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Klinger CM, Jimenez-Ruiz E, Mourier T, Klingl A, Lemgruber L, Pain A, Dacks JB, Meissner M. Evolutionary analysis identifies a Golgi pathway and correlates lineage-specific factors with endomembrane organelle emergence in apicomplexans. Cell Rep 2024; 43:113740. [PMID: 38363682 DOI: 10.1016/j.celrep.2024.113740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/20/2023] [Accepted: 01/18/2024] [Indexed: 02/18/2024] Open
Abstract
The organelle paralogy hypothesis (OPH) aims to explain the evolution of non-endosymbiotically derived organelles. It predicts that lineage-specific pathways or organelles should result when identity-encoding membrane-trafficking components duplicate and co-evolve. Here, we investigate the presence of such lineage-specific membrane-trafficking machinery paralogs in Apicomplexa, a globally important parasitic lineage. We are able to identify 18 paralogs of known membrane-trafficking machinery, in several cases co-incident with the presence of new endomembrane organelles in apicomplexans or their parent lineage, the Alveolata. Moreover, focused analysis of the apicomplexan Arf-like small GTPases (i.e., ArlX3) revealed a specific post-Golgi trafficking pathway. This pathway appears involved in delivery of proteins to micronemes and rhoptries, with knockdown demonstrating reduced invasion capacity. Overall, our data have identified an unforeseen post-Golgi trafficking pathway in apicomplexans and are consistent with the OPH mechanism acting to produce endomembrane pathways or organelles at various evolutionary stages across the alveolate lineage.
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Affiliation(s)
- Christen M Klinger
- Division of Infectious Diseases, Department of Medicine and Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada; Women and Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada
| | - Elena Jimenez-Ruiz
- Experimental Parasitology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, LMU, Munich, Germany
| | - Tobias Mourier
- Pathogen Genomics Laboratory, Bioscience Programme, Biological, and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Andreas Klingl
- Pflanzliche Entwicklungsbiologie, Biozentrum der Ludwig-Maximilians-Universität, Munich, Germany
| | - Leandro Lemgruber
- Cellular Analysis Facility, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Arnab Pain
- Pathogen Genomics Laboratory, Bioscience Programme, Biological, and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; International Institute for Zoonosis Control, GI-CoRE, Hokkaido University, Sapporo, Japan
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine and Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada; Women and Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Centre for Life's Origin and Evolution, Department of Genetics, Evolution & Environment, University College London, London, UK.
| | - Markus Meissner
- Experimental Parasitology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, LMU, Munich, Germany.
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2
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Paul P, Tiwari B. Organelles are miscommunicating: Membrane contact sites getting hijacked by pathogens. Virulence 2023; 14:2265095. [PMID: 37862470 PMCID: PMC10591786 DOI: 10.1080/21505594.2023.2265095] [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: 01/30/2023] [Accepted: 09/25/2023] [Indexed: 10/22/2023] Open
Abstract
Membrane Contact Sites (MCS) are areas of close apposition of organelles that serve as hotspots for crosstalk and direct transport of lipids, proteins and metabolites. Contact sites play an important role in Ca2+ signalling, phospholipid synthesis, and micro autophagy. Initially, altered regulation of vesicular trafficking was regarded as the key mechanism for intracellular pathogen survival. However, emerging studies indicate that pathogens hijack MCS elements - a novel strategy for survival and replication in an intracellular environment. Several pathogens exploit MCS to establish direct contact between organelles and replication inclusion bodies, which are essential for their survival within the cell. By establishing this direct control, pathogens gain access to cytosolic compounds necessary for replication, maintenance, escaping endocytic maturation and circumventing lysosome fusion. MCS components such as VAP A/B, OSBP, and STIM1 are targeted by pathogens through their effectors and secretion systems. In this review, we delve into the mechanisms which operate in the evasion of the host immune system when intracellular pathogens hostage MCS. We explore targeting MCS components as a novel therapeutic approach, modifying molecular pathways and signalling to address the disease's mechanisms and offer more effective, tailored treatments for affected individuals.
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Affiliation(s)
- Pratyashaa Paul
- Department of Biological Sciences, Indian Institute of Science Education and Research, India
| | - Bhavana Tiwari
- Department of Biological Sciences, Indian Institute of Science Education and Research, India
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3
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Meissner JM, Akhmetova K, Szul T, Viktorova EG, Sha B, Bhatt JM, Lee EJ, Kahn RA, Belov GA, Chesnokov I, Sztul E. The Arf-GEF GBF1 undergoes multi-domain structural shifts to activate Arf at the Golgi. Front Cell Dev Biol 2023; 11:1233272. [PMID: 37745300 PMCID: PMC10512945 DOI: 10.3389/fcell.2023.1233272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/29/2023] [Indexed: 09/26/2023] Open
Abstract
Golgi homeostasis require the activation of Arf GTPases by the guanine-nucleotide exchange factor requires GBF1, whose recruitment to the Golgi represents a rate limiting step in the process. GBF1 contains a conserved, catalytic, Sec7 domain (Sec7d) and five additional (DCB, HUS, HDS1-3) domains. Herein, we identify the HDS3 domain as essential for GBF1 membrane association in mammalian cells and document the critical role of HDS3 during the development of Drosophila melanogaster. We show that upon binding to Golgi membranes, GBF1 undergoes conformational changes in regions bracketing the catalytic Sec7d. We illuminate GBF1 interdomain arrangements by negative staining electron microscopy of full-length human GBF1 to show that GBF1 forms an anti-parallel dimer held together by the paired central DCB-HUS core, with two sets of HDS1-3 arms extending outward in opposite directions. The catalytic Sec7d protrudes from the central core as a largely independent domain, but is closely opposed to a previously unassigned α-helix from the HDS1 domain. Based on our data, we propose models of GBF1 engagement on the membrane to provide a paradigm for understanding GBF1-mediated Arf activation required for cellular and organismal function.
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Affiliation(s)
- Justyna M. Meissner
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Katarina Akhmetova
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Tomasz Szul
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ekaterina G. Viktorova
- Department of Veterinary Medicine, Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, MD, United States
| | - Bingdong Sha
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jay M. Bhatt
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Eunjoo J. Lee
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Richard A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
| | - George A. Belov
- Department of Veterinary Medicine, Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, MD, United States
| | - Igor Chesnokov
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Elizabeth Sztul
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
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4
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Yang C, Fan H, Ge L, Ma Q, Jiang M, Wen H. Comparative analysis of quantitative phosphoproteomics between two tilapias ( Oreochromis niloticus and Oreochromis aureus) under low-temperature stress. PeerJ 2023; 11:e15599. [PMID: 37456864 PMCID: PMC10340112 DOI: 10.7717/peerj.15599] [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] [Received: 02/02/2023] [Accepted: 05/30/2023] [Indexed: 07/18/2023] Open
Abstract
As an important farmed fish, tilapia has poor tolerance to low-temperatures. At the same time, different tilapia strains have apparent differences in low-temperature tolerance. In this study, using the iTRAQ method, the phosphorylated proteomics of two tilapia strains (Oreochromis niloticus and Oreochromis aureus) with different tolerances to low-temperature stress were quantitatively and comparatively analyzed, to clarify the physiological mechanism of tilapia's response to low-temperature stress. Through the GO and IPR analyses of differentially phosphorylated proteins, a number of similarities in physiological activities and regulatory effects were found between the two tilapias in response to low-temperature stress. Many differentially phosphorylated proteins are mainly involved in lipid metabolism, cell proliferation and apoptosis. However, the difference in endurance of low temperature of these two tilapias might be related to the differences in categories, expression and modification level of genetic products which were involved in the aforementioned physiological processes. And meanwhile, the enrichment results of KEGG showed the changes of multiple immune-related and growth-related phosphorylated proteins in the cytokine-cytokine receptor interaction pathway in O. aureus are more prominent. Furthermore, the significantly enriched pathway of carbohydrate digestion and absorption in O. niloticus may indicate that low-temperature stress exerts a more severe impact on energy metabolism. The relative results would help elucidating the molecular mechanism by which tilapia responds to low-temperature stress, and developing culture of tilapia species.
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Affiliation(s)
- Changgeng Yang
- Life Science & Technology School, Lingnan Normal University, Zhanjiang, China
| | - Hua Fan
- Life Science & Technology School, Lingnan Normal University, Zhanjiang, China
| | - Liya Ge
- Life Science & Technology School, Lingnan Normal University, Zhanjiang, China
| | - Qian Ma
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Ming Jiang
- Fish Nutrition and Feed Division, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Hua Wen
- Fish Nutrition and Feed Division, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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Brumm S, Singh MK, Kriechbaum C, Richter S, Huhn K, Kucera T, Baumann S, Wolters H, Takada S, Jürgens G. N-terminal domain of ARF-GEF GNOM prevents heterodimerization with functionally divergent GNL1 in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:772-785. [PMID: 36106415 DOI: 10.1111/tpj.15979] [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: 05/20/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 06/15/2023]
Abstract
Evolutionary change following gene duplication can lead to functionally divergent paralogous proteins. If comprising identical subunits their random assortment would also form potentially detrimental heteromeric proteins. In Arabidopsis, the ARF GTPase guanine-nucleotide exchange factor GNOM is essential for polar recycling of auxin-efflux transporter PIN1 from endosomes to the basal plasma membrane whereas its paralog GNL1 mediates retrograde Golgi-endoplasmic reticulum traffic. Here we show that both GNOM and GNL1 form homodimers but no heterodimers. To assess the biological significance of this, we generated transgenic plants expressing engineered heterodimer-compatible GNOM variants. Those plants showed developmental defects such as the failure to produce lateral roots. To identify mechanisms underlying heterodimer prevention, we analyzed interactions of the N-terminal dimerization and cyclophilin-binding (DCB) domain. Each DCB domain interacted with the complementary fragment (ΔDCB) both of their own and of the paralogous protein. However, only DCBGNOM interacted with itself whereas DCBGNL1 failed to interact with itself and with DCBGNOM . GNOM variants in which the DCB domain was removed or replaced by DCBGNL1 revealed a role for DCB-DCB interaction in the prevention of GNOM-GNL1 heterodimers whereas DCB-ΔDCB interaction was essential for dimer formation and GNOM function. Our data suggest a model of early DCB-DCB interaction that facilitates GNOM homodimer formation, indirectly precluding formation of detrimental heterodimers.
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Affiliation(s)
- Sabine Brumm
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Manoj K Singh
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Choy Kriechbaum
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Sandra Richter
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Kerstin Huhn
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Tim Kucera
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Sarah Baumann
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Hanno Wolters
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Shinobu Takada
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Gerd Jürgens
- Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
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6
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Ito A, Fukaya M, Okamoto H, Sakagami H. Physiological and Pathological Roles of the Cytohesin Family in Neurons. Int J Mol Sci 2022; 23:5087. [PMID: 35563476 PMCID: PMC9104363 DOI: 10.3390/ijms23095087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 02/05/2023] Open
Abstract
The cytohesin proteins, consisting of four closely related members (cytohesins-1, -2, -3, and -4), are a subfamily of the Sec7 domain-containing guanine nucleotide exchange factors for ADP ribosylation factors (Arfs), which are critical regulators of membrane trafficking and actin cytoskeleton remodeling. Recent advances in molecular biological techniques and the development of a specific pharmacological inhibitor for cytohesins, SecinH3, have revealed the functional involvement of the cytohesin-Arf pathway in diverse neuronal functions from the formation of axons and dendrites, axonal pathfinding, and synaptic vesicle recycling, to pathophysiological processes including chronic pain and neurotoxicity induced by proteins related to neurodegenerative disorders, such as amyotrophic lateral sclerosis and Alzheimer's disease. Here, we review the physiological and pathological roles of the cytohesin-Arf pathway in neurons and discuss the future directions of this research field.
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Affiliation(s)
- Akiko Ito
- Department of Anesthesiology, Kitasato University School of Medicine, Sagamihara 252-0374, Kanagawa, Japan; (A.I.); (H.O.)
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara 252-0374, Kanagawa, Japan;
| | - Masahiro Fukaya
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara 252-0374, Kanagawa, Japan;
| | - Hirotsugu Okamoto
- Department of Anesthesiology, Kitasato University School of Medicine, Sagamihara 252-0374, Kanagawa, Japan; (A.I.); (H.O.)
| | - Hiroyuki Sakagami
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara 252-0374, Kanagawa, Japan;
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7
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Saito-Nakano Y, Makiuchi T, Tochikura M, Gilchrist CA, Petri WA, Nozaki T. ArfX2 GTPase Regulates Trafficking From the Trans-Golgi to Lysosomes and Is Necessary for Liver Abscess Formation in the Protozoan Parasite Entamoeba histolytica. Front Cell Infect Microbiol 2022; 11:794152. [PMID: 34976870 PMCID: PMC8719317 DOI: 10.3389/fcimb.2021.794152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/24/2021] [Indexed: 02/03/2023] Open
Abstract
Entamoeba histolytica is the causative agent of amoebic dysentery and liver abscess in humans. The parasitic lifestyle and the virulence of the protist require elaborate biological processes, including vesicular traffic and stress management against a variety of reactive oxygen and nitrogen species produced by the host immune response. Although the mechanisms for intracellular traffic of representative virulence factors have been investigated at molecular levels, it remains poorly understood whether and how intracellular traffic is involved in the defense against reactive oxygen and nitrogen species. Here, we demonstrate that EhArfX2, one of the Arf family of GTPases known to be involved in the regulation of vesicular traffic, was identified by comparative transcriptomic analysis of two isogenic strains: an animal-passaged highly virulent HM-1:IMSS Cl6 and in vitro maintained attenuated avirulent strain. EhArfX2 was identified as one of the most highly upregulated genes in the highly virulent strain. EhArfX2 was localized to small vesicle-like structures and largely colocalized with the marker for the trans-Golgi network SNARE, EhYkt6, but neither with the endoplasmic reticulum (ER)-resident chaperon, EhBip, nor the cis-Golgi SNARE, EhSed5, and Golgi-luminal galactosyl transferase, EhGalT. Expression of the dominant-active mutant form of EhArfX2 caused an increase in the number of lysosomes, while expression of the dominant-negative mutant led to a defect in lysosome formation and cysteine protease transport to lysosomes. Expression of the dominant-negative mutant in the virulent E. histolytica strain caused a reduction of the size of liver abscesses in a hamster model. This defect in liver abscess formation was likely at least partially attributed to reduced resistance to nitrosative, but not oxidative stress in vitro. These results showed that the EhArfX2-mediated traffic is necessary for the nitrosative stress response and virulence in the host.
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Affiliation(s)
- Yumiko Saito-Nakano
- Department of Parasitology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Takashi Makiuchi
- Department of Infectious Diseases, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Mami Tochikura
- Department of Parasitology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Carol A Gilchrist
- Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - William A Petri
- Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Tomoyoshi Nozaki
- Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo, Japan
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8
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Pipaliya SV, Santos R, Salas-Leiva D, Balmer EA, Wirdnam CD, Roger AJ, Hehl AB, Faso C, Dacks JB. Unexpected organellar locations of ESCRT machinery in Giardia intestinalis and complex evolutionary dynamics spanning the transition to parasitism in the lineage Fornicata. BMC Biol 2021; 19:167. [PMID: 34446013 PMCID: PMC8394649 DOI: 10.1186/s12915-021-01077-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/23/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Comparing a parasitic lineage to its free-living relatives is a powerful way to understand how that evolutionary transition to parasitism occurred. Giardia intestinalis (Fornicata) is a leading cause of gastrointestinal disease world-wide and is famous for its unusual complement of cellular compartments, such as having peripheral vacuoles instead of typical endosomal compartments. Endocytosis plays an important role in Giardia's pathogenesis. Endosomal sorting complexes required for transport (ESCRT) are membrane-deforming proteins associated with the late endosome/multivesicular body (MVB). MVBs are ill-defined in G. intestinalis, and roles for identified ESCRT-related proteins are not fully understood in the context of its unique endocytic system. Furthermore, components thought to be required for full ESCRT functionality have not yet been documented in this species. RESULTS We used genomic and transcriptomic data from several Fornicata species to clarify the evolutionary genome streamlining observed in Giardia, as well as to detect any divergent orthologs of the Fornicata ESCRT subunits. We observed differences in the ESCRT machinery complement between Giardia strains. Microscopy-based investigations of key components of ESCRT machinery such as GiVPS36 and GiVPS25 link them to peripheral vacuoles, highlighting these organelles as simplified MVB equivalents. Unexpectedly, we show ESCRT components associated with the endoplasmic reticulum and, for the first time, mitosomes. Finally, we identified the rare ESCRT component CHMP7 in several fornicate representatives, including Giardia and show that contrary to current understanding, CHMP7 evolved from a gene fusion of VPS25 and SNF7 domains, prior to the last eukaryotic common ancestor, over 1.5 billion years ago. CONCLUSIONS Our findings show that ESCRT machinery in G. intestinalis is far more varied and complete than previously thought, associates to multiple cellular locations, and presents changes in ESCRT complement which pre-date adoption of a parasitic lifestyle.
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Affiliation(s)
- Shweta V Pipaliya
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Rui Santos
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Dayana Salas-Leiva
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Erina A Balmer
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Corina D Wirdnam
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Adrian B Hehl
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Carmen Faso
- Institute of Cell Biology, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, 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.
- Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College of London, London, UK.
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9
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More K, Klinger CM, Barlow LD, Dacks JB. Evolution and Natural History of Membrane Trafficking in Eukaryotes. Curr Biol 2021; 30:R553-R564. [PMID: 32428497 DOI: 10.1016/j.cub.2020.03.068] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The membrane-trafficking system is a defining facet of eukaryotic cells. The best-known organelles and major protein families of this system are largely conserved across the vast diversity of eukaryotes, implying both ancient organization and functional unity. Nonetheless, intriguing variation exists that speaks to the evolutionary forces that have shaped the endomembrane system in eukaryotes and highlights ways in which membrane trafficking in protists differs from that in our well-understood models of mammalian and yeast cells. Both parasites and free-living protists possess specialized trafficking organelles, some lineage specific, others more widely distributed - the evolution and function of these organelles begs exploration. Novel members of protein families are present across eukaryotes but have been lost in humans. These proteins may well hold clues to understanding differences in cellular function in organisms that are of pressing importance for planetary health.
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Affiliation(s)
- Kira More
- Division of Infectious Disease, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton, Alberta T6G 2G3, Canada; Department of Biological Sciences, University of Alberta, P217 Biological Sciences Building, Edmonton, Alberta T6G 2E9, Canada
| | - Christen M Klinger
- Division of Infectious Disease, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton, Alberta T6G 2G3, Canada
| | - Lael D Barlow
- Division of Infectious Disease, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton, Alberta T6G 2G3, Canada; Department of Biological Sciences, University of Alberta, P217 Biological Sciences Building, Edmonton, Alberta T6G 2E9, Canada
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton, Alberta T6G 2G3, Canada; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 Ceske Budejovice, Czech Republic.
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10
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Vargová R, Wideman JG, Derelle R, Klimeš V, Kahn RA, Dacks JB, Eliáš M. A Eukaryote-Wide Perspective on the Diversity and Evolution of the ARF GTPase Protein Family. Genome Biol Evol 2021; 13:6319025. [PMID: 34247240 PMCID: PMC8358228 DOI: 10.1093/gbe/evab157] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 12/21/2022] Open
Abstract
The evolution of eukaryotic cellular complexity is interwoven with the extensive diversification of many protein families. One key family is the ARF GTPases that act in eukaryote-specific processes, including membrane traffic, tubulin assembly, actin dynamics, and cilia-related functions. Unfortunately, our understanding of the evolution of this family is limited. Sampling an extensive set of available genome and transcriptome sequences, we have assembled a data set of over 2,000 manually curated ARF family genes from 114 eukaryotic species, including many deeply diverged protist lineages, and carried out comprehensive molecular phylogenetic analyses. These reconstructed as many as 16 ARF family members present in the last eukaryotic common ancestor, nearly doubling the previously inferred ancient system complexity. Evidence for the wide occurrence and ancestral origin of Arf6, Arl13, and Arl16 is presented for the first time. Moreover, Arl17, Arl18, and SarB, newly described here, are absent from well-studied model organisms and as a result their function(s) remain unknown. Analyses of our data set revealed a previously unsuspected diversity of membrane association modes and domain architectures within the ARF family. We detail the step-wise expansion of the ARF family in the metazoan lineage, including discovery of several new animal-specific family members. Delving back to its earliest evolution in eukaryotes, the resolved relationship observed between the ARF family paralogs sets boundaries for scenarios of vesicle coat origins during eukaryogenesis. Altogether, our work fundamentally broadens the understanding of the diversity and evolution of a protein family underpinning the structural and functional complexity of the eukaryote cells.
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Affiliation(s)
- Romana Vargová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
| | - Jeremy G Wideman
- Biodesign Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Romain Derelle
- Station d'Ecologie Théorique et Expérimentale, UMR CNRS 5321, Moulis, France
| | - Vladimír Klimeš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.,Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College of London, United Kingdom
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
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11
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Bäck N, Mains RE, Eipper BA. PAM: diverse roles in neuroendocrine cells, cardiomyocytes, and green algae. FEBS J 2021; 289:4470-4496. [PMID: 34089560 DOI: 10.1111/febs.16049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/28/2021] [Accepted: 06/02/2021] [Indexed: 12/13/2022]
Abstract
Our understanding of the ways in which peptides are used for communication in the nervous and endocrine systems began with the identification of oxytocin, vasopressin, and insulin, each of which is stored in electron-dense granules, ready for release in response to an appropriate stimulus. For each of these peptides, entry of its newly synthesized precursor into the ER lumen is followed by transport through the secretory pathway, exposing the precursor to a sequence of environments and enzymes that produce the bioactive products stored in mature granules. A final step in the biosynthesis of many peptides is C-terminal amidation by peptidylglycine α-amidating monooxygenase (PAM), an ascorbate- and copper-dependent membrane enzyme that enters secretory granules along with its soluble substrates. Biochemical and cell biological studies elucidated the highly conserved mechanism for amidated peptide production and raised many questions about PAM trafficking and the effects of PAM on cytoskeletal organization and gene expression. Phylogenetic studies and the discovery of active PAM in the ciliary membranes of Chlamydomonas reinhardtii, a green alga lacking secretory granules, suggested that a PAM-like enzyme was present in the last eukaryotic common ancestor. While the catalytic features of human and C. reinhardtii PAM are strikingly similar, the trafficking of PAM in C. reinhardtii and neuroendocrine cells and secretion of its amidated products differ. A comparison of PAM function in neuroendocrine cells, atrial myocytes, and C. reinhardtii reveals multiple ways in which altered trafficking allows PAM to accomplish different tasks in different species and cell types.
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Affiliation(s)
- Nils Bäck
- Department of Anatomy, University of Helsinki, Finland
| | - Richard E Mains
- Department of Neuroscience, UConn Health, Farmington, CT, USA
| | - Betty A Eipper
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA
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12
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Pipaliya SV, Thompson LA, Dacks JB. The reduced ARF regulatory system in Giardia intestinalis pre-dates the transition to parasitism in the lineage Fornicata. Int J Parasitol 2021; 51:825-839. [PMID: 33848497 DOI: 10.1016/j.ijpara.2021.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/18/2022]
Abstract
Giardia intestinalis is an enteric pathogen with an extremely modified membrane trafficking system, lacking canonical compartments such as the Golgi, endosomes, and intermediate vesicle carriers. By comparison the fornicate relatives of Giardia possess greater endomembrane system complexity. In eukaryotes, the ADP ribosylation factor (ARF) GTPase regulatory system proteins, which consist of the small GTPase ARF1, and its guanine exchange nucleotide factors (GEFs) and GTPase activating proteins (GAPs), coordinate temporal and directional trafficking of cargo vesicles by recognizing and interacting with heterotetrameric coat complexes at pre-Golgi and post-Golgi interfaces. To understand the evolution of this regulatory system across the fornicate lineage, we have performed comparative genomic and phylogenetic analyses of the ARF GTPases, and their regulatory GAPs and GEFs in fornicate genomes and transcriptomes. Prior to our analysis of the fornicates, we first establish that the ARF GAP sub-family ArfGAP with dual PH domains (ADAP) is sparsely distributed but present in at least four eukaryotic supergroups and thus was likely present in the Last Eukaryotic Common Ancestor (LECA). Next, our collective comparative genomic and phylogenetic investigations into the ARF regulatory proteins in fornicates identify a duplication of ARF1 GTPase yielding two paralogues of ARF1F proteins, ancestral to all fornicates and present in all examined isolates of Giardia. However, the ARF GEF and ARF GAP complement is reduced compared with the LECA. This investigation shows that the system was significantly streamlined prior to the fornicate ancestor but was not further reduced concurrent with a transition into a parasitic lifestyle.
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Affiliation(s)
- Shweta V Pipaliya
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.
| | - L Alexa Thompson
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - 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.
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13
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Gonçalves-Pimentel C, Mazaud D, Kottler B, Proelss S, Hirth F, Fanto M. A miRNA screen procedure identifies garz as an essential factor in adult glia functions and validates Drosophila as a beneficial 3Rs model to study glial functions and GBF1 biology. F1000Res 2020; 9:317. [PMID: 32595956 PMCID: PMC7309417 DOI: 10.12688/f1000research.23154.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/21/2020] [Indexed: 03/21/2024] Open
Abstract
Invertebrate glia performs most of the key functions controlled by mammalian glia in the nervous system and provides an ideal model for genetic studies of glial functions. To study the influence of adult glial cells in ageing we have performed a genetic screen in Drosophila using a collection of transgenic lines providing conditional expression of micro-RNAs (miRNAs). Here, we describe a methodological algorithm to identify and rank genes that are candidate to be targeted by miRNAs that shorten lifespan when expressed in adult glia. We have used four different databases for miRNA target prediction in Drosophila but find little agreement between them, overall. However, top candidate gene analysis shows potential to identify essential genes involved in adult glial functions. One example from our top candidates' analysis is gartenzwerg ( garz). We establish that garz is necessary in many glial cell types, that it affects motor behaviour and, at the sub-cellular level, is responsible for defects in cellular membranes, autophagy and mitochondria quality control. We also verify the remarkable conservation of functions between garz and its mammalian orthologue, GBF1, validating the use of Drosophila as an alternative 3Rs-beneficial model to knock-out mice for studying the biology of GBF1, potentially involved in human neurodegenerative diseases.
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Affiliation(s)
- Catarina Gonçalves-Pimentel
- Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9NU, UK
- Champalimaud Research, Champalimaud Foundation, Av. Brasília, Lisbon, 1400-038, Portugal
| | - David Mazaud
- Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9NU, UK
| | - Benjamin Kottler
- Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9NU, UK
| | - Sandra Proelss
- Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9NU, UK
| | - Frank Hirth
- Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9NU, UK
| | - Manolis Fanto
- Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9NU, UK
- Institut du Cerveau et de la Moelle épinière (ICM), 47, bd de l'hôpital, Paris, F-75013, France
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14
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Gonçalves-Pimentel C, Mazaud D, Kottler B, Proelss S, Hirth F, Fanto M. A miRNA screen procedure identifies garz as an essential factor in adult glia functions and validates Drosophila as a beneficial 3Rs model to study glial functions and GBF1 biology. F1000Res 2020; 9:317. [PMID: 32595956 PMCID: PMC7309417 DOI: 10.12688/f1000research.23154.2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/20/2020] [Indexed: 11/25/2022] Open
Abstract
Invertebrate glia performs most of the key functions controlled by mammalian glia in the nervous system and provides an ideal model for genetic studies of glial functions. To study the influence of adult glial cells in ageing we have performed a genetic screen in Drosophila using a collection of transgenic lines providing conditional expression of micro-RNAs (miRNAs). Here, we describe a methodological algorithm to identify and rank genes that are candidate to be targeted by miRNAs that shorten lifespan when expressed in adult glia. We have used four different databases for miRNA target prediction in Drosophila but find little agreement between them, overall. However, top candidate gene analysis shows potential to identify essential genes involved in adult glial functions. One example from our top candidates' analysis is gartenzwerg ( garz). We establish that garz is necessary in many glial cell types, that it affects motor behaviour and, at the sub-cellular level, is responsible for defects in cellular membranes, autophagy and mitochondria quality control. We also verify the remarkable conservation of functions between garz and its mammalian orthologue, GBF1, validating the use of Drosophila as an alternative 3Rs-beneficial model to knock-out mice for studying the biology of GBF1, potentially involved in human neurodegenerative diseases.
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Affiliation(s)
- Catarina Gonçalves-Pimentel
- Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9NU, UK
- Champalimaud Research, Champalimaud Foundation, Av. Brasília, Lisbon, 1400-038, Portugal
| | - David Mazaud
- Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9NU, UK
| | - Benjamin Kottler
- Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9NU, UK
| | - Sandra Proelss
- Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9NU, UK
| | - Frank Hirth
- Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9NU, UK
| | - Manolis Fanto
- Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9NU, UK
- Institut du Cerveau et de la Moelle épinière (ICM), 47, bd de l'hôpital, Paris, F-75013, France
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15
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Anandapadamanaban M, Williams RL. Prime Time for Dimeric Cytohesins: Surveying the Membrane with One Foot at a Time. Structure 2019; 27:1739-1741. [PMID: 31801096 DOI: 10.1016/j.str.2019.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this issue of Structure, Das et al. (2019) probe the structure and dynamics of dimeric cytohesins (guanine nucleotide exchange factors for ADP-ribosylation factors), in solution and on membranes. Unleashing an arsenal of methods, they demonstrate that a pleckstrin-homology domain-mediated membrane recruitment promotes conformational changes that prime cytohesins for allosteric activation.
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Affiliation(s)
| | - Roger L Williams
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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