon in its native membrane environment. Life Sci Alliance 2024; 7:e202302496. [PMID: 38866426 PMCID: PMC11169918 DOI: 10.26508/lsa.202302496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024] Open
Abstract
Multispanning membrane proteins are inserted into the endoplasmic reticulum membrane by the ribosome-bound multipass translocon (MPT) machinery. Based on cryo-electron tomography and extensive subtomogram analysis, we reveal the composition and arrangement of ribosome-bound MPT components in their native membrane environment. The intramembrane chaperone complex PAT and the translocon-associated protein (TRAP) complex associate substoichiometrically with the MPT in a translation-dependent manner. Although PAT is preferentially part of MPTs bound to translating ribosomes, the abundance of TRAP is highest in MPTs associated with non-translating ribosomes. The subtomogram average of the TRAP-containing MPT reveals intermolecular contacts between the luminal domains of TRAP and an unknown subunit of the back-of-Sec61 complex. AlphaFold modeling suggests this protein is nodal modulator, bridging the luminal domains of nicalin and TRAPα. Collectively, our results visualize the variability of MPT factors in the native membrane environment dependent on the translational activity of the bound ribosome.
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Affiliation(s)
- Max Gemmer
- https://ror.org/04pp8hn57 Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Marten L Chaillet
- https://ror.org/04pp8hn57 Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Friedrich Förster
- https://ror.org/04pp8hn57 Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
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5
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Sanderlin AG, Kurka Margolis H, Meyer AF, Lamason RL. Cell-selective proteomics reveal novel effectors secreted by an obligate intracellular bacterial pathogen. Nat Commun 2024; 15:6073. [PMID: 39025857 PMCID: PMC11258249 DOI: 10.1038/s41467-024-50493-9] [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: 11/27/2023] [Accepted: 07/11/2024] [Indexed: 07/20/2024] Open
Abstract
Pathogenic bacteria secrete protein effectors to hijack host machinery and remodel their infectious niche. Rickettsia spp. are obligate intracellular bacteria that can cause life-threatening disease, but their absolute dependence on the host cell has impeded discovery of rickettsial effectors and their host targets. We implemented bioorthogonal non-canonical amino acid tagging (BONCAT) during R. parkeri infection to selectively label, isolate, and identify effectors delivered into the host cell. As the first use of BONCAT in an obligate intracellular bacterium, our screen more than doubles the number of experimentally validated effectors for the genus. The seven novel secreted rickettsial factors (Srfs) we identified include Rickettsia-specific proteins of unknown function that localize to the host cytoplasm, mitochondria, and ER. We further show that one such effector, SrfD, interacts with the host Sec61 translocon. Altogether, our work uncovers a diverse set of previously uncharacterized rickettsial effectors and lays the foundation for a deeper exploration of the host-pathogen interface.
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Affiliation(s)
- Allen G Sanderlin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Abigail F Meyer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rebecca L Lamason
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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6
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Liu L, Wang H, Liu L, Cheng F, Aisa HA, Li C, Meng S. Rupestonic Acid Derivative YZH-106 Promotes Lysosomal Degradation of HBV L- and M-HBsAg via Direct Interaction with PreS2 Domain. Viruses 2024; 16:1151. [PMID: 39066313 PMCID: PMC11281537 DOI: 10.3390/v16071151] [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: 05/18/2024] [Revised: 07/13/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Hepatitis B surface antigen (HBsAg) is not only the biomarker of hepatitis B virus (HBV) infection and expression activity in hepatocytes, but it also contributes to viral specific T cell exhaustion and HBV persistent infection. Therefore, anti-HBV therapies targeting HBsAg to achieve HBsAg loss are key approaches for an HBV functional cure. In this study, we found that YZH-106, a rupestonic acid derivative, inhibited HBsAg secretion and viral replication. Further investigation demonstrated that YZH-106 promoted the lysosomal degradation of viral L- and M-HBs proteins. A mechanistic study using Biacore and docking analysis revealed that YZH-106 bound directly to the PreS2 domain of L- and M-HBsAg, thereby blocking their entry into the endoplasmic reticulum (ER) and promoting their degradation in cytoplasm. Our work thereby provides the basis for the design of a novel compound therapy to target HBsAg against HBV infection.
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Affiliation(s)
- Lanlan Liu
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (H.W.); (L.L.)
| | - Haoyu Wang
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (H.W.); (L.L.)
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Lulu Liu
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (H.W.); (L.L.)
| | - Fang Cheng
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (H.W.); (L.L.)
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Haji Akber Aisa
- State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
| | - Changfei Li
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (H.W.); (L.L.)
| | - Songdong Meng
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (H.W.); (L.L.)
- University of Chinese Academy of Sciences, Beijing 100101, China
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7
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Lewis AJO, Zhong F, Keenan RJ, Hegde RS. Structural analysis of the dynamic ribosome-translocon complex. eLife 2024; 13:RP95814. [PMID: 38896445 PMCID: PMC11186639 DOI: 10.7554/elife.95814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024] Open
Abstract
The protein translocon at the endoplasmic reticulum comprises the Sec61 translocation channel and numerous accessory factors that collectively facilitate the biogenesis of secretory and membrane proteins. Here, we leveraged recent advances in cryo-electron microscopy (cryo-EM) and structure prediction to derive insights into several novel configurations of the ribosome-translocon complex. We show how a transmembrane domain (TMD) in a looped configuration passes through the Sec61 lateral gate during membrane insertion; how a nascent chain can bind and constrain the conformation of ribosomal protein uL22; and how the translocon-associated protein (TRAP) complex can adjust its position during different stages of protein biogenesis. Most unexpectedly, we find that a large proportion of translocon complexes contains RAMP4 intercalated into Sec61's lateral gate, widening Sec61's central pore and contributing to its hydrophilic interior. These structures lead to mechanistic hypotheses for translocon function and highlight a remarkably plastic machinery whose conformations and composition adjust dynamically to its diverse range of substrates.
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Affiliation(s)
- Aaron JO Lewis
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Frank Zhong
- Department of Molecular Genetics and Cell Biology, The University of ChicagoChicagoUnited States
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
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8
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Vismpas D, Förster F. RAMPing up knowledge of the translocon. eLife 2024; 13:e98548. [PMID: 38787756 PMCID: PMC11126307 DOI: 10.7554/elife.98548] [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] [Indexed: 05/26/2024] Open
Abstract
Advanced cryo-EM approaches reveal surprising insights into the molecular structure that allows nascent proteins to be inserted into the membrane of the endoplasmic reticulum.
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Affiliation(s)
- Dimitrios Vismpas
- Bijvoet Center for Biomolecular Research, Utrecht UniversityUtrechtNetherlands
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht UniversityUtrechtNetherlands
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9
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Morgan CJ, Enustun E, Armbruster EG, Birkholz EA, Prichard A, Forman T, Aindow A, Wannasrichan W, Peters S, Inlow K, Shepherd IL, Razavilar A, Chaikeeratisak V, Adler BA, Cress BF, Doudna JA, Pogliano K, Villa E, Corbett KD, Pogliano J. An essential and highly selective protein import pathway encoded by nucleus-forming phage. Proc Natl Acad Sci U S A 2024; 121:e2321190121. [PMID: 38687783 PMCID: PMC11087766 DOI: 10.1073/pnas.2321190121] [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: 12/20/2023] [Accepted: 04/04/2024] [Indexed: 05/02/2024] Open
Abstract
Targeting proteins to specific subcellular destinations is essential in prokaryotes, eukaryotes, and the viruses that infect them. Chimalliviridae phages encapsulate their genomes in a nucleus-like replication compartment composed of the protein chimallin (ChmA) that excludes ribosomes and decouples transcription from translation. These phages selectively partition proteins between the phage nucleus and the bacterial cytoplasm. Currently, the genes and signals that govern selective protein import into the phage nucleus are unknown. Here, we identify two components of this protein import pathway: a species-specific surface-exposed region of a phage intranuclear protein required for nuclear entry and a conserved protein, PicA (Protein importer of chimalliviruses A), that facilitates cargo protein trafficking across the phage nuclear shell. We also identify a defective cargo protein that is targeted to PicA on the nuclear periphery but fails to enter the nucleus, providing insight into the mechanism of nuclear protein trafficking. Using CRISPRi-ART protein expression knockdown of PicA, we show that PicA is essential early in the chimallivirus replication cycle. Together, our results allow us to propose a multistep model for the Protein Import Chimallivirus pathway, where proteins are targeted to PicA by amino acids on their surface and then licensed by PicA for nuclear entry. The divergence in the selectivity of this pathway between closely related chimalliviruses implicates its role as a key player in the evolutionary arms race between competing phages and their hosts.
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Affiliation(s)
- Chase J. Morgan
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Eray Enustun
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Emily G. Armbruster
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Erica A. Birkholz
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Amy Prichard
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Taylor Forman
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Ann Aindow
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Wichanan Wannasrichan
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand 10330
| | - Sela Peters
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Koe Inlow
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Isabelle L. Shepherd
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Alma Razavilar
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Vorrapon Chaikeeratisak
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand 10330
| | - Benjamin A. Adler
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Innovative Genomics Institute, University of California, Berkeley, CA94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Brady F. Cress
- Innovative Genomics Institute, University of California, Berkeley, CA94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Jennifer A. Doudna
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Innovative Genomics Institute, University of California, Berkeley, CA94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Department of Chemistry, University of California, Berkeley, CA94720
- HHMI, University of California, Berkeley, CA94720
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Kit Pogliano
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Elizabeth Villa
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
- HHMI, University of California San Diego, La Jolla, CA92093
| | - Kevin D. Corbett
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Joe Pogliano
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
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10
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Morgan CJ, Enustun E, Armbruster EG, Birkholz EA, Prichard A, Forman T, Aindow A, Wannasrichan W, Peters S, Inlow K, Shepherd IL, Razavilar A, Chaikeeratisak V, Adler BA, Cress BF, Doudna JA, Pogliano K, Villa E, Corbett KD, Pogliano J. An essential and highly selective protein import pathway encoded by nucleus-forming phage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.585822. [PMID: 38562762 PMCID: PMC10983916 DOI: 10.1101/2024.03.21.585822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Targeting proteins to specific subcellular destinations is essential in prokaryotes, eukaryotes, and the viruses that infect them. Chimalliviridae phages encapsulate their genomes in a nucleus-like replication compartment composed of the protein chimallin (ChmA) that excludes ribosomes and decouples transcription from translation. These phages selectively partition proteins between the phage nucleus and the bacterial cytoplasm. Currently, the genes and signals that govern selective protein import into the phage nucleus are unknown. Here we identify two components of this novel protein import pathway: a species-specific surface-exposed region of a phage intranuclear protein required for nuclear entry and a conserved protein, PicA, that facilitates cargo protein trafficking across the phage nuclear shell. We also identify a defective cargo protein that is targeted to PicA on the nuclear periphery but fails to enter the nucleus, providing insight into the mechanism of nuclear protein trafficking. Using CRISPRi-ART protein expression knockdown of PicA, we show that PicA is essential early in the chimallivirus replication cycle. Together our results allow us to propose a multistep model for the Protein Import Chimallivirus (PIC) pathway, where proteins are targeted to PicA by amino acids on their surface, and then licensed by PicA for nuclear entry. The divergence in the selectivity of this pathway between closely-related chimalliviruses implicates its role as a key player in the evolutionary arms race between competing phages and their hosts. Significance Statement The phage nucleus is an enclosed replication compartment built by Chimalliviridae phages that, similar to the eukaryotic nucleus, separates transcription from translation and selectively imports certain proteins. This allows the phage to concentrate proteins required for DNA replication and transcription while excluding DNA-targeting host defense proteins. However, the mechanism of selective trafficking into the phage nucleus is currently unknown. Here we determine the region of a phage nuclear protein that targets it for nuclear import and identify a conserved, essential nuclear shell-associated protein that plays a key role in this process. This work provides the first mechanistic model of selective import into the phage nucleus.
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11
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Makhlouf L, Peter JJ, Magnussen HM, Thakur R, Millrine D, Minshull TC, Harrison G, Varghese J, Lamoliatte F, Foglizzo M, Macartney T, Calabrese AN, Zeqiraj E, Kulathu Y. The UFM1 E3 ligase recognizes and releases 60S ribosomes from ER translocons. Nature 2024; 627:437-444. [PMID: 38383789 PMCID: PMC10937380 DOI: 10.1038/s41586-024-07093-w] [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: 04/03/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024]
Abstract
Stalled ribosomes at the endoplasmic reticulum (ER) are covalently modified with the ubiquitin-like protein UFM1 on the 60S ribosomal subunit protein RPL26 (also known as uL24)1,2. This modification, which is known as UFMylation, is orchestrated by the UFM1 ribosome E3 ligase (UREL) complex, comprising UFL1, UFBP1 and CDK5RAP3 (ref. 3). However, the catalytic mechanism of UREL and the functional consequences of UFMylation are unclear. Here we present cryo-electron microscopy structures of UREL bound to 60S ribosomes, revealing the basis of its substrate specificity. UREL wraps around the 60S subunit to form a C-shaped clamp architecture that blocks the tRNA-binding sites at one end, and the peptide exit tunnel at the other. A UFL1 loop inserts into and remodels the peptidyl transferase centre. These features of UREL suggest a crucial function for UFMylation in the release and recycling of stalled or terminated ribosomes from the ER membrane. In the absence of functional UREL, 60S-SEC61 translocon complexes accumulate at the ER membrane, demonstrating that UFMylation is necessary for releasing SEC61 from 60S subunits. Notably, this release is facilitated by a functional switch of UREL from a 'writer' to a 'reader' module that recognizes its product-UFMylated 60S ribosomes. Collectively, we identify a fundamental role for UREL in dissociating 60S subunits from the SEC61 translocon and the basis for UFMylation in regulating protein homeostasis at the ER.
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Affiliation(s)
- Linda Makhlouf
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Joshua J Peter
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Helge M Magnussen
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Rohan Thakur
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - David Millrine
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
- Translational Immunology, Cancer Biomarker Centre, Manchester CRUK Institute, Manchester, UK
| | - Thomas C Minshull
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Grace Harrison
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Joby Varghese
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Frederic Lamoliatte
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Martina Foglizzo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Thomas Macartney
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Elton Zeqiraj
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
| | - Yogesh Kulathu
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
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12
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Karki S, Javanainen M, Rehan S, Tranter D, Kellosalo J, Huiskonen JT, Happonen L, Paavilainen V. Molecular view of ER membrane remodeling by the Sec61/TRAP translocon. EMBO Rep 2023; 24:e57910. [PMID: 37983950 DOI: 10.15252/embr.202357910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
Protein translocation across the endoplasmic reticulum (ER) membrane is an essential step during protein entry into the secretory pathway. The conserved Sec61 protein-conducting channel facilitates polypeptide translocation and coordinates cotranslational polypeptide-processing events. In cells, the majority of Sec61 is stably associated with a heterotetrameric membrane protein complex, the translocon-associated protein complex (TRAP), yet the mechanism by which TRAP assists in polypeptide translocation remains unknown. Here, we present the structure of the core Sec61/TRAP complex bound to a mammalian ribosome by cryogenic electron microscopy (cryo-EM). Ribosome interactions anchor the Sec61/TRAP complex in a conformation that renders the ER membrane locally thinner by significantly curving its lumenal leaflet. We propose that TRAP stabilizes the ribosome exit tunnel to assist nascent polypeptide insertion through Sec61 and provides a ratcheting mechanism into the ER lumen mediated by direct polypeptide interactions.
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Affiliation(s)
- Sudeep Karki
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Matti Javanainen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Shahid Rehan
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Protein Biochemistry and Structural Biology, Omass Therapeutics Ltd, Oxford, UK
| | - Dale Tranter
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Juho Kellosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Juha T Huiskonen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Lotta Happonen
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Ville Paavilainen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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13
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Sanderlin AG, Margolis HK, Meyer AF, Lamason RL. Cell-selective proteomics reveal novel effectors secreted by an obligate intracellular bacterial pathogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.17.567466. [PMID: 38014272 PMCID: PMC10680844 DOI: 10.1101/2023.11.17.567466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Pathogenic bacteria secrete protein effectors to hijack host machinery and remodel their infectious niche. Rickettsia spp. are obligate intracellular bacteria that can cause life-threatening disease, but their absolute dependence on the host cell environment has impeded discovery of rickettsial effectors and their host targets. We implemented bioorthogonal non-canonical amino acid tagging (BONCAT) during R. parkeri infection to selectively label, isolate, and identify secreted effectors. As the first use of BONCAT in an obligate intracellular bacterium, our screen more than doubles the number of experimentally validated effectors for R. parkeri. The novel secreted rickettsial factors (Srfs) we identified include Rickettsia-specific proteins of unknown function that localize to the host cytoplasm, mitochondria, and ER. We further show that one such effector, SrfD, interacts with the host Sec61 translocon. Altogether, our work uncovers a diverse set of previously uncharacterized rickettsial effectors and lays the foundation for a deeper exploration of the host-pathogen interface.
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Affiliation(s)
- Allen G Sanderlin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Hannah K Margolis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Abigail F Meyer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rebecca L Lamason
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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14
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Jackson KG, Way GW, Zeng J, Lipp MK, Zhou H. The Dynamic Role of Endoplasmic Reticulum Stress in Chronic Liver Disease. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:1389-1399. [PMID: 37028592 PMCID: PMC10548273 DOI: 10.1016/j.ajpath.2023.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/10/2023] [Accepted: 03/27/2023] [Indexed: 04/08/2023]
Abstract
Chronic liver disease (CLD) is a major worldwide public health threat, with an estimated prevalence of 1.5 billion individuals with CLD in 2020. Chronic activation of endoplasmic reticulum (ER) stress-related pathways is recognized as substantially contributing to the pathologic progression of CLD. The ER is an intracellular organelle that folds proteins into their correct three-dimensional shapes. ER-associated enzymes and chaperone proteins highly regulate this process. Perturbations in protein folding lead to misfolded or unfolded protein accumulation in the ER lumen, resulting in ER stress and concomitant activation of the unfolded protein response (UPR). The adaptive UPR is a set of signal transduction pathways evolved in mammalian cells that attempts to reestablish ER protein homeostasis by reducing protein load and increasing ER-associated degradation. However, maladaptive UPR responses in CLD occur due to prolonged UPR activation, leading to concomitant inflammation and cell death. This review assesses the current understanding of the cellular and molecular mechanisms that regulate ER stress and the UPR in the progression of various liver diseases and the potential pharmacologic and biological interventions that target the UPR.
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Affiliation(s)
- Kaitlyn G Jackson
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Grayson W Way
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia; Center for Clinical and Translational Research, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Jing Zeng
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia; Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Marissa K Lipp
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Huiping Zhou
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia; Central Virginia Veterans Healthcare System, Richmond, Virginia.
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15
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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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16
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Yao Z, Ramachandran S, Huang S, Jami-Alahmadi Y, Wohlschlegel JA, Li MMH. Chikungunya virus glycoproteins transform macrophages into productive viral dissemination vessels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542714. [PMID: 37398144 PMCID: PMC10312455 DOI: 10.1101/2023.05.29.542714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Despite their role as innate sentinels, macrophages are cellular reservoirs for chikungunya virus (CHIKV), a highly pathogenic arthropod-borne alphavirus that has caused unprecedented epidemics worldwide. Here, we took interdisciplinary approaches to elucidate the CHIKV determinants that subvert macrophages into virion dissemination vessels. Through comparative infection using chimeric alphaviruses and evolutionary selection analyses, we discovered for the first time that CHIKV glycoproteins E2 and E1 coordinate efficient virion production in macrophages with the domains involved under positive selection. We performed proteomics on CHIKV-infected macrophages to identify cellular proteins interacting with the precursor and/or mature forms of viral glycoproteins. We uncovered two E1-binding proteins, signal peptidase complex subunit 3 (SPCS3) and eukaryotic translation initiation factor 3 (eIF3k), with novel inhibitory activities against CHIKV production. These results highlight how CHIKV E2 and E1 have been evolutionarily selected for viral dissemination likely through counteracting host restriction factors, making them attractive targets for therapeutic intervention.
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Affiliation(s)
- Zhenlan Yao
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sangeetha Ramachandran
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Serina Huang
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Melody M H Li
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
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17
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Bai L, Li H. Structural insights into the membrane chaperones for multi-pass membrane protein biogenesis. Curr Opin Struct Biol 2023; 79:102563. [PMID: 36863267 DOI: 10.1016/j.sbi.2023.102563] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/22/2023] [Accepted: 01/28/2023] [Indexed: 03/04/2023]
Abstract
Certain transmembrane α-helices of multi-pass membrane proteins line substrate transport paths or catalytic pockets and, therefore, are partially hydrophilic. Sec61 alone is insufficient to insert these less hydrophobic segments into the membrane and needs to work with dedicated membrane chaperones. Three such membrane chaperones have been described in the literature-the endoplasmic reticulum membrane protein complex (EMC), the TMCO1 complex, and the PAT complex. Recent structural studies on these membrane chaperones have revealed their overall architecture, multi-subunit assembly, putative substrate transmembrane helix-binding pockets, and cooperative mechanisms with the ribosome and Sec61 translocon. These structures are providing initial insights into the poorly understood processes of multi-pass membrane protein biogenesis.
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Affiliation(s)
- Lin Bai
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, 100083, China.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, 49503, United States.
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18
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Biasini E, Faccioli P. Functional, pathogenic, and pharmacological roles of protein folding intermediates. Proteins 2023. [PMID: 36779817 DOI: 10.1002/prot.26479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
Protein expression and function in eukaryotic cells are tightly harmonized processes modulated by the combination of different layers of regulation, including transcription, processing, stability, and translation of messenger RNA, as well as assembly, maturation, sorting, recycling, and degradation of polypeptides. Integrating all these pathways and the protein quality control machinery, deputed to avoid the production and accumulation of aberrantly folded proteins, determines protein homeostasis. Over the last decade, the combined development of accurate time-resolved experimental techniques and efficient computer simulations has opened the possibility of investigating biological mechanisms at atomic resolution with physics-based models. A meaningful example is the reconstruction of protein folding pathways at atomic resolution, which has enabled the characterization of the folding kinetics of biologically relevant globular proteins consisting of a few hundred amino acids. Combining these innovative computational technologies with rigorous experimental approaches reveals the existence of non-native metastable states transiently appearing along the folding process of such proteins. Here, we review the primary evidence indicating that these protein folding intermediates could play roles in disparate biological processes, from the posttranslational regulation of protein expression to disease-relevant protein misfolding mechanisms. Finally, we discuss how the information encoded into protein folding pathways could be exploited to design an entirely new generation of pharmacological agents capable of promoting the selective degradation of protein targets.
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Affiliation(s)
- Emiliano Biasini
- Department of Cellular Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Pietro Faccioli
- Department of Physics, University of Trento, Trento, Italy
- Trento Institute for Fundamental Physics and Applications, Italian Institute for Nuclear Physics, Trento, Italy
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19
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Melnyk A, Lang S, Sicking M, Zimmermann R, Jung M. Co-chaperones of the Human Endoplasmic Reticulum: An Update. Subcell Biochem 2023; 101:247-291. [PMID: 36520310 DOI: 10.1007/978-3-031-14740-1_9] [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] [Indexed: 06/17/2023]
Abstract
In mammalian cells, the rough endoplasmic reticulum (ER) plays central roles in the biogenesis of extracellular plus organellar proteins and in various signal transduction pathways. For these reasons, the ER comprises molecular chaperones, which are involved in import, folding, assembly, export, plus degradation of polypeptides, and signal transduction components, such as calcium channels, calcium pumps, and UPR transducers plus adenine nucleotide carriers/exchangers in the ER membrane. The calcium- and ATP-dependent ER lumenal Hsp70, termed immunoglobulin heavy-chain-binding protein or BiP, is the central player in all these activities and involves up to nine different Hsp40-type co-chaperones, i.e., ER membrane integrated as well as ER lumenal J-domain proteins, termed ERj or ERdj proteins, two nucleotide exchange factors or NEFs (Grp170 and Sil1), and NEF-antagonists, such as MANF. Here we summarize the current knowledge on the ER-resident BiP/ERj chaperone network and focus on the interaction of BiP with the polypeptide-conducting and calcium-permeable Sec61 channel of the ER membrane as an example for BiP action and how its functional cycle is linked to ER protein import and various calcium-dependent signal transduction pathways.
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Affiliation(s)
- Armin Melnyk
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
| | - Sven Lang
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
| | - Mark Sicking
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
| | - Richard Zimmermann
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany.
| | - Martin Jung
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
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20
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Visualization of translation and protein biogenesis at the ER membrane. Nature 2023; 614:160-167. [PMID: 36697828 PMCID: PMC9892003 DOI: 10.1038/s41586-022-05638-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 12/07/2022] [Indexed: 01/26/2023]
Abstract
The dynamic ribosome-translocon complex, which resides at the endoplasmic reticulum (ER) membrane, produces a major fraction of the human proteome1,2. It governs the synthesis, translocation, membrane insertion, N-glycosylation, folding and disulfide-bond formation of nascent proteins. Although individual components of this machinery have been studied at high resolution in isolation3-7, insights into their interplay in the native membrane remain limited. Here we use cryo-electron tomography, extensive classification and molecular modelling to capture snapshots of mRNA translation and protein maturation at the ER membrane at molecular resolution. We identify a highly abundant classical pre-translocation intermediate with eukaryotic elongation factor 1a (eEF1a) in an extended conformation, suggesting that eEF1a may remain associated with the ribosome after GTP hydrolysis during proofreading. At the ER membrane, distinct polysomes bind to different ER translocons specialized in the synthesis of proteins with signal peptides or multipass transmembrane proteins with the translocon-associated protein complex (TRAP) present in both. The near-complete atomic model of the most abundant ER translocon variant comprising the protein-conducting channel SEC61, TRAP and the oligosaccharyltransferase complex A (OSTA) reveals specific interactions of TRAP with other translocon components. We observe stoichiometric and sub-stoichiometric cofactors associated with OSTA, which are likely to include protein isomerases. In sum, we visualize ER-bound polysomes with their coordinated downstream machinery.
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21
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Zhang Z, Zhou H, Ouyang X, Dong Y, Sarapultsev A, Luo S, Hu D. Multifaceted functions of STING in human health and disease: from molecular mechanism to targeted strategy. Signal Transduct Target Ther 2022; 7:394. [PMID: 36550103 PMCID: PMC9780328 DOI: 10.1038/s41392-022-01252-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/25/2022] [Accepted: 11/09/2022] [Indexed: 12/24/2022] Open
Abstract
Since the discovery of Stimulator of Interferon Genes (STING) as an important pivot for cytosolic DNA sensation and interferon (IFN) induction, intensive efforts have been endeavored to clarify the molecular mechanism of its activation, its physiological function as a ubiquitously expressed protein, and to explore its potential as a therapeutic target in a wide range of immune-related diseases. With its orthodox ligand 2'3'-cyclic GMP-AMP (2'3'-cGAMP) and the upstream sensor 2'3'-cGAMP synthase (cGAS) to be found, STING acquires its central functionality in the best-studied signaling cascade, namely the cGAS-STING-IFN pathway. However, recently updated research through structural research, genetic screening, and biochemical assay greatly extends the current knowledge of STING biology. A second ligand pocket was recently discovered in the transmembrane domain for a synthetic agonist. On its downstream outputs, accumulating studies sketch primordial and multifaceted roles of STING beyond its cytokine-inducing function, such as autophagy, cell death, metabolic modulation, endoplasmic reticulum (ER) stress, and RNA virus restriction. Furthermore, with the expansion of the STING interactome, the details of STING trafficking also get clearer. After retrospecting the brief history of viral interference and the milestone events since the discovery of STING, we present a vivid panorama of STING biology taking into account the details of the biochemical assay and structural information, especially its versatile outputs and functions beyond IFN induction. We also summarize the roles of STING in the pathogenesis of various diseases and highlight the development of small-molecular compounds targeting STING for disease treatment in combination with the latest research. Finally, we discuss the open questions imperative to answer.
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Affiliation(s)
- Zili Zhang
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Haifeng Zhou
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Xiaohu Ouyang
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Yalan Dong
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Alexey Sarapultsev
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049, Ekaterinburg, Russia
| | - Shanshan Luo
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Desheng Hu
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China.
- Key Laboratory of Biological Targeted Therapy, The Ministry of Education, 430022, Wuhan, China.
- Clinical Research Center of Cancer Immunotherapy, 430022, Hubei, Wuhan, China.
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22
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Yuan W, Cui CC, Li J, Xu YH, Fan CE, Chen YC, Fan HW, Hu BX, Shi MY, Sun ZY, Wang P, Ma TX, Zhang Z, Zhu MS, Chen HQ. Intracellular TMEM16A is necessary for myogenesis of skeletal muscle. iScience 2022; 25:105446. [DOI: 10.1016/j.isci.2022.105446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 08/08/2022] [Accepted: 10/21/2022] [Indexed: 11/09/2022] Open
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23
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O'Keefe S, Pool MR, High S. Membrane protein biogenesis at the ER: the highways and byways. FEBS J 2022; 289:6835-6862. [PMID: 33960686 DOI: 10.1111/febs.15905] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/19/2021] [Accepted: 04/28/2021] [Indexed: 01/13/2023]
Abstract
The Sec61 complex is the major protein translocation channel of the endoplasmic reticulum (ER), where it plays a central role in the biogenesis of membrane and secretory proteins. Whilst Sec61-mediated protein translocation is typically coupled to polypeptide synthesis, suggestive of significant complexity, an obvious characteristic of this core translocation machinery is its surprising simplicity. Over thirty years after its initial discovery, we now understand that the Sec61 complex is in fact the central piece of an elaborate jigsaw puzzle, which can be partly solved using new research findings. We propose that the Sec61 complex acts as a dynamic hub for co-translational protein translocation at the ER, proactively recruiting a range of accessory complexes that enhance and regulate its function in response to different protein clients. It is now clear that the Sec61 complex does not have a monopoly on co-translational insertion, with some transmembrane proteins preferentially utilising the ER membrane complex instead. We also have a better understanding of post-insertion events, where at least one membrane-embedded chaperone complex can capture the newly inserted transmembrane domains of multi-span proteins and co-ordinate their assembly into a native structure. Having discovered this array of Sec61-associated components and competitors, our next challenge is to understand how they act together in order to expand the range and complexity of the membrane proteins that can be synthesised at the ER. Furthermore, this diversity of components and pathways may open up new opportunities for targeted therapeutic interventions designed to selectively modulate protein biogenesis at the ER.
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Affiliation(s)
- Sarah O'Keefe
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Martin R Pool
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Stephen High
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
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24
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Substrate-driven assembly of a translocon for multipass membrane proteins. Nature 2022; 611:167-172. [PMID: 36261522 PMCID: PMC9630114 DOI: 10.1038/s41586-022-05330-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 09/07/2022] [Indexed: 11/19/2022]
Abstract
Most membrane proteins are synthesized on endoplasmic reticulum (ER)-bound ribosomes docked at the translocon, a heterogeneous ensemble of transmembrane factors operating on the nascent chain1,2. How the translocon coordinates the actions of these factors to accommodate its different substrates is not well understood. Here we define the composition, function and assembly of a translocon specialized for multipass membrane protein biogenesis3. This ‘multipass translocon’ is distinguished by three components that selectively bind the ribosome–Sec61 complex during multipass protein synthesis: the GET- and EMC-like (GEL), protein associated with translocon (PAT) and back of Sec61 (BOS) complexes. Analysis of insertion intermediates reveals how features of the nascent chain trigger multipass translocon assembly. Reconstitution studies demonstrate a role for multipass translocon components in protein topogenesis, and cells lacking these components show reduced multipass protein stability. These results establish the mechanism by which nascent multipass proteins selectively recruit the multipass translocon to facilitate their biogenesis. More broadly, they define the ER translocon as a dynamic assembly whose subunit composition adjusts co-translationally to accommodate the biosynthetic needs of its diverse range of substrates. Biochemical reconstitution and functional analysis reveal how newly synthesized multipass membrane proteins dynamically remodel the translocon to facilitate their successful biogenesis.
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25
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Parys JB, Van Coppenolle F. Sec61 complex/translocon: The role of an atypical ER Ca 2+-leak channel in health and disease. Front Physiol 2022; 13:991149. [PMID: 36277220 PMCID: PMC9582130 DOI: 10.3389/fphys.2022.991149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/20/2022] [Indexed: 11/02/2023] Open
Abstract
The heterotrimeric Sec61 protein complex forms the functional core of the so-called translocon that forms an aqueous channel in the endoplasmic reticulum (ER). The primary role of the Sec61 complex is to allow protein import in the ER during translation. Surprisingly, a completely different function in intracellular Ca2+ homeostasis has emerged for the Sec61 complex, and the latter is now accepted as one of the major Ca2+-leak pathways of the ER. In this review, we first discuss the structure of the Sec61 complex and focus on the pharmacology and regulation of the Sec61 complex as a Ca2+-leak channel. Subsequently, we will pay particular attention to pathologies that are linked to Sec61 mutations, such as plasma cell deficiency and congenital neutropenia. Finally, we will explore the relevance of the Sec61 complex as a Ca2+-leak channel in various pathophysiological (ER stress, apoptosis, ischemia-reperfusion) and pathological (type 2 diabetes, cancer) settings.
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Affiliation(s)
- Jan B. Parys
- Laboratory for Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, KU Leuven, Leuven, Belgium
| | - Fabien Van Coppenolle
- CarMeN Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Groupement Hospitalier EST, Department of Cardiology, Hospices Civils de Lyon, Lyon, France
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26
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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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27
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Fels JA, Dash J, Leslie K, Manfredi G, Kawamata H. Effects of
PB‐TURSO
on the transcriptional and metabolic landscape of sporadic
ALS
fibroblasts. Ann Clin Transl Neurol 2022; 9:1551-1564. [PMID: 36083004 PMCID: PMC9539390 DOI: 10.1002/acn3.51648] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/02/2022] [Accepted: 07/22/2022] [Indexed: 11/09/2022] Open
Abstract
Objective Methods Results Interpretation
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Affiliation(s)
- Jasmine A. Fels
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine 407 East 61st Street New York New York 10065 USA
- Neuroscience Graduate Program Weill Cornell Graduate School of Medical Sciences 1300 York Ave New York New York 10065 USA
| | - Jalia Dash
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine 407 East 61st Street New York New York 10065 USA
| | - Kent Leslie
- Amylyx Pharmaceuticals 43 Thorndike Street Cambridge Massachusetts 02141 USA
| | - Giovanni Manfredi
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine 407 East 61st Street New York New York 10065 USA
| | - Hibiki Kawamata
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine 407 East 61st Street New York New York 10065 USA
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28
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Hirata T, Yang J, Tomida S, Tokoro Y, Kinoshita T, Fujita M, Kizuka Y. ER entry pathway and glycosylation of GPI-anchored proteins are determined by N-terminal signal sequence and C-terminal GPI-attachment sequence. J Biol Chem 2022; 298:102444. [PMID: 36055406 PMCID: PMC9520029 DOI: 10.1016/j.jbc.2022.102444] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/20/2022] [Accepted: 08/25/2022] [Indexed: 11/15/2022] Open
Abstract
Newly synthesized proteins in the secretory pathway, including glycosylphosphatidylinositol (GPI)-anchored proteins (GPI-APs), need to be correctly targeted and imported into the endoplasmic reticulum (ER) lumen. GPI-APs are synthesized in the cytosol as preproproteins, which contain an N-terminal signal sequence (SS), mature protein part, and C-terminal GPI-attachment sequence (GPI-AS), and translocated into the ER lumen where SS and GPI-AS are removed, generating mature GPI-APs. However, how various GPI-APs are translocated into the ER lumen in mammalian cells is unclear. Here, we investigated the ER entry pathways of GPI-APs using a panel of KO cells defective in each signal recognition particle–independent ER entry pathway—namely, Sec62, GET, or SND pathway. We found GPI-AP CD59 largely depends on the SND pathway for ER entry, whereas prion protein (Prion) and LY6K depend on both Sec62 and GET pathways. Using chimeric Prion and LY6K constructs in which the N-terminal SS or C-terminal GPI-AS was replaced with that of CD59, we revealed that the hydrophobicity of the SSs and GPI-ASs contributes to the dependence on Sec62 and GET pathways, respectively. Moreover, the ER entry route of chimeric Prion constructs with the C-terminal GPI-ASs replaced with that of CD59 was changed to the SND pathway. Simultaneously, their GPI structures and which oligosaccharyltransferase isoforms modify the constructs were altered without any amino acid change in the mature protein part. Taking these findings together, this study revealed N- and C-terminal sequences of GPI-APs determine the selective ER entry route, which in turn regulates subsequent maturation processes of GPI-APs.
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Affiliation(s)
- Tetsuya Hirata
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Jing Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Seita Tomida
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan; Graduate School of Natural Science and Technology, Gifu University, Gifu 501-1193, Japan
| | - Yuko Tokoro
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Taroh Kinoshita
- Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita 565-0871, Japan
| | - Morihisa Fujita
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yasuhiko Kizuka
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan.
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29
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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] [Key Words] [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
| | - 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
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30
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Synthesis, Biological Evaluation and Docking Studies of Ring-Opened Analogues of Ipomoeassin F. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27144419. [PMID: 35889292 PMCID: PMC9320607 DOI: 10.3390/molecules27144419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/04/2022] [Accepted: 07/07/2022] [Indexed: 11/17/2022]
Abstract
The plant-derived macrocyclic resin glycoside ipomoeassin F (Ipom-F) binds to Sec61α and significantly disrupts multiple aspects of Sec61-mediated protein biogenesis at the endoplasmic reticulum, ultimately leading to cell death. However, extensive assessment of Ipom-F as a molecular tool and a therapeutic lead is hampered by its limited production scale, largely caused by intramolecular assembly of the macrocyclic ring. Here, using in vitro and/or in cellula biological assays to explore the first series of ring-opened analogues for the ipomoeassins, and indeed all resin glycosides, we provide clear evidence that macrocyclic integrity is not required for the cytotoxic inhibition of Sec61-dependent protein translocation by Ipom-F. Furthermore, our modeling suggests that open-chain analogues of Ipom-F can interact with multiple sites on the Sec61α subunit, most likely located at a previously identified binding site for mycolactone and/or the so-called lateral gate. Subsequent in silico-aided design led to the discovery of the stereochemically simplified analogue 3 as a potent, alternative lead compound that could be synthesized much more efficiently than Ipom-F and will accelerate future ipomoeassin research in chemical biology and drug discovery. Our work may also inspire further exploration of ring-opened analogues of other resin glycosides.
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31
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Regulation of Translation, Translocation, and Degradation of Proteins at the Membrane of the Endoplasmic Reticulum. Int J Mol Sci 2022; 23:ijms23105576. [PMID: 35628387 PMCID: PMC9147092 DOI: 10.3390/ijms23105576] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 11/21/2022] Open
Abstract
The endoplasmic reticulum (ER) of mammalian cells is the central organelle for the maturation and folding of transmembrane proteins and for proteins destined to be secreted into the extracellular space. The proper folding of target proteins is achieved and supervised by a complex endogenous chaperone machinery. BiP, a member of the Hsp70 protein family, is the central chaperone in the ER. The chaperoning activity of BiP is assisted by ER-resident DnaJ (ERdj) proteins due to their ability to stimulate the low, intrinsic ATPase activity of BiP. Besides their co-chaperoning activity, ERdj proteins also regulate and tightly control the translation, translocation, and degradation of proteins. Disturbances in the luminal homeostasis result in the accumulation of unfolded proteins, thereby eliciting a stress response, the so-called unfolded protein response (UPR). Accumulated proteins are either deleterious due to the functional loss of the respective protein and/or due to their deposition as intra- or extracellular protein aggregates. A variety of metabolic diseases are known to date, which are associated with the dysfunction of components of the chaperone machinery. In this review, we will delineate the impact of ERdj proteins in controlling protein synthesis and translocation under physiological and under stress conditions. A second aspect of this review is dedicated to the role of ERdj proteins in the ER-associated degradation pathway, by which unfolded or misfolded proteins are discharged from the ER. We will refer to some of the most prominent diseases known to be based on the dysfunction of ERdj proteins.
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32
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Iyer U, Park JE, Sze SK, Bozdech Z, Featherstone M. Mediator Complex of the Malaria Parasite Plasmodium falciparum Associates with Evolutionarily Novel Subunits. ACS OMEGA 2022; 7:14867-14874. [PMID: 35557691 PMCID: PMC9088918 DOI: 10.1021/acsomega.2c00368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
The eukaryotic Mediator is a large and conserved multisubunit protein complex that directly contacts RNA polymerase II and impinges on multiple aspects of gene expression. The genome of the human malaria parasite Plasmodium falciparum has been predicted to encode several Mediator subunits. We provide physical evidence for the presence of a Mediator complex in P. falciparum by using coimmunoprecipitation and mass spectrometry to identify interaction partners of the highly conserved Mediator subunit PfMed31. We identify 11 of 14 predicted Mediator subunits and the products of two uncharacterized genes, PF3D7_0526800 and PF3D7_1363600, which are strongly associated with PfMed31. As expected, several additional interaction partners have known roles in the transcriptional control of gene expression and mRNA processing. Intriguingly, multiple interaction partners are implicated in endoplasmic reticulum function and the ER stress (ERS) response, suggesting crosstalk between the ERS response and the transcriptional machinery. Our results establish for the first time the physical presence of the Mediator complex within P. falciparum and strongly suggest that it plays both conserved and unique roles in the control of gene expression. Data are available via ProteomeXchange with the identifier PXD027640.
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33
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Sicking M, Živná M, Bhadra P, Barešová V, Tirincsi A, Hadzibeganovic D, Hodaňová K, Vyleťal P, Sovová J, Jedličková I, Jung M, Bell T, Helms V, Bleyer AJ, Kmoch S, Cavalié A, Lang S. Phenylbutyrate rescues the transport defect of the Sec61α mutations V67G and T185A for renin. Life Sci Alliance 2022; 5:e202101150. [PMID: 35064074 PMCID: PMC8807872 DOI: 10.26508/lsa.202101150] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 11/24/2022] Open
Abstract
The human Sec61 complex is a widely distributed and abundant molecular machine. It resides in the membrane of the endoplasmic reticulum to channel two types of cargo: protein substrates and calcium ions. The SEC61A1 gene encodes for the pore-forming Sec61α subunit of the Sec61 complex. Despite their ubiquitous expression, the idiopathic SEC61A1 missense mutations p.V67G and p.T185A trigger a localized disease pattern diagnosed as autosomal dominant tubulointerstitial kidney disease (ADTKD-SEC61A1). Using cellular disease models for ADTKD-SEC61A1, we identified an impaired protein transport of the renal secretory protein renin and a reduced abundance of regulatory calcium transporters, including SERCA2. Treatment with the molecular chaperone phenylbutyrate reversed the defective protein transport of renin and the imbalanced calcium homeostasis. Signal peptide substitution experiments pointed at targeting sequences as the cause for the substrate-specific impairment of protein transport in the presence of the V67G or T185A mutations. Similarly, dominant mutations in the signal peptide of renin also cause ADTKD and point to impaired transport of this renal hormone as important pathogenic feature for ADTKD-SEC61A1 patients as well.
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Affiliation(s)
- Mark Sicking
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Martina Živná
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Pratiti Bhadra
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Veronika Barešová
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Andrea Tirincsi
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Drazena Hadzibeganovic
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Petr Vyleťal
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jana Sovová
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ivana Jedličková
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martin Jung
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Thomas Bell
- Department of Chemistry, University of Nevada, Reno, NV, USA
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Anthony J Bleyer
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Adolfo Cavalié
- Experimental and Clinical Pharmacology and Toxicology, Pre-clinical Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
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Dhayalan B, Glidden MD, Zaykov AN, Chen YS, Yang Y, Phillips NB, Ismail-Beigi F, Jarosinski MA, DiMarchi RD, Weiss MA. Peptide Model of the Mutant Proinsulin Syndrome. I. Design and Clinical Correlation. Front Endocrinol (Lausanne) 2022; 13:821069. [PMID: 35299972 PMCID: PMC8922534 DOI: 10.3389/fendo.2022.821069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/17/2022] [Indexed: 12/16/2022] Open
Abstract
The mutant proinsulin syndrome is a monogenic cause of diabetes mellitus due to toxic misfolding of insulin's biosynthetic precursor. Also designated mutant INS-gene induced diabetes of the young (MIDY), this syndrome defines molecular determinants of foldability in the endoplasmic reticulum (ER) of β-cells. Here, we describe a peptide model of a key proinsulin folding intermediate and variants containing representative clinical mutations; the latter perturb invariant core sites in native proinsulin (LeuB15→Pro, LeuA16→Pro, and PheB24→Ser). The studies exploited a 49-residue single-chain synthetic precursor (designated DesDi), previously shown to optimize in vitro efficiency of disulfide pairing. Parent and variant peptides contain a single disulfide bridge (cystine B19-A20) to provide a model of proinsulin's first oxidative folding intermediate. The peptides were characterized by circular dichroism and redox stability in relation to effects of the mutations on (a) in vitro foldability of the corresponding insulin analogs and (b) ER stress induced in cell culture on expression of the corresponding variant proinsulins. Striking correlations were observed between peptide biophysical properties, degree of ER stress and age of diabetes onset (neonatal or adolescent). Our findings suggest that age of onset reflects the extent to which nascent structure is destabilized in proinsulin's putative folding nucleus. We envisage that such peptide models will enable high-resolution structural studies of key folding determinants and in turn permit molecular dissection of phenotype-genotype relationships in this monogenic diabetes syndrome. Our companion study (next article in this issue) employs two-dimensional heteronuclear NMR spectroscopy to define site-specific perturbations in the variant peptides.
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Affiliation(s)
- Balamurugan Dhayalan
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Michael D. Glidden
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Department of Physiology & Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | | | - Yen-Shan Chen
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Yanwu Yang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Nelson B. Phillips
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Faramarz Ismail-Beigi
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Department of Physiology & Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Mark A. Jarosinski
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | | | - Michael A. Weiss
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
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35
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Xu X, Huang Y, Li X, Arvan P, Liu M. The Role of TRAPγ/SSR3 in Preproinsulin Translocation Into the Endoplasmic Reticulum. Diabetes 2022; 71:440-452. [PMID: 34857543 PMCID: PMC8893945 DOI: 10.2337/db21-0638] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/18/2021] [Indexed: 11/13/2022]
Abstract
In the endoplasmic reticulum (ER), the translocation-associated protein complex (TRAP), also called signal sequence receptor (SSR), includes four integral membrane proteins TRAPα/SSR1, TRAPβ/SSR2, and TRAPδ/SSR4 with the bulk of their extramembranous portions primarily in the ER lumen, whereas the extramembranous portion of TRAPγ/SSR3 is primarily cytosolic. Individually diminished expression of either TRAPα/SSR1, TRAPβ/SSR2, or TRAPδ/SSR4 mRNA is known in each case to lower TRAPα/SSR1 protein levels, leading to impaired proinsulin biosynthesis, whereas forced expression of TRAPα/SSR1 at least partially suppresses the proinsulin biosynthetic defect. Here, we report that diminished TRAPγ/SSR3 expression in pancreatic β-cells leaves TRAPα/SSR1 levels unaffected while nevertheless inhibiting cotranslational and posttranslational translocation of preproinsulin into the ER. Crucially, acute exposure to high glucose leads to a rapid upregulation of both TRAPγ/SSR3 and proinsulin protein without change in the respective mRNA levels, as observed in cultured rodent β-cell lines and confirmed in human islets. Strikingly, pancreatic β-cells with suppressed TRAPγ/SSR3 expression are blocked in glucose-dependent upregulation of proinsulin (or insulin) biosynthesis. Most remarkably, overexpression of TRAPγ/SSR3 in control β-cells raises proinsulin levels, even without boosting extracellular glucose. The data suggest the possibility that TRAPγ/SSR3 may fulfill a rate-limiting function in preproinsulin translocation across the ER membrane for proinsulin biosynthesis.
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Affiliation(s)
- Xiaoxi Xu
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical Center, Ann Arbor, MI
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China
| | - Yumeng Huang
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical Center, Ann Arbor, MI
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China
| | - Xin Li
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical Center, Ann Arbor, MI
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China
| | - Peter Arvan
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical Center, Ann Arbor, MI
- Corresponding authors: Peter Arvan, , and Ming Liu,
| | - Ming Liu
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China
- Corresponding authors: Peter Arvan, , and Ming Liu,
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36
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Schirrmacher V. Molecular Mechanisms of Anti-Neoplastic and Immune Stimulatory Properties of Oncolytic Newcastle Disease Virus. Biomedicines 2022; 10:562. [PMID: 35327364 PMCID: PMC8945571 DOI: 10.3390/biomedicines10030562] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/18/2022] [Accepted: 02/25/2022] [Indexed: 12/25/2022] Open
Abstract
Oncolytic viruses represent interesting anti-cancer agents with high tumor selectivity and immune stimulatory potential. The present review provides an update of the molecular mechanisms of the anti-neoplastic and immune stimulatory properties of the avian paramyxovirus, Newcastle Disease Virus (NDV). The anti-neoplastic activities of NDV include (i) the endocytic targeting of the GTPase Rac1 in Ras-transformed human tumorigenic cells; (ii) the switch from cellular protein to viral protein synthesis and the induction of autophagy mediated by viral nucleoprotein NP; (iii) the virus replication mediated by viral RNA polymerase (large protein (L), associated with phosphoprotein (P)); (iv) the facilitation of NDV spread in tumors via the membrane budding of the virus progeny with the help of matrix protein (M) and fusion protein (F); and (v) the oncolysis via apoptosis, necroptosis, pyroptosis, or ferroptosis associated with immunogenic cell death. A special property of this oncolytic virus consists of its potential for breaking therapy resistance in human cancer cells. Eight examples of this important property are presented and explained. In healthy human cells, NDV infection activates the RIG-MAVs immune signaling pathway and establishes an anti-viral state based on a strong and uninhibited interferon α,ß response. The review also describes the molecular determinants and mechanisms of the NDV-mediated immune stimulatory effects, in which the viral hemagglutinin-neuraminidase (HN) protein plays a prominent role. The six viral proteins provide oncolytic NDV with a special profile in the treatment of cancer.
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Reduced DNAJC3 Expression Affects Protein Translocation across the ER Membrane and Attenuates the Down-Modulating Effect of the Translocation Inhibitor Cyclotriazadisulfonamide. Int J Mol Sci 2022; 23:ijms23020584. [PMID: 35054769 PMCID: PMC8775681 DOI: 10.3390/ijms23020584] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/03/2022] [Accepted: 01/05/2022] [Indexed: 12/20/2022] Open
Abstract
One of the reported substrates for the endoplasmic reticulum (ER) translocation inhibitor cyclotriazadisulfonamide (CADA) is DNAJC3, a chaperone of the unfolded protein response during ER stress. In this study, we investigated the impact of altered DNAJC3 protein levels on the inhibitory activity of CADA. By comparing WT DNAJC3 with a CADA-resistant DNAJC3 mutant, we observed the enhanced sensitivity of human CD4, PTK7 and ERLEC1 for CADA when DNAJC3 was expressed at high levels. Combined treatment of CADA with a proteasome inhibitor resulted in synergistic inhibition of protein translocation and in the rescue of a small preprotein fraction, which presumably corresponds to the CADA affected protein fraction that is stalled at the Sec61 translocon. We demonstrate that DNAJC3 enhances the protein translation of a reporter protein that is expressed downstream of the CADA-stalled substrate, suggesting that DNAJC3 promotes the clearance of the clogged translocon. We propose a model in which a reduced DNAJC3 level by CADA slows down the clearance of CADA-stalled substrates. This results in higher residual translocation into the ER lumen due to the longer dwelling time of the temporarily stalled substrates in the translocon. Thus, by directly reducing DNAJC3 protein levels, CADA attenuates its net down-modulating effect on its substrates.
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Randzavola LO, Mortimer PM, Garside E, Dufficy ER, Schejtman A, Roumelioti G, Yu L, Pardo M, Spirohn K, Tolley C, Brandt C, Harcourt K, Nichols E, Nahorski M, Woods G, Williamson JC, Suresh S, Sowerby JM, Matsumoto M, Santos CXC, Kiar CS, Mukhopadhyay S, Rae WM, Dougan GJ, Grainger J, Lehner PJ, Calderwood MA, Choudhary J, Clare S, Speak A, Santilli G, Bateman A, Smith KGC, Magnani F, Thomas DC. EROS is a selective chaperone regulating the phagocyte NADPH oxidase and purinergic signalling. eLife 2022; 11:76387. [PMID: 36421765 PMCID: PMC9767466 DOI: 10.7554/elife.76387] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 10/31/2022] [Indexed: 11/25/2022] Open
Abstract
EROS (essential for reactive oxygen species) protein is indispensable for expression of gp91phox, the catalytic core of the phagocyte NADPH oxidase. EROS deficiency in humans is a novel cause of the severe immunodeficiency, chronic granulomatous disease, but its mechanism of action was unknown until now. We elucidate the role of EROS, showing it acts at the earliest stages of gp91phox maturation. It binds the immature 58 kDa gp91phox directly, preventing gp91phox degradation and allowing glycosylation via the oligosaccharyltransferase machinery and the incorporation of the heme prosthetic groups essential for catalysis. EROS also regulates the purine receptors P2X7 and P2X1 through direct interactions, and P2X7 is almost absent in EROS-deficient mouse and human primary cells. Accordingly, lack of murine EROS results in markedly abnormal P2X7 signalling, inflammasome activation, and T cell responses. The loss of both ROS and P2X7 signalling leads to resistance to influenza infection in mice. Our work identifies EROS as a highly selective chaperone for key proteins in innate and adaptive immunity and a rheostat for immunity to infection. It has profound implications for our understanding of immune physiology, ROS dysregulation, and possibly gene therapy.
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Affiliation(s)
- Lyra O Randzavola
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College LondonLondonUnited Kingdom
| | - Paige M Mortimer
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College LondonLondonUnited Kingdom
| | - Emma Garside
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College LondonLondonUnited Kingdom
| | - Elizabeth R Dufficy
- The Department of Medicine, University of Cambridge School of Clinical MedicineCambridgeUnited Kingdom
| | - Andrea Schejtman
- Molecular Immunology Unit, UCL Great Ormond Street Institute of Child HealthLondonUnited Kingdom
| | - Georgia Roumelioti
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer ResearchLondonUnited Kingdom
| | - Lu Yu
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer ResearchLondonUnited Kingdom
| | - Mercedes Pardo
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer ResearchLondonUnited Kingdom
| | - Kerstin Spirohn
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer InstituteBostonUnited States,Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States,Department of Cancer Biology, Dana-Farber Cancer InstituteBostonUnited States
| | | | | | | | - Esme Nichols
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College LondonLondonUnited Kingdom
| | - Mike Nahorski
- Cambridge Institute of Medical Research, University of CambridgeCambridgeUnited Kingdom
| | - Geoff Woods
- Cambridge Institute of Medical Research, University of CambridgeCambridgeUnited Kingdom
| | - James C Williamson
- The Department of Medicine, University of Cambridge School of Clinical MedicineCambridgeUnited Kingdom,Cambridge Institute of Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Shreehari Suresh
- The Department of Medicine, University of Cambridge School of Clinical MedicineCambridgeUnited Kingdom
| | - John M Sowerby
- The Department of Medicine, University of Cambridge School of Clinical MedicineCambridgeUnited Kingdom,Cambridge Institute of Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Misaki Matsumoto
- Department of Pharmacology, Kyoto Prefectural University of MedicineKyotoJapan
| | - Celio XC Santos
- School of Cardiovascular Medicine and Sciences, James Black Centre, King's College LondonLondonUnited Kingdom
| | - Cher Shen Kiar
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
| | - Subhankar Mukhopadhyay
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
| | - William M Rae
- The Department of Medicine, University of Cambridge School of Clinical MedicineCambridgeUnited Kingdom,Cambridge Institute of Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Gordon J Dougan
- The Department of Medicine, University of Cambridge School of Clinical MedicineCambridgeUnited Kingdom
| | - John Grainger
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer ResearchLondonUnited Kingdom,Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Paul J Lehner
- The Department of Medicine, University of Cambridge School of Clinical MedicineCambridgeUnited Kingdom,Cambridge Institute of Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer InstituteBostonUnited States,Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States,Department of Cancer Biology, Dana-Farber Cancer InstituteBostonUnited States
| | - Jyoti Choudhary
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer ResearchLondonUnited Kingdom
| | - Simon Clare
- Wellcome Trust Sanger InstituteHinxtonUnited Kingdom
| | | | - Giorgia Santilli
- Molecular Immunology Unit, UCL Great Ormond Street Institute of Child HealthLondonUnited Kingdom
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome CampusHinxtonUnited Kingdom
| | - Kenneth GC Smith
- The Department of Medicine, University of Cambridge School of Clinical MedicineCambridgeUnited Kingdom,Cambridge Institute of Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Francesca Magnani
- Department of Biology and Biotechnology, University of PaviaPaviaItaly
| | - David C Thomas
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College LondonLondonUnited Kingdom
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Tirincsi A, Sicking M, Hadzibeganovic D, Haßdenteufel S, Lang S. The Molecular Biodiversity of Protein Targeting and Protein Transport Related to the Endoplasmic Reticulum. Int J Mol Sci 2021; 23:143. [PMID: 35008565 PMCID: PMC8745461 DOI: 10.3390/ijms23010143] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
Looking at the variety of the thousands of different polypeptides that have been focused on in the research on the endoplasmic reticulum from the last five decades taught us one humble lesson: no one size fits all. Cells use an impressive array of components to enable the safe transport of protein cargo from the cytosolic ribosomes to the endoplasmic reticulum. Safety during the transit is warranted by the interplay of cytosolic chaperones, membrane receptors, and protein translocases that together form functional networks and serve as protein targeting and translocation routes. While two targeting routes to the endoplasmic reticulum, SRP (signal recognition particle) and GET (guided entry of tail-anchored proteins), prefer targeting determinants at the N- and C-terminus of the cargo polypeptide, respectively, the recently discovered SND (SRP-independent) route seems to preferentially cater for cargos with non-generic targeting signals that are less hydrophobic or more distant from the termini. With an emphasis on targeting routes and protein translocases, we will discuss those functional networks that drive efficient protein topogenesis and shed light on their redundant and dynamic nature in health and disease.
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Affiliation(s)
- Andrea Tirincsi
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Mark Sicking
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Drazena Hadzibeganovic
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Sarah Haßdenteufel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
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Ackermann B, Dünschede B, Pietzenuk B, Justesen BH, Krämer U, Hofmann E, Günther Pomorski T, Schünemann D. Chloroplast Ribosomes Interact With the Insertase Alb3 in the Thylakoid Membrane. FRONTIERS IN PLANT SCIENCE 2021; 12:781857. [PMID: 35003166 PMCID: PMC8733628 DOI: 10.3389/fpls.2021.781857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/27/2021] [Indexed: 06/14/2023]
Abstract
Members of the Oxa1/YidC/Alb3 protein family are involved in the insertion, folding, and assembly of membrane proteins in mitochondria, bacteria, and chloroplasts. The thylakoid membrane protein Alb3 mediates the chloroplast signal recognition particle (cpSRP)-dependent posttranslational insertion of nuclear-encoded light harvesting chlorophyll a/b-binding proteins and participates in the biogenesis of plastid-encoded subunits of the photosynthetic complexes. These subunits are cotranslationally inserted into the thylakoid membrane, yet very little is known about the molecular mechanisms underlying docking of the ribosome-nascent chain complexes to the chloroplast SecY/Alb3 insertion machinery. Here, we show that nanodisc-embedded Alb3 interacts with ribosomes, while the homolog Alb4, also located in the thylakoid membrane, shows no ribosome binding. Alb3 contacts the ribosome with its C-terminal region and at least one additional binding site within its hydrophobic core region. Within the C-terminal region, two conserved motifs (motifs III and IV) are cooperatively required to enable the ribosome contact. Furthermore, our data suggest that the negatively charged C-terminus of the ribosomal subunit uL4c is involved in Alb3 binding. Phylogenetic analyses of uL4 demonstrate that this region newly evolved in the green lineage during the transition from aquatic to terrestrial life.
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Affiliation(s)
- Bernd Ackermann
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Beatrix Dünschede
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Björn Pietzenuk
- Department of Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Bo Højen Justesen
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Ute Krämer
- Department of Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
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41
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Zimmermann R, Lang S, Lerner M, Förster F, Nguyen D, Helms V, Schrul B. Quantitative Proteomics and Differential Protein Abundance Analysis after the Depletion of PEX3 from Human Cells Identifies Additional Aspects of Protein Targeting to the ER. Int J Mol Sci 2021; 22:ijms222313028. [PMID: 34884833 PMCID: PMC8658024 DOI: 10.3390/ijms222313028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/19/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022] Open
Abstract
Protein import into the endoplasmic reticulum (ER) is the first step in the biogenesis of around 10,000 different soluble and membrane proteins in humans. It involves the co- or post-translational targeting of precursor polypeptides to the ER, and their subsequent membrane insertion or translocation. So far, three pathways for the ER targeting of precursor polypeptides and four pathways for the ER targeting of mRNAs have been described. Typically, these pathways deliver their substrates to the Sec61 polypeptide-conducting channel in the ER membrane. Next, the precursor polypeptides are inserted into the ER membrane or translocated into the ER lumen, which may involve auxiliary translocation components, such as the TRAP and Sec62/Sec63 complexes, or auxiliary membrane protein insertases, such as EMC and the TMCO1 complex. Recently, the PEX19/PEX3-dependent pathway, which has a well-known function in targeting and inserting various peroxisomal membrane proteins into pre-existent peroxisomal membranes, was also found to act in the targeting and, putatively, insertion of monotopic hairpin proteins into the ER. These either remain in the ER as resident ER membrane proteins, or are pinched off from the ER as components of new lipid droplets. Therefore, the question arose as to whether this pathway may play a more general role in ER protein targeting, i.e., whether it represents a fourth pathway for the ER targeting of precursor polypeptides. Thus, we addressed the client spectrum of the PEX19/PEX3-dependent pathway in both PEX3-depleted HeLa cells and PEX3-deficient Zellweger patient fibroblasts by an established approach which involved the label-free quantitative mass spectrometry of the total proteome of depleted or deficient cells, as well as differential protein abundance analysis. The negatively affected proteins included twelve peroxisomal proteins and two hairpin proteins of the ER, thus confirming two previously identified classes of putative PEX19/PEX3 clients in human cells. Interestingly, fourteen collagen-related proteins with signal peptides or N-terminal transmembrane helices belonging to the secretory pathway were also negatively affected by PEX3 deficiency, which may suggest compromised collagen biogenesis as a hitherto-unknown contributor to organ failures in the respective Zellweger patients.
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Affiliation(s)
- Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.L.); (M.L.)
- Correspondence: (R.Z.); (B.S.)
| | - Sven Lang
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.L.); (M.L.)
| | - Monika Lerner
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.L.); (M.L.)
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands;
| | - Duy Nguyen
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66041 Saarbrücken, Germany; (D.N.); (V.H.)
| | - Volkhard Helms
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66041 Saarbrücken, Germany; (D.N.); (V.H.)
| | - Bianca Schrul
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.L.); (M.L.)
- Correspondence: (R.Z.); (B.S.)
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42
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Whitley P, Grau B, Gumbart JC, Martínez-Gil L, Mingarro I. Folding and Insertion of Transmembrane Helices at the ER. Int J Mol Sci 2021; 22:ijms222312778. [PMID: 34884581 PMCID: PMC8657811 DOI: 10.3390/ijms222312778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 01/16/2023] Open
Abstract
In eukaryotic cells, the endoplasmic reticulum (ER) is the entry point for newly synthesized proteins that are subsequently distributed to organelles of the endomembrane system. Some of these proteins are completely translocated into the lumen of the ER while others integrate stretches of amino acids into the greasy 30 Å wide interior of the ER membrane bilayer. It is generally accepted that to exist in this non-aqueous environment the majority of membrane integrated amino acids are primarily non-polar/hydrophobic and adopt an α-helical conformation. These stretches are typically around 20 amino acids long and are known as transmembrane (TM) helices. In this review, we will consider how transmembrane helices achieve membrane integration. We will address questions such as: Where do the stretches of amino acids fold into a helical conformation? What is/are the route/routes that these stretches take from synthesis at the ribosome to integration through the ER translocon? How do these stretches ‘know’ to integrate and in which orientation? How do marginally hydrophobic stretches of amino acids integrate and survive as transmembrane helices?
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Affiliation(s)
- Paul Whitley
- Department of Biology and Biochemistry, Centre for Regenerative Medicine, University of Bath, Bath BA2 7AY, UK;
| | - Brayan Grau
- Department of Biochemistry and Molecular Biology, Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain; (B.G.); (L.M.-G.)
| | - James C. Gumbart
- School of Physics, School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Luis Martínez-Gil
- Department of Biochemistry and Molecular Biology, Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain; (B.G.); (L.M.-G.)
| | - Ismael Mingarro
- Department of Biochemistry and Molecular Biology, Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain; (B.G.); (L.M.-G.)
- Correspondence: ; Tel.: +34-963543796
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Take Me Home, Protein Roads: Structural Insights into Signal Peptide Interactions during ER Translocation. Int J Mol Sci 2021; 22:ijms222111871. [PMID: 34769302 PMCID: PMC8584900 DOI: 10.3390/ijms222111871] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/14/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
Cleavable endoplasmic reticulum (ER) signal peptides (SPs) and other non-cleavable signal sequences target roughly a quarter of the human proteome to the ER. These short peptides, mostly located at the N-termini of proteins, are highly diverse. For most proteins targeted to the ER, it is the interactions between the signal sequences and the various ER targeting and translocation machineries such as the signal recognition particle (SRP), the protein-conducting channel Sec61, and the signal peptidase complex (SPC) that determine the proteins’ target location and provide translocation fidelity. In this review, we follow the signal peptide into the ER and discuss the recent insights that structural biology has provided on the governing principles of those interactions.
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Sicking M, Jung M, Lang S. Lights, Camera, Interaction: Studying Protein-Protein Interactions of the ER Protein Translocase in Living Cells. Int J Mol Sci 2021; 22:10358. [PMID: 34638699 PMCID: PMC8508666 DOI: 10.3390/ijms221910358] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 12/12/2022] Open
Abstract
Various landmark studies have revealed structures and functions of the Sec61/SecY complex in all domains of live demonstrating the conserved nature of this ancestral protein translocase. While the bacterial homolog of the Sec61 complex resides in the plasma membrane, the eukaryotic counterpart manages the transfer of precursor proteins into or across the membrane of the endoplasmic reticulum (ER). Sec61 complexes are accompanied by a set of dynamically recruited auxiliary proteins assisting the transport of certain precursor polypeptides. TRAP and Sec62/Sec63 are two auxiliary protein complexes in mammalian cells that have been characterized by structural and biochemical methods. Using these ER membrane protein complexes for our proof-of-concept study, we aimed to detect interactions of membrane proteins in living mammalian cells under physiological conditions. Bimolecular luminescence complementation and competition was used to demonstrate multiple protein-protein interactions of different topological layouts. In addition to the interaction of the soluble catalytic and regulatory subunits of the cytosolic protein kinase A, we detected interactions of ER membrane proteins that either belong to the same multimeric protein complex (intra-complex interactions: Sec61α-Sec61β, TRAPα-TRAPβ) or protein complexes in juxtaposition (inter-complex interactions: Sec61α-TRAPα, Sec61α-Sec63, and Sec61β-Sec63). In the process, we established further control elements like synthetic peptide complementation for expression profiling of fusion constructs and protease-mediated reporter degradation demonstrating the cytosolic localization of a reporter complementation. Ease of use and flexibility of the approach presented here will spur further research regarding the dynamics of protein-protein interactions in response to changing cellular conditions in living cells.
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Affiliation(s)
| | | | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (M.S.); (M.J.)
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45
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Pauwels E, Rutz C, Provinciael B, Stroobants J, Schols D, Hartmann E, Krause E, Stephanowitz H, Schülein R, Vermeire K. A Proteomic Study on the Membrane Protein Fraction of T Cells Confirms High Substrate Selectivity for the ER Translocation Inhibitor Cyclotriazadisulfonamide. Mol Cell Proteomics 2021; 20:100144. [PMID: 34481949 PMCID: PMC8477212 DOI: 10.1016/j.mcpro.2021.100144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/09/2021] [Accepted: 08/30/2021] [Indexed: 11/15/2022] Open
Abstract
Cyclotriazadisulfonamide (CADA) inhibits the cotranslational translocation of type I integral membrane protein human CD4 (huCD4) across the endoplasmic reticulum in a signal peptide (SP)–dependent way. Previously, sortilin was identified as a secondary substrate for CADA but showed reduced CADA sensitivity as compared with huCD4. Here, we performed a quantitative proteomic study on the crude membrane fraction of human T-cells to analyze how many proteins are sensitive to CADA. To screen for these proteins, we employed stable isotope labeling by amino acids in cell culture technique in combination with quantitative MS on CADA-treated human T-lymphoid SUP-T1 cells expressing high levels of huCD4. In line with our previous reports, our current proteomic analysis (data available via ProteomeXchange with identifier PXD027712) demonstrated that only a very small subset of proteins is depleted by CADA. Our data also confirmed that cellular expression of both huCD4 and sortilin are affected by CADA treatment of SUP-T1 cells. Furthermore, three additional targets for CADA are identified, namely, endoplasmic reticulum lectin 1 (ERLEC1), inactive tyrosine-protein kinase 7 (PTK7), and DnaJ homolog subfamily C member 3 (DNAJC3). Western blot and flow cytometry analysis of ERLEC1, PTK7, and DNAJC3 protein expression validated susceptibility of these substrates to CADA, although with varying degrees of sensitivity. Additional cell-free in vitro translation/translocation data demonstrated that the new substrates for CADA carry cleavable SPs that are targets for the cotranslational translocation inhibition exerted by CADA. Thus, our quantitative proteomic analysis demonstrates that ERLEC1, PTK7, and DNAJC3 are validated additional substrates of CADA; however, huCD4 remains the most sensitive integral membrane protein for the endoplasmic reticulum translocation inhibitor CADA. Furthermore, to our knowledge, CADA is the first compound that specifically interferes with only a very small subset of SPs and does not affect signal anchor sequences. About 3007 proteins quantified in SILAC/MS study on CD4+ T-cells treated with CADA. Three new targets for CADA were identified: ERLEC1, PTK7, and DNAJC3. All CADA substrates carry cleavable signal peptides for translocation into ER. huCD4 remains the most sensitive substrate for the ER translocation inhibitor CADA.
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Affiliation(s)
- Eva Pauwels
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
| | - Claudia Rutz
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Becky Provinciael
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
| | - Joren Stroobants
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
| | - Enno Hartmann
- Centre for Structural and Cell Biology in Medicine, Institute of Biology, University of Lübeck, Lübeck, Germany
| | - Eberhard Krause
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Heike Stephanowitz
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Ralf Schülein
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Kurt Vermeire
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium.
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Liaci AM, Steigenberger B, Telles de Souza PC, Tamara S, Gröllers-Mulderij M, Ogrissek P, Marrink SJ, Scheltema RA, Förster F. Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. Mol Cell 2021; 81:3934-3948.e11. [PMID: 34388369 DOI: 10.1016/j.molcel.2021.07.031] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/02/2021] [Accepted: 07/26/2021] [Indexed: 12/18/2022]
Abstract
The signal peptidase complex (SPC) is an essential membrane complex in the endoplasmic reticulum (ER), where it removes signal peptides (SPs) from a large variety of secretory pre-proteins with exquisite specificity. Although the determinants of this process have been established empirically, the molecular details of SP recognition and removal remain elusive. Here, we show that the human SPC exists in two functional paralogs with distinct proteolytic subunits. We determined the atomic structures of both paralogs using electron cryo-microscopy and structural proteomics. The active site is formed by a catalytic triad and abuts the ER membrane, where a transmembrane window collectively formed by all subunits locally thins the bilayer. Molecular dynamics simulations indicate that this unique architecture generates specificity for SPs based on the length of their hydrophobic segments.
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Affiliation(s)
- A Manuel Liaci
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands
| | - Barbara Steigenberger
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Paulo Cesar Telles de Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands; Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS and University of Lyon, Lyon, France
| | - Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Mariska Gröllers-Mulderij
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands
| | - Patrick Ogrissek
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands; Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Material, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, the Netherlands.
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Dual topology of co-chaperones at the membrane of the endoplasmic reticulum. Cell Death Discov 2021; 7:203. [PMID: 34354047 PMCID: PMC8342575 DOI: 10.1038/s41420-021-00594-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/08/2021] [Accepted: 07/22/2021] [Indexed: 11/08/2022] Open
Abstract
Dual topologies of proteins at the ER membrane are known for a variety of proteins allowing the same protein to exert different functions according to the topology adopted. A dual topology of the co-chaperone ERdj4, which resides in the endoplasmic reticulum (ER), was proposed recently, a thesis that we found to align all published data and existing controversies into one whole picture. The aim of this review is to reassess all primary data available in the literature on ER-resident Hsp40 co-chaperones with respect to their topology. After careful and critical analyses of all experimental data published so far, we identified, next to ERdj4, two other co-chaperones, ERdj3 and ERdj6, that also display features of a dual topology at the ER membrane. We assume that during cellular stress subpools of some ER-resident J protein can alter their topology so that these proteins can exert different functions in order to adapt to cellular stress.
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48
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Huang Y, Xu X, Arvan P, Liu M. Deficient endoplasmic reticulum translocon-associated protein complex limits the biosynthesis of proinsulin and insulin. FASEB J 2021; 35:e21515. [PMID: 33811688 DOI: 10.1096/fj.202002774r] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/14/2021] [Accepted: 02/24/2021] [Indexed: 01/22/2023]
Abstract
The conserved endoplasmic reticulum (ER) membrane protein TRAPα (translocon-associated protein, also known as signal sequence receptor 1, SSR1) has been reported to play a critical but unclear role in insulin biosynthesis. TRAPα/SSR1 is one component of a four-protein complex including TRAPβ/SSR2, TRAPγ/SSR3, and TRAPδ/SSR4. The TRAP complex topologically has a small exposure on the cytosolic side of the ER via its TRAPγ/SSR3 subunit, whereas TRAPβ/SSR2 and TRAPδ/SSR4 function along with TRAPα/SSR1 largely on the luminal side of the ER membrane. Here, we have examined pancreatic β-cells with deficient expression of either TRAPβ/SSR2 or TRAPδ/SSR4, which does not perturb mRNA expression levels of other TRAP subunits, or insulin mRNA. However, deficient protein expression of TRAPβ/SSR2 and, to a lesser degree, TRAPδ/SSR4, diminishes the protein levels of other TRAP subunits, concomitant with deficient steady-state levels of proinsulin and insulin. Deficient TRAPβ/SSR2 or TRAPδ/SSR4 is not associated with any apparent defect of exocytotic mechanism but rather by a decreased abundance of the proinsulin and insulin that accompanies glucose-stimulated secretion. Amino acid pulse labeling directly establishes that much of the steady-state deficiency of intracellular proinsulin can be accounted for by diminished proinsulin biosynthesis, observed in a pulse-labeling as short as 5 minutes. The proinsulin and insulin levels in TRAPβ/SSR2 or TRAPδ/SSR4 null mutant β-cells are notably recovered upon re-expression of the missing TRAP subunit, accompanying a rebound of proinsulin biosynthesis. Remarkably, overexpression of TRAPα/SSR1 can also suppress defects in β-cells with diminished expression of TRAPβ/SSR2, strongly suggesting that TRAPβ/SSR2 is needed to support TRAPα/SSR1 function.
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Affiliation(s)
- Yumeng Huang
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China.,Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Xiaoxi Xu
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China.,Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Peter Arvan
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Ming Liu
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China.,Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical Center, Ann Arbor, MI, USA
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49
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O’Keefe S, Zong G, Duah KB, Andrews LE, Shi WQ, High S. An alternative pathway for membrane protein biogenesis at the endoplasmic reticulum. Commun Biol 2021; 4:828. [PMID: 34211117 PMCID: PMC8249459 DOI: 10.1038/s42003-021-02363-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 06/17/2021] [Indexed: 02/06/2023] Open
Abstract
The heterotrimeric Sec61 complex is a major site for the biogenesis of transmembrane proteins (TMPs), accepting nascent TMP precursors that are targeted to the endoplasmic reticulum (ER) by the signal recognition particle (SRP). Unlike most single-spanning membrane proteins, the integration of type III TMPs is completely resistant to small molecule inhibitors of the Sec61 translocon. Using siRNA-mediated depletion of specific ER components, in combination with the potent Sec61 inhibitor ipomoeassin F (Ipom-F), we show that type III TMPs utilise a distinct pathway for membrane integration at the ER. Hence, following SRP-mediated delivery to the ER, type III TMPs can uniquely access the membrane insertase activity of the ER membrane complex (EMC) via a mechanism that is facilitated by the Sec61 translocon. This alternative EMC-mediated insertion pathway allows type III TMPs to bypass the Ipom-F-mediated blockade of membrane integration that is seen with obligate Sec61 clients.
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Affiliation(s)
- Sarah O’Keefe
- grid.5379.80000000121662407School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Guanghui Zong
- grid.164295.d0000 0001 0941 7177Department of Chemistry and Biochemistry, University of Maryland, College Park, MD USA
| | - Kwabena B. Duah
- grid.252754.30000 0001 2111 9017Department of Chemistry, Ball State University, Muncie, IN USA
| | - Lauren E. Andrews
- grid.252754.30000 0001 2111 9017Department of Chemistry, Ball State University, Muncie, IN USA
| | - Wei Q. Shi
- grid.252754.30000 0001 2111 9017Department of Chemistry, Ball State University, Muncie, IN USA
| | - Stephen High
- grid.5379.80000000121662407School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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50
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Bhadra P, Schorr S, Lerner M, Nguyen D, Dudek J, Förster F, Helms V, Lang S, Zimmermann R. Quantitative Proteomics and Differential Protein Abundance Analysis after Depletion of Putative mRNA Receptors in the ER Membrane of Human Cells Identifies Novel Aspects of mRNA Targeting to the ER. Molecules 2021; 26:3591. [PMID: 34208277 PMCID: PMC8230838 DOI: 10.3390/molecules26123591] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 11/28/2022] Open
Abstract
In human cells, one-third of all polypeptides enter the secretory pathway at the endoplasmic reticulum (ER). The specificity and efficiency of this process are guaranteed by targeting of mRNAs and/or polypeptides to the ER membrane. Cytosolic SRP and its receptor in the ER membrane facilitate the cotranslational targeting of most ribosome-nascent precursor polypeptide chain (RNC) complexes together with the respective mRNAs to the Sec61 complex in the ER membrane. Alternatively, fully synthesized precursor polypeptides are targeted to the ER membrane post-translationally by either the TRC, SND, or PEX19/3 pathway. Furthermore, there is targeting of mRNAs to the ER membrane, which does not involve SRP but involves mRNA- or RNC-binding proteins on the ER surface, such as RRBP1 or KTN1. Traditionally, the targeting reactions were studied in cell-free or cellular assays, which focus on a single precursor polypeptide and allow the conclusion of whether a certain precursor can use a certain pathway. Recently, cellular approaches such as proximity-based ribosome profiling or quantitative proteomics were employed to address the question of which precursors use certain pathways under physiological conditions. Here, we combined siRNA-mediated depletion of putative mRNA receptors in HeLa cells with label-free quantitative proteomics and differential protein abundance analysis to characterize RRBP1- or KTN1-involving precursors and to identify possible genetic interactions between the various targeting pathways. Furthermore, we discuss the possible implications on the so-called TIGER domains and critically discuss the pros and cons of this experimental approach.
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Affiliation(s)
- Pratiti Bhadra
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66041 Saarbrücken, Germany; (P.B.); (D.N.); (V.H.)
| | - Stefan Schorr
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.S.); (M.L.); (J.D.); (S.L.)
| | - Monika Lerner
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.S.); (M.L.); (J.D.); (S.L.)
| | - Duy Nguyen
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66041 Saarbrücken, Germany; (P.B.); (D.N.); (V.H.)
| | - Johanna Dudek
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.S.); (M.L.); (J.D.); (S.L.)
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands;
| | - Volkhard Helms
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66041 Saarbrücken, Germany; (P.B.); (D.N.); (V.H.)
| | - Sven Lang
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.S.); (M.L.); (J.D.); (S.L.)
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.S.); (M.L.); (J.D.); (S.L.)
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