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Grijaldo-Alvarez SJB, Alvarez MRS, Schindler RL, Oloumi A, Hernandez N, Seales T, Angeles JGC, Nacario RC, Completo GC, Zivkovic AM, Bruce German J, Lebrilla CB. N-Glycan profile of the cell membrane as a probe for lipopolysaccharide-induced microglial neuroinflammation uncovers the effects of common fatty acid supplementation. Food Funct 2024. [PMID: 39011570 DOI: 10.1039/d4fo01598c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Altered N-glycosylation of proteins on the cell membrane is associated with several neurodegenerative diseases. Microglia are an ideal model for studying glycosylation and neuroinflammation, but whether aberrant N-glycosylation in microglia can be restored by diet remains unknown. Herein, we profiled the N-glycome, proteome, and glycoproteome of the human microglia following lipopolysaccharide (LPS) induction to probe the impact of dietary and gut microbe-derived fatty acids-oleic acid, lauric acid, palmitic acid, valeric acid, butyric acid, isobutyric acid, and propionic acid-on neuroinflammation using liquid chromatography-tandem mass spectrometry. LPS changed N-glycosylation in the microglial glycocalyx altering high mannose and sialofucosylated N-glycans, suggesting the dysregulation of mannosidases, fucosyltransferases, and sialyltransferases. The results were consistent as we observed the restoration effect of the fatty acids, especially oleic acid, on the LPS-treated microglia, specifically on the high mannose and sialofucosylated glycoforms of translocon-associated proteins, SSRA and SSRB along with the cell surface proteins, CD63 and CD166. In addition, proteomic analysis and in silico modeling substantiated the potential of fatty acids in reverting the effects of LPS on microglial N-glycosylation. Our results showed that N-glycosylation is likely affected by diet by restoring alterations following LPS challenge, which may then influence the disease state.
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Affiliation(s)
- Sheryl Joyce B Grijaldo-Alvarez
- Department of Chemistry, University of California, Davis, 95616, USA.
- Institute of Chemistry, University of the Philippines Los Baños, Philippines, 4031.
| | | | | | - Armin Oloumi
- Department of Chemistry, University of California, Davis, 95616, USA.
| | - Noah Hernandez
- Department of Chemistry, University of California, Davis, 95616, USA.
| | - Tristan Seales
- Department of Chemistry, University of California, Davis, 95616, USA.
| | - Jorge Gil C Angeles
- Philippine Genome Center - Program for Agriculture, Livestock, Fisheries and Forestry, University of the Philippines Los Baños, Philippines, 4031.
| | - Ruel C Nacario
- Institute of Chemistry, University of the Philippines Los Baños, Philippines, 4031.
| | - Gladys C Completo
- Institute of Chemistry, University of the Philippines Los Baños, Philippines, 4031.
| | - Angela M Zivkovic
- Department of Nutrition, University of California, Davis, 95616, USA.
| | - J Bruce German
- Department of Food Science and Technology, University of California, Davis, 95616, USA.
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2
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Voss M. Proteolytic cleavage of Golgi glycosyltransferases by SPPL3 and other proteases and its implications for cellular glycosylation. Biochim Biophys Acta Gen Subj 2024; 1868:130668. [PMID: 38992482 DOI: 10.1016/j.bbagen.2024.130668] [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: 06/04/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/13/2024]
Abstract
Glycosylation of proteins and lipids is of fundamental importance in multicellular eukaryotes. The vast diversity of glycan structures observed is generated in the Golgi apparatus by the concerted activity of >100 distinct enzymes, which include glycosyltransferases and other glycan-modifying enzymes. Well-known for decades, the majority of these enzymes is released from the Golgi apparatus and subsequently secreted into the extracellular space following endoproteolytic cleavage, but the underlying molecular mechanisms and the physiological implications have remained unexplored. This review will summarize our current knowledge of Golgi enzyme proteolysis and secretion and will discuss its conceptual implications for the regulation of cellular glycosylation and the organization of the Golgi apparatus. A particular focus will lie on the intramembrane protease SPPL3, which recently emerged as key protease facilitating Golgi enzyme release and has since been shown to affect a multitude of glycosylation-dependent physiological processes.
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Affiliation(s)
- Matthias Voss
- Institute of Biochemistry, Kiel University, Kiel, Germany.
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3
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Zhao R, Liao W, Tan D, Huang H, Hu C, Chen M. Comparative analysis of the expression patterns of TM9SF family members in mice. Gene Expr Patterns 2024; 52:119366. [PMID: 38719197 DOI: 10.1016/j.gep.2024.119366] [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: 11/23/2023] [Revised: 03/05/2024] [Accepted: 05/05/2024] [Indexed: 05/19/2024]
Abstract
Transmembrane 9 superfamily proteins (TM9SFs) define a highly conserved protein family, each member of which is characterized by a variable extracellular domain and presumably nine transmembrane domains. Although previous studies have delineated the potential cytological roles of TM9SFs like autophagy and secretory pathway, their functions during development are largely unknown. To establish the basis for dissecting the functions of TM9SFs in vivo, we employed the open-source database, structure prediction, immunofluorescence and Western blot to describe the gene and protein expression patterns of TM9SFs in human and mouse. While TM9SFs are ubiquitously and homogeneously expressed in all tissues in human with RNA sequencing and proteomics analysis, we found that all mice Tm9sf proteins are preferentially expressed in lung except Tm9sf1 which is enriched in brain although they all distributed in various tissues we examined. In addition, we further explored their expression patterns in the mice central nervous system (CNS) and its extension tissue retina. Interestingly, we could show that Tm9sf1is developmentally up-regulated in brain. In addition, we also detected all Tm9sf proteins are located in neurons and microglia instead of astrocytes. Importantly, Tm9sf3 is localized in the nuclei which is distinct from the other members that are dominantly targeted to the plasma membrane/cytoplasm as expected. Finally, we also found that Tm9sf family members are broadly expressed in the layers of INL, OPL, and GCL of retina and likely targeted to the plasma membrane of retinal cells. Thus, our data provided a comprehensive overview of TM9SFs expression patterns, illustrating their ubiquitous roles in different organs, implying the possible roles of Tm9sf2/3/4 in lung functions and Tm9sf1 in neurodevelopment, and highlighting a unique cell biological functions of TM9SF3 in neuronal and microglia.
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Affiliation(s)
- Rui Zhao
- Guangdong Second Provincial General Hospital, Guangzhou, 510317, China; Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Institute for Brain Research and Rehabilitation, South China Normal University, 510631, Guangzhou, China
| | - Wenxiong Liao
- Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Duo Tan
- Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Haiyou Huang
- Jianghai Street Community Health Service Center, Haizhu District, Guangzhou, Guangzhou, 510305, China
| | - Chun Hu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Institute for Brain Research and Rehabilitation, South China Normal University, 510631, Guangzhou, China
| | - Meilan Chen
- Guangdong Second Provincial General Hospital, Guangzhou, 510317, China.
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4
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Arab M, Chen T, Lowe M. Mechanisms governing vesicle traffic at the Golgi apparatus. Curr Opin Cell Biol 2024; 88:102365. [PMID: 38705050 DOI: 10.1016/j.ceb.2024.102365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/04/2024] [Accepted: 04/11/2024] [Indexed: 05/07/2024]
Abstract
Vesicle transport at the Golgi apparatus is a well-described process, and the major protein components involved have been identified. This includes the coat proteins that function in cargo sorting and vesicle formation, and the proteins that mediate the downstream events of vesicle tethering and membrane fusion. However, despite this knowledge, there remain significant gaps in our mechanistic understanding of these processes which includes how they are coordinated in space and time. In this review we discuss recent advances that have provided new insights into the mechanisms of Golgi trafficking, focussing on vesicle formation and cargo sorting, and vesicle tethering and fusion. These studies point to a high degree of spatial organisation of trafficking components at the Golgi and indicate an inherent plasticity of trafficking. Going forward, further advancements in technology and more sophisticated functional assays are expected to yield greater understanding of the mechanisms that govern Golgi trafficking events.
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Affiliation(s)
- Maryam Arab
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Tong Chen
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Martin Lowe
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
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5
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Lin J, Miao J, Schaefer KG, Russell CM, Pyron RJ, Zhang F, Phan QT, Solis-Swidergall NV, Liu H, Tashiro M, Dordick JS, Linhardt RJ, Yeaman MR, King GM, Barrera FN, Peters BM, Filler SG. A genome-scale screen identifies sulfated glycosaminoglycans as pivotal in epithelial cell damage by Candida albicans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595417. [PMID: 38826446 PMCID: PMC11142209 DOI: 10.1101/2024.05.23.595417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Candidalysin is a cytolytic peptide produced by the opportunistic fungal pathogen Candida albicans. This peptide is a key virulence factor in mouse models of mucosal and hematogenously disseminated candidiasis. Despite intense interest in the role of candidalysin in C. albicans pathogenicity, its host cell targets have remained elusive. To fill this knowledge gap, we performed a genome-wide loss-of-function CRISPR screen in a human oral epithelial cell line to identify specific host factors required for susceptibility to candidalysin-induced cellular damage. Among the top hits were XYLT2, B3GALT6 and B3GAT3, genes that function in glycosaminoglycan (GAG) biosynthesis. Deletion of these genes led to the absence of GAGs such as heparan sulfate on the epithelial cell surface and increased resistance to damage induced by both candidalysin and live C. albicans. Biophysical analyses including surface plasmon resonance and atomic force and electron microscopy indicated that candidalysin physically binds to sulfated GAGs, facilitating its oligomerization or enrichment on the host cell surface. The addition of exogenous sulfated GAGs or the GAG analogue dextran sulfate protected cells against candidalysin-induced damage. Dextran sulfate, but not non-sulfated dextran, also inhibited epithelial cell endocytosis of C. albicans and fungal-induced epithelial cell cytokine and chemokine production. In a murine model of vulvovaginal candidiasis, topical dextran sulfate administration reduced host tissue damage and decreased intravaginal IL-1β and neutrophil levels. Collectively, these data indicate that GAGs are epithelial cell targets of candidalysin and can be used therapeutically to protect cells from candidalysin-induced damage.
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Affiliation(s)
- Jianfeng Lin
- Institute for Infection and Immunity, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Jian Miao
- Pharmaceutical Sciences Program, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Katherine G Schaefer
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri United States
| | - Charles M Russell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee United States
| | - Robert J Pyron
- Genome Science and Technology, University of Tennessee, Knoxville, United States
| | - Fuming Zhang
- Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Quynh T Phan
- Institute for Infection and Immunity, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Norma V Solis-Swidergall
- Institute for Infection and Immunity, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Hong Liu
- Institute for Infection and Immunity, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Masato Tashiro
- Institute for Infection and Immunity, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Robert J Linhardt
- Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Michael R Yeaman
- Institute for Infection and Immunity, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Division of Infectious Diseases, Department of Medicine, Harbor-UCLA Medical Center, Torrance, California, USA
- Division of Molecular Medicine, Department of Medicine, Harbor-UCLA Medical Center, Torrance, California, USA
| | - Gavin M King
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri United States
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee United States
| | - Brian M Peters
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Scott G Filler
- Institute for Infection and Immunity, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Division of Infectious Diseases, Department of Medicine, Harbor-UCLA Medical Center, Torrance, California, USA
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6
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Hollingsworth LR, Veeraraghavan P, Paulo JA, Harper JW, Rauch I. Spatiotemporal proteomic profiling of cellular responses to NLRP3 agonists. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590338. [PMID: 38659763 PMCID: PMC11042255 DOI: 10.1101/2024.04.19.590338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Nucleotide-binding domain and leucine-rich repeat pyrin-domain containing protein 3 (NLRP3) is an innate immune sensor that forms an inflammasome in response to various cellular stressors. Gain-of-function mutations in NLRP3 cause autoinflammatory diseases and NLRP3 signalling itself exacerbates the pathogenesis of many other human diseases. Despite considerable therapeutic interest, the primary drivers of NLRP3 activation remain controversial due to the diverse array of signals that are integrated through NLRP3. Here, we mapped subcellular proteome changes to lysosomes, mitochondrion, EEA1-positive endosomes, and Golgi caused by the NLRP3 inflammasome agonists nigericin and CL097. We identified several common disruptions to retrograde trafficking pathways, including COPI and Shiga toxin-related transport, in line with recent studies. We further characterized mouse NLRP3 trafficking throughout its activation using temporal proximity proteomics, which supports a recent model of NLRP3 recruitment to endosomes during inflammasome activation. Collectively, these findings provide additional granularity to our understanding of the molecular events driving NLRP3 activation and serve as a valuable resource for cell biological research. We have made our proteomics data accessible through an open-access Shiny browser to facilitate future research within the community, available at: https://harperlab.connect.hms.harvard.edu/inflame/. We will display anonymous peer review for this manuscript on pubpub.org (https://harperlab.pubpub.org/pub/nlrp3/) rather than a traditional journal. Moreover, we invite community feedback on the pubpub version of this manuscript, and we will address criticisms accordingly.
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Affiliation(s)
- L. Robert Hollingsworth
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | | | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Isabella Rauch
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University
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7
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Liu N, Hou L, Chen X, Bao J, Chen F, Cai W, Zhu H, Wang L, Chen X. Arabidopsis TETRASPANIN8 mediates exosome secretion and glycosyl inositol phosphoceramide sorting and trafficking. THE PLANT CELL 2024; 36:626-641. [PMID: 37950906 PMCID: PMC11024842 DOI: 10.1093/plcell/koad285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/16/2023] [Accepted: 11/07/2023] [Indexed: 11/13/2023]
Abstract
Sphingolipids are components of plant membranes, and their heterogeneous distribution gives different membrane systems distinct properties. For example, glycosyl inositol phosphoceramides (GIPCs), 1 major type of sphingolipids, aggregate in the outer layer of the plasma membrane (PM), as well as in extracellular vesicles (EVs), including the small (30 to 100 nm) EVs termed exosomes. How these sphingolipids are sorted and trafficked is not clear. In this work, we report that Arabidopsis thaliana TETRASPANIN8 (TET8) acts as a sphingolipid carrier and thus regulates the export of GIPCs from the Golgi apparatus. TET8 recognized the coat protein complex I (COPI) subunit γ2-COPI and moved to its proper location in the PM; this recognition required the TET8 C-terminal tail. Deleting the C-terminal tail of TET8 largely restricted its roles in GIPC transport and endosomal trafficking. Further, we show that TET8 affects EV secretion in association with GIPCs. Thus, our findings shed light on GIPC transport and the molecular machinery involved in EV biogenesis.
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Affiliation(s)
- Ningjing Liu
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Lipan Hou
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xin Chen
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Jingjing Bao
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Fangyan Chen
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wenjuan Cai
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Huixian Zhu
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Lingjian Wang
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaoya Chen
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
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8
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Botelho FD, Franca TCC, LaPlante SR. The Search for Antidotes Against Ricin. Mini Rev Med Chem 2024; 24:1148-1161. [PMID: 38350844 DOI: 10.2174/0113895575270509231121060105] [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: 07/04/2023] [Revised: 09/30/2023] [Accepted: 10/18/2023] [Indexed: 02/15/2024]
Abstract
The castor plant (Ricinus communis) is primarily known for its seeds, which contain a unique fatty acid called ricinoleic acid with several industrial and commercial applications. Castor seeds also contain ricin, a toxin considered a chemical and biological warfare agent. Despite years of investigation, there is still no effective antidote or vaccine available. However, some progress has been made, and the development of an effective treatment may be on the horizon. To provide an updated overview of this issue, we have conducted a comprehensive review of the literature on the current state of research in the fight against ricin. This review is based on the reported research and aims to address the challenges faced by researchers, as well as highlight the most successful cases achieved thus far. Our goal is to encourage the scientific community to continue their efforts in this critical search.
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Affiliation(s)
- Fernanda Diniz Botelho
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Praça General Tibúrcio 80, 22290-270, Rio de Janeiro, RJ, Brazil
| | - Tanos Celmar Costa Franca
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Praça General Tibúrcio 80, 22290-270, Rio de Janeiro, RJ, Brazil
- Université de Québec, INRS - Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec, H7V 1B7, Canada
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, Czech Republic
| | - Steven R LaPlante
- Université de Québec, INRS - Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec, H7V 1B7, Canada
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9
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Tian S, Zhou N. Gaining New Insights into Fundamental Biological Pathways by Bacterial Toxin-Based Genetic Screens. Bioengineering (Basel) 2023; 10:884. [PMID: 37627769 PMCID: PMC10451959 DOI: 10.3390/bioengineering10080884] [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: 05/15/2023] [Revised: 07/11/2023] [Accepted: 07/22/2023] [Indexed: 08/27/2023] Open
Abstract
Genetic screen technology has been applied to study the mechanism of action of bacterial toxins-a special class of virulence factors that contribute to the pathogenesis caused by bacterial infections. These screens aim to identify host factors that directly or indirectly facilitate toxin intoxication. Additionally, specific properties of certain toxins, such as membrane interaction, retrograde trafficking, and carbohydrate binding, provide robust probes to comprehensively investigate the lipid biosynthesis, membrane vesicle transport, and glycosylation pathways, respectively. This review specifically focuses on recent representative toxin-based genetic screens that have identified new players involved in and provided new insights into fundamental biological pathways, such as glycosphingolipid biosynthesis, protein glycosylation, and membrane vesicle trafficking pathways. Functionally characterizing these newly identified factors not only expands our current understanding of toxin biology but also enables a deeper comprehension of fundamental biological questions. Consequently, it stimulates the development of new therapeutic approaches targeting both bacterial infectious diseases and genetic disorders with defects in these factors and pathways.
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Affiliation(s)
- Songhai Tian
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA;
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Nini Zhou
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA;
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
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10
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Jeon Y, Chow SH, Stuart I, Weir A, Yeung AT, Hale C, Sridhar S, Dougan G, Vince JE, Naderer T. FBXO11 governs macrophage cell death and inflammation in response to bacterial toxins. Life Sci Alliance 2023; 6:e202201735. [PMID: 36977592 PMCID: PMC10053445 DOI: 10.26508/lsa.202201735] [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: 09/25/2022] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Staphylococcus aureus causes severe infections such as pneumonia and sepsis depending on the pore-forming toxin Panton-Valentine leukocidin (PVL). PVL kills and induces inflammation in macrophages and other myeloid cells by interacting with the human cell surface receptor, complement 5a receptor 1 (C5aR1). C5aR1 expression is tighly regulated and may thus modulate PVL activity, although the mechanisms involved remain incompletely understood. Here, we used a genome-wide CRISPR/Cas9 screen and identified F-box protein 11 (FBXO11), an E3 ubiquitin ligase complex member, to promote PVL toxicity. Genetic deletion of FBXO11 reduced the expression of C5aR1 at the mRNA level, whereas ectopic expression of C5aR1 in FBXO11-/- macrophages, or priming with LPS, restored C5aR1 expression and thereby PVL toxicity. In addition to promoting PVL-mediated killing, FBXO11 dampens secretion of IL-1β after NLRP3 activation in response to bacterial toxins by reducing mRNA levels in a BCL-6-dependent and BCL-6-independent manner. Overall, these findings highlight that FBXO11 regulates C5aR1 and IL-1β expression and controls macrophage cell death and inflammation following PVL exposure.
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Affiliation(s)
- Yusun Jeon
- Department of Biochemistry & Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Seong H Chow
- Department of Biochemistry & Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Isabella Stuart
- Department of Biochemistry & Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Ashley Weir
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Amy Ty Yeung
- The Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Christine Hale
- The Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Sushmita Sridhar
- The Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gordon Dougan
- The Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - James E Vince
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Thomas Naderer
- Department of Biochemistry & Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
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11
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Targeting the Inside of Cells with Biologicals: Toxin Routes in a Therapeutic Context. BioDrugs 2023; 37:181-203. [PMID: 36729328 PMCID: PMC9893211 DOI: 10.1007/s40259-023-00580-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2023] [Indexed: 02/03/2023]
Abstract
Numerous toxins translocate to the cytosol in order to fulfil their function. This demonstrates the existence of routes for proteins from the extracellular space to the cytosol. Understanding these routes is relevant to multiple aspects related to therapeutic applications. These include the development of anti-toxin treatments, the potential use of toxins as shuttles for delivering macromolecular cargo to the cytosol or the use of drugs based on toxins. Compared with other strategies for delivery, such as chemicals as carriers for macromolecular delivery or physical methods like electroporation, toxin routes present paths into the cell that potentially cause less damage and can be specifically targeted. The efficiency of delivery via toxin routes is limited. However, low-delivery efficiencies can be entirely sufficient, if delivered cargoes possess an amplification effect or if very few molecules are sufficient for inducing the desired effects. This is known for example from RNA-based vaccines that have been developed during the coronavirus disease 2019 pandemic as well as for other approved RNA-based drugs, which elicited the desired effect despite their typically low delivery efficiencies. The different mechanisms by which toxins enter cells may have implications for their technological utility. We review the mechanistic principles of the translocation pathway of toxins from the extracellular space to the cytosol, the delivery efficiencies, and therapeutic strategies or applications that exploit toxin routes for intracellular delivery.
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12
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Tian S, Xiong X, Zeng J, Wang S, Tremblay BJM, Chen P, Chen B, Liu M, Chen P, Sheng K, Zeve D, Qi W, Breault DT, Rodríguez C, Gerhard R, Jin R, Doxey AC, Dong M. Identification of TFPI as a receptor reveals recombination-driven receptor switching in Clostridioides difficile toxin B variants. Nat Commun 2022; 13:6786. [PMID: 36351897 PMCID: PMC9646764 DOI: 10.1038/s41467-022-33964-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022] Open
Abstract
Toxin B (TcdB) is a major exotoxin responsible for diseases associated with Clostridioides difficile infection. Its sequence variations among clinical isolates may contribute to the difficulty in developing effective therapeutics. Here, we investigate receptor-binding specificity of major TcdB subtypes (TcdB1 to TcdB12). We find that representative members of subtypes 2, 4, 7, 10, 11, and 12 do not recognize the established host receptor, frizzled proteins (FZDs). Using a genome-wide CRISPR-Cas9-mediated screen, we identify tissue factor pathway inhibitor (TFPI) as a host receptor for TcdB4. TFPI is recognized by a region in TcdB4 that is homologous to the FZD-binding site in TcdB1. Analysis of 206 TcdB variant sequences reveals a set of six residues within this receptor-binding site that defines a TFPI binding-associated haplotype (designated B4/B7) that is present in all TcdB4 members, a subset of TcdB7, and one member of TcdB2. Intragenic micro-recombination (IR) events have occurred around this receptor-binding region in TcdB7 and TcdB2 members, resulting in either TFPI- or FZD-binding capabilities. Introduction of B4/B7-haplotype residues into TcdB1 enables dual recognition of TFPI and FZDs. Finally, TcdB10 also recognizes TFPI, although it does not belong to the B4/B7 haplotype, and shows species selectivity: it recognizes TFPI of chicken and to a lesser degree mouse, but not human, dog, or cattle versions. These findings identify TFPI as a TcdB receptor and reveal IR-driven changes on receptor-specificity among TcdB variants.
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Affiliation(s)
- Songhai Tian
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA.
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA.
| | - Xiaozhe Xiong
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Ji Zeng
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Siyu Wang
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Benjamin Jean-Marie Tremblay
- Department of Biology, Cheriton School of Computer Science, and Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Peng Chen
- Department of Physiology and Biophysics, School of Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | - Baohua Chen
- Department of Physiology and Biophysics, School of Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | - Min Liu
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Pengsheng Chen
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Kuanwei Sheng
- Wyss Institute for Bioinspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Daniel Zeve
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Wanshu Qi
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - David T Breault
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA, 02138, USA
| | - César Rodríguez
- Faculty of Microbiology & CIET, University of Costa Rica, San José, Costa Rica
| | - Ralf Gerhard
- Institute of Toxicology, Hannover Medical School, 30625, Hannover, Germany
| | - Rongsheng Jin
- Department of Physiology and Biophysics, School of Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | - Andrew C Doxey
- Department of Biology, Cheriton School of Computer Science, and Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA.
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA.
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13
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Truberg J, Hobohm L, Jochimsen A, Desel C, Schweizer M, Voss M. Endogenous tagging reveals a mid-Golgi localization of the glycosyltransferase-cleaving intramembrane protease SPPL3. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119345. [PMID: 36007678 DOI: 10.1016/j.bbamcr.2022.119345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Numerous Golgi-resident enzymes implicated in glycosylation are regulated by the conserved intramembrane protease SPPL3. SPPL3-catalyzed endoproteolysis separates Golgi enzymes from their membrane anchors, enabling subsequent release from the Golgi and secretion. Experimentally altered SPPL3 expression changes glycosylation patterns, yet the regulation of SPPL3-mediated Golgi enzyme cleavage is not understood and conflicting results regarding the subcellular localization of SPPL3 have been reported. Here, we used precise genome editing to generate isogenic cell lines expressing N- or C-terminally tagged SPPL3 from its endogenous locus. Using these cells, we conducted co-localization analyses of tagged endogenous SPPL3 and Golgi markers under steady-state conditions and upon treatment with drugs disrupting Golgi organization. Our data demonstrate that endogenous SPPL3 is Golgi-resident and found predominantly in the mid-Golgi. We find that endogenous SPPL3 co-localizes with its substrates but similarly with non-substrate type II proteins, demonstrating that in addition to co-localization in the Golgi other substrate-intrinsic properties govern SPPL3-mediated intramembrane proteolysis. Given the prevalence of SPPL3-mediated cleavage among Golgi-resident proteins our results have important implications for the regulation of SPPL3 and its role in the organization of the Golgi glycosylation machinery.
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Affiliation(s)
- Jule Truberg
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, D-24118 Kiel, Germany
| | - Laura Hobohm
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, D-24118 Kiel, Germany
| | - Alexander Jochimsen
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, D-24118 Kiel, Germany
| | - Christine Desel
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, D-24118 Kiel, Germany
| | - Michaela Schweizer
- Morphology and Electron Microscopy, University Medical Center Hamburg-Eppendorf, Center for Molecular Neurobiology (ZMNH), 20251 Hamburg, Germany
| | - Matthias Voss
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, D-24118 Kiel, Germany.
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14
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Gyimesi G, Hediger MA. Systematic in silico discovery of novel solute carrier-like proteins from proteomes. PLoS One 2022; 17:e0271062. [PMID: 35901096 PMCID: PMC9333335 DOI: 10.1371/journal.pone.0271062] [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: 12/01/2021] [Accepted: 06/22/2022] [Indexed: 12/26/2022] Open
Abstract
Solute carrier (SLC) proteins represent the largest superfamily of transmembrane transporters. While many of them play key biological roles, their systematic analysis has been hampered by their functional and structural heterogeneity. Based on available nomenclature systems, we hypothesized that many as yet unidentified SLC transporters exist in the human genome, which await further systematic analysis. Here, we present criteria for defining "SLC-likeness" to curate a set of "SLC-like" protein families from the Transporter Classification Database (TCDB) and Protein families (Pfam) databases. Computational sequence similarity searches surprisingly identified ~120 more proteins in human with potential SLC-like properties compared to previous annotations. Interestingly, several of these have documented transport activity in the scientific literature. To complete the overview of the "SLC-ome", we present an algorithm to classify SLC-like proteins into protein families, investigating their known functions and evolutionary relationships to similar proteins from 6 other clinically relevant experimental organisms, and pinpoint structural orphans. We envision that our work will serve as a stepping stone for future studies of the biological function and the identification of the natural substrates of the many under-explored SLC transporters, as well as for the development of new therapeutic applications, including strategies for personalized medicine and drug delivery.
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Affiliation(s)
- Gergely Gyimesi
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department for BioMedical Research, Inselspital, University of Bern, Bern, Switzerland
- * E-mail: (GG); (MAH)
| | - Matthias A. Hediger
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department for BioMedical Research, Inselspital, University of Bern, Bern, Switzerland
- * E-mail: (GG); (MAH)
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15
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Stewart N, Wisnovsky S. Bridging Glycomics and Genomics: New Uses of Functional Genetics in the Study of Cellular Glycosylation. Front Mol Biosci 2022; 9:934584. [PMID: 35782863 PMCID: PMC9243437 DOI: 10.3389/fmolb.2022.934584] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
All living cells are coated with a diverse collection of carbohydrate molecules called glycans. Glycans are key regulators of cell behavior and important therapeutic targets for human disease. Unlike proteins, glycans are not directly templated by discrete genes. Instead, they are produced through multi-gene pathways that generate a heterogenous array of glycoprotein and glycolipid antigens on the cell surface. This genetic complexity has sometimes made it challenging to understand how glycosylation is regulated and how it becomes altered in disease. Recent years, however, have seen the emergence of powerful new functional genomics technologies that allow high-throughput characterization of genetically complex cellular phenotypes. In this review, we discuss how these techniques are now being applied to achieve a deeper understanding of glyco-genomic regulation. We highlight specifically how methods like ChIP-seq, RNA-seq, CRISPR genomic screening and scRNA-seq are being used to map the genomic basis for various cell-surface glycosylation states in normal and diseased cell types. We also offer a perspective on how emerging functional genomics technologies are likely to create further opportunities for studying cellular glycobiology in the future. Taken together, we hope this review serves as a primer to recent developments at the glycomics-genomics interface.
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Affiliation(s)
- Natalie Stewart
- Biochemistry and Microbiology Dept, University of Victoria, Victoria, BC, Canada
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Simon Wisnovsky
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Simon Wisnovsky,
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16
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Kono M, Hoachlander-Hobby LE, Majumder S, Schwartz R, Byrnes C, Zhu H, Proia RL. Identification of two lipid phosphatases that regulate sphingosine-1-phosphate cellular uptake and recycling. J Lipid Res 2022; 63:100225. [PMID: 35568252 PMCID: PMC9213771 DOI: 10.1016/j.jlr.2022.100225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/06/2022] [Accepted: 05/07/2022] [Indexed: 12/29/2022] Open
Abstract
Sphingosine-1-phosphate (S1P) is a sphingolipid metabolite that serves as a potent extracellular signaling molecule. Metabolic regulation of extracellular S1P levels impacts key cellular activities through altered S1P receptor signaling. Although the pathway through which S1P is degraded within the cell and thereby eliminated from reuse has been previously described, the mechanism used for S1P cellular uptake and the subsequent recycling of its sphingoid base into the sphingolipid synthesis pathway is not completely understood. To identify the genes within this S1P uptake and recycling pathway, we performed a genome-wide CRISPR/Cas9 KO screen using a positive-selection scheme with Shiga toxin, which binds a cell-surface glycosphingolipid receptor, globotriaosylceramide (Gb3), and causes lethality upon internalization. The screen was performed in HeLa cells with their sphingolipid de novo pathway disabled so that Gb3 cell-surface expression was dependent on salvage of the sphingoid base of S1P taken up from the medium. The screen identified a suite of genes necessary for S1P uptake and the recycling of its sphingoid base to synthesize Gb3, including two lipid phosphatases, PLPP3 (phospholipid phosphatase 3) and SGPP1 (S1P phosphatase 1). The results delineate a pathway in which plasma membrane–bound PLPP3 dephosphorylates extracellular S1P to sphingosine, which then enters cells and is rephosphorylated to S1P by the sphingosine kinases. This rephosphorylation step is important to regenerate intracellular S1P as a branch-point substrate that can be routed either for dephosphorylation to salvage sphingosine for recycling into complex sphingolipid synthesis or for degradation to remove it from the sphingolipid synthesis pathway.
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Affiliation(s)
- Mari Kono
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Lila E Hoachlander-Hobby
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Saurav Majumder
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Ronit Schwartz
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Colleen Byrnes
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Hongling Zhu
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Richard L Proia
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
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17
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Xiong X, Tian S, Yang P, Lebreton F, Bao H, Sheng K, Yin L, Chen P, Zhang J, Qi W, Ruan J, Wu H, Chen H, Breault DT, Wu H, Earl AM, Gilmore MS, Abraham J, Dong M. Emerging enterococcus pore-forming toxins with MHC/HLA-I as receptors. Cell 2022; 185:1157-1171.e22. [PMID: 35259335 PMCID: PMC8978092 DOI: 10.1016/j.cell.2022.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 12/15/2021] [Accepted: 02/01/2022] [Indexed: 01/12/2023]
Abstract
Enterococci are a part of human microbiota and a leading cause of multidrug resistant infections. Here, we identify a family of Enterococcus pore-forming toxins (Epxs) in E. faecalis, E. faecium, and E. hirae strains isolated across the globe. Structural studies reveal that Epxs form a branch of β-barrel pore-forming toxins with a β-barrel protrusion (designated the top domain) sitting atop the cap domain. Through a genome-wide CRISPR-Cas9 screen, we identify human leukocyte antigen class I (HLA-I) complex as a receptor for two members (Epx2 and Epx3), which preferentially recognize human HLA-I and homologous MHC-I of equine, bovine, and porcine, but not murine, origin. Interferon exposure, which stimulates MHC-I expression, sensitizes human cells and intestinal organoids to Epx2 and Epx3 toxicity. Co-culture with Epx2-harboring E. faecium damages human peripheral blood mononuclear cells and intestinal organoids, and this toxicity is neutralized by an Epx2 antibody, demonstrating the toxin-mediated virulence of Epx-carrying Enterococcus.
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Affiliation(s)
- Xiaozhe Xiong
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Songhai Tian
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Pan Yang
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Francois Lebreton
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Huan Bao
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Kuanwei Sheng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| | - Linxiang Yin
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Pengsheng Chen
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jie Zhang
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Wanshu Qi
- Division of Endocrinology, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jianbin Ruan
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology, University of Connecticut Health School of Medicine, Farmington, CT 06030, USA
| | - Hao Wu
- Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hong Chen
- Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - David T Breault
- Division of Endocrinology, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Hao Wu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ashlee M Earl
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael S Gilmore
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Jonathan Abraham
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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18
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Hobohm L, Koudelka T, Bahr FH, Truberg J, Kapell S, Schacht SS, Meisinger D, Mengel M, Jochimsen A, Hofmann A, Heintz L, Tholey A, Voss M. N-terminome analyses underscore the prevalence of SPPL3-mediated intramembrane proteolysis among Golgi-resident enzymes and its role in Golgi enzyme secretion. Cell Mol Life Sci 2022; 79:185. [PMID: 35279766 PMCID: PMC8918473 DOI: 10.1007/s00018-022-04163-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/07/2022] [Accepted: 01/22/2022] [Indexed: 12/17/2022]
Abstract
Golgi membrane proteins such as glycosyltransferases and other glycan-modifying enzymes are key to glycosylation of proteins and lipids. Secretion of soluble Golgi enzymes that are released from their membrane anchor by endoprotease activity is a wide-spread yet largely unexplored phenomenon. The intramembrane protease SPPL3 can specifically cleave select Golgi enzymes, enabling their secretion and concomitantly altering global cellular glycosylation, yet the entire range of Golgi enzymes cleaved by SPPL3 under physiological conditions remains to be defined. Here, we established isogenic SPPL3-deficient HEK293 and HeLa cell lines and applied N-terminomics to identify substrates cleaved by SPPL3 and released into cell culture supernatants. With high confidence, our study identifies more than 20 substrates of SPPL3, including entirely novel substrates. Notably, our N-terminome analyses provide a comprehensive list of SPPL3 cleavage sites demonstrating that SPPL3-mediated shedding of Golgi enzymes occurs through intramembrane proteolysis. Through the use of chimeric glycosyltransferase constructs we show that transmembrane domains can determine cleavage by SPPL3. Using our cleavage site data, we surveyed public proteome data and found that SPPL3 cleavage products are present in human blood. We also generated HEK293 knock-in cells expressing the active site mutant D271A from the endogenous SPPL3 locus. Immunoblot analyses revealed that secretion of select novel substrates such as the key mucin-type O-glycosylation enzyme GALNT2 is dependent on endogenous SPPL3 protease activity. In sum, our study expands the spectrum of known physiological substrates of SPPL3 corroborating its significant role in Golgi enzyme turnover and secretion as well as in the regulation of global glycosylation pathways.
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Affiliation(s)
- Laura Hobohm
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
| | - Tomas Koudelka
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Kiel University, 24105, Kiel, Germany
| | - Fenja H Bahr
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
| | - Jule Truberg
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
| | - Sebastian Kapell
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - Sarah-Sophie Schacht
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
- Institute of Immunology, University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Daniel Meisinger
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
| | - Marion Mengel
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
| | - Alexander Jochimsen
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
| | - Anna Hofmann
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
| | - Lukas Heintz
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany
- Institute for Cellular and Integrative Physiology, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Kiel University, 24105, Kiel, Germany
| | - Matthias Voss
- Institute of Biochemistry, Kiel University, Rudolf-Höber-Str. 1, 24118, Kiel, Germany.
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19
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The application of genome-wide CRISPR-Cas9 screens to dissect the molecular mechanisms of toxins. Comput Struct Biotechnol J 2022; 20:5076-5084. [PMID: 36187925 PMCID: PMC9489804 DOI: 10.1016/j.csbj.2022.09.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
Many toxins are life-threatening to both animals and humans. However, specific antidotes are not available for most of those toxins. The molecular mechanisms underlying the toxicology of well-known toxins are not yet fully characterized. Recently, the advance in CRISPR-Cas9 technologies has greatly accelerated the process of revealing the toxic mechanisms of some common toxins on hosts from a genome-wide perspective. The high-throughput CRISPR screen has made it feasible to untangle complicated interactions between a particular toxin and its corresponding targeting tissue(s). In this review, we present an overview of recent advances in molecular dissection of toxins’ cytotoxicity by using genome-wide CRISPR screens, summarize the components essential for toxin-specific CRISPR screens, and propose new strategies for future research.
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20
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Riyad JM, Weber T. Intracellular trafficking of adeno-associated virus (AAV) vectors: challenges and future directions. Gene Ther 2021; 28:683-696. [PMID: 33658649 PMCID: PMC8413391 DOI: 10.1038/s41434-021-00243-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/27/2021] [Accepted: 02/05/2021] [Indexed: 02/07/2023]
Abstract
In the last two decades, recombinant adeno-associated virus has emerged as the most popular gene therapy vector. Recently AAV gene therapy has been approved by the FDA for the treatment of two rare genetic disorders, namely the early childhood blindness disease Leber congenital amaurosis and spinal muscular atrophy (SMA). As is the case for the treatment of SMA, if the AAV vector must be administered systemically, very high vector doses are often required for therapeutic efficacy. But higher vector doses inevitably increase the risk of adverse events. The tragic death of three children in a clinical trial to treat X-linked myotubular myopathy with an AAV vector has thrown this limitation into sharp relief. Regardless of the precise cause(s) that led to the death of the two children, it is critical that we develop better AAV vectors to achieve therapeutic levels of expression with lower vector doses. To transduce successfully a target cell, AAV has to overcome both systemic as well as cellular roadblocks. In this review, we discuss some of the most prominent cellular roadblocks that AAV must get past to deliver successfully its therapeutic payload. We also highlight recent advancements in our knowledge of AAV biology that can potentially be harnessed to improve AAV vector performance and thereby make AAV gene therapy safer.
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Affiliation(s)
- Jalish M Riyad
- Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Weber
- Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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21
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Sardana R, Highland CM, Straight BE, Chavez CF, Fromme JC, Emr SD. Golgi membrane protein Erd1 Is essential for recycling a subset of Golgi glycosyltransferases. eLife 2021; 10:e70774. [PMID: 34821548 PMCID: PMC8616560 DOI: 10.7554/elife.70774] [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: 05/28/2021] [Accepted: 11/17/2021] [Indexed: 12/24/2022] Open
Abstract
Protein glycosylation in the Golgi is a sequential process that requires proper distribution of transmembrane glycosyltransferase enzymes in the appropriate Golgi compartments. Some of the cytosolic machinery required for the steady-state localization of some Golgi enzymes are known but existing models do not explain how many of these enzymes are localized. Here, we uncover the role of an integral membrane protein in yeast, Erd1, as a key facilitator of Golgi glycosyltransferase recycling by directly interacting with both the Golgi enzymes and the cytosolic receptor, Vps74. Loss of Erd1 function results in mislocalization of Golgi enzymes to the vacuole/lysosome. We present evidence that Erd1 forms an integral part of the recycling machinery and ensures productive recycling of several early Golgi enzymes. Our work provides new insights on how the localization of Golgi glycosyltransferases is spatially and temporally regulated, and is finely tuned to the cues of Golgi maturation.
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Affiliation(s)
- Richa Sardana
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Medicine, Cornell UniversityIthacaUnited States
| | - Carolyn M Highland
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Beth E Straight
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Christopher F Chavez
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Scott D Emr
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
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22
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Liu NJ, Hou LP, Bao JJ, Wang LJ, Chen XY. Sphingolipid metabolism, transport, and functions in plants: Recent progress and future perspectives. PLANT COMMUNICATIONS 2021; 2:100214. [PMID: 34746760 PMCID: PMC8553973 DOI: 10.1016/j.xplc.2021.100214] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 05/12/2021] [Accepted: 06/26/2021] [Indexed: 05/08/2023]
Abstract
Sphingolipids, which comprise membrane systems together with other lipids, are ubiquitous in cellular organisms. They show a high degree of diversity across plant species and vary in their structures, properties, and functions. Benefiting from the development of lipidomic techniques, over 300 plant sphingolipids have been identified. Generally divided into free long-chain bases (LCBs), ceramides, glycosylceramides (GlcCers) and glycosyl inositol phosphoceramides (GIPCs), plant sphingolipids exhibit organized aggregation within lipid membranes to form raft domains with sterols. Accumulating evidence has revealed that sphingolipids obey certain trafficking and distribution rules and confer unique properties to membranes. Functional studies using sphingolipid biosynthetic mutants demonstrate that sphingolipids participate in plant developmental regulation, stimulus sensing, and stress responses. Here, we present an updated metabolism/degradation map and summarize the structures of plant sphingolipids, review recent progress in understanding the functions of sphingolipids in plant development and stress responses, and review sphingolipid distribution and trafficking in plant cells. We also highlight some important challenges and issues that we may face during the process of studying sphingolipids.
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Affiliation(s)
- Ning-Jing Liu
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
- Corresponding author
| | - Li-Pan Hou
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Jing-Jing Bao
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Ling-Jian Wang
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
| | - Xiao-Ya Chen
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
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23
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Bereznicka A, Mikolajczyk K, Szymczak-Kulus K, Kapczynska K, Majorczyk E, Modlinska A, Piasecki T, Kaczmarek R, Czerwinski M. Two Paralogous Gb3/CD77 Synthases in Birds Show Different Preferences for Their Glycoprotein and Glycosphingolipid Substrates. Int J Mol Sci 2021; 22:9761. [PMID: 34575935 PMCID: PMC8466213 DOI: 10.3390/ijms22189761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/06/2021] [Accepted: 09/06/2021] [Indexed: 11/22/2022] Open
Abstract
Most glycosyltransferases show remarkable gross and fine substrate specificity, which is reflected in the old one enzyme-one linkage paradigm. While human Gb3/CD77 synthase is a glycosyltransferase that synthesizes the Galα1→4Gal moiety mainly on glycosphingolipids, its pigeon homolog prefers glycoproteins as acceptors. In this study, we characterized two Gb3/CD77 synthase paralogs found in pigeons (Columba livia). We evaluated their specificities in transfected human teratocarcinoma 2102Ep cells by flow cytofluorometry, Western blotting, high-performance thin-layer chromatography, mass spectrometry and metabolic labelling with 14C-galactose. We found that the previously described pigeon Gb3/CD77 synthase (called P) can use predominately glycoproteins as acceptors, while its paralog (called M), which we serendipitously discovered while conducting this study, efficiently synthesizes Galα1→4Gal caps on both glycoproteins and glycosphingolipids. These two paralogs may underlie the difference in expression profiles of Galα1→4Gal-terminated glycoconjugates between neoavians and mammals.
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Affiliation(s)
- Anna Bereznicka
- Laboratory of Glycobiology, Department of Immunochemistry, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.B.); (K.M.); (K.S.-K.); (R.K.)
| | - Krzysztof Mikolajczyk
- Laboratory of Glycobiology, Department of Immunochemistry, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.B.); (K.M.); (K.S.-K.); (R.K.)
| | - Katarzyna Szymczak-Kulus
- Laboratory of Glycobiology, Department of Immunochemistry, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.B.); (K.M.); (K.S.-K.); (R.K.)
| | - Katarzyna Kapczynska
- Laboratory of Medical Microbiology, Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland;
| | - Edyta Majorczyk
- Faculty of Physical Education and Physiotherapy, Opole University of Technology, 45-758 Opole, Poland;
| | - Anna Modlinska
- Department of Epizootiology and Clinic of Birds and Exotic Animals, Wroclaw University of Environmental Sciences, 50-366 Wroclaw, Poland; (A.M.); (T.P.)
| | - Tomasz Piasecki
- Department of Epizootiology and Clinic of Birds and Exotic Animals, Wroclaw University of Environmental Sciences, 50-366 Wroclaw, Poland; (A.M.); (T.P.)
| | - Radoslaw Kaczmarek
- Laboratory of Glycobiology, Department of Immunochemistry, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.B.); (K.M.); (K.S.-K.); (R.K.)
| | - Marcin Czerwinski
- Laboratory of Glycobiology, Department of Immunochemistry, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.B.); (K.M.); (K.S.-K.); (R.K.)
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24
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Regional Heritability Mapping of Quantitative Trait Loci Controlling Traits Related to Growth and Productivity in Popcorn (Zea mays L.). PLANTS 2021; 10:plants10091845. [PMID: 34579378 PMCID: PMC8466968 DOI: 10.3390/plants10091845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/16/2021] [Accepted: 08/31/2021] [Indexed: 11/17/2022]
Abstract
The method of regional heritability mapping (RHM) has become an important tool in the identification of quantitative trait loci (QTLs) controlling traits of interest in plants. Here, RHM was first applied in a breeding population of popcorn, to identify the QTLs and candidate genes involved in grain yield, plant height, kernel popping expansion, and first ear height, as well as determining the heritability of each significant genomic region. The study population consisted of 98 S1 families derived from the 9th recurrent selection cycle (C-9) of the open-pollinated variety UENF-14, which were genetically evaluated in two environments (ENV1 and ENV2). Seventeen and five genomic regions were mapped by the RHM method in ENV1 and ENV2, respectively. Subsequent genome-wide analysis based on the reference genome B73 revealed associations with forty-six candidate genes within these genomic regions, some of them are considered to be biologically important due to the proteins that they encode. The results obtained by the RHM method have the potential to contribute to knowledge on the genetic architecture of the growth and yield traits of popcorn, which might be used for marker-assisted selection in breeding programs.
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25
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Lujan P, Campelo F. Should I stay or should I go? Golgi membrane spatial organization for protein sorting and retention. Arch Biochem Biophys 2021; 707:108921. [PMID: 34038703 DOI: 10.1016/j.abb.2021.108921] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/12/2021] [Accepted: 05/03/2021] [Indexed: 12/23/2022]
Abstract
The Golgi complex is the membrane-bound organelle that lies at the center of the secretory pathway. Its main functions are to maintain cellular lipid homeostasis, to orchestrate protein processing and maturation, and to mediate protein sorting and export. These functions are not independent of one another, and they all require that the membranes of the Golgi complex have a well-defined biochemical composition. Importantly, a finely-regulated spatiotemporal organization of the Golgi membrane components is essential for the correct performance of the organelle. In here, we review our current mechanistic and molecular understanding of how Golgi membranes are spatially organized in the lateral and axial directions to fulfill their functions. In particular, we highlight the current evidence and proposed models of intra-Golgi transport, as well as the known mechanisms for the retention of Golgi residents and for the sorting and export of transmembrane cargo proteins. Despite the controversies, conflicting evidence, clashes between models, and technical limitations, the field has moved forward and we have gained extensive knowledge in this fascinating topic. However, there are still many important questions that remain to be completely answered. We hope that this review will help boost future investigations on these issues.
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Affiliation(s)
- Pablo Lujan
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860, Barcelona, Spain.
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860, Barcelona, Spain.
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26
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Zhang W, Yang X, Chen L, Liu YY, Venkatarangan V, Reist L, Hanson P, Xu H, Wang Y, Li M. A conserved ubiquitin- and ESCRT-dependent pathway internalizes human lysosomal membrane proteins for degradation. PLoS Biol 2021; 19:e3001361. [PMID: 34297722 PMCID: PMC8337054 DOI: 10.1371/journal.pbio.3001361] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/04/2021] [Accepted: 07/09/2021] [Indexed: 12/15/2022] Open
Abstract
The lysosome is an essential organelle to recycle cellular materials and maintain nutrient homeostasis, but the mechanism to down-regulate its membrane proteins is poorly understood. In this study, we performed a cycloheximide (CHX) chase assay to measure the half-lives of approximately 30 human lysosomal membrane proteins (LMPs) and identified RNF152 and LAPTM4A as short-lived membrane proteins. The degradation of both proteins is ubiquitin dependent. RNF152 is a transmembrane E3 ligase that ubiquitinates itself, whereas LAPTM4A uses its carboxyl-terminal PY motifs to recruit NEDD4-1 for ubiquitination. After ubiquitination, they are internalized into the lysosome lumen by the endosomal sorting complexes required for transport (ESCRT) machinery for degradation. Strikingly, when ectopically expressed in budding yeast, human RNF152 is still degraded by the vacuole (yeast lysosome) in an ESCRT-dependent manner. Thus, our study uncovered a conserved mechanism to down-regulate lysosome membrane proteins.
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Affiliation(s)
- Weichao Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Xi Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Liang Chen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yun-Yu Liu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Varsha Venkatarangan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lucas Reist
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Phyllis Hanson
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Haoxing Xu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yanzhuang Wang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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27
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Abaandou L, Quan D, Shiloach J. Affecting HEK293 Cell Growth and Production Performance by Modifying the Expression of Specific Genes. Cells 2021; 10:cells10071667. [PMID: 34359846 PMCID: PMC8304725 DOI: 10.3390/cells10071667] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/22/2022] Open
Abstract
The HEK293 cell line has earned its place as a producer of biotherapeutics. In addition to its ease of growth in serum-free suspension culture and its amenability to transfection, this cell line’s most important attribute is its human origin, which makes it suitable to produce biologics intended for human use. At the present time, the growth and production properties of the HEK293 cell line are inferior to those of non-human cell lines, such as the Chinese hamster ovary (CHO) and the murine myeloma NSO cell lines. However, the modification of genes involved in cellular processes, such as cell proliferation, apoptosis, metabolism, glycosylation, secretion, and protein folding, in addition to bioprocess, media, and vector optimization, have greatly improved the performance of this cell line. This review provides a comprehensive summary of important achievements in HEK293 cell line engineering and on the global engineering approaches and functional genomic tools that have been employed to identify relevant genes for targeted engineering.
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Affiliation(s)
- Laura Abaandou
- Biotechnology Core Laboratory National Institutes of Diabetes, Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA; (L.A.); (D.Q.)
- Department of Chemistry and Biochemistry, College of Science, George Mason University, Fairfax, VA 22030, USA
| | - David Quan
- Biotechnology Core Laboratory National Institutes of Diabetes, Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA; (L.A.); (D.Q.)
| | - Joseph Shiloach
- Biotechnology Core Laboratory National Institutes of Diabetes, Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA; (L.A.); (D.Q.)
- Correspondence:
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28
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The ER membrane protein complex subunit Emc3 controls angiogenesis via the FZD4/WNT signaling axis. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1868-1883. [PMID: 34128175 DOI: 10.1007/s11427-021-1941-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/29/2021] [Indexed: 02/08/2023]
Abstract
The endoplasmic reticulum (ER) membrane protein complex (EMC) regulates the synthesis and quality control of membrane proteins with multiple transmembrane domains. One of the membrane spanning subunits, EMC3, is a core member of the EMC complex that provides essential hydrophilic vestibule for substrate insertion. Here, we show that the EMC subunit Emc3 plays critical roles in the retinal vascular angiogenesis by regulating Norrin/Wnt signaling. Postnatal endothelial cell (EC)-specific deletion of Emc3 led to retarded retinal vascular development with a hyperpruned vascular network, the appearance of blunt-ended, aneurysm-like tip endothelial cells (ECs) with reduced numbers of filopodia and leakage of erythrocytes at the vascular front. Diminished tube formation and cell proliferation were also observed in EMC3 depleted human retinal endothelial cells (HRECs). We then discovered a critical role for EMC3 in expression of FZD4 receptor of β-catenin signaling using RNA sequencing, real-time quantitative PCR (RT-qPCR) and luciferase reporter assay. Moreover, augmentation of Wnt activity via lithium chloride (LiCl) treatment remarkably enhanced β-catenin signaling and cell proliferation of HRECs. Additionally, LiCl partially reversed the angiogenesis defects in Emc3-cKO mice. Our data reveal that Emc3 plays essential roles in angiogenesis through direct control of FZD4 expression and Norrin/β-catenin signaling.
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29
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Weiss RJ, Spahn PN, Chiang AW, Liu Q, Li J, Hamill KM, Rother S, Clausen TM, Hoeksema MA, Timm BM, Godula K, Glass CK, Tor Y, Gordts PL, Lewis NE, Esko JD. Genome-wide screens uncover KDM2B as a modifier of protein binding to heparan sulfate. Nat Chem Biol 2021; 17:684-692. [PMID: 33846619 PMCID: PMC8159865 DOI: 10.1038/s41589-021-00776-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 02/18/2021] [Indexed: 02/01/2023]
Abstract
Heparan sulfate (HS) proteoglycans bind extracellular proteins that participate in cell signaling, attachment and endocytosis. These interactions depend on the arrangement of sulfated sugars in the HS chains generated by well-characterized biosynthetic enzymes; however, the regulation of these enzymes is largely unknown. We conducted genome-wide CRISPR-Cas9 screens with a small-molecule ligand that binds to HS. Screening of A375 melanoma cells uncovered additional genes and pathways impacting HS formation. The top hit was the epigenetic factor KDM2B, a histone demethylase. KDM2B inactivation suppressed multiple HS sulfotransferases and upregulated the sulfatase SULF1. These changes differentially affected the interaction of HS-binding proteins. KDM2B-deficient cells displayed decreased growth rates, which was rescued by SULF1 inactivation. In addition, KDM2B deficiency altered the expression of many extracellular matrix genes. Thus, KDM2B controls proliferation of A375 cells through the regulation of HS structure and serves as a master regulator of the extracellular matrix.
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Affiliation(s)
- Ryan J. Weiss
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Philipp N. Spahn
- Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Austin W.T. Chiang
- Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Qing Liu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Jing Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Kristina M. Hamill
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA
| | - Sandra Rother
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Thomas M. Clausen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA,Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, 2200 Copenhagen, Denmark
| | - Marten A. Hoeksema
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Bryce M. Timm
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA
| | - Kamil Godula
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA,Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA,Department of Medicine, Copenhagen University Hospital, 2200 Copenhagen, Denmark
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA,Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA
| | - Philip L.S.M. Gordts
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA,Department of Medicine, Copenhagen University Hospital, 2200 Copenhagen, Denmark
| | - Nathan E. Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA,Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA,Co-corresponding authors
| | - Jeffrey D. Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA,Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA,Co-corresponding authors
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30
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Sakuma C, Sekizuka T, Kuroda M, Hanada K, Yamaji T. Identification of SYS1 as a Host Factor Required for Shiga Toxin-Mediated Cytotoxicity in Vero Cells. Int J Mol Sci 2021; 22:ijms22094936. [PMID: 34066520 PMCID: PMC8124574 DOI: 10.3390/ijms22094936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 12/12/2022] Open
Abstract
Shiga toxin (STx) or Vero toxin is a virulence factor produced by enterohemorrhagic Escherichia coli. The toxin binds to the glycosphingolipid globotriaosylceramide (Gb3) for its entry, and causes cell death by inhibiting ribosome function. Previously, we performed a loss-of-function screen in HeLa cells using a human CRISPR knockout (KO) library and identified various host genes required for STx-induced cell death. To determine whether this library targeted to the human genome is applicable to non-human primate cells and to identify previously unrecognized factors crucial for STx-induced cell death, we herein performed a similar screen in the African green monkey kidney-derived Vero C1008 subline. Many genes relevant to metabolic enzymes and membrane trafficking were enriched, although the number of enriched genes was less than that obtained in the screening for HeLa cells. Of note, several genes that had not been enriched in the previous screening were enriched: one of these genes was SYS1, which encodes a multi-spanning membrane protein in the Golgi apparatus. In SYS1 KO Vero cells, expression of Gb3 and sphingomyelin was decreased, while that of glucosylceramide and lactosylceramide was increased. In addition, loss of SYS1 inhibited the biosynthesis of protein glycans, deformed the Golgi apparatus, and perturbed the localization of trans-Golgi network protein (TGN) 46. These results indicate that the human CRISPR KO library is applicable to Vero cell lines, and SYS1 has a widespread effect on glycan biosynthesis via regulation of intra-Golgi and endosome–TGN retrograde transports.
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Affiliation(s)
- Chisato Sakuma
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan; (C.S.); (K.H.)
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan; (T.S.); (M.K.)
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan; (T.S.); (M.K.)
| | - Kentaro Hanada
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan; (C.S.); (K.H.)
| | - Toshiyuki Yamaji
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan; (C.S.); (K.H.)
- Correspondence:
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31
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Liu Y, Tian S, Thaker H, Dong M. Shiga Toxins: An Update on Host Factors and Biomedical Applications. Toxins (Basel) 2021; 13:222. [PMID: 33803852 PMCID: PMC8003205 DOI: 10.3390/toxins13030222] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 12/18/2022] Open
Abstract
Shiga toxins (Stxs) are classic bacterial toxins and major virulence factors of toxigenic Shigella dysenteriae and enterohemorrhagic Escherichia coli (EHEC). These toxins recognize a glycosphingolipid globotriaosylceramide (Gb3/CD77) as their receptor and inhibit protein synthesis in cells by cleaving 28S ribosomal RNA. They are the major cause of life-threatening complications such as hemolytic uremic syndrome (HUS), associated with severe cases of EHEC infection, which is the leading cause of acute kidney injury in children. The threat of Stxs is exacerbated by the lack of toxin inhibitors and effective treatment for HUS. Here, we briefly summarize the Stx structure, subtypes, in vitro and in vivo models, Gb3 expression and HUS, and then introduce recent studies using CRISPR-Cas9-mediated genome-wide screens to identify the host cell factors required for Stx action. We also summarize the latest progress in utilizing and engineering Stx components for biomedical applications.
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Affiliation(s)
- Yang Liu
- Department of Nephrology, The First Hospital of Jilin University, Changchun 130021, China
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA; (S.T.); (H.T.)
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Songhai Tian
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA; (S.T.); (H.T.)
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Hatim Thaker
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA; (S.T.); (H.T.)
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Min Dong
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA; (S.T.); (H.T.)
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
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Genetic glycoengineering in mammalian cells. J Biol Chem 2021; 296:100448. [PMID: 33617880 PMCID: PMC8042171 DOI: 10.1016/j.jbc.2021.100448] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023] Open
Abstract
Advances in nuclease-based gene-editing technologies have enabled precise, stable, and systematic genetic engineering of glycosylation capacities in mammalian cells, opening up a plethora of opportunities for studying the glycome and exploiting glycans in biomedicine. Glycoengineering using chemical, enzymatic, and genetic approaches has a long history, and precise gene editing provides a nearly unlimited playground for stable engineering of glycosylation in mammalian cells to explore and dissect the glycome and its many biological functions. Genetic engineering of glycosylation in cells also brings studies of the glycome to the single cell level and opens up wider use and integration of data in traditional omics workflows in cell biology. The last few years have seen new applications of glycoengineering in mammalian cells with perspectives for wider use in basic and applied glycosciences, and these have already led to discoveries of functions of glycans and improved designs of glycoprotein therapeutics. Here, we review the current state of the art of genetic glycoengineering in mammalian cells and highlight emerging opportunities.
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Drabavicius G, Daelemans D. Intermedilysin cytolytic activity depends on heparan sulfates and membrane composition. PLoS Genet 2021; 17:e1009387. [PMID: 33577603 PMCID: PMC7906465 DOI: 10.1371/journal.pgen.1009387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 02/25/2021] [Accepted: 01/27/2021] [Indexed: 12/26/2022] Open
Abstract
Cholesterol-dependent cytolysins (CDCs), of which intermedilysin (ILY) is an archetypal member, are a group of pore-forming toxins secreted by a large variety of pathogenic bacteria. These toxins, secreted as soluble monomers, oligomerize upon interaction with cholesterol in the target membrane and transect it as pores of diameters of up to 100 to 300 Å. These pores disrupt cell membranes and result in cell lysis. The immune receptor CD59 is a well-established cellular factor required for intermedilysin pore formation. In this study, we applied genome-wide CRISPR-Cas9 knock-out screening to reveal additional cellular co-factors essential for ILY-mediated cell lysis. We discovered a plethora of genes previously not associated with ILY, many of which are important for membrane constitution. We show that heparan sulfates facilitate ILY activity, which can be inhibited by heparin. Furthermore, we identified hits in both protein and lipid glycosylation pathways and show a role for glucosylceramide, demonstrating that membrane organization is important for ILY activity. We also cross-validated identified genes with vaginolysin and pneumolysin and found that pneumolysin's cytolytic activity strongly depends on the asymmetric distribution of membrane phospholipids. This study shows that membrane-targeting toxins combined with genetic screening can identify genes involved in biological membrane composition and metabolism.
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Affiliation(s)
- Gediminas Drabavicius
- KU Leuven Department of Microbiology, Immunology, and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
- Vilnius University, Life Sciences Center, Institute of Biotechnology, Vilnius, Lithuania
| | - Dirk Daelemans
- KU Leuven Department of Microbiology, Immunology, and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
- * E-mail:
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Kok K, Zwiers KC, Boot RG, Overkleeft HS, Aerts JMFG, Artola M. Fabry Disease: Molecular Basis, Pathophysiology, Diagnostics and Potential Therapeutic Directions. Biomolecules 2021; 11:271. [PMID: 33673160 PMCID: PMC7918333 DOI: 10.3390/biom11020271] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 02/06/2023] Open
Abstract
Fabry disease (FD) is a lysosomal storage disorder (LSD) characterized by the deficiency of α-galactosidase A (α-GalA) and the consequent accumulation of toxic metabolites such as globotriaosylceramide (Gb3) and globotriaosylsphingosine (lysoGb3). Early diagnosis and appropriate timely treatment of FD patients are crucial to prevent tissue damage and organ failure which no treatment can reverse. LSDs might profit from four main therapeutic strategies, but hitherto there is no cure. Among the therapeutic possibilities are intravenous administered enzyme replacement therapy (ERT), oral pharmacological chaperone therapy (PCT) or enzyme stabilizers, substrate reduction therapy (SRT) and the more recent gene/RNA therapy. Unfortunately, FD patients can only benefit from ERT and, since 2016, PCT, both always combined with supportive adjunctive and preventive therapies to clinically manage FD-related chronic renal, cardiac and neurological complications. Gene therapy for FD is currently studied and further strategies such as substrate reduction therapy (SRT) and novel PCTs are under investigation. In this review, we discuss the molecular basis of FD, the pathophysiology and diagnostic procedures, together with the current treatments and potential therapeutic avenues that FD patients could benefit from in the future.
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Affiliation(s)
- Ken Kok
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Kimberley C Zwiers
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Rolf G Boot
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Hermen S Overkleeft
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Johannes M F G Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Marta Artola
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Song N, Chen L, Ren X, Waterfield NR, Yang J, Yang G. N-Glycans and sulfated glycosaminoglycans contribute to the action of diverse Tc toxins on mammalian cells. PLoS Pathog 2021; 17:e1009244. [PMID: 33539469 PMCID: PMC7861375 DOI: 10.1371/journal.ppat.1009244] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/18/2020] [Indexed: 01/11/2023] Open
Abstract
Tc toxin is an exotoxin composed of three subunits named TcA, TcB and TcC. Structural analysis revealed that TcA can form homopentamer that mediates the cellular recognition and delivery processes, thus contributing to the host tropism of Tc toxin. N-glycans and heparan sulfates have been shown to act as receptors for several Tc toxins. Here, we performed two independent genome-wide CRISPR-Cas9 screens, and have validated glycans and sulfated glycosaminoglycans (sGAGs) as Tc toxin receptors also for previously uncharacterized Tc toxins. We found that TcdA1 form Photorhabdus luminescens W14 (TcdA1W14) can recognize N-glycans via the RBD-D domain, corroborating previous findings. Knockout of N-glycan processing enzymes specifically blocks the intoxication of TcdA1W14-assembled Tc toxin. On the other hand, our results showed that sGAG biosynthesis pathway is involved in the cell surface binding of TcdA2TT01 (TcdA2 from P. luminescens TT01). Competition assays and biolayer interferometry demonstrated that the sulfation group in sGAGs is required for the binding of TcdA2TT01. Finally, based on the conserved domains of representative TcA proteins, we have identified 1,189 putative TcAs from 1,039 bacterial genomes. These TcAs are categorized into five subfamilies. Each subfamily shows a good correlation with both genetic organization of the TcA protein(s) and taxonomic origin of the genomes, suggesting these subfamilies may utilize different mechanisms for cellular recognition. Taken together, our results support the previously described two different binding modalities of Tc toxins, leading to unique host targeting properties. We also present the bioinformatics data and receptor screening strategies for TcA proteins, provide new insights into understanding host specificity and biomedical applications of Tc toxins. The Toxin complexes, also referred to as Tc toxins, are a family of A5BC exotoxins widely distributed among Gram-negative and positive bacteria. First identified in Entomopathogenic bacteria as key virulence factors to combat insect hosts, putative Tc toxin loci are also encoded by a range of human pathogens such as Salmonella and Yersinia. Previous studies indicated that several Tc toxins can target invertebrate and vertebrate cells via binding with N-glycans and heparan sulfates. Here our genome-wide CRISPR-Cas9 screens validated that different Tc toxins utilized distinct receptors for the adhesion to their targets, which is determined by TcA homopentamer. For example, TcdA1 from Photorhabdus luminescens W14 (TcdA1W14) relies on N-glycan binding to exert its toxic effects, while sulfate groups of sulfated glycosaminoglycans are critical for the cell targeting of other TcAs such as TcdA2TT01 (TcdA2 from P. luminescens TT01). Consistent with the previously described different binding modalities of Tc toxins, our results confirm that the receptor selectivity of TcAs contribute to the cellular tropism of Tc toxins. Furthermore we has also identified 1,189 TcA homologues and categorized them into five subfamilies. Each TcA subfamily shows a good correlation with the taxonomic origin of the genomes, suggesting these subfamilies are linked to diverse host tropisms via different binding modalities. Together, our findings provide mechanistic insights into understanding host specificity of distinct Tc toxins and the development of therapeutics for Tc toxin-related infections, as well as the adaptation of Tc-injectisomes as potential biotechnology tools and pest-control weapons.
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Affiliation(s)
- Nan Song
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Lihong Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xingmei Ren
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | | | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guowei Yang
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- * E-mail:
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Dichlberger A, Zhou K, Bäck N, Nyholm T, Backman A, Mattjus P, Ikonen E, Blom T. LAPTM4B controls the sphingolipid and ether lipid signature of small extracellular vesicles. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1866:158855. [PMID: 33181324 DOI: 10.1016/j.bbalip.2020.158855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 01/08/2023]
Abstract
Lysosome Associated Protein Transmembrane 4B (LAPTM4B) is a four-membrane spanning ceramide interacting protein that regulates mTORC1 signaling. Here, we show that LAPTM4B is sorted into intraluminal vesicles (ILVs) of multivesicular endosomes (MVEs) and released in small extracellular vesicles (sEVs) into conditioned cell culture medium and human urine. Efficient sorting of LAPTM4B into ILV membranes depends on its third transmembrane domain containing a sphingolipid interaction motif (SLim). Unbiased lipidomic analysis reveals a strong enrichment of glycosphingolipids in sEVs secreted from LAPTM4B knockout cells and from cells expressing a SLim-deficient LAPTM4B mutant. The altered sphingolipid profile is accompanied by a distinct SLim-dependent co-modulation of ether lipid species. The changes in the lipid composition of sEVs derived from LAPTM4B knockout cells is reflected by an increased stability of membrane nanodomains of sEVs. These results identify LAPTM4B as a determinant of the glycosphingolipid profile and membrane properties of sEVs.
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Affiliation(s)
- Andrea Dichlberger
- Department of Anatomy and Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Minerva Foundation Institute for Medical Research, Helsinki, Finland.
| | - Kecheng Zhou
- Department of Anatomy and Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Minerva Foundation Institute for Medical Research, Helsinki, Finland.
| | - Nils Bäck
- Department of Anatomy and Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Thomas Nyholm
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland.
| | - Anders Backman
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland.
| | - Peter Mattjus
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland.
| | - Elina Ikonen
- Department of Anatomy and Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Minerva Foundation Institute for Medical Research, Helsinki, Finland.
| | - Tomas Blom
- Department of Anatomy and Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Minerva Foundation Institute for Medical Research, Helsinki, Finland.
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Global view of human protein glycosylation pathways and functions. Nat Rev Mol Cell Biol 2020; 21:729-749. [PMID: 33087899 DOI: 10.1038/s41580-020-00294-x] [Citation(s) in RCA: 515] [Impact Index Per Article: 128.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 02/07/2023]
Abstract
Glycosylation is the most abundant and diverse form of post-translational modification of proteins that is common to all eukaryotic cells. Enzymatic glycosylation of proteins involves a complex metabolic network and different types of glycosylation pathways that orchestrate enormous amplification of the proteome in producing diversity of proteoforms and its biological functions. The tremendous structural diversity of glycans attached to proteins poses analytical challenges that limit exploration of specific functions of glycosylation. Major advances in quantitative transcriptomics, proteomics and nuclease-based gene editing are now opening new global ways to explore protein glycosylation through analysing and targeting enzymes involved in glycosylation processes. In silico models predicting cellular glycosylation capacities and glycosylation outcomes are emerging, and refined maps of the glycosylation pathways facilitate genetic approaches to address functions of the vast glycoproteome. These approaches apply commonly available cell biology tools, and we predict that use of (single-cell) transcriptomics, genetic screens, genetic engineering of cellular glycosylation capacities and custom design of glycoprotein therapeutics are advancements that will ignite wider integration of glycosylation in general cell biology.
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38
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Tian S, Wu Q, Zhou B, Choi MY, Ding B, Yang W, Dong M. Proteomic Analysis Identifies Membrane Proteins Dependent on the ER Membrane Protein Complex. Cell Rep 2020; 28:2517-2526.e5. [PMID: 31484065 PMCID: PMC6749609 DOI: 10.1016/j.celrep.2019.08.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 06/18/2019] [Accepted: 07/30/2019] [Indexed: 02/04/2023] Open
Abstract
The endoplasmic reticulum (ER) membrane protein complex (EMC) is a key contributor to biogenesis and membrane integration of transmembrane proteins, but our understanding of its mechanisms and the range of EMC-dependent proteins remains incomplete. Here, we carried out an unbiased mass spectrometry (MS)-based quantitative proteomic analysis comparing membrane proteins in EMC-deficient cells to wild-type (WT) cells and identified 36 EMC-dependent membrane proteins and 171 EMC-independent membrane proteins. Of these, six EMC-dependent and six EMC-independent proteins were further independently validated. We found that a common feature among EMC-dependent proteins is that they contain transmembrane domains (TMDs) with polar and/or charged residues. Mutagenesis studies demonstrate that EMC dependency can be converted in cells by removing or introducing polar and/or charged residues within TMDs. Our studies expand the list of validated EMC-dependent and EMC-independent proteins and suggest that the EMC is involved in handling TMDs with residues challenging for membrane integration. The endoplasmic reticulum membrane protein complex (EMC) contributes to the biogenesis of transmembrane proteins. Using mass spectrometry-based quantitative proteomic analysis, Tian et al. identify EMC-dependent and EMC-independent proteins. The authors find evidence that the EMC is involved in handling transmembrane domains with polar and/or charged residues that are challenging for membrane integration.
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Affiliation(s)
- Songhai Tian
- Department of Urology, Boston Children's Hospital, and Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Quan Wu
- Department of Urology, Boston Children's Hospital, and Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Central Laboratory of Medical Research Centre, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, People's Republic of China
| | - Bo Zhou
- Division of Cancer Biology and Therapeutics, Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mei Yuk Choi
- Division of Genetics, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA 02115, USA
| | - Bo Ding
- Bonacept LLC, San Diego, CA 92122, USA
| | - Wei Yang
- Division of Cancer Biology and Therapeutics, Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Min Dong
- Department of Urology, Boston Children's Hospital, and Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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39
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De Cesco S, Davis JB, Brennan PE. TargetDB: A target information aggregation tool and tractability predictor. PLoS One 2020; 15:e0232644. [PMID: 32877430 PMCID: PMC7467329 DOI: 10.1371/journal.pone.0232644] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
When trying to identify new potential therapeutic protein targets, access to data and knowledge is increasingly important. In a field where new resources and data sources become available every day, it is crucial to be able to take a step back and look at the wider picture in order to identify potential drug targets. While this task is routinely performed by bespoke literature searches, it is often time-consuming and lacks uniformity when comparing multiple targets at one time. To address this challenge, we developed TargetDB, a tool that aggregates public information available on given target(s) (links to disease, safety, 3D structures, ligandability, novelty, etc.) and assembles it in an easy to read output ready for the researcher to analyze. In addition, we developed a target scoring system based on the desirable attributes of good therapeutic targets and machine learning classification system to categorize novel targets as having promising or challenging tractrability. In this manuscript, we present the methodology used to develop TargetDB as well as test cases.
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Affiliation(s)
- Stephane De Cesco
- Nuffield Department of Medicine, ARUK Oxford Drug Discovery Institute, Target Discovery Institute, University of Oxford, Oxford, United-Kingdom
- * E-mail: (PEB); (SDC)
| | - John B. Davis
- Nuffield Department of Medicine, ARUK Oxford Drug Discovery Institute, Target Discovery Institute, University of Oxford, Oxford, United-Kingdom
| | - Paul E. Brennan
- Nuffield Department of Medicine, ARUK Oxford Drug Discovery Institute, Target Discovery Institute, University of Oxford, Oxford, United-Kingdom
- * E-mail: (PEB); (SDC)
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40
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Murali P, Johnson BP, Lu Z, Climer L, Scott DA, Foulquier F, Oprea-Ilies G, Lupashin V, Drake RR, Abbott KL. Novel role for the Golgi membrane protein TMEM165 in control of migration and invasion for breast carcinoma. Oncotarget 2020; 11:2747-2762. [PMID: 32733646 PMCID: PMC7367651 DOI: 10.18632/oncotarget.27668] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/20/2020] [Indexed: 12/21/2022] Open
Abstract
The TMEM165 gene encodes for a multiple pass membrane protein localized in the Golgi that has been linked to congenital disorders of glycosylation. The TMEM165 protein is a putative ion transporter that regulates H+/Ca++/Mn++ homeostasis and pH in the Golgi. Previously, we identified TMEM165 as a potential biomarker for breast carcinoma in a glycoproteomic study using late stage invasive ductal carcinoma tissues with patient- matched adjacent normal tissues. The TMEM165 protein was not detected in non-malignant matched breast tissues and was detected in invasive ductal breast carcinoma tissues by mass spectrometry. Our hypothesis is that the TMEM165 protein confers a growth advantage to breast cancer. In this preliminary study we have investigated the expression of TMEM165 in earlier stage invasive ductal carcinoma and ductal carcinoma in situ cases. We created a CRISPR/Cas9 knockout of TMEM165 in the human invasive breast cancer cell line MDAMB231. Our results indicate that removal of TMEM165 in these cells results in a significant reduction of cell migration, tumor growth, and tumor vascularization in vivo. Furthermore, we find that TMEM165 expression alters the glycosylation of breast cancer cells and these changes promote the invasion and growth of breast cancer by altering the expression levels of key glycoproteins involved in regulation of the epithelial to mesenchymal transition such as E-cadherin. These studies illustrate new potential functions for this Golgi membrane protein in the control of breast cancer growth and invasion.
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Affiliation(s)
- Pavitra Murali
- University of Oklahoma Health Sciences Center, Department of Biochemistry and Molecular Biology, Oklahoma City, OK, United States
| | - Blake P Johnson
- Ouchita Baptist University, Department of Biology, Arkadelphia, AR, United States
| | - Zhongpeng Lu
- University of Oklahoma Health Sciences Center, Department of Biochemistry and Molecular Biology, Oklahoma City, OK, United States
| | - Leslie Climer
- University of Arkansas for Medical Sciences, Department of Biophysics and Physiology, Little Rock, AR, United States
| | - Danielle A Scott
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, SC, United States
| | - Francois Foulquier
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche, Unité de Glycobiologie Structurale et Fonctionnelle, University of Lille, Lille, France
| | | | - Vladimir Lupashin
- University of Arkansas for Medical Sciences, Department of Biophysics and Physiology, Little Rock, AR, United States
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, SC, United States
| | - Karen L Abbott
- University of Oklahoma Health Sciences Center, Department of Biochemistry and Molecular Biology, Oklahoma City, OK, United States
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Meisen WH, Nejad ZB, Hardy M, Zhao H, Oliverio O, Wang S, Hale C, Ollmann MM, Collins PJ. Pooled Screens Identify GPR108 and TM9SF2 as Host Cell Factors Critical for AAV Transduction. Mol Ther Methods Clin Dev 2020; 17:601-611. [PMID: 32280726 PMCID: PMC7139131 DOI: 10.1016/j.omtm.2020.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 03/12/2020] [Indexed: 12/19/2022]
Abstract
Adeno-associated virus (AAV) has been used extensively as a vector for gene therapy. Despite its widespread use, the mechanisms by which AAV enters the cell and is trafficked to the nucleus are poorly understood. In this study, we performed two pooled, genome-wide screens to identify positive and negative factors modulating AAV2 transduction. Genome-wide libraries directed against all human genes with four designs per gene or eight designs per gene were transduced into U-2 OS cells. These pools were transduced with AAV2 encoding EGFP and sorted based on the intensity of EGFP expression. Analysis of enriched and depleted barcodes in the sorted samples identified several genes that putatively decreased AAV2 transduction. A subset of screen hits was validated in flow cytometry and imaging studies. In addition to KIAA0319L (AAVR), we confirmed the role of two genes, GPR108 and TM9SF2, in mediating viral transduction in eight different AAV serotypes. Interestingly, GPR108 displayed serotype selectivity and was not required for AAV5 transduction. Follow-up studies suggested that GPR108 localized primarily to the Golgi, where it may interact with AAV and play a critical role in mediating virus escape or trafficking. Cumulatively, these results expand our understanding of the process of AAV transduction in different cell types and serotypes.
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Affiliation(s)
- W. Hans Meisen
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
| | | | - Miki Hardy
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
| | - Huiren Zhao
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
| | - Oliver Oliverio
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
| | - Songli Wang
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
| | - Christopher Hale
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
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Baddal B. Next-generation technologies for studying host-pathogen interactions: a focus on dual transcriptomics, CRISPR/Cas9 screening and organs-on-chips. Pathog Dis 2020; 77:5593955. [PMID: 31626299 DOI: 10.1093/femspd/ftz060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/16/2019] [Indexed: 12/13/2022] Open
Abstract
Pathogens constantly interact with their hosts and the environment, and therefore have evolved unique virulence mechanisms to target and breach host defense barriers and manipulate host immune response to establish an infection. Advances in technologies that allow genome mining, gene editing such as CRISPR/Cas9, genomic, epigenomic and transcriptomic studies such as dual RNA-seq, coupled with bioinformatics, have accelerated the field of host-pathogen interactions within a broad range of infection models. Underpinning of the molecular changes that accompany invasion of eukaryotic cells with pathogenic microorganisms at the intersection of host, pathogen and their local environment has provided a better understanding of infectious disease mechanisms and antimicrobial strategies. The recent evolution of physiologically relevant three-dimensional (3-D) tissue/organ models and microfluidic organ-on-chip devices also provided a window to a more predictive framework of infectious disease processes. These approaches combined hold the potential to highly impact discovery of novel drug targets and vaccine candidates of the future. Here, we review three of the available and emerging technologies-dual RNA-seq, CRISPR/Cas9 screening and organs-on-chips, applicable to the high throughput study and deciphering of interaction networks between pathogens and their hosts that are critical for the development of novel therapeutics.
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Affiliation(s)
- Buket Baddal
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, Near East Boulevard, Nicosia 99010, Cyprus
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43
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Majumder S, Kono M, Lee YT, Byrnes C, Li C, Tuymetova G, Proia RL. A genome-wide CRISPR/Cas9 screen reveals that the aryl hydrocarbon receptor stimulates sphingolipid levels. J Biol Chem 2020; 295:4341-4349. [PMID: 32029474 PMCID: PMC7105297 DOI: 10.1074/jbc.ac119.011170] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/28/2020] [Indexed: 01/12/2023] Open
Abstract
Sphingolipid biosynthesis generates lipids for membranes and signaling that are crucial for many developmental and physiological processes. In some cases, large amounts of specific sphingolipids must be synthesized for specialized physiological functions, such as during axon myelination. How sphingolipid synthesis is regulated to fulfill these physiological requirements is not known. To identify genes that positively regulate membrane sphingolipid levels, here we employed a genome-wide CRISPR/Cas9 loss-of-function screen in HeLa cells using selection for resistance to Shiga toxin, which uses a plasma membrane-associated glycosphingolipid, globotriaosylceramide (Gb3), for its uptake. The screen identified several genes in the sphingolipid biosynthetic pathway that are required for Gb3 synthesis, and it also identified the aryl hydrocarbon receptor (AHR), a ligand-activated transcription factor widely involved in development and physiology, as being required for Gb3 biosynthesis. AHR bound and activated the gene promoter of serine palmitoyltransferase small subunit A (SPTSSA), which encodes a subunit of the serine palmitoyltransferase that catalyzes the first and rate-limiting step in de novo sphingolipid biosynthesis. AHR knockout HeLa cells exhibited significantly reduced levels of cell-surface Gb3, and both AHR knockout HeLa cells and tissues from Ahr knockout mice displayed decreased sphingolipid content as well as significantly reduced expression of several key genes in the sphingolipid biosynthetic pathway. The sciatic nerve of Ahr knockout mice exhibited both reduced ceramide content and reduced myelin thickness. These results indicate that AHR up-regulates sphingolipid levels and is important for full axon myelination, which requires elevated levels of membrane sphingolipids.
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Affiliation(s)
- Saurav Majumder
- Genetics of Development and Disease Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Mari Kono
- Genetics of Development and Disease Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Y Terry Lee
- Genetics of Development and Disease Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Colleen Byrnes
- Genetics of Development and Disease Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Cuiling Li
- Genetics of Development and Disease Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Galina Tuymetova
- Genetics of Development and Disease Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Richard L Proia
- Genetics of Development and Disease Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892.
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Mesquita FS, van der Goot FG, Sergeeva OA. Mammalian membrane trafficking as seen through the lens of bacterial toxins. Cell Microbiol 2020; 22:e13167. [PMID: 32185902 PMCID: PMC7154709 DOI: 10.1111/cmi.13167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 12/12/2022]
Abstract
A fundamental question of eukaryotic cell biology is how membrane organelles are organised and interact with each other. Cell biologists address these questions by characterising the structural features of membrane compartments and the mechanisms that coordinate their exchange. To do so, they must rely on variety of cargo molecules and treatments that enable targeted perturbation, localisation, and labelling of specific compartments. In this context, bacterial toxins emerged in cell biology as paradigm shifting molecules that enabled scientists to not only study them from the side of bacterial infection but also from the side of the mammalian host. Their selectivity, potency, and versatility made them exquisite tools for uncovering much of our current understanding of membrane trafficking mechanisms. Here, we will follow the steps that lead toxins until their intracellular targets, highlighting how specific events helped us comprehend membrane trafficking and establish the fundamentals of various cellular organelles and processes. Bacterial toxins will continue to guide us in answering crucial questions in cellular biology while also acting as probes for new technologies and applications.
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Affiliation(s)
| | | | - Oksana A Sergeeva
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
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RAB5A and TRAPPC6B are novel targets for Shiga toxin 2a inactivation in kidney epithelial cells. Sci Rep 2020; 10:4945. [PMID: 32188865 PMCID: PMC7080763 DOI: 10.1038/s41598-020-59694-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/30/2020] [Indexed: 12/21/2022] Open
Abstract
The cardinal virulence factor of human-pathogenic enterohaemorrhagic Escherichia coli (EHEC) is Shiga toxin (Stx), which causes severe extraintestinal complications including kidney failure by damaging renal endothelial cells. In EHEC pathogenesis, the disturbance of the kidney epithelium by Stx becomes increasingly recognised, but how this exactly occurs is unknown. To explore this molecularly, we investigated the Stx receptor content and transcriptomic profile of two human renal epithelial cell lines: highly Stx-sensitive ACHN cells and largely Stx-insensitive Caki-2 cells. Though both lines exhibited the Stx receptor globotriaosylceramide, RNAseq revealed strikingly different transcriptomic responses to an Stx challenge. Using RNAi to silence factors involved in ACHN cells’ Stx response, the greatest protection occurred when silencing RAB5A and TRAPPC6B, two host factors that we newly link to Stx trafficking. Silencing these factors alongside YKT6 fully prevented the cytotoxic Stx effect. Overall, our approach reveals novel subcellular targets for potential therapies against Stx-mediated kidney failure.
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Li D, Mukhopadhyay S. Functional analyses of the UDP-galactose transporter SLC35A2 using the binding of bacterial Shiga toxins as a novel activity assay. Glycobiology 2020; 29:490-503. [PMID: 30834435 DOI: 10.1093/glycob/cwz016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/17/2019] [Accepted: 02/28/2019] [Indexed: 01/13/2023] Open
Abstract
SLC35A2 transports UDP-galactose from the cytosol to the lumen of the Golgi apparatus and endoplasmic reticulum for glycosylation. Mutations in SLC35A2 induce a congenital disorder of glycosylation. Despite the biomedical relevance, mechanisms of transport via SLC35A2 and the impact of disease-associated mutations on activity are unclear. To address these issues, we generated a predicted structure of SLC35A2 and assayed for the effects of a set of structural and disease-associated mutations. Activity assays were performed using a rescue approach in ΔSLC35A2 cells and took advantage of the fact that SLC35A2 is required for expression of the glycosphingolipid globotriaosylceramide (Gb3), the cell surface receptor for Shiga toxin 1 (STx1) and 2 (STx2). The N- and C-terminal cytoplasmic loops of SLC35A2 were dispensable for activity, but two critical glycine (Gly-202 and Gly-214) and lysine (Lys-78 and Lys-297) residues in transmembrane segments were required. Residues corresponding to Gly-202 and Gly-214 in the related transporter SLC35A1 form a substrate-translocating channel, suggesting that a similar mechanism may be involved in SLC35A2. Among the eight disease-associated mutations tested, SLC35A2 function was completely inhibited by two (S213F and G282R) and partially inhibited by three (R55L, G266V, and S304P), providing a straight-forward mechanism of disease. Interestingly, the remaining three (V331I, V258M, and Y267C) did not impact SLC35A2 function, suggesting that complexities beyond loss of transporter activity may underlie disease due to these mutations. Overall, our results provide new insights into the mechanisms of transport of SLC35A2 and improve understanding of the relationship between SLC35A2 mutations and disease.
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Affiliation(s)
- Danyang Li
- Division of Pharmacology & Toxicology, College of Pharmacy, Institute for Cellular & Molecular Biology, and Institute for Neuroscience, The University of Texas at Austin, Austin, TX, USA
| | - Somshuvra Mukhopadhyay
- Division of Pharmacology & Toxicology, College of Pharmacy, Institute for Cellular & Molecular Biology, and Institute for Neuroscience, The University of Texas at Austin, Austin, TX, USA
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Preparation of Fluorescent Recombinant Shiga Toxin B Subunit and Its Application to Flow Cytometry. Methods Mol Biol 2020; 2132:463-474. [PMID: 32306353 DOI: 10.1007/978-1-0716-0430-4_45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Shiga toxin (Stx) is a major virulence factor of enterohemorrhagic Escherichia coli (E. coli). Stx consists of one enzymatic A subunit and five B subunits (StxB) that are involved in binding. The StxB pentamer specifically recognizes a glycosphingolipid, globotriaosylceramide (Gb3), as a receptor; therefore, it can be used as a probe to detect Gb3. This chapter describes the preparation of recombinant Stx1B proteins using E. coli, their conjugation with fluorescent dyes, and their application for flow cytometry. The prepared fluorescent StxB proteins bound to cells of several lines, including the HeLa human cervix adenocarcinoma cell line and the THP-1 human monocytic leukemia cell line. Furthermore, the probe was useful for confirmation of several sphingolipid-deficient HeLa cell lines that were constructed using genome editing.
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Welch LG, Munro S. A tale of short tails, through thick and thin: investigating the sorting mechanisms of Golgi enzymes. FEBS Lett 2019; 593:2452-2465. [DOI: 10.1002/1873-3468.13553] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Lawrence G. Welch
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge UK
| | - Sean Munro
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge UK
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Sulfated glycosaminoglycans and low-density lipoprotein receptor contribute to Clostridium difficile toxin A entry into cells. Nat Microbiol 2019; 4:1760-1769. [PMID: 31160825 PMCID: PMC6754795 DOI: 10.1038/s41564-019-0464-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/19/2019] [Indexed: 12/18/2022]
Abstract
Clostridium difficile toxin A (TcdA) is a major exotoxin contributing to disruption of the colonic epithelium during C. difficile infection. TcdA contains a carbohydrate-binding combined repetitive oligopeptides (CROPs) domain that mediates its attachment to cell surfaces, but recent data suggest the existence of CROPs-independent receptors. Here, we carried out genome-wide clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated screens using a truncated TcdA lacking the CROPs, and identified sulfated glycosaminoglycans (sGAGs) and low-density lipoprotein receptor (LDLR) as host factors contributing to binding and entry of TcdA. TcdA recognizes the sulfation group in sGAGs. Blocking sulfation and glycosaminoglycan synthesis reduces TcdA binding and entry into cells. Binding of TcdA to the colonic epithelium can be reduced by surfen, a small molecule that masks sGAGs, by GM-1111, a sulfated heparan sulfate analogue, and by sulfated cyclodextrin, a sulfated small molecule. Cells lacking LDLR also show reduced sensitivity to TcdA, although binding between LDLR and TcdA are not detected, suggesting that LDLR may facilitate endocytosis of TcdA. Finally, GM-1111 reduces TcdA-induced fluid accumulation and tissue damage in the colon in a mouse model in which TcdA is injected into the caecum. These data demonstrate in vivo and pathological relevance of TcdA-sGAGs interactions, and reveal a potential therapeutic approach of protecting colonic tissues by blocking these interactions.
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