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Shinde AP, Kučerová J, Dacks JB, Tachezy J. The retromer and retriever systems are conserved and differentially expanded in parabasalids. J Cell Sci 2024; 137:jcs261949. [PMID: 38884339 PMCID: PMC11267458 DOI: 10.1242/jcs.261949] [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: 01/09/2024] [Accepted: 06/06/2024] [Indexed: 06/18/2024] Open
Abstract
Early endosomes sort transmembrane cargo either for lysosomal degradation or retrieval to the plasma membrane or the Golgi complex. Endosomal retrieval in eukaryotes is governed by the anciently homologous retromer or retriever complexes. Each comprises a core tri-protein subcomplex, membrane-deformation proteins and interacting partner complexes, together retrieving a variety of known cargo proteins. Trichomonas vaginalis, a sexually transmitted human parasite, uses the endomembrane system for pathogenesis. It has massively and selectively expanded its endomembrane protein complement, the evolutionary path of which has been largely unexplored. Our molecular evolutionary study of retromer, retriever and associated machinery in parabasalids and its free-living sister lineage of Anaeramoeba demonstrates specific expansion of the retromer machinery, contrasting with the retriever components. We also observed partial loss of the Commander complex and sorting nexins in Parabasalia but complete retention in Anaeramoeba. Notably, we identified putative parabasalid sorting nexin analogs. Finally, we report the first retriever protein localization in a non-metazoan group along with retromer protein localization in T. vaginalis.
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Affiliation(s)
- Abhishek Prakash Shinde
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
- Division of Infectious Diseases, Department of Medicine and Department of Biological Sciences,University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Jitka Kučerová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
| | - Joel Bryan Dacks
- Division of Infectious Diseases, Department of Medicine and Department of Biological Sciences,University of Alberta, Edmonton, Alberta T6G 2G3, Canada
- Women and Children's Health Research Institute, University of Alberta, Edmonton, Alberta, Canada
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, Darwin Building, 99-105 Gower Street, WC1E 6BT, London, UK
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005České Budějovice (Budweis), Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
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2
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Jetishi C, Balmer EA, Berger BM, Faso C, Ochsenreiter T. Expansion of metabolically labelled endocytic organelles and cytoskeletal cell structures in Giardia lamblia using optimised U-ExM protocols. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:198-206. [PMID: 38975021 PMCID: PMC11224680 DOI: 10.15698/mic2024.06.825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/08/2024] [Accepted: 04/17/2024] [Indexed: 07/09/2024]
Abstract
Understanding cellular ultrastructure is tightly bound to microscopic resolution and the ability to identify individual components at that resolution. Expansion microscopy has revolutionised this topic. Here we present and compare two protocols of ultrastructure expansion microscopy that allow for 4.5-fold mostly isotropic expansion and the use of antibodies, metabolic labelling, and DNA stains to demarcate individual regions such as the endoplasmic reticulum, the nuclei, the peripheral endocytic compartments as well as the ventral disc and the cytoskeleton in Giardia lamblia. We present an optimised, shortened, and modular protocol that can be swiftly adjusted to the investigators needs in this important protozoan model organism.
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Affiliation(s)
- Clirim Jetishi
- Institute of Cell Biology, University of BernBernSwitzerland
- Graduate School for Cellular and Biomedical Sciences, University of BernBernSwitzerland
| | - Erina A Balmer
- Institute of Cell Biology, University of BernBernSwitzerland
- Graduate School for Cellular and Biomedical Sciences, University of BernBernSwitzerland
| | - Bianca M Berger
- Institute of Cell Biology, University of BernBernSwitzerland
- Graduate School for Cellular and Biomedical Sciences, University of BernBernSwitzerland
| | - Carmen Faso
- Institute of Cell Biology, University of BernBernSwitzerland
- Multidisciplinary Center for Infectious Diseases, University of BernBernSwitzerland
- Institute of Infectious Diseases, University of BernBernSwitzerland.
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3
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Balmer EA, Wirdnam CD, Faso C. A core UPS molecular complement implicates unique endocytic compartments at the parasite-host interface in Giardia lamblia. Virulence 2023; 14:2174288. [PMID: 36730629 PMCID: PMC9928461 DOI: 10.1080/21505594.2023.2174288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Unconventional protein secretion (UPS) plays important roles in cell physiology. In contrast to canonical secretory routes, UPS does not generally require secretory signal sequences and often bypasses secretory compartments such as the ER and the Golgi apparatus. Giardia lamblia is a protist parasite with reduced subcellular complexity which releases several proteins, some of them virulence factors, without canonical secretory signals. This implicates UPS at the parasite-host interface. No dedicated machinery nor mechanism(s) for UPS in Giardia are currently known, although speculations on the involvement of endocytic organelles called PV/PECs, have been put forth. To begin to address the question of whether PV/PECs are implicated in virulence-associated UPS and to define the composition of molecular machinery involved in protein release, we employed affinity purification and mass spectrometry, coupled to microscopy-based subcellular localization and signal correlation quantification to investigate the interactomes of 11 reported unconventionally secreted proteins, all predicted to be cytosolic. A subset of these are associated with PV/PECs. Extended and validated interactomes point to a core PV/PECs-associated UPS machinery, which includes uncharacterized and Giardia-specific coiled-coil proteins and NEK kinases. Finally, a subset of the alpha-giardin protein family was enriched in all PV/PECs-associated protein interactomes, highlighting a previously unappreciated role for these proteins at PV/PECs and in UPS. Taken together, our results provide the first characterization of a virulence-associated UPS protein complex in Giardia lamblia at PV/PECs, suggesting a novel link between these primarily endocytic and feeding organelles and UPS at the parasite-host interface.
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Affiliation(s)
- Erina A. Balmer
- Institute of Cell Biology, University of Bern, Bern, Switzerland,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Carmen Faso
- Institute of Cell Biology, University of Bern, Bern, Switzerland,Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland,CONTACT Carmen Faso
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4
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Maciejowski WJ, Gile GH, Jerlström-Hultqvist J, Dacks JB. Ancient and pervasive expansion of adaptin-related vesicle coat machinery across Parabasalia. Int J Parasitol 2023; 53:233-245. [PMID: 36898426 DOI: 10.1016/j.ijpara.2023.01.002] [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: 10/10/2022] [Revised: 01/30/2023] [Accepted: 01/30/2023] [Indexed: 03/11/2023]
Abstract
The eukaryotic phylum Parabasalia is composed primarily of anaerobic, endobiotic organisms such as the veterinary parasite Tritrichomonas foetus and the human parasite Trichomonas vaginalis, the latter causing the most prevalent, non-viral, sexually transmitted disease world-wide. Although a parasitic lifestyle is generally associated with a reduction in cell biology, T. vaginalis provides a striking counter-example. The 2007 T. vaginalis genome paper reported a massive and selective expansion of encoded proteins involved in vesicle trafficking, particularly those implicated in the late secretory and endocytic systems. Chief amongst these were the hetero-tetrameric adaptor proteins or 'adaptins', with T. vaginalis encoding ∼3.5 times more such proteins than do humans. The provenance of such a complement, and how it relates to the transition from a free-living or endobiotic state to parasitism, remains unclear. In this study, we performed a comprehensive bioinformatic and molecular evolutionary investigation of the heterotetrameric cargo adaptor-derived coats, comparing the molecular complement and evolution of these proteins between T. vaginalis, T. foetus and the available diversity of endobiotic parabasalids. Notably, with the recent discovery of Anaeramoeba spp. as the free-living sister lineage to all parabasalids, we were able to delve back to time points earlier in the lineage's history than ever before. We found that, although T. vaginalis still encodes the most HTAC subunits amongst parabasalids, the duplications giving rise to the complement took place more deeply and at various stages across the lineage. While some duplications appear to have convergently shaped the parasitic lineages, the largest jump is in the transition from free-living to endobiotic lifestyle with both gains and losses shaping the encoded complement. This work details the evolution of a cellular system across an important lineage of parasites and provides insight into the evolutionary dynamics of an example of expansion of protein machinery, counter to the more common trends observed in many parasitic systems.
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Affiliation(s)
- William J Maciejowski
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada; Department of Biological Sciences, University of Alberta, Edmonton, Canada; Women and Children's Health Research Institute, University of Alberta, Edmonton, Canada
| | - Gillian H Gile
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, Arizona, USA
| | - Jon Jerlström-Hultqvist
- Department of Cell and Molecular Biology, BMC, Box 586, Uppsala Universitet, SE-751 24 Uppsala, Sweden. https://twitter.com/jon_hultqvist
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada; Department of Biological Sciences, University of Alberta, Edmonton, Canada; Women and Children's Health Research Institute, University of Alberta, Edmonton, Canada; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.
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5
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Thattai M. Molecular and cellular constraints on vesicle traffic evolution. Curr Opin Cell Biol 2023; 80:102151. [PMID: 36610080 DOI: 10.1016/j.ceb.2022.102151] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/30/2022] [Accepted: 12/08/2022] [Indexed: 01/07/2023]
Abstract
In eukaryotic cells, the budding and fusion of intracellular transport vesicles is carefully orchestrated in space and time. Locally, a vesicle's source compartment, its cargo, and its destination compartment are controlled by dynamic multi-protein specificity modules. Globally, vesicle constituents must be recycled to ensure homeostasis of compartment compositions. The emergence of a novel vesicle pathway therefore requires new specificity modules as well as new recycling routes. Here, we review recent research on local (molecular) constraints on gene module duplication and global (cellular) constraints on intracellular recycling. By studying the evolution of vesicle traffic, we may discover general principles of how complex traits arise via multiple intermediate steps.
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Affiliation(s)
- Mukund Thattai
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, TIFR, Bangalore, India.
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6
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Zhang S, Yazaki E, Sakamoto H, Yamamoto H, Mizushima N. Evolutionary diversification of the autophagy-related ubiquitin-like conjugation systems. Autophagy 2022; 18:2969-2984. [PMID: 35427200 PMCID: PMC9673942 DOI: 10.1080/15548627.2022.2059168] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Two autophagy-related (ATG) ubiquitin-like conjugation systems, the ATG12 and ATG8 systems, play important roles in macroautophagy. While multiple duplications and losses of the ATG conjugation system proteins are found in different lineages, the extent to which the underlying systems diversified across eukaryotes is not fully understood. Here, in order to understand the evolution of the ATG conjugation systems, we constructed a transcriptome database consisting of 94 eukaryotic species covering major eukaryotic clades and systematically identified ATG conjugation system components. Both ATG10 and the C-terminal glycine of ATG12 are essential for the canonical ubiquitin-like conjugation of ATG12 and ATG5. However, loss of ATG10 or the C-terminal glycine of ATG12 occurred at least 16 times in a wide range of lineages, suggesting that possible covalent-to-non-covalent transition is not limited to the species that we previously reported such as Alveolata and some yeast species. Some species have only the ATG8 system (with conjugation enzymes) or only ATG8 (without conjugation enzymes). More than 10 species have ATG8 homologs without the conserved C-terminal glycine, and Tetrahymena has an ATG8 homolog with a predicted transmembrane domain, which may be able to anchor to the membrane independent of the ATG conjugation systems. We discuss the possibility that the ancestor of the ATG12 and ATG8 systems is more similar to ATG8. Overall, our study offers a whole picture of the evolution and diversity of the ATG conjugation systems among eukaryotes, and provides evidence that functional diversifications of the systems are more common than previously thought.Abbreviations: APEAR: ATG8-PE association region; ATG: autophagy-related; LIR: LC3-interacting region; NEDD8: neural precursor cell expressed, developmentally down-regulated gene 8; PE: phosphatidylethanolamine; SAMP: small archaeal modifier protein; SAR: Stramenopiles, Alveolata, and Rhizaria; SMC: structural maintenance of chromosomes; SUMO: small ubiquitin like modifier; TACK: Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota; UBA: ubiquitin like modifier activating enzyme; UFM: ubiquitin fold modifier; URM: ubiquitin related modifier.
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Affiliation(s)
- Sidi Zhang
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Euki Yazaki
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS), RIKEN, Saitama, Japan
| | - Hirokazu Sakamoto
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,Department of Infection and Host Defense, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hayashi Yamamoto
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,CONTACT Noboru Mizushima Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
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7
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Santos R, Ástvaldsson Á, Pipaliya SV, Zumthor JP, Dacks JB, Svärd S, Hehl AB, Faso C. Combined nanometric and phylogenetic analysis of unique endocytic compartments in Giardia lamblia sheds light on the evolution of endocytosis in Metamonada. BMC Biol 2022; 20:206. [PMID: 36127707 PMCID: PMC9490929 DOI: 10.1186/s12915-022-01402-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/06/2022] [Indexed: 11/27/2022] Open
Abstract
Background Giardia lamblia, a parasitic protist of the Metamonada supergroup, has evolved one of the most diverged endocytic compartment systems investigated so far. Peripheral endocytic compartments, currently known as peripheral vesicles or vacuoles (PVs), perform bulk uptake of fluid phase material which is then digested and sorted either to the cell cytosol or back to the extracellular space. Results Here, we present a quantitative morphological characterization of these organelles using volumetric electron microscopy and super-resolution microscopy (SRM). We defined a morphological classification for the heterogenous population of PVs and performed a comparative analysis of PVs and endosome-like organelles in representatives of phylogenetically related taxa, Spironucleus spp. and Tritrichomonas foetus. To investigate the as-yet insufficiently understood connection between PVs and clathrin assemblies in G. lamblia, we further performed an in-depth search for two key elements of the endocytic machinery, clathrin heavy chain (CHC) and clathrin light chain (CLC), across different lineages in Metamonada. Our data point to the loss of a bona fide CLC in the last Fornicata common ancestor (LFCA) with the emergence of a protein analogous to CLC (GlACLC) in the Giardia genus. Finally, the location of clathrin in the various compartments was quantified. Conclusions Taken together, this provides the first comprehensive nanometric view of Giardia’s endocytic system architecture and sheds light on the evolution of GlACLC analogues in the Fornicata supergroup and, specific to Giardia, as a possible adaptation to the formation and maintenance of stable clathrin assemblies at PVs. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01402-3.
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Affiliation(s)
- Rui Santos
- Institute of Parasitology, University of Zürich, Winterthurerstrasse 266a, 8057, Zürich, Switzerland.,Institute of Anatomy, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Ásgeir Ástvaldsson
- Department of Cell and Molecular Biology, University of Uppsala, Husargatan 3, 752 37, Uppsala, Sweden.,Department of Microbiology, National Veterinary Institute, 751 23, Uppsala, Sweden
| | - Shweta V Pipaliya
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.,School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jon Paulin Zumthor
- Amt für Lebensmittelsicherheit und Tiergesundheit Graubünden, Chur, Switzerland
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.,Institute of Parasitology, Biology Centre, CAS, v.v.i., Branisovska 31, 370 05, Ceske Budejovice, Czech Republic
| | - Staffan Svärd
- Department of Cell and Molecular Biology, University of Uppsala, Husargatan 3, 752 37, Uppsala, Sweden
| | - Adrian B Hehl
- Institute of Parasitology, University of Zürich, Winterthurerstrasse 266a, 8057, Zürich, Switzerland
| | - Carmen Faso
- Institute of Cell Biology, University of Bern, Bern, Switzerland. .,Multidisciplinary Center for Infectious Diseases, Vetsuisse, University of Bern, Bern, Switzerland.
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8
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Benchimol M, de Souza W. Giardia intestinalis and its Endomembrane System. J Eukaryot Microbiol 2022; 69:e12893. [PMID: 35148450 DOI: 10.1111/jeu.12893] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 11/29/2022]
Abstract
Giardia intestinalis has unique characteristics, even in the absence of certain organelles. For instance, Golgi and mitochondria are not found. On the other hand, there is a network of peripheral vacuoles (PVs) and mitosomes. The endoplasmic reticulum (ER), nuclear membrane, peroxisomes, and lipid bodies are present. The peripheral vacuole system seems to play several simultaneous roles. It is involved in the endocytic activity of the trophozoite but also has characteristics of early and late endosomes and even lysosomes, establishing a connection with the ER. Some of the PVs contain small vesicles, acting as multivesicular bodies, including the release of exosomes. The mitosomes are surrounded by two membranes, divide during mitosis, and are distributed throughout the cell. They do not contain DNA, enzymes involved in the citric acid cycle, respiratory chain, or ATP synthesis. However, they contain the iron-sulfur complex and transporters as TOM and TIM. Some mitosomes are linked to flagellar axonemes through a fibrillar connection. During encystation, two types of larger cytoplasmic vesicles appear. One originating from the ER contains the cyst wall proteins. Another contains carbohydrates. Both migrate to the cell periphery and fuse with plasma membrane secreting their contents to give rise to the cell wall.
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Affiliation(s)
- Marlene Benchimol
- Universidade do Grande Rio (UNIGRANRIO), Rio de Janeiro Duque de Caxias, RJ, Brazil.,Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens, Centro Nacional de Biologia Estrutural e Bioimagens, CENABIO-Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Wanderley de Souza
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens, Centro Nacional de Biologia Estrutural e Bioimagens, CENABIO-Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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