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Williams SK, Jerlström Hultqvist J, Eglit Y, Salas-Leiva DE, Curtis B, Orr RJS, Stairs CW, Atalay TN, MacMillan N, Simpson AGB, Roger AJ. Extreme mitochondrial reduction in a novel group of free-living metamonads. Nat Commun 2024; 15:6805. [PMID: 39122691 PMCID: PMC11316075 DOI: 10.1038/s41467-024-50991-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 07/15/2024] [Indexed: 08/12/2024] Open
Abstract
Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered 'mitochondrion-related organelles' (MROs) with reduced functions, however the degree of reduction varies. Here, we generate high-quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we name the 'BaSk' (Barthelonids+Skoliomonads) clade, a deeply branching sister group to the Fornicata, a phylum that includes parasitic and free-living flagellates. Bioinformatic analyses of gene models shows that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system Fe/S cluster pathway by lateral gene transfer. One of the isolates, Skoliomonas litria, appears to have lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade demonstrates that mitochondrial functions may be completely lost even in free-living organisms.
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Affiliation(s)
- Shelby K Williams
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Jon Jerlström Hultqvist
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Yana Eglit
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biology, Dalhousie University, Halifax, Canada
| | - Dayana E Salas-Leiva
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry, Cambridge University, Cambridge, UK
| | - Bruce Curtis
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Russell J S Orr
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Tuğba N Atalay
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Naomi MacMillan
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Alastair G B Simpson
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biology, Dalhousie University, Halifax, Canada
| | - Andrew J Roger
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada.
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.
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Suzuki-Tellier S, Miano F, Asadzadeh SS, Simpson AGB, Kiørboe T. Foraging mechanisms in excavate flagellates shed light on the functional ecology of early eukaryotes. Proc Natl Acad Sci U S A 2024; 121:e2317264121. [PMID: 38781211 PMCID: PMC11145212 DOI: 10.1073/pnas.2317264121] [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: 10/06/2023] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
The phagotrophic flagellates described as "typical excavates" have been hypothesized to be morphologically similar to the Last Eukaryotic Common Ancestor and understanding the functional ecology of excavates may therefore help shed light on the ecology of these early eukaryotes. Typical excavates are characterized by a posterior flagellum equipped with a vane that beats in a ventral groove. Here, we combined flow visualization and observations of prey capture in representatives of the three clades of excavates with computational fluid dynamic modeling, to understand the functional significance of this cell architecture. We record substantial differences amongst species in the orientation of the vane and the beat plane of the posterior flagellum. Clearance rate magnitudes estimated from flow visualization and modeling are both like that of other similarly sized flagellates. The interaction between a vaned flagellum beating in a confinement is modeled to produce a very efficient feeding current at low energy costs, irrespective of the beat plane and vane orientation and of all other morphological variations. Given this predicted uniformity of function, we suggest that the foraging systems of typical excavates studied here may be good proxies to understand those potentially used by our distant ancestors more than 1 billion years ago.
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Affiliation(s)
- Sei Suzuki-Tellier
- Centre for Ocean Life, National Institute of Aquatic Resources, Technical University of Denmark, Kgs Lyngby2800, Denmark
| | - Federica Miano
- Centre for Ocean Life, National Institute of Aquatic Resources, Technical University of Denmark, Kgs Lyngby2800, Denmark
| | - Seyed Saeed Asadzadeh
- Centre for Ocean Life, National Institute of Aquatic Resources, Technical University of Denmark, Kgs Lyngby2800, Denmark
| | - Alastair G. B. Simpson
- Department of Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, HalifaxNSB3H 4R2, Canada
| | - Thomas Kiørboe
- Centre for Ocean Life, National Institute of Aquatic Resources, Technical University of Denmark, Kgs Lyngby2800, Denmark
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Suzuki-Tellier S, Kiørboe T, Simpson AGB. The function of the feeding groove of 'typical excavate' flagellates. J Eukaryot Microbiol 2024; 71:e13016. [PMID: 38108228 DOI: 10.1111/jeu.13016] [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: 10/09/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/19/2023]
Abstract
Phagotrophic flagellates are the main consumers of bacteria and picophytoplankton. Despite their ecological significance in the 'microbial loop', many of their predation mechanisms remain unclear. 'Typical excavates' bear a ventral groove, where prey is captured for ingestion. The consequences of feeding through a 'semi-rigid' furrow on the prey size range have not been explored. An unidentified moving element called 'the wave' that sweeps along the bottom of the groove toward the site of phagocytosis has been observed in a few species; its function is unclear. We investigated the presence, behavior, and function of the wave in four species from the three excavate clades (Discoba, Metamonada, and Malawimonadida) and found it present in all studied cases, suggesting the potential homology of this feature across all three groups. The wave displayed a species-specific behavior and was crucial for phagocytosis. The morphology of the feeding groove had an upper-prey size limit for successful prey captures, but smaller particles were not constrained. Additionally, the ingestion efficiencies were species dependent. By jointly studying these feeding traits, we speculate on adaptations to differences in food availability to better understand their ecological functions.
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Affiliation(s)
- Sei Suzuki-Tellier
- Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Thomas Kiørboe
- Centre for Ocean Life, DTU Aqua, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Alastair G B Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
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