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Irisarri I, Lorente-Martínez H, Strassert JFH, Agorreta A, Zardoya R, San Mauro D, de Vries J. Early Diversification of Membrane Intrinsic Proteins (MIPs) in Eukaryotes. Genome Biol Evol 2024; 16:evae164. [PMID: 39058319 PMCID: PMC11316224 DOI: 10.1093/gbe/evae164] [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: 08/03/2023] [Revised: 07/01/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Membrane intrinsic proteins (MIPs), including aquaporins (AQPs) and aquaglyceroporins (GLPs), form an ancient family of transporters for water and small solutes across biological membranes. The evolutionary history and functions of MIPs have been extensively studied in vertebrates and land plants, but their widespread presence across the eukaryotic tree of life suggests both a more complex evolutionary history and a broader set of functions than previously thought. That said, the early evolution of MIPs remains obscure. The presence of one GLP and four AQP clades across both bacteria and archaea suggests that the first eukaryotes could have possessed up to five MIPs. Here, we report on a previously unknown richness in MIP diversity across all major eukaryotic lineages, including unicellular eukaryotes, which make up the bulk of eukaryotic diversity. Three MIP clades have likely deep evolutionary origins, dating back to the last eukaryotic common ancestor (LECA), and support the presence of a complex MIP repertoire in early eukaryotes. Overall, our findings highlight the growing complexity of the reconstructed LECA genome: the dynamic evolutionary history of MIPs was set in motion when eukaryotes were in their infancy followed by radiative bursts across all main eukaryotic lineages.
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Affiliation(s)
- Iker Irisarri
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, 37077 Göttingen, Germany
- Campus Institute Data Science (CIDAS), 37077 Göttingen, Germany
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, 20146 Hamburg, Germany
| | - Héctor Lorente-Martínez
- Department of Biodiversity Ecology and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| | - Jürgen F H Strassert
- Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 12587 Berlin, Germany
| | - Ainhoa Agorreta
- Department of Biodiversity Ecology and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| | - Rafael Zardoya
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), 28006 Madrid, Spain
| | - Diego San Mauro
- Department of Biodiversity Ecology and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| | - Jan de Vries
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, 37077 Göttingen, Germany
- Campus Institute Data Science (CIDAS), 37077 Göttingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, University of Goettingen, 37077 Göttingen, Germany
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Byrt CS, Zhang RY, Magrath I, Chan KX, De Rosa A, McGaughey S. Exploring aquaporin functions during changes in leaf water potential. FRONTIERS IN PLANT SCIENCE 2023; 14:1213454. [PMID: 37615024 PMCID: PMC10442719 DOI: 10.3389/fpls.2023.1213454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/04/2023] [Indexed: 08/25/2023]
Abstract
Maintenance of optimal leaf tissue humidity is important for plant productivity and food security. Leaf humidity is influenced by soil and atmospheric water availability, by transpiration and by the coordination of water flux across cell membranes throughout the plant. Flux of water and solutes across plant cell membranes is influenced by the function of aquaporin proteins. Plants have numerous aquaporin proteins required for a multitude of physiological roles in various plant tissues and the membrane flux contribution of each aquaporin can be regulated by changes in protein abundance, gating, localisation, post-translational modifications, protein:protein interactions and aquaporin stoichiometry. Resolving which aquaporins are candidates for influencing leaf humidity and determining how their regulation impacts changes in leaf cell solute flux and leaf cavity humidity is challenging. This challenge involves resolving the dynamics of the cell membrane aquaporin abundance, aquaporin sub-cellular localisation and location-specific post-translational regulation of aquaporins in membranes of leaf cells during plant responses to changes in water availability and determining the influence of cell signalling on aquaporin permeability to a range of relevant solutes, as well as determining aquaporin influence on cell signalling. Here we review recent developments, current challenges and suggest open opportunities for assessing the role of aquaporins in leaf substomatal cavity humidity regulation.
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Ishibashi K, Tanaka Y, Morishita Y. Evolutionary Overview of Aquaporin Superfamily. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1398:81-98. [PMID: 36717488 DOI: 10.1007/978-981-19-7415-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Aquaporins (AQPs) are present not only in three domains of life, bacteria, eukaryotes, and archaea, but also in viruses. With the accumulating arrays of AQP superfamily, the evolutional relationship has attracted much attention with multiple publications on "the genome-wide identification and phylogenetic analysis" of AQP superfamily. A pair of NPA boxes forming a pore is highly conserved throughout the evolution and renders key residues for the classification of AQP superfamily into four groups: AQP1-like, AQP3-like, AQP8-like, and AQP11-like. The complexity of AQP family has mostly been achieved in nematodes and subsequent evolution has been directed toward increasing the number of AQPs through whole-genome duplications (WGDs) to extend the tissue specific expression and regulation. The discovery of the intracellular AQP (iAQP: AQP8-like and AQP11-like) and substrate transports by the plasma membrane AQP (pAQP: AQP1-like and AQP3-like) have accelerated the AQP research much more toward the transport of substrates with complex profiles. This evolutionary overview based on a simple classification of AQPs into four subfamilies will provide putative structural, functional, and localization information and insights into the role of AQP as well as clues to understand the complex diversity of AQP superfamily.
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Affiliation(s)
- Kenichi Ishibashi
- Division of Pathophysiology, Meiji Pharmaceutical University, Tokyo, Japan.
| | - Yasuko Tanaka
- Division of Pathophysiology, Meiji Pharmaceutical University, Tokyo, Japan
| | - Yoshiyuki Morishita
- Division of Nephrology, Saitama Medical Center, Jichi Medical University, Ohmiya, Saitama-City, Saitama, Japan
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Shanmugasundram A, Starns D, Böhme U, Amos B, Wilkinson PA, Harb OS, Warrenfeltz S, Kissinger JC, McDowell MA, Roos DS, Crouch K, Jones AR. TriTrypDB: An integrated functional genomics resource for kinetoplastida. PLoS Negl Trop Dis 2023; 17:e0011058. [PMID: 36656904 PMCID: PMC9888696 DOI: 10.1371/journal.pntd.0011058] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/31/2023] [Accepted: 12/23/2022] [Indexed: 01/20/2023] Open
Abstract
Parasitic diseases caused by kinetoplastid parasites are a burden to public health throughout tropical and subtropical regions of the world. TriTrypDB (https://tritrypdb.org) is a free online resource for data mining of genomic and functional data from these kinetoplastid parasites and is part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org). As of release 59, TriTrypDB hosts 83 kinetoplastid genomes, nine of which, including Trypanosoma brucei brucei TREU927, Trypanosoma cruzi CL Brener and Leishmania major Friedlin, undergo manual curation by integrating information from scientific publications, high-throughput assays and user submitted comments. TriTrypDB also integrates transcriptomic, proteomic, epigenomic, population-level and isolate data, functional information from genome-wide RNAi knock-down and fluorescent tagging, and results from automated bioinformatics analysis pipelines. TriTrypDB offers a user-friendly web interface embedded with a genome browser, search strategy system and bioinformatics tools to support custom in silico experiments that leverage integrated data. A Galaxy workspace enables users to analyze their private data (e.g., RNA-sequencing, variant calling, etc.) and explore their results privately in the context of publicly available information in the database. The recent addition of an annotation platform based on Apollo enables users to provide both functional and structural changes that will appear as 'community annotations' immediately and, pending curatorial review, will be integrated into the official genome annotation.
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Affiliation(s)
- Achchuthan Shanmugasundram
- Department of Biochemistry and Systems Biology, Institute of Integrative, Systems and Molecular Biology, University of Liverpool, Liverpool, United Kingdom
| | - David Starns
- Department of Biochemistry and Systems Biology, Institute of Integrative, Systems and Molecular Biology, University of Liverpool, Liverpool, United Kingdom
| | - Ulrike Böhme
- Department of Biochemistry and Systems Biology, Institute of Integrative, Systems and Molecular Biology, University of Liverpool, Liverpool, United Kingdom
| | - Beatrice Amos
- Department of Biochemistry and Systems Biology, Institute of Integrative, Systems and Molecular Biology, University of Liverpool, Liverpool, United Kingdom
| | - Paul A. Wilkinson
- Department of Biochemistry and Systems Biology, Institute of Integrative, Systems and Molecular Biology, University of Liverpool, Liverpool, United Kingdom
| | - Omar S. Harb
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Susanne Warrenfeltz
- Center for Tropical & Emerging Global Diseases, Department of Genetics, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Jessica C. Kissinger
- Center for Tropical & Emerging Global Diseases, Department of Genetics, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Mary Ann McDowell
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - David S. Roos
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kathryn Crouch
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Andrew R. Jones
- Department of Biochemistry and Systems Biology, Institute of Integrative, Systems and Molecular Biology, University of Liverpool, Liverpool, United Kingdom
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Down the membrane hole: Ion channels in protozoan parasites. PLoS Pathog 2022; 18:e1011004. [PMID: 36580479 PMCID: PMC9799330 DOI: 10.1371/journal.ppat.1011004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Parasitic diseases caused by protozoans are highly prevalent around the world, disproportionally affecting developing countries, where coinfection with other microorganisms is common. Control and treatment of parasitic infections are constrained by the lack of specific and effective drugs, plus the rapid emergence of resistance. Ion channels are main drug targets for numerous diseases, but their potential against protozoan parasites is still untapped. Ion channels are membrane proteins expressed in all types of cells, allowing for the flow of ions between compartments, and regulating cellular functions such as membrane potential, excitability, volume, signaling, and death. Channels and transporters reside at the interface between parasites and their hosts, controlling nutrient uptake, viability, replication, and infectivity. To understand how ion channels control protozoan parasites fate and to evaluate their suitability for therapeutics, we must deepen our knowledge of their structure, function, and modulation. However, methodological approaches commonly used in mammalian cells have proven difficult to apply in protozoans. This review focuses on ion channels described in protozoan parasites of clinical relevance, mainly apicomplexans and trypanosomatids, highlighting proteins for which molecular and functional evidence has been correlated with their physiological functions.
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