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Mendes LFS, Gimenes CO, da Silva MDO, Rout SK, Riek R, Costa‐Filho AJ. The potential role of liquid-liquid phase separation in the cellular fate of the compartments for unconventional protein secretion. Protein Sci 2024; 33:e5085. [PMID: 38923199 PMCID: PMC11201811 DOI: 10.1002/pro.5085] [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: 02/27/2024] [Revised: 04/30/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
Eukaryotic cells have developed intricate mechanisms for biomolecule transport, particularly in stressful conditions. This interdisciplinary study delves into unconventional protein secretion (UPS) pathways activated during starvation, facilitating the export of proteins bypassing most of the components of the classical secretory machinery. Specifically, we focus on the underexplored mechanisms of the GRASP's role in UPS, particularly in biogenesis and cargo recruitment for the vesicular-like compartment for UPS. Our results show that liquid-liquid phase separation (LLPS) plays a key role in the coacervation of Grh1, the GRASP yeast homologue, under starvation-like conditions. This association seems a precursor to the Compartment for Unconventional Protein Secretion (CUPS) biogenesis. Grh1's self-association is regulated by electrostatic, hydrophobic, and hydrogen-bonding interactions. Importantly, our study demonstrates that phase-separated states of Grh1 can recruit UPS cargo under starvation-like situations. Additionally, we explore how the coacervate liquid-to-solid transition could impact cells' ability to return to normal post-stress states. Our findings offer insights into intracellular protein dynamics and cell adaptive responses to stress.
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Affiliation(s)
- Luis Felipe S. Mendes
- Group of Biophysics and Structural Biology "Sergio Mascarenhas". São Carlos Institute of PhysicsUniversity of São PauloSão CarlosSão PauloBrazil
- Department of Physics, Ribeirão Preto School of Philosophy, Science, and LiteratureUniversity of São PauloRibeirão PretoSão PauloBrazil
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH HönggerbergZürichSwitzerland
| | - Carolina O. Gimenes
- Department of Physics, Ribeirão Preto School of Philosophy, Science, and LiteratureUniversity of São PauloRibeirão PretoSão PauloBrazil
| | - Marília D. O. da Silva
- Group of Biophysics and Structural Biology "Sergio Mascarenhas". São Carlos Institute of PhysicsUniversity of São PauloSão CarlosSão PauloBrazil
| | - Saroj K. Rout
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH HönggerbergZürichSwitzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH HönggerbergZürichSwitzerland
| | - Antonio J. Costa‐Filho
- Department of Physics, Ribeirão Preto School of Philosophy, Science, and LiteratureUniversity of São PauloRibeirão PretoSão PauloBrazil
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2
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DeKryger W, Chroneos ZC. Emerging concepts of myosin 18A isoform mechanobiology in organismal and immune system physiology, development, and function. FASEB J 2024; 38:e23649. [PMID: 38776246 DOI: 10.1096/fj.202400350r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/24/2024]
Abstract
Alternative and combinatorial splicing of myosin 18A (MYO18A) gene transcripts results in expression of MYO18A protein isoforms and isoform variants with different membrane and subcellular localizations, and functional properties. MYO18A proteins are members of the myosin superfamily consisting of a myosin-like motor domain, an IQ motif, and a coiled-coil domain. MYO18A isoforms, however, lack the ability to hydrolyze ATP and do not perform ATP-dependent motor activity. MYO18A isoforms are distinguished by different amino- and carboxy-terminal extensions and domains. The domain organization and functions of MYO18Aα, MYO18Aβ, and MYO18Aγ have been studied experimentally. MYO18Aα and MYO18Aβ have a common carboxy-terminal extension but differ by the presence or absence of an amino-terminal KE repeat and PDZ domain, respectively. The amino- and carboxy-terminal extensions of MYO18Aγ contain unique proline and serine-rich domains. Computationally predicted MYO18Aε and MYO18Aδ isoforms contain the carboxy-terminal serine-rich extension but differ by the presence or absence of the amino-terminal KE/PDZ extension. Additional isoform variants within each category arise by alternative utilization or inclusion/exclusion of small exons. MYO18Aα variants are expressed in somatic cells and mature immune cells, whereas MYO18Aβ variants occur mainly in myeloid and natural killer cells. MYO18Aγ expression is selective to cardiac and skeletal muscle. In the present review perspective, we discuss current and emerging concepts of the functional specialization of MYO18A proteins in membrane and cytoskeletal dynamics, cellular communication and signaling, endocytic and exocytic organelle movement, viral infection, and as the SP-R210 receptor for surfactant protein A.
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Affiliation(s)
- William DeKryger
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Zissis C Chroneos
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, Pulmonary Immunology and Physiology Laboratory, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
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3
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Denus M, Fargues W, Filaquier A, Néel É, Marin P, Parmentier ML, Villeneuve J. [Unconventional protein secretion - new perspectives in protein trafficking]. Med Sci (Paris) 2024; 40:267-274. [PMID: 38520102 DOI: 10.1051/medsci/2024013] [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] [Indexed: 03/25/2024] Open
Abstract
The characterization of the structural and functional organization of eukaryotic cells has revealed the membrane compartments and machinery required for vesicular protein transport. Most proteins essential for intercellular communication contain an N-terminal signal sequence enabling them to be incorporated into the biosynthetic or conventional secretory pathway, in which proteins are sequentially transported through the endoplasmic reticulum (ER) and the Golgi apparatus. However, major research studies have shown the existence of alternative secretory routes that are independent of the ER-Golgi and designated as unconventional secretory pathways. These pathways involve a large number of players that may divert specific compartments from their primary function in favor of secretory roles. The comprehensive description of these processes is therefore of utmost importance to unveil how proteins secreted through these alternative pathways control cell homeostasis or contribute to disease development.
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Affiliation(s)
- Morgane Denus
- Institut de génomique fonctionnelle,Université de Montpellier, CNRS UMR 5 203. Inserm U1191, Montpellier, France
| | - William Fargues
- Institut de génomique fonctionnelle,Université de Montpellier, CNRS UMR 5 203. Inserm U1191, Montpellier, France
| | - Aurore Filaquier
- Institut de génomique fonctionnelle,Université de Montpellier, CNRS UMR 5 203. Inserm U1191, Montpellier, France
| | - Éloïse Néel
- Institut de génomique fonctionnelle,Université de Montpellier, CNRS UMR 5 203. Inserm U1191, Montpellier, France
| | - Philippe Marin
- Institut de génomique fonctionnelle,Université de Montpellier, CNRS UMR 5 203. Inserm U1191, Montpellier, France
| | - Marie-Laure Parmentier
- Institut de génomique fonctionnelle,Université de Montpellier, CNRS UMR 5 203. Inserm U1191, Montpellier, France
| | - Julien Villeneuve
- Institut de génomique fonctionnelle,Université de Montpellier, CNRS UMR 5 203. Inserm U1191, Montpellier, France
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4
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Li X, Liu B, Wen Y, Wang J, Guo YR, Shi A, Lin L. Coordination of RAB-8 and RAB-11 during unconventional protein secretion. J Cell Biol 2024; 223:e202306107. [PMID: 38019180 PMCID: PMC10686230 DOI: 10.1083/jcb.202306107] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/17/2023] [Accepted: 11/16/2023] [Indexed: 11/30/2023] Open
Abstract
Multiple physiology-pertinent transmembrane proteins reach the cell surface via the Golgi-bypassing unconventional protein secretion (UcPS) pathway. By employing C. elegans-polarized intestine epithelia, we recently have revealed that the small GTPase RAB-8/Rab8 serves as an important player in the process. Nonetheless, its function and the relevant UcPS itinerary remain poorly understood. Here, we show that deregulated RAB-8 activity resulted in impaired apical UcPS, which increased sensitivity to infection and environmental stress. We also identified the SNARE VTI-1/Vti1a/b as a new RAB-8-interacting factor involved in the apical UcPS. Besides, RAB-11/Rab11 was capable of recruiting RABI-8/Rabin8 to reduce the guanine nucleotide exchange activity of SMGL-1/GEF toward RAB-8, indicating the necessity of a finely tuned RAB-8/RAB-11 network. Populations of RAB-8- and RAB-11-positive endosomal structures containing the apical UcPS cargo moved toward the apical side. In the absence of RAB-11 or its effectors, the cargo was retained in RAB-8- and RAB-11-positive endosomes, respectively, suggesting that these endosomes are utilized as intermediate carriers for the UcPS.
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Affiliation(s)
- Xinxin Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bowen Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yue Wen
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiabin Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yusong R. Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Anbing Shi
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Long Lin
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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5
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Tiberti N, Manfredi M, Piubelli C, Buonfrate D. Progresses and challenges in Strongyloides spp. proteomics. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220447. [PMID: 38008115 PMCID: PMC10676815 DOI: 10.1098/rstb.2022.0447] [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: 03/31/2023] [Accepted: 08/09/2023] [Indexed: 11/28/2023] Open
Abstract
The availability of high-quality data of helminth genomes provided over the past two decades has supported and accelerated large-scale 'omics studies and, consequently, the achievement of a more in-depth molecular characterization of a number of pathogens. This has also involved Strongyloides spp. and since their genome was made available transcriptomics has been rather frequently applied to investigate gene expression regulation across their life cycle. Strongyloides proteomics characterization has instead been somehow neglected, with only a few reports performing high-throughput or targeted analyses associated with protein identification by tandem mass spectrometry. Such investigations are however necessary in order to discern important aspects associated with human strongyloidiasis, including understanding parasite biology and the mechanisms of host-parasite interaction, but also to identify novel diagnostic and therapeutic targets. In this review article, we will give an overview of the published proteomics studies investigating strongyloidiasis at different levels, spanning from the characterization of the somatic proteome and excretory/secretory products of different parasite stages to the investigation of potentially immunogenic proteins. Moreover, in the effort to try to start filling the current gap in host-proteomics, we will also present the first serum proteomics analysis in patients suffering from human strongyloidiasis. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.
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Affiliation(s)
- Natalia Tiberti
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, 37024 Negrar di Valpolicella (Verona), Italy
| | - Marcello Manfredi
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
| | - Chiara Piubelli
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, 37024 Negrar di Valpolicella (Verona), Italy
| | - Dora Buonfrate
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, 37024 Negrar di Valpolicella (Verona), Italy
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6
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Huber RJ, Kim WD, Wilson-Smillie MLDM. Mechanisms regulating the intracellular trafficking and release of CLN5 and CTSD. Traffic 2024; 25:e12925. [PMID: 38272448 DOI: 10.1111/tra.12925] [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: 08/01/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/27/2024]
Abstract
Ceroid lipofuscinosis neuronal 5 (CLN5) and cathepsin D (CTSD) are soluble lysosomal enzymes that also localize extracellularly. In humans, homozygous mutations in CLN5 and CTSD cause CLN5 disease and CLN10 disease, respectively, which are two subtypes of neuronal ceroid lipofuscinosis (commonly known as Batten disease). The mechanisms regulating the intracellular trafficking of CLN5 and CTSD and their release from cells are not well understood. Here, we used the social amoeba Dictyostelium discoideum as a model system to examine the pathways and cellular components that regulate the intracellular trafficking and release of the D. discoideum homologs of human CLN5 (Cln5) and CTSD (CtsD). We show that both Cln5 and CtsD contain signal peptides for secretion that facilitate their release from cells. Like Cln5, extracellular CtsD is glycosylated. In addition, Cln5 release is regulated by the amount of extracellular CtsD. Autophagy induction promotes the release of Cln5, and to a lesser extent CtsD. Release of Cln5 requires the autophagy proteins Atg1, Atg5, and Atg9, as well as autophagosomal-lysosomal fusion. Atg1 and Atg5 are required for the release of CtsD. Together, these data support a model where Cln5 and CtsD are actively released from cells via their signal peptides for secretion and pathways linked to autophagy. The release of Cln5 and CtsD from cells also requires microfilaments and the D. discoideum homologs of human AP-3 complex mu subunit, the lysosomal-trafficking regulator LYST, mucopilin-1, and the Wiskott-Aldrich syndrome-associated protein WASH, which all regulate lysosomal exocytosis in this model organism. These findings suggest that lysosomal exocytosis also facilitates the release of Cln5 and CtsD from cells. In addition, we report the roles of ABC transporters, microtubules, osmotic stress, and the putative D. discoideum homologs of human sortilin and cation-independent mannose-6-phosphate receptor in regulating the intracellular/extracellular distribution of Cln5 and CtsD. In total, this study identifies the cellular mechanisms regulating the release of Cln5 and CtsD from D. discoideum cells and provides insight into how altered trafficking of CLN5 and CTSD causes disease in humans.
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Affiliation(s)
- Robert J Huber
- Department of Biology, Trent University, Peterborough, Ontario, Canada
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - William D Kim
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
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7
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Wu W, Krijgsveld J. Secretome Analysis: Reading Cellular Sign Language to Understand Intercellular Communication. Mol Cell Proteomics 2024; 23:100692. [PMID: 38081362 PMCID: PMC10793180 DOI: 10.1016/j.mcpro.2023.100692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/06/2024] Open
Abstract
A significant portion of mammalian proteomes is secreted to the extracellular space to fulfill crucial roles in cell-to-cell communication. To best recapitulate the intricate and multi-faceted crosstalk between cells in a live organism, there is an ever-increasing need for methods to study protein secretion in model systems that include multiple cell types. In addition, posttranslational modifications further expand the complexity and versatility of cellular communication. This review aims to summarize recent strategies and model systems that employ cellular coculture, chemical biology tools, protein enrichment, and proteomic methods to characterize the composition and function of cellular secretomes. This is all geared towards gaining better understanding of organismal biology in vivo mediated by secretory signaling.
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Affiliation(s)
- Wei Wu
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore; Department of Pharmacy, National University of Singapore, Singapore, Singapore.
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany; Medical Faculty, Heidelberg University, Heidelberg, Germany.
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8
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Parvanian S, Coelho-Rato LS, Patteson AE, Eriksson JE. Vimentin takes a hike - Emerging roles of extracellular vimentin in cancer and wound healing. Curr Opin Cell Biol 2023; 85:102246. [PMID: 37783033 PMCID: PMC11214764 DOI: 10.1016/j.ceb.2023.102246] [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: 07/10/2023] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 10/04/2023]
Abstract
Vimentin is a cytoskeletal protein important for many cellular processes, including proliferation, migration, invasion, stress resistance, signaling, and many more. The vimentin-deficient mouse has revealed many of these functions as it has numerous severe phenotypes, many of which are found only following a suitable challenge or stress. While these functions are usually related to vimentin as a major intracellular protein, vimentin is also emerging as an extracellular protein, exposed at the cell surface in an oligomeric form or secreted to the extracellular environment in soluble and vesicle-bound forms. Thus, this review explores the roles of the extracellular pool of vimentin (eVIM), identified in both normal and pathological states. It focuses specifically on the recent advances regarding the role of eVIM in wound healing and cancer. Finally, it discusses new technologies and future perspectives for the clinical application of eVIM.
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Affiliation(s)
- Sepideh Parvanian
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland; Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland; Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Leila S Coelho-Rato
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland; Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland
| | - Alison E Patteson
- Physics Department and BioInspired Institute, Syracuse University, Syracuse, NY, 13244, USA
| | - John E Eriksson
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland; Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland; Euro-Bioimaging ERIC, 20520 Turku, Finland.
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9
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Parvanian S, Coelho-Rato LS, Eriksson JE, Patteson AE. The molecular biophysics of extracellular vimentin and its role in pathogen-host interactions. Curr Opin Cell Biol 2023; 85:102233. [PMID: 37677998 PMCID: PMC10841047 DOI: 10.1016/j.ceb.2023.102233] [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: 05/31/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 09/09/2023]
Abstract
Vimentin, an intermediate filament protein typically located in the cytoplasm of mesenchymal cells, can also be secreted as an extracellular protein. The organization of extracellular vimentin strongly determines its functions in physiological and pathological conditions, making it a promising target for future therapeutic interventions. The extracellular form of vimentin has been found to play a role in the interaction between host cells and pathogens. In this review, we first discuss the molecular biophysics of extracellular vimentin, including its structure, secretion, and adhesion properties. We then provide a general overview of the role of extracellular vimentin in mediating pathogen-host interactions, with a focus on its interactions with viruses and bacteria. We also discuss the implications of these findings for the development of new therapeutic strategies for combating infectious diseases.
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Affiliation(s)
- Sepideh Parvanian
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland; Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520, Turku, Finland; Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Leila S Coelho-Rato
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland; Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520, Turku, Finland
| | - John E Eriksson
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland; Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520, Turku, Finland; Euro-Bioimaging ERIC, 20520, Turku, Finland
| | - Alison E Patteson
- Physics Department and BioInspired Institute, Syracuse University, Syracuse, NY, 13244, USA.
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10
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Huber RJ, Gray J, Kim WD. Loss of mfsd8 alters the secretome during Dictyostelium aggregation. Eur J Cell Biol 2023; 102:151361. [PMID: 37742391 DOI: 10.1016/j.ejcb.2023.151361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/26/2023] Open
Abstract
Major facilitator superfamily domain-containing protein 8 (MFSD8) is a transmembrane protein that has been reported to function as a lysosomal chloride channel. In humans, homozygous mutations in MFSD8 cause a late-infantile form of neuronal ceroid lipofuscinosis (NCL) called CLN7 disease. In the social amoeba Dictyostelium discoideum, Mfsd8 localizes to cytoplasmic puncta and vesicles, and regulates conserved processes during the organism's life cycle. Here, we used D. discoideum to examine the effect of mfsd8-deficiency on the secretome during the early stages of multicellular development. Mass spectrometry revealed 61 proteins that were differentially released by cells after 4 and 8 h of starvation. Most proteins were present in increased amounts in mfsd8- conditioned buffer compared to WT indicating that loss of mfsd8 deregulates protein secretion and/or causes the release of proteins not normally secreted by WT cells. GO term enrichment analyses showed that many of the proteins aberrantly released by mfsd8- cells localize to compartments and regions of the cell associated with the endo-lysosomal and secretory pathways. Mass spectrometry also revealed proteins previously known to be impacted by the loss of mfsd8 (e.g., cathepsin D), as well as proteins that may underlie mfsd8-deficiency phenotypes during aggregation. Finally, we show that mfsd8-deficiency reduces intracellular proteasome 20S activity due to the abnormal release of at least one proteasomal subunit. Together, this study reveals the impact of mfsd8 loss on the secretome during D. discoideum aggregation and lays the foundation for follow up work that investigates the role of altered protein release in CLN7 disease.
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Affiliation(s)
- Robert J Huber
- Department of Biology, Trent University, Peterborough, Ontario, Canada; Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada.
| | - Joshua Gray
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - William D Kim
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
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11
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Lonsdale A, Ceballos-Laita L, Takahashi D, Uemura M, Abadía J, Davis MJ, Bacic A, Doblin MS. LSPpred Suite: Tools for Leaderless Secretory Protein Prediction in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:1428. [PMID: 37050054 PMCID: PMC10097205 DOI: 10.3390/plants12071428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/24/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Plant proteins that are secreted without a classical signal peptide leader sequence are termed leaderless secretory proteins (LSPs) and are implicated in both plant development and (a)biotic stress responses. In plant proteomics experimental workflows, identification of LSPs is hindered by the possibility of contamination from other subcellar compartments upon purification of the secretome. Applying machine learning algorithms to predict LSPs in plants is also challenging due to the rarity of experimentally validated examples for training purposes. This work attempts to address this issue by establishing criteria for identifying potential plant LSPs based on experimental observations and training random forest classifiers on the putative datasets. The resultant plant protein database LSPDB and bioinformatic prediction tools LSPpred and SPLpred are available at lsppred.lspdb.org. The LSPpred and SPLpred modules are internally validated on the training dataset, with false positives controlled at 5%, and are also able to classify the limited number of established plant LSPs (SPLpred (3/4, LSPpred 4/4). Until such time as a larger set of bona fide (independently experimentally validated) LSPs is established using imaging technologies (light/fluorescence/electron microscopy) to confirm sub-cellular location, these tools represent a bridging method for predicting and identifying plant putative LSPs for subsequent experimental validation.
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Affiliation(s)
- Andrew Lonsdale
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Laura Ceballos-Laita
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Daisuke Takahashi
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan
| | - Matsuo Uemura
- Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Javier Abadía
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Melissa J. Davis
- Bioinformatics, Walter and Eliza Hall Institute for Medical Research, Melbourne, VIC 3052, Australia
| | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Monika S. Doblin
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
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12
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Remtulla AAN, Huber RJ. The conserved cellular roles of CLN proteins: Novel insights from Dictyostelium discoideum. Eur J Cell Biol 2023; 102:151305. [PMID: 36917916 DOI: 10.1016/j.ejcb.2023.151305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/15/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023] Open
Abstract
The neuronal ceroid lipofuscinoses (NCLs), collectively referred to as Batten disease, are a group of fatal neurodegenerative disorders that primarily affect children. The etiology of Batten disease is linked to mutations in 13 genes that encode distinct CLN proteins, whose functions have yet to be fully elucidated. The social amoeba Dictyostelium discoideum has been adopted as an efficient and powerful model system for studying the diverse cellular roles of CLN proteins. The genome of D. discoideum encodes several homologs of human CLN proteins, and a growing body of literature supports the conserved roles and networking of CLN proteins in D. discoideum and humans. In humans, CLN proteins have diverse cellular roles related to autophagy, signal transduction, lipid homeostasis, lysosomal ion homeostasis, and intracellular trafficking. Recent work also indicates that CLN proteins play an important role in protein secretion. Remarkably, many of these findings have found parallels in studies with D. discoideum. Accordingly, this review will highlight the translatable value of novel work with D. discoideum in the field of NCL research and propose further avenues of research using this biomedical model organism for studying the NCLs.
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Affiliation(s)
- Adam A N Remtulla
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Robert J Huber
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada; Department of Biology, Trent University, Peterborough, Ontario, Canada.
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13
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Tang VT, Ginsburg D. Cargo selection in endoplasmic reticulum-to-Golgi transport and relevant diseases. J Clin Invest 2023; 133:163838. [PMID: 36594468 PMCID: PMC9797344 DOI: 10.1172/jci163838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Most proteins destined for the extracellular space or various intracellular compartments must traverse the intracellular secretory pathway. The first step is the recruitment and transport of cargoes from the endoplasmic reticulum (ER) lumen to the Golgi apparatus by coat protein complex II (COPII), consisting of five core proteins. Additional ER transmembrane proteins that aid cargo recruitment are referred to as cargo receptors. Gene duplication events have resulted in multiple COPII paralogs present in the mammalian genome. Here, we review the functions of each COPII protein, human disorders associated with each paralog, and evidence for functional conservation between paralogs. We also provide a summary of current knowledge regarding two prototypical cargo receptors in mammals, LMAN1 and SURF4, and their roles in human health and disease.
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Affiliation(s)
- Vi T. Tang
- Department of Molecular and Integrative Physiology,,Life Sciences Institute
| | - David Ginsburg
- Life Sciences Institute,,Department of Internal Medicine,,Department of Human Genetics,,Department of Pediatrics and Communicable Diseases, and,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA
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14
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Yang L, Zhu H, Li M, Yu Q. The Tricalbin-Family Endoplasmic Reticulum-Plasma Membrane Tethering Proteins Attenuate ROS-Involved Caspofungin Sensitivity in Candida albicans. Microbiol Spectr 2022; 10:e0207922. [PMID: 36445092 PMCID: PMC9769562 DOI: 10.1128/spectrum.02079-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 11/07/2022] [Indexed: 12/02/2022] Open
Abstract
The endoplasmic reticulum-plasma membrane (ER-PM) contacts are one kind of important membrane contact structures in eukaryotic cells, which mediate material and message exchange between the ER and the PM. However, the specific types and functions of ER-PM tethering proteins are poorly understood in the human fungal pathogen Candida albicans. In this study, we observed that the two tricalbin-family proteins, i.e., Tcb1 and Tcb3, were colocalized with the ER-PM contacts in C. albicans. Deletion of the tricalbin-encoding genes TCB1 and TCB3 remarkably reduced ER-PM contacts, suggesting that tricalbins are ER-PM tethering proteins of C. albicans. Stress sensitivity assays showed that the TCB-deleted strains, including tcb1Δ/Δ, tcb3Δ/Δ, and tcb1Δ/Δ tcb3Δ/Δ, exhibited hypersensitivity to cell wall stress induced by caspofungin. Further investigation revealed that caspofungin induced drastic reactive oxygen species (ROS) accumulation in the mutants, which was attributed to enhanced oxidation of Ero1 in the ER lumen. Removal of intracellular ROS by the ROS scavenger vitamin C rescued the growth of the mutants under caspofungin treatment, indicating that Ero1 oxidation-related ROS accumulation was involved in caspofungin hypersensitivity of the mutants. Moreover, deletion of the TCB genes decreased secretion of extracellular aspartyl proteinases, reduced transport of the cell wall protein Hwp1 from the cytoplasm to the cell wall, and attenuated virulence of the fungal pathogen. This study sheds a light on the role of ER-PM tethering proteins in maintenance of cell wall integrity and virulence in fungal pathogens. IMPORTANCE The endoplasmic reticulum-plasma membrane contacts are important membrane contact structures in eukaryotic cells, functioning in material and message exchange between the ER and the PM. We observed that the two tricalbin-family endoplasmic reticulum-plasma membrane contact proteins are required for tolerance to caspofungin-induced cell wall stress in the pathogenic fungus Candida albicans. The tricalbin mutants exhibited hypersensitivity to cell wall stress induced by caspofungin. Further investigation revealed that Ero1 oxidation-related reactive species oxygen accumulation was involved in caspofungin hypersensitivity of the tricalbin mutants. Moreover, loss of tricalbins reduced secretion of extracellular aspartyl proteinases, decreased transport of the cell wall proteins from the cytoplasm to the cell wall, and attenuated virulence of the fungal pathogen. This study uncovers the role of ER-PM tethering proteins in sustaining protein secretion, maintenance of cell wall integrity and virulence in fungal pathogens.
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Affiliation(s)
- Li Yang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, People’s Republic of China
| | - Hangqi Zhu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, People’s Republic of China
| | - Mingchun Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, People’s Republic of China
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, People’s Republic of China
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15
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Chiritoiu-Butnaru M, Stewart SE, Zhang M, Malhotra V, Villeneuve J. Editorial: Unconventional protein secretion: From basic mechanisms to dysregulation in disease. Front Cell Dev Biol 2022; 10:1088002. [DOI: 10.3389/fcell.2022.1088002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022] Open
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