1
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Cooney EC, Holt CC, Hehenberger E, Adams JA, Leander BS, Keeling PJ. Investigation of heterotrophs reveals new insights in dinoflagellate evolution. Mol Phylogenet Evol 2024; 196:108086. [PMID: 38677354 DOI: 10.1016/j.ympev.2024.108086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Dinoflagellates are diverse and ecologically important protists characterized by many morphological and molecular traits that set them apart from other eukaryotes. These features include, but are not limited to, massive genomes organized using bacterially-derived histone-like proteins (HLPs) and dinoflagellate viral nucleoproteins (DVNP) rather than histones, and a complex history of photobiology with many independent losses of photosynthesis, numerous cases of serial secondary and tertiary plastid gains, and the presence of horizontally acquired bacterial rhodopsins and type II RuBisCo. Elucidating how this all evolved depends on knowing the phylogenetic relationships between dinoflagellate lineages. Half of these species are heterotrophic, but existing molecular data is strongly biased toward the photosynthetic dinoflagellates due to their amenability to cultivation and prevalence in culture collections. These biases make it impossible to interpret the evolution of photosynthesis, but may also affect phylogenetic inferences that impact our understanding of character evolution. Here, we address this problem by isolating individual cells from the Salish Sea and using single cell, culture-free transcriptomics to expand molecular data for dinoflagellates to include 27 more heterotrophic taxa, resulting in a roughly balanced representation. Using these data, we performed a comprehensive search for proteins involved in chromatin packaging, plastid function, and photoactivity across all dinoflagellates. These searches reveal that 1) photosynthesis was lost at least 21 times, 2) two known types of HLP were horizontally acquired around the same time rather than sequentially as previously thought; 3) multiple rhodopsins are present across the dinoflagellates, acquired multiple times from different donors; 4) kleptoplastic species have nucleus-encoded genes for proteins targeted to their temporary plastids and they are derived from multiple lineages, and 5) warnowiids are the only heterotrophs that retain a whole photosystem, although some photosynthesis-related electron transport genes are widely retained in heterotrophs, likely as part of the iron-sulfur cluster pathway that persists in non-photosynthetic plastids.
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Affiliation(s)
- Elizabeth C Cooney
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; Hakai Institute, 1747 Hyacinthe Bay Rd., Heriot Bay, BC V0P 1H0, Canada.
| | - Corey C Holt
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; Hakai Institute, 1747 Hyacinthe Bay Rd., Heriot Bay, BC V0P 1H0, Canada.
| | - Elisabeth Hehenberger
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice, Czech Republic.
| | - Jayd A Adams
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.
| | - Brian S Leander
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; Department of Zoology, University of British Columbia, 4200 - 6270, University Blvd., Vancouver, BC V6T 1Z4, Canada.
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.
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2
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Na I, Campos C, Lax G, Kwong WK, Keeling PJ. Phylogenomics reveals Adeleorina are an ancient and distinct subgroup of Apicomplexa. Mol Phylogenet Evol 2024; 195:108060. [PMID: 38485105 DOI: 10.1016/j.ympev.2024.108060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/21/2024] [Accepted: 03/11/2024] [Indexed: 03/17/2024]
Abstract
Apicomplexans are a diverse phylum of unicellular eukaryotes that share obligate relationships with terrestrial and aquatic animal hosts. Many well-studied apicomplexans are responsible for several deadly zoonotic and human diseases, most notably malaria caused by Plasmodium. Interest in the evolutionary origin of apicomplexans has also spurred recent work on other more deeply-branching lineages, especially gregarines and sister groups like squirmids and chrompodellids. But a full picture of apicomplexan evolution is still lacking several lineages, and one major, diverse lineage that is notably absent is the adeleorinids. Adeleorina apicomplexans comprises hundreds of described species that infect invertebrate and vertebrate hosts across the globe. Although historically considered coccidians, phylogenetic trees based on limited data have shown conflicting branch positions for this subgroup, leaving this question unresolved. Phylogenomic trees and large-scale analyses comparing cellular functions and metabolism between major subgroups of apicomplexans have not incorporated Adeleorina because only a handful of molecular markers and a couple organellar genomes are available, ultimately excluding this group from contributing to our understanding of apicomplexan evolution and biology. To address this gap, we have generated complete genomes from mitochondria and plastids, as well as multiple deep-coverage single-cell transcriptomes of nuclear genes from two Adeleorina species, Klossia helicina and Legerella nova, and inferred a 206-protein phylogenomic tree of Apicomplexa. We observed distinct structures reported in species descriptions as remnant host structures surrounding adeleorinid oocysts. Klossia helicina and L. nova branched, as expected, with monoxenous adeleorinids within the Adeleorina and their mitochondrial and plastid genomes exhibited similarity to published organellar adeleorinid genomes. We show with a phylogeneomic tree and subsequent phylogenomic analyses that Adeleorina are not closely related to any of the currently sampled apicomplexan subgroups, and instead fall as a sister to a large clade encompassing Coccidia, Protococcidia, Hematozoa, and Nephromycida, collectively. This resolves Adeleorina as a key independently-branching group, separate from coccidians, on the tree of Apicomplexa, which now has all known major lineages sampled.
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Affiliation(s)
- Ina Na
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
| | - Claudia Campos
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Gordon Lax
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Waldan K Kwong
- Department of Botany, University of British Columbia, Vancouver, BC, Canada; Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
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Keeling PJ. Horizontal gene transfer in eukaryotes: aligning theory with data. Nat Rev Genet 2024; 25:416-430. [PMID: 38263430 DOI: 10.1038/s41576-023-00688-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2023] [Indexed: 01/25/2024]
Abstract
Horizontal gene transfer (HGT), or lateral gene transfer, is the non-sexual movement of genetic information between genomes. It has played a pronounced part in bacterial and archaeal evolution, but its role in eukaryotes is less clear. Behaviours unique to eukaryotic cells - phagocytosis and endosymbiosis - have been proposed to increase the frequency of HGT, but nuclear genomes encode fewer HGTs than bacteria and archaea. Here, I review the existing theory in the context of the growing body of data on HGT in eukaryotes, which suggests that any increased chance of acquiring new genes through phagocytosis and endosymbiosis is offset by a reduced need for these genes in eukaryotes, because selection in most eukaryotes operates on variation not readily generated by HGT.
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Affiliation(s)
- Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
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4
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Trznadel M, Holt CC, Livingston SJ, Kwong WK, Keeling PJ. Coral-infecting parasites in cold marine ecosystems. Curr Biol 2024; 34:1810-1816.e4. [PMID: 38608678 DOI: 10.1016/j.cub.2024.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/17/2024] [Accepted: 03/14/2024] [Indexed: 04/14/2024]
Abstract
Coral reefs are a biodiversity hotspot,1,2 and the association between coral and intracellular dinoflagellates is a model for endosymbiosis.3,4 Recently, corals and related anthozoans have also been found to harbor another kind of endosymbiont, apicomplexans called corallicolids.5 Apicomplexans are a diverse lineage of obligate intracellular parasites6 that include human pathogens such as the malaria parasite, Plasmodium.7 Global environmental sequencing shows corallicolids are tightly associated with tropical and subtropical reef environments,5,8,9 where they infect diverse corals across a range of depths in many reef systems, and correlate with host mortality during bleaching events.10 All of this points to corallicolids being ecologically significant to coral reefs, but it is also possible they are even more widely distributed because most environmental sampling is biased against parasites that maintain a tight association with their hosts throughout their life cycle. We tested the global distribution of corallicolids using a more direct approach, by specifically targeting potential anthozoan host animals from cold/temperate marine waters outside the coral reef context. We found that corallicolids are in fact common in such hosts, in some cases at high frequency, and that they infect the same tissue as parasites from topical coral reefs. Parasite phylogeny suggests corallicolids move between hosts and habitats relatively frequently, but that biogeography is more conserved. Overall, these results greatly expand the range of corallicolids beyond coral reefs, suggesting they are globally distributed parasites of marine anthozoans, which also illustrates significant blind spots that result from strategies commonly used to sample microbial biodiversity.
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Affiliation(s)
- Morelia Trznadel
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Corey C Holt
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Samuel J Livingston
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Waldan K Kwong
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Patrick J Keeling
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada.
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5
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Cho A, Lax G, Livingston SJ, Masukagami Y, Naumova M, Millar O, Husnik F, Keeling PJ. Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but does reveal the presence of giant viruses. PLoS Genet 2024; 20:e1011218. [PMID: 38557755 PMCID: PMC11008856 DOI: 10.1371/journal.pgen.1011218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/11/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Symbiomonas scintillans Guillou et Chrétiennot-Dinet, 1999 is a tiny (1.4 μm) heterotrophic microbial eukaryote. The genus was named based on the presence of endosymbiotic bacteria in its endoplasmic reticulum, however, like most such endosymbionts neither the identity nor functional association with its host were known. We generated both amplification-free shotgun metagenomics and whole genome amplification sequencing data from S. scintillans strains RCC257 and RCC24, but were unable to detect any sequences from known lineages of endosymbiotic bacteria. The absence of endobacteria was further verified with FISH analyses. Instead, numerous contigs in assemblies from both RCC24 and RCC257 were closely related to prasinoviruses infecting the green algae Ostreococcus lucimarinus, Bathycoccus prasinos, and Micromonas pusilla (OlV, BpV, and MpV, respectively). Using the BpV genome as a reference, we assembled a near-complete 190 kbp draft genome encoding all hallmark prasinovirus genes, as well as two additional incomplete assemblies of closely related but distinct viruses from RCC257, and three similar draft viral genomes from RCC24, which we collectively call SsVs. A multi-gene tree showed the three SsV genome types branched within highly supported clades with each of BpV2, OlVs, and MpVs, respectively. Interestingly, transmission electron microscopy also revealed a 190 nm virus-like particle similar the morphology and size of the endosymbiont originally reported in S. scintillans. Overall, we conclude that S. scintillans currently does not harbour an endosymbiotic bacterium, but is associated with giant viruses.
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Affiliation(s)
- Anna Cho
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gordon Lax
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Samuel J. Livingston
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yumiko Masukagami
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Mariia Naumova
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Olivia Millar
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Filip Husnik
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Patrick J. Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Keeling PJ, Mtawali M, Trznadel M, Livingston SJ, Wakeman KC. Parallel functional reduction in the mitochondria of apicomplexan parasites. Eur J Protistol 2024; 94:126065. [PMID: 38492251 DOI: 10.1016/j.ejop.2024.126065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/18/2024]
Abstract
Extreme functional reduction of mitochondria has taken place in parallel in many distantly related lineages of eukaryotes, leading to a number of recurring metabolic states with variously lost electron transport chain (ETC) complexes, loss of the tricarboxylic acid (TCA) cycle, and/or loss of the mitochondrial genome. The resulting mitochondria-related organelles (MROs) are generally structurally reduced and in the most extreme cases barely recognizable features of the cell with no role in energy metabolism whatsoever (e.g., mitosomes, which generally only make iron-sulfur clusters). Recently, a wide diversity of MROs were discovered to be hiding in plain sight: in gregarine apicomplexans. This diverse group of invertebrate parasites has been known and observed for centuries, but until recent applications of culture-free genomics, their mitochondria were unremarkable. The genomics, however, showed that mitochondrial function has reduced in parallel in multiple gregarine lineages to several different endpoints, including the most reduced mitosomes. Here we review this remarkable case of parallel evolution of MROs, and some of the interesting questions this work raises.
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Affiliation(s)
- Patrick J Keeling
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver V6T 1Z4, BC, Canada.
| | - Mahara Mtawali
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver V6T 1Z4, BC, Canada
| | - Morelia Trznadel
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver V6T 1Z4, BC, Canada
| | - Samuel J Livingston
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver V6T 1Z4, BC, Canada
| | - Kevin C Wakeman
- Institute for the Advancement of Higher Education, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan
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7
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Jinkerson RE, Poveda-Huertes D, Cooney EC, Cho A, Ochoa-Fernandez R, Keeling PJ, Xiang T, Andersen-Ranberg J. Biosynthesis of chlorophyll c in a dinoflagellate and heterologous production in planta. Curr Biol 2024; 34:594-605.e4. [PMID: 38157859 DOI: 10.1016/j.cub.2023.12.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Chlorophyll c is a key photosynthetic pigment that has been used historically to classify eukaryotic algae. Despite its importance in global photosynthetic productivity, the pathway for its biosynthesis has remained elusive. Here we define the CHLOROPHYLL C SYNTHASE (CHLCS) discovered through investigation of a dinoflagellate mutant deficient in chlorophyll c. CHLCSs are proteins with chlorophyll a/b binding and 2-oxoglutarate-Fe(II) dioxygenase (2OGD) domains found in peridinin-containing dinoflagellates; other chlorophyll c-containing algae utilize enzymes with only the 2OGD domain or an unknown synthase to produce chlorophyll c. 2OGD-containing synthases across dinoflagellate, diatom, cryptophyte, and haptophyte lineages form a monophyletic group, 8 members of which were also shown to produce chlorophyll c. Chlorophyll c1 to c2 ratios in marine algae are dictated in part by chlorophyll c synthases. CHLCS heterologously expressed in planta results in the accumulation of chlorophyll c1 and c2, demonstrating a path to augment plant pigment composition with algal counterparts.
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Affiliation(s)
- Robert E Jinkerson
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, USA; Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.
| | - Daniel Poveda-Huertes
- Department of Plant and Environmental Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Elizabeth C Cooney
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Anna Cho
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Rocio Ochoa-Fernandez
- Department of Plant and Environmental Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Tingting Xiang
- Department of Bioengineering, University of California, Riverside, Riverside, CA 92521, USA.
| | - Johan Andersen-Ranberg
- Department of Plant and Environmental Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
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Lax G, Okamoto N, Keeling PJ. Phylogenomic position of eupelagonemids, abundant, and diverse deep-ocean heterotrophs. ISME J 2024; 18:wrae040. [PMID: 38457644 PMCID: PMC10987973 DOI: 10.1093/ismejo/wrae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/02/2024] [Accepted: 03/06/2024] [Indexed: 03/10/2024]
Abstract
Eupelagonemids, formerly known as Deep Sea Pelagic Diplonemids I (DSPD I), are among the most abundant and diverse heterotrophic protists in the deep ocean, but little else is known about their ecology, evolution, or biology in general. Originally recognized solely as a large clade of environmental ribosomal subunit RNA gene sequences (SSU rRNA), branching with a smaller sister group DSPD II, they were postulated to be diplonemids, a poorly studied branch of Euglenozoa. Although new diplonemids have been cultivated and studied in depth in recent years, the lack of cultured eupelagonemids has limited data to a handful of light micrographs, partial SSU rRNA gene sequences, a small number of genes from single amplified genomes, and only a single formal described species, Eupelagonema oceanica. To determine exactly where this clade goes in the tree of eukaryotes and begin to address the overall absence of biological information about this apparently ecologically important group, we conducted single-cell transcriptomics from two eupelagonemid cells. A SSU rRNA gene phylogeny shows that these two cells represent distinct subclades within eupelagonemids, each different from E. oceanica. Phylogenomic analysis based on a 125-gene matrix contrasts with the findings based on ecological survey data and shows eupelagonemids branch sister to the diplonemid subgroup Hemistasiidae.
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Affiliation(s)
- Gordon Lax
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Noriko Okamoto
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Hakai Institute, Heriot Bay, BC, V0P 1H0, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Cho A, Tikhonenkov DV, Lax G, Prokina KI, Keeling PJ. Phylogenomic position of genetically diverse phagotrophic stramenopile flagellates in the sediment-associated MAST-6 lineage and a potentially halotolerant placididean. Mol Phylogenet Evol 2024; 190:107964. [PMID: 37951557 DOI: 10.1016/j.ympev.2023.107964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 11/02/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023]
Abstract
Unlike morphologically conspicuous ochrophytes, many flagellates belonging to basally branching stramenopiles are small and often overlooked. As a result, many of these lineages are known only through molecular surveys and identified as MArine STramenopiles (MAST), and remain largely uncharacterized at the cellular or genomic level. These likely phagotrophic flagellates are not only phylogenetically diverse, but also extremely abundant in some environments, making their characterization all the more important. MAST-6 is one example of a phylogenetically distinct group that has been known to be associated with sediments, but little else is known about it. Indeed, until the present study, only a single species from this group, Pseudophyllomitus vesiculosus (Pseudophyllomitidae), has been both formally described and associated with genomic information. Here, we describe four new species including two new genera of sediment-dwelling MAST-6, Vomastramonas tehuelche gen. et sp. nov., Mastreximonas tlaamin gen. et sp. nov., one undescribed Pseudophyllomitus sp., BSC2, and a new species belonging to Placididea, the potentially halotolerant Haloplacidia sinai sp. nov. We also provide two additional bikosian transcriptomes from a public culture collection, to allow for better phylogenetic reconstructions of deep-branching stramenopiles. With the SSU rRNA sequences of the new MAST-6 species, we investigate the phylogenetic diversity of the MAST-6 group and show a high relative abundance of MAST-6 related to M. tlaamin in samples across various depths and geographical locations. Using the new MAST-6 species, we also update the phylogenomic tree of stramenopiles, particularly focusing on the paraphyly of Bigyra.
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Affiliation(s)
- Anna Cho
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada.
| | - Denis V Tikhonenkov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Science, Borok 152742, Russia
| | - Gordon Lax
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
| | - Kristina I Prokina
- Papanin Institute for Biology of Inland Waters, Russian Academy of Science, Borok 152742, Russia; Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
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10
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Holt CC, Hehenberger E, Tikhonenkov DV, Jacko-Reynolds VKL, Okamoto N, Cooney EC, Irwin NAT, Keeling PJ. Multiple parallel origins of parasitic Marine Alveolates. Nat Commun 2023; 14:7049. [PMID: 37923716 PMCID: PMC10624901 DOI: 10.1038/s41467-023-42807-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/20/2023] [Indexed: 11/06/2023] Open
Abstract
Microbial eukaryotes are important components of marine ecosystems, and the Marine Alveolates (MALVs) are consistently both abundant and diverse in global environmental sequencing surveys. MALVs are dinoflagellates that are thought to be parasites of other protists and animals, but the lack of data beyond ribosomal RNA gene sequences from all but a few described species means much of their biology and evolution remain unknown. Using single-cell transcriptomes from several MALVs and their free-living relatives, we show that MALVs evolved independently from two distinct, free-living ancestors and that their parasitism evolved in parallel. Phylogenomics shows one subgroup (MALV-II and -IV, or Syndiniales) is related to a novel lineage of free-living, eukaryovorous predators, the eleftherids, while the other (MALV-I, or Ichthyodinida) is related to the free-living predator Oxyrrhis and retains proteins targeted to a non-photosynthetic plastid. Reconstructing the evolution of photosynthesis, plastids, and parasitism in early-diverging dinoflagellates shows a number of parallels with the evolution of their apicomplexan sisters. In both groups, similar forms of parasitism evolved multiple times and photosynthesis was lost many times. By contrast, complete loss of the plastid organelle is infrequent and, when this does happen, leaves no residual genes.
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Affiliation(s)
- Corey C Holt
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
- Hakai Institute, Heriot Bay, British Columbia, Canada.
| | - Elisabeth Hehenberger
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice, Czech Republic.
| | - Denis V Tikhonenkov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
- AquaBioSafe Laboratory, University of Tyumen, Tyumen, Russia
| | | | - Noriko Okamoto
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Elizabeth C Cooney
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Merton College, University of Oxford, Oxford, UK
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
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11
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Keeling PJ, Eglit Y. Openly available illustrations as tools to describe eukaryotic microbial diversity. PLoS Biol 2023; 21:e3002395. [PMID: 37988341 PMCID: PMC10662721 DOI: 10.1371/journal.pbio.3002395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Microbial life maintains nearly all the support systems that keep the Earth habitable, yet the diversity of this vast microbial world is greatly understudied, misrepresented, and misunderstood. Even what we do know is difficult to communicate broadly because an intuitive grasp of what these tiny organisms are like is abstract, and we lack tools that would help to describe them. In this Essay, we present a series of openly available technical diagrams that illustrate the diverse range of complex body plans of microbial eukaryotes (or "protists"), as well as an illustrated tree to show the vast diversity they encompass and how they are related to the more familiar macroscopic animals, fungi, and plants. These sorts of tools are desperately needed for teaching and communication about the microbial world, which is a pressingly important problem where much improvement is needed.
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Affiliation(s)
| | - Yana Eglit
- Botany Department, University of British Columbia, Vancouver, Canada
- Department of Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Canada
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12
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Cooney EC, Holt CC, Jacko-Reynolds VKL, Leander BS, Keeling PJ. Photosystems in the eye-like organelles of heterotrophic warnowiid dinoflagellates. Curr Biol 2023; 33:4252-4260.e3. [PMID: 37703877 DOI: 10.1016/j.cub.2023.08.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/03/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023]
Abstract
Warnowiid dinoflagellates contain a highly complex camera-eye-like structure called the ocelloid that is composed of different organelles resembling parts of metazoan eyes, including a modified plastid that serves as the retinal body.1 The overall structure of the ocelloid has been investigated by microscopy; because warnowiids are not in culture and are rare in nature, we know little about their function.1,2 Here, we generate single-cell transcriptomes from 18 warnowiid cells collected directly from the marine environment representing all 4 known genera and 1 previously undescribed genus, as well as 8 cells from a related lineage, the polykrikoids. Phylogenomic analyses show that photosynthesis was independently lost twice in warnowiids. Interestingly, the non-photosynthetic taxa still express a variety of photosynthesis-related proteins. Nematodinium and Warnowia (known or suspected to be photosynthetic1,3) unsurprisingly express a full complement of photosynthetic pathway components. However, non-photosynthetic genera with ocelloids were also found to express light-harvesting complexes, photosystem I, photosynthetic electron transport (PET), cytochrome b6f, and, in Erythropsidinium, plastid ATPase, representing all major complexes except photosystem II and the Calvin cycle. This suggests that the non-photosynthetic retinal body has retained a reduced but still substantial photosynthetic apparatus that perhaps functions using cyclic electron flow (CEF). This may support ATP synthesis in a reduced capacity, but it is also possible that the photosystem has been co-opted to function as a light-driven proton pump at the heart of the sensory mechanism within the complex architecture of ocelloids.
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Affiliation(s)
- Elizabeth C Cooney
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Hakai Institute, Heriot Bay, BC V9W 5E3, Canada.
| | - Corey C Holt
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Hakai Institute, Heriot Bay, BC V9W 5E3, Canada
| | | | - Brian S Leander
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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13
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Lax G, Keeling PJ. Molecular phylogenetics of sessile Dolium sedentarium, a petalomonad euglenid. J Eukaryot Microbiol 2023; 70:e12991. [PMID: 37424051 DOI: 10.1111/jeu.12991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 07/11/2023]
Abstract
The euglenids are a species-rich group of flagellates with varying modes of nutrition that can be found in diverse habitats. Phagotrophic members of this group gave rise to phototrophs and hold the key to understanding the evolution of euglenids as a whole, including the evolution of complex morphological characters like the euglenid pellicle. Yet to understand the evolution of these characters, a comprehensive sampling of molecular data is needed to correlate morphological and molecular data, and to estimate a basic phylogenetic backbone of the group. While the availability of SSU rDNA and, more recently, multigene data from phagotrophic euglenids has improved, several "orphan" taxa remain without any molecular data whatsoever. Dolium sedentarium is one such taxon: It is a rarely-observed phagotrophic euglenid that inhabits tropical benthic environments and is one of few known sessile euglenids. Based on morphological characters, it has been thought of as part of the earliest branch of euglenids, the Petalomonadida. We report the first molecular sequencing data for Dolium using single-cell transcriptomics, adding another small piece in the puzzle of euglenid evolution. Both SSU rDNA and multigene phylogenies confirm it as a solitary branch within Petalomonadida.
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Affiliation(s)
- Gordon Lax
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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14
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Hehenberger E, Boscaro V, James ER, Hirakawa Y, Trznadel M, Mtawali M, Fiorito R, Del Campo J, Karnkowska A, Kolisko M, Irwin NAT, Mathur V, Scheffrahn RH, Keeling PJ. New Parabasalia symbionts Snyderella spp. and Daimonympha gen. nov. from South American Rugitermes termites and the parallel evolution of a cell with a rotating "head". J Eukaryot Microbiol 2023; 70:e12987. [PMID: 37282792 DOI: 10.1111/jeu.12987] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/24/2023] [Accepted: 05/28/2023] [Indexed: 06/08/2023]
Abstract
Most Parabasalia are symbionts in the hindgut of "lower" (non-Termitidae) termites, where they widely vary in morphology and degree of morphological complexity. Large and complex cells in the class Cristamonadea evolved by replicating a fundamental unit, the karyomastigont, in various ways. We describe here four new species of Calonymphidae (Cristamonadea) from Rugitermes hosts, assigned to the genus Snyderella based on diagnostic features (including the karyomastigont pattern) and molecular phylogeny. We also report a new genus of Calonymphidae, Daimonympha, from Rugitermes laticollis. Daimonympha's morphology does not match that of any known Parabasalia, and its SSU rRNA gene sequence corroborates this distinction. Daimonympha does however share a puzzling feature with a few previously described, but distantly related, Cristamonadea: a rapid, smooth, and continuous rotation of the anterior end of the cell, including the many karyomastigont nuclei. The function of this rotatory movement, the cellular mechanisms enabling it, and the way the cell deals with the consequent cell membrane shear, are all unknown. "Rotating wheel" structures are famously rare in biology, with prokaryotic flagella being the main exception; these mysterious spinning cells found only among Parabasalia are another, far less understood, example.
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Affiliation(s)
- Elisabeth Hehenberger
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Erick R James
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yoshihisa Hirakawa
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Morelia Trznadel
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mahara Mtawali
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rebecca Fiorito
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Javier Del Campo
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Anna Karnkowska
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Martin Kolisko
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Merton College, University of Oxford, Oxford, UK
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biology, University of Oxford, Oxford, UK
| | | | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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15
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Tikhonenkov DV, Mikhailov KV, Gawryluk RMR, Keeling PJ. Provora. Curr Biol 2023; 33:R790-R791. [PMID: 37552939 DOI: 10.1016/j.cub.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Tikhonenkov et al. introduce the Provora-a newly described, yet ancient, supergroup of unicellular protists encompassing as much genetic diversity as animals and fungi combined.
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Affiliation(s)
- Denis V Tikhonenkov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, 152742, Russian Federation.
| | - Kirill V Mikhailov
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russian Federation; Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russian Federation
| | - Ryan M R Gawryluk
- Department of Biology, University of Victoria, Victoria, V8P5C2 BC, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, V6T1Z4 BC, Canada
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16
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Lax G, Cho A, Keeling PJ. Phylogenomics of novel ploeotid taxa contribute to the backbone of the euglenid tree. J Eukaryot Microbiol 2023; 70:e12973. [PMID: 36912454 DOI: 10.1111/jeu.12973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/14/2023]
Abstract
Euglenids are a diverse group of flagellates that inhabit most environments and exhibit many different nutritional modes. The most prominent euglenids are phototrophs, but phagotrophs constitute the majority of phylogenetic diversity of euglenids. They are pivotal to our understanding of euglenid evolution, yet we are only starting to understand relationships amongst phagotrophs, with the backbone of the tree being most elusive. Ploeotids make up most of this backbone diversity-yet despite their morphological similarities, SSU rDNA analyses and multigene analyses show that they are non-monophyletic. As more ploeotid diversity is sampled, known taxa have coalesced into some subgroups (e.g. Alistosa), but the relationships amongst these are not always supported and some taxa remain unsampled for multigene phylogenetics. Here, we used light microscopy and single-cell transcriptomics to characterize five ploeotid euglenids and place them into a multigene phylogenetic framework. Our analyses place Decastava in Alistosa; while Hemiolia branches with Liburna, establishing the novel clade Karavia. We describe Hemiolia limna, a freshwater-dwelling species in an otherwise marine clade. Intriguingly, two undescribed ploeotids are found to occupy pivotal positions in the tree: Chelandium granulatum nov. gen. nov. sp. branches as sister to Olkasia, and Gaulosia striata nov. gen. nov. sp. remains an orphan taxon.
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Affiliation(s)
- Gordon Lax
- Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, British Columbia, Canada
| | - Anna Cho
- Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, British Columbia, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, British Columbia, Canada
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17
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Žárský V, Karnkowska A, Boscaro V, Trznadel M, Whelan TA, Hiltunen-Thorén M, Onut-Brännström I, Abbott CL, Fast NM, Burki F, Keeling PJ. Contrasting outcomes of genome reduction in mikrocytids and microsporidians. BMC Biol 2023; 21:137. [PMID: 37280585 DOI: 10.1186/s12915-023-01635-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/26/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Intracellular symbionts often undergo genome reduction, losing both coding and non-coding DNA in a process that ultimately produces small, gene-dense genomes with few genes. Among eukaryotes, an extreme example is found in microsporidians, which are anaerobic, obligate intracellular parasites related to fungi that have the smallest nuclear genomes known (except for the relic nucleomorphs of some secondary plastids). Mikrocytids are superficially similar to microsporidians: they are also small, reduced, obligate parasites; however, as they belong to a very different branch of the tree of eukaryotes, the rhizarians, such similarities must have evolved in parallel. Since little genomic data are available from mikrocytids, we assembled a draft genome of the type species, Mikrocytos mackini, and compared the genomic architecture and content of microsporidians and mikrocytids to identify common characteristics of reduction and possible convergent evolution. RESULTS At the coarsest level, the genome of M. mackini does not exhibit signs of extreme genome reduction; at 49.7 Mbp with 14,372 genes, the assembly is much larger and gene-rich than those of microsporidians. However, much of the genomic sequence and most (8075) of the protein-coding genes code for transposons, and may not contribute much of functional relevance to the parasite. Indeed, the energy and carbon metabolism of M. mackini share several similarities with those of microsporidians. Overall, the predicted proteome involved in cellular functions is quite reduced and gene sequences are extremely divergent. Microsporidians and mikrocytids also share highly reduced spliceosomes that have retained a strikingly similar subset of proteins despite having reduced independently. In contrast, the spliceosomal introns in mikrocytids are very different from those of microsporidians in that they are numerous, conserved in sequence, and constrained to an exceptionally narrow size range (all 16 or 17 nucleotides long) at the shortest extreme of known intron lengths. CONCLUSIONS Nuclear genome reduction has taken place many times and has proceeded along different routes in different lineages. Mikrocytids show a mix of similarities and differences with other extreme cases, including uncoupling the actual size of a genome with its functional reduction.
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Affiliation(s)
- Vojtečh Žárský
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada
| | - Anna Karnkowska
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada
- Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw, 02-089, Warsaw, Poland
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada.
| | - Morelia Trznadel
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada
| | - Thomas A Whelan
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada
| | - Markus Hiltunen-Thorén
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, 752 36, Uppsala, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Ioana Onut-Brännström
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, 752 36, Uppsala, Sweden
- Department of Ecology and Genetics, Uppsala University, 752 36, Uppsala, Sweden
- Natural History Museum, University of Oslo, 0562, Oslo, Norway
| | - Cathryn L Abbott
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, V9T 6N7, Canada
| | - Naomi M Fast
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada
| | - Fabien Burki
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, 752 36, Uppsala, Sweden
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, V6T 1Z4, Vancouver, 3529-6270 University Boulevard, BC, Canada.
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18
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George EE, Barcytė D, Lax G, Livingston S, Tashyreva D, Husnik F, Lukeš J, Eliáš M, Keeling PJ. A single cryptomonad cell harbors a complex community of organelles, bacteria, a phage, and selfish elements. Curr Biol 2023; 33:1982-1996.e4. [PMID: 37116483 DOI: 10.1016/j.cub.2023.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/20/2023] [Accepted: 04/06/2023] [Indexed: 04/30/2023]
Abstract
Symbiosis between prokaryotes and microbial eukaryotes (protists) has broadly impacted both evolution and ecology. Endosymbiosis led to mitochondria and plastids, the latter spreading across the tree of eukaryotes by subsequent rounds of endosymbiosis. Present-day endosymbionts in protists remain both common and diverse, although what function they serve is often unknown. Here, we describe a highly complex community of endosymbionts and a bacteriophage (phage) within a single cryptomonad cell. Cryptomonads are a model for organelle evolution because their secondary plastid retains a relict endosymbiont nucleus, but only one previously unidentified Cryptomonas strain (SAG 25.80) is known to harbor bacterial endosymbionts. We carried out electron microscopy and FISH imaging as well as genomic sequencing on Cryptomonas SAG 25.80, which revealed a stable, complex community even after over 50 years in continuous cultivation. We identified the host strain as Cryptomonas gyropyrenoidosa, and sequenced genomes from its mitochondria, plastid, and nucleomorph (and partially its nucleus), as well as two symbionts, Megaira polyxenophila and Grellia numerosa, and one phage (MAnkyphage) infecting M. polyxenophila. Comparing closely related endosymbionts from other hosts revealed similar metabolic and genomic features, with the exception of abundant transposons and genome plasticity in M. polyxenophila from Cryptomonas. We found an abundance of eukaryote-interacting genes as well as many toxin-antitoxin systems, including in the MAnkyphage genome that also encodes several eukaryotic-like proteins. Overall, the Cryptomonas cell is an endosymbiotic conglomeration with seven distinct evolving genomes that all show evidence of inter-lineage conflict but nevertheless remain stable, even after more than 4,000 generations in culture.
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Affiliation(s)
- Emma E George
- University of British Columbia, Department of Botany, Vancouver V6T 1Z4, Canada.
| | - Dovilė Barcytė
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, 701 00 Ostrava, Czech Republic; Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
| | - Gordon Lax
- University of British Columbia, Department of Botany, Vancouver V6T 1Z4, Canada
| | - Sam Livingston
- University of British Columbia, Department of Botany, Vancouver V6T 1Z4, Canada
| | - Daria Tashyreva
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Filip Husnik
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
| | - Julius Lukeš
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic; University of South Bohemia, Faculty of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Marek Eliáš
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, 701 00 Ostrava, Czech Republic
| | - Patrick J Keeling
- University of British Columbia, Department of Botany, Vancouver V6T 1Z4, Canada
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19
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Onuț-Brännström I, Stairs CW, Campos KIA, Thorén MH, Ettema TJG, Keeling PJ, Bass D, Burki F. A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea). Genome Biol Evol 2023; 15:7039708. [PMID: 36790104 PMCID: PMC9998036 DOI: 10.1093/gbe/evad022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/13/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
Ascetosporea are endoparasites of marine invertebrates that include economically important pathogens of aquaculture species. Owing to their often-minuscule cell sizes, strict intracellular lifestyle, lack of cultured representatives and minimal availability of molecular data, these unicellular parasites remain poorly studied. Here, we sequenced and assembled the genome and transcriptome of Paramikrocytos canceri, an endoparasite isolated from the European edible crab Cancer pagurus. Using bioinformatic predictions, we show that P. canceri likely possesses a mitochondrion-related organelle (MRO) with highly reduced metabolism, resembling the mitosomes of other parasites but with key differences. Like other mitosomes, this MRO is predicted to have reduced metabolic capacity and lack an organellar genome and function in iron-sulfur cluster (ISC) pathway-mediated Fe-S cluster biosynthesis. However, the MRO in P. canceri is uniquely predicted to produce ATP via a partial glycolytic pathway and synthesize phospholipids de novo through the CDP-DAG pathway. Heterologous gene expression confirmed that proteins from the ISC and CDP-DAG pathways retain mitochondrial targeting sequences that are recognized by yeast mitochondria. This represents a unique combination of metabolic pathways in an MRO, including the first reported case of a mitosome-like organelle able to synthesize phospholipids de novo. Some of these phospholipids, such as phosphatidylserine, are vital in other protist endoparasites that invade their host through apoptotic mimicry.
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Affiliation(s)
- Ioana Onuț-Brännström
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden
| | - Courtney W Stairs
- Microbiology Research Group, Department of Biology, Lund University, Lund, Sweden
| | | | - Markus Hiltunen Thorén
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Bass
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, United Kingdom.,Department of Life Sciences, The Natural History Museum, London, United Kingdom.,Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Fabien Burki
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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20
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Boscaro V, Keeling PJ. How ciliates got their nuclei. Proc Natl Acad Sci U S A 2023; 120:e2221818120. [PMID: 36763531 PMCID: PMC9963403 DOI: 10.1073/pnas.2221818120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Affiliation(s)
- Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, BCB6T 1Z4, Canada
| | - Patrick J. Keeling
- Department of Botany, University of British Columbia, Vancouver, BCB6T 1Z4, Canada
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21
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Mathur V, Salomaki ED, Wakeman KC, Na I, Kwong WK, Kolisko M, Keeling PJ. Reconstruction of Plastid Proteomes of Apicomplexans and Close Relatives Reveals the Major Evolutionary Outcomes of Cryptic Plastids. Mol Biol Evol 2023; 40:6969433. [PMID: 36610734 PMCID: PMC9847631 DOI: 10.1093/molbev/msad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/18/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
Apicomplexans and related lineages comprise many obligate symbionts of animals; some of which cause notorious diseases such as malaria. They evolved from photosynthetic ancestors and transitioned into a symbiotic lifestyle several times, giving rise to species with diverse non-photosynthetic plastids. Here, we sought to reconstruct the evolution of the cryptic plastids in the apicomplexans, chrompodellids, and squirmids (ACS clade) by generating five new single-cell transcriptomes from understudied gregarine lineages, constructing a robust phylogenomic tree incorporating all ACS clade sequencing datasets available, and using these to examine in detail, the evolutionary distribution of all 162 proteins recently shown to be in the apicoplast by spatial proteomics in Toxoplasma. This expanded homology-based reconstruction of plastid proteins found in the ACS clade confirms earlier work showing convergence in the overall metabolic pathways retained once photosynthesis is lost, but also reveals differences in the degrees of plastid reduction in specific lineages. We show that the loss of the plastid genome is common and unexpectedly find many lineage- and species-specific plastid proteins, suggesting the presence of evolutionary innovations and neofunctionalizations that may confer new functional and metabolic capabilities that are yet to be discovered in these enigmatic organelles.
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Affiliation(s)
| | - Eric D Salomaki
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Kevin C Wakeman
- Institute for the Advancement of Higher Education, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan
| | - Ina Na
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver V6T 1Z4, BC, Canada
| | - Waldan K Kwong
- Present address: Instituto Gulbenkian de Ciência (IGC) Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Martin Kolisko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver V6T 1Z4, BC, Canada
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22
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Boscaro V, Manassero V, Keeling PJ, Vannini C. Single-cell Microbiomics Unveils Distribution and Patterns of Microbial Symbioses in the Natural Environment. Microb Ecol 2023; 85:307-316. [PMID: 35048168 DOI: 10.1007/s00248-021-01938-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
Protist-bacteria associations are extremely common. Among them, those involving ciliates of the genus Euplotes are emerging as models for symbioses between prokaryotes and eukaryotes, and a great deal of information is available from cultured representatives of this system. Even so, as for most known microbial symbioses, data on natural populations is lacking, and their ecology remains largely unexplored; how well lab cultures represent actual diversity is untested. Here, we describe a survey on natural populations of Euplotes based on a single-cell microbiomic approach, focusing on taxa that include known endosymbionts of this ciliate. The results reveal an unexpected variability in symbiotic communities, with individual hosts of the same population harboring different sets of bacterial endosymbionts. Co-occurring Euplotes individuals of the same population can even have different essential symbionts, Polynucleobacter and "Candidatus Protistobacter," which might suggest that replacement events could be more frequent in nature than previously hypothesized. Accessory symbionts are even more variable: some showed a strong affinity for one host species, some for a sampling site, and two ("Candidatus Cyrtobacter" and "Candidatus Anadelfobacter") displayed an unusual pattern of competitive exclusion. These data represent the first insight into the prevalence and patterns of bacterial symbionts in natural populations of free-living protists.
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Affiliation(s)
- Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Claudia Vannini
- Department of Biology, University of Pisa, 56126, Pisa, Italy.
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23
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Giannotti D, Boscaro V, Husnik F, Vannini C, Keeling PJ. At the threshold of symbiosis: the genome of obligately endosymbiotic ' Candidatus Nebulobacter yamunensis' is almost indistinguishable from that of a cultivable strain. Microb Genom 2022; 8:mgen000909. [PMID: 36748607 PMCID: PMC9837558 DOI: 10.1099/mgen.0.000909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Comparing obligate endosymbionts with their free-living relatives is a powerful approach to investigate the evolution of symbioses, and it has led to the identification of several genomic traits consistently associated with the establishment of symbiosis. 'Candidatus Nebulobacter yamunensis' is an obligate bacterial endosymbiont of the ciliate Euplotes that seemingly depends on its host for survival. A subsequently characterized bacterial strain with an identical 16S rRNA gene sequence, named Fastidiosibacter lacustris, can instead be maintained in pure culture. We analysed the genomes of 'Candidatus Nebulobacter' and Fastidiosibacter seeking to identify key differences between their functional traits and genomic structure that might shed light on a recent transition to obligate endosymbiosis. Surprisingly, we found almost no such differences: the two genomes share a high level of sequence identity, the same overall structure, and largely overlapping sets of genes. The similarities between the genomes of the two strains are at odds with their different ecological niches, confirmed here with a parallel growth experiment. Although other pairs of closely related symbiotic/free-living bacteria have been compared in the past, 'Candidatus Nebulobacter' and Fastidiosibacter represent an extreme example proving that a small number of (unknown) factors might play a pivotal role in the earliest stages of obligate endosymbiosis establishment.
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Affiliation(s)
- Daniele Giannotti
- Department of Biology, University of Pisa, Pisa, Italy,Department of Botany, University of British Columbia, Vancouver, Canada
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, Canada,*Correspondence: Vittorio Boscaro,
| | - Filip Husnik
- Department of Botany, University of British Columbia, Vancouver, Canada,Okinawa Institute of Science and Technology, Okinawa, Japan
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24
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Tikhonenkov DV, Mikhailov KV, Gawryluk RMR, Belyaev AO, Mathur V, Karpov SA, Zagumyonnyi DG, Borodina AS, Prokina KI, Mylnikov AP, Aleoshin VV, Keeling PJ. Microbial predators form a new supergroup of eukaryotes. Nature 2022; 612:714-719. [PMID: 36477531 DOI: 10.1038/s41586-022-05511-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022]
Abstract
Molecular phylogenetics of microbial eukaryotes has reshaped the tree of life by establishing broad taxonomic divisions, termed supergroups, that supersede the traditional kingdoms of animals, fungi and plants, and encompass a much greater breadth of eukaryotic diversity1. The vast majority of newly discovered species fall into a small number of known supergroups. Recently, however, a handful of species with no clear relationship to other supergroups have been described2-4, raising questions about the nature and degree of undiscovered diversity, and exposing the limitations of strictly molecular-based exploration. Here we report ten previously undescribed strains of microbial predators isolated through culture that collectively form a diverse new supergroup of eukaryotes, termed Provora. The Provora supergroup is genetically, morphologically and behaviourally distinct from other eukaryotes, and comprises two divergent clades of predators-Nebulidia and Nibbleridia-that are superficially similar to each other, but differ fundamentally in ultrastructure, behaviour and gene content. These predators are globally distributed in marine and freshwater environments, but are numerically rare and have consequently been overlooked by molecular-diversity surveys. In the age of high-throughput analyses, investigation of eukaryotic diversity through culture remains indispensable for the discovery of rare but ecologically and evolutionarily important eukaryotes.
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Affiliation(s)
- Denis V Tikhonenkov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation. .,AquaBioSafe Laboratory, University of Tyumen, Tyumen, Russian Federation.
| | - Kirill V Mikhailov
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ryan M R Gawryluk
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Artem O Belyaev
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation.,Department of Zoology and Ecology, Penza State University, Penza, Russian Federation
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Zoology, University of Oxford, Oxford, UK
| | - Sergey A Karpov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russian Federation.,Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russian Federation
| | - Dmitry G Zagumyonnyi
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation.,AquaBioSafe Laboratory, University of Tyumen, Tyumen, Russian Federation
| | - Anastasia S Borodina
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation.,Department of Zoology and Parasitology, Voronezh State University, Voronezh, Russian Federation
| | - Kristina I Prokina
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation.,Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Alexander P Mylnikov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation
| | - Vladimir V Aleoshin
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Holt CC, Boscaro V, Van Steenkiste NWL, Herranz M, Mathur V, Irwin NAT, Buckholtz G, Leander BS, Keeling PJ. Microscopic marine invertebrates are reservoirs for cryptic and diverse protists and fungi. Microbiome 2022; 10:161. [PMID: 36180959 PMCID: PMC9523941 DOI: 10.1186/s40168-022-01363-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Microbial symbioses in marine invertebrates are commonplace. However, characterizations of invertebrate microbiomes are vastly outnumbered by those of vertebrates. Protists and fungi run the gamut of symbiosis, yet eukaryotic microbiome sequencing is rarely undertaken, with much of the focus on bacteria. To explore the importance of microscopic marine invertebrates as potential symbiont reservoirs, we used a phylogenetic-focused approach to analyze the host-associated eukaryotic microbiomes of 220 animal specimens spanning nine different animal phyla. RESULTS Our data expanded the traditional host range of several microbial taxa and identified numerous undescribed lineages. A lack of comparable reference sequences resulted in several cryptic clades within the Apicomplexa and Ciliophora and emphasized the potential for microbial invertebrates to harbor novel protistan and fungal diversity. CONCLUSIONS Microscopic marine invertebrates, spanning a wide range of animal phyla, host various protist and fungal sequences and may therefore serve as a useful resource in the detection and characterization of undescribed symbioses. Video Abstract.
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Affiliation(s)
- Corey C Holt
- Department of Botany, University of British Columbia, Vancouver, Canada.
- Hakai Institute, Heriot Bay, Canada.
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
| | - Niels W L Van Steenkiste
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Maria Herranz
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Gracy Buckholtz
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Brian S Leander
- Department of Botany, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada.
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26
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Cooney EC, Leander BS, Keeling PJ. Phylogenomics shows unique traits in Noctilucales are derived rather than ancestral. PNAS Nexus 2022; 1:pgac202. [PMID: 36714854 PMCID: PMC9802342 DOI: 10.1093/pnasnexus/pgac202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/19/2022] [Indexed: 02/01/2023]
Abstract
Dinoflagellates are a diverse protist group possessing many unique traits. These include (but are not limited to) expansive genomes packaged into permanently condensed chromosomes, photosynthetic or cryptic plastids acquired vertically or horizontally in serial endosymbioses, and a ruffle-like transverse flagellum attached along its length to the cell. When reconstructing character evolution, early branching lineages with unusual features that distinguish them from the rest of the group have proven useful for inferring ancestral states. The Noctilucales are one such lineage, possessing relaxed chromosomes in some life stages and a trailing, thread-like transverse flagellum. However, most of the cellular and molecular data for the entire group come from a single cultured species, Noctiluca scintillans, and because its phylogenetic position is unresolved it remains unclear if these traits are ancestral or derived. Here, we use single cell transcriptomics to characterize three diverse Noctilucales genera: Spatulodinium, Kofoidinium, and a new lineage, Fabadinium gen. nov. We also provide transcriptomes for undescribed species in Amphidinium and Abediniales, critical taxa for clarifying the phylogenetic position of Noctilucales. Phylogenomic analyses suggests that the Noctilucales are sister to Amphidinium rather than an independent branch outside the core dinoflagellates. This topology is consistent with observations of shared characteristics between some members of Noctilucales and Amphidinium and provides the most compelling evidence to date that the unusual traits within this group are derived rather than ancestral. We also confirm that Spatulodinium plastids are photosynthetic and of ancestral origin, and show that all non-photosynthetic Noctilucales retain plastid genes indicating a cryptic organelle.
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Affiliation(s)
| | - Brian S Leander
- Department of Botany, University of British Columbia, British Columbia, Vancouver V6T 1Z4, Canada,Department of Zoology, University of British Columbia, British Columbia, Vancouver V6T 1Z4, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, British Columbia, Vancouver V6T 1Z4, Canada
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27
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Boscaro V, Syberg-Olsen MJ, Irwin NAT, George EE, Vannini C, Husnik F, Keeling PJ. All essential endosymbionts of the ciliate Euplotes are cyclically replaced. Curr Biol 2022; 32:R826-R827. [PMID: 35839761 DOI: 10.1016/j.cub.2022.06.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Symbiotic systems vary in the degree to which the partners are bound to each other1. At one extreme, there are intracellular endosymbionts in mutually obligate relationships with their host, often interpreted as mutualistic. The symbiosis between the betaproteobacterium Polynucleobacter and the ciliate Euplotes (clade B) challenges this view2: although freshwater Euplotes species long ago became dependent on endosymbionts, the many extant Polynucleobacter lineages they harbour arose recently and in parallel from different free-living ancestors2. The host requires the endosymbionts for reproduction and survival3, but each newly established symbiont is ultimately driven to extinction in a cycle of establishment, degeneration, and replacement. Similar replacement events have been observed in sap-feeding insects4-6, a model for bacteria-eukaryote symbioses7, but usually only affect a small subset of the host populations. Most insects retain an ancient coevolving symbiont, suggesting that long-term mutualism and permanent integration remains the rule and symbiont turnovers are mere evolutionary side-stories. Here we show that this is not the case for Euplotes. We examined all known essential Euplotes symbionts and found that none are ancient or coevolving; rather, all are recently established and continuously replaced over relatively short evolutionary time spans, making the symbiosis ancient for the host but not for any bacterial lineage.
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Affiliation(s)
- Vittorio Boscaro
- University of British Columbia, Department of Botany, Vancouver, BC, V6T 1Z4, Canada.
| | | | - Nicholas A T Irwin
- University of British Columbia, Department of Botany, Vancouver, BC, V6T 1Z4, Canada; University of Oxford, Merton College, Oxford, OX1 4JD, UK
| | - Emma E George
- University of British Columbia, Department of Botany, Vancouver, BC, V6T 1Z4, Canada
| | - Claudia Vannini
- Department of Biology, University of Pisa, Pisa, 56126, Italy
| | - Filip Husnik
- University of British Columbia, Department of Botany, Vancouver, BC, V6T 1Z4, Canada; Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
| | - Patrick J Keeling
- University of British Columbia, Department of Botany, Vancouver, BC, V6T 1Z4, Canada
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28
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Abstract
Prokaryotic genomes are usually densely packed with intact and functional genes. However, in certain contexts, such as after recent ecological shifts or extreme population bottlenecks, broken and nonfunctional gene fragments can quickly accumulate and form a substantial fraction of the genome. Identification of these broken genes, called pseudogenes, is a critical step for understanding the evolutionary forces acting upon, and the functional potential encoded within, prokaryotic genomes. Here, we present Pseudofinder, an open-source software dedicated to pseudogene identification and analysis in bacterial and archaeal genomes. We demonstrate that Pseudofinder’s multi-pronged, reference-based approach can detect a wide variety of pseudogenes, including those that are highly degraded and typically missed by gene-calling pipelines, as well newly formed pseudogenes containing only one or a few inactivating mutations. Additionally, Pseudofinder can detect genes that lack inactivating substitutions but experiencing relaxed selection. Implementation of Pseudofinder in annotation pipelines will allow more precise estimations of the functional potential of sequenced microbes, while also generating new hypotheses related to the evolutionary dynamics of bacterial and archaeal genomes.
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Affiliation(s)
| | - Arkadiy I Garber
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - John P McCutcheon
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA.,Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland, USA
| | - Filip Husnik
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Okinawa Institute of Science and Technology, Okinawa, Japan
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29
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George EE, Tashyreva D, Kwong WK, Okamoto N, Horák A, Husnik F, Lukeš J, Keeling PJ. Gene Transfer Agents in Bacterial Endosymbionts of Microbial Eukaryotes. Genome Biol Evol 2022; 14:6615375. [PMID: 35738252 PMCID: PMC9254644 DOI: 10.1093/gbe/evac099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2022] [Indexed: 11/14/2022] Open
Abstract
Gene transfer agents (GTAs) are virus-like structures that package and transfer prokaryotic DNA from donor to recipient prokaryotic cells. Here, we describe widespread GTA gene clusters in the highly reduced genomes of bacterial endosymbionts from microbial eukaryotes (protists). Homologs of the GTA capsid and portal complexes were initially found to be present in several highly reduced alphaproteobacterial endosymbionts of diplonemid protists (Rickettsiales and Rhodospirillales). Evidence of GTA expression was found in polyA-enriched metatranscriptomes of the diplonemid hosts and their endosymbionts, but due to biases in the polyA-enrichment methods, levels of GTA expression could not be determined. Examining the genomes of closely related bacteria revealed that the pattern of retained GTA head/capsid complexes with missing tail components was common across Rickettsiales and Holosporaceae (Rhodospirillales), all obligate symbionts with a wide variety of eukaryotic hosts. A dN/dS analysis of Rickettsiales and Holosporaceae symbionts revealed that purifying selection is likely the main driver of GTA evolution in symbionts, suggesting they remain functional, but the ecological function of GTAs in bacterial symbionts is unknown. In particular, it is unclear how increasing horizontal gene transfer in small, largely clonal endosymbiont populations can explain GTA retention, and, therefore, the structures may have been repurposed in endosymbionts for host interactions. Either way, their widespread retention and conservation in endosymbionts of diverse eukaryotes suggests an important role in symbiosis.
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Affiliation(s)
- Emma E George
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada
| | - Daria Tashyreva
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Waldan K Kwong
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada.,Instituto Gulbenkian de Ciência, 6, 2780-156 Oeiras, Portugal
| | - Noriko Okamoto
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada.,Hakai Institute, Quadra Island, British Columbia, Canada
| | - Aleš Horák
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic.,University of South Bohemia, Faculty of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Filip Husnik
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada.,Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
| | - Julius Lukeš
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic.,University of South Bohemia, Faculty of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Patrick J Keeling
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada
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30
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Okamoto N, Keeling PJ, Leander BS, Tai V. Microbial communities in sandy beaches from the three domains of life differ by microhabitat and intertidal location. Mol Ecol 2022; 31:3210-3227. [PMID: 35364623 DOI: 10.1111/mec.16453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/28/2022]
Abstract
The microbial communities of sandy beaches are poorly described despite the biogeochemical importance and ubiquity of these ecosystems. Using metabarcoding of the 16S and 18S rRNA genes, we investigated the diversity, microhabitats (with or between sand grains), and intertidal distributions of microorganisms (including meiofauna) from pristine sandy beaches in British Columbia, Canada, and hypothesized that abiotic variations due to microhabitat or intertidal gradients influences the distribution of microorganisms on local scales. Bacterial, archaeal, and protistan communities of the sand were clearly distinct from interstitial communities, and from planktonic communities of the overlying seawater, which correlated with differences in function and lifestyle, e.g., sulfur reduction and gliding motility. In contrast, meiofaunal communities could not be distinguished by sample type, suggesting that they are more frequently mobilized between these microhabitats. Across intertidal zones, high intertidal, mid intertidal, and low intertidal/swash communities were distinct and correlated with moisture, organic carbon and phosphate content, implying that the distribution of microorganisms is influenced by intertidal abiotic gradients. However, few taxa at the genus or species level individually contributed to this zonation pattern; rather, a unique combination of multiple microbial taxa was more likely responsible. Although significant differences in microbial community composition on sandy beaches can be attributed to microhabitat and intertidal gradients, further investigations are needed to assess community assembly processes, the consistency of these distributions, and the functions of the majority of the microorganisms observed in the sand and their effects on the biogeochemistry and ecology of sandy beaches.
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Affiliation(s)
- Noriko Okamoto
- University of British Columbia, Vancouver, British Columbia, Canada.,Hakai Institute, Quadra Island, British Columbia, Canada
| | | | - Brian S Leander
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Vera Tai
- University of British Columbia, Vancouver, British Columbia, Canada.,University of Western Ontario, London, Ontario, Canada
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31
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Tashyreva D, Simpson A, Prokopchuk G, Škodová-Sveráková I, Butenko A, Hammond M, George EE, Flegontova O, Záhonová K, Faktorová D, Yabuki A, Horák A, Keeling PJ, Lukeš J. Diplonemids – A Review on “New“ Flagellates on the Oceanic Block. Protist 2022; 173:125868. [DOI: 10.1016/j.protis.2022.125868] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/26/2022] [Accepted: 02/28/2022] [Indexed: 11/15/2022]
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32
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Cho A, Tikhonenkov DV, Hehenberger E, Karnkowska A, Mylnikov AP, Keeling PJ. Monophyly of Diverse Bigyromonadea and their Impact on Phylogenomic Relationships Within Stramenopiles. Mol Phylogenet Evol 2022; 171:107468. [DOI: 10.1016/j.ympev.2022.107468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/11/2022] [Accepted: 02/22/2022] [Indexed: 10/18/2022]
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Irwin NAT, Pittis AA, Richards TA, Keeling PJ. Systematic evaluation of horizontal gene transfer between eukaryotes and viruses. Nat Microbiol 2021; 7:327-336. [PMID: 34972821 DOI: 10.1038/s41564-021-01026-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 11/12/2021] [Indexed: 01/19/2023]
Abstract
Gene exchange between viruses and their hosts acts as a key facilitator of horizontal gene transfer and is hypothesized to be a major driver of evolutionary change. Our understanding of this process comes primarily from bacteria and phage co-evolution, but the mode and functional importance of gene transfers between eukaryotes and their viruses remain anecdotal. Here we systematically characterized viral-eukaryotic gene exchange across eukaryotic and viral diversity, identifying thousands of transfers and revealing their frequency, taxonomic distribution and projected functions. Eukaryote-derived viral genes, abundant in the Nucleocytoviricota, highlighted common strategies for viral host-manipulation, including metabolic reprogramming, proteolytic degradation and extracellular modification. Furthermore, viral-derived eukaryotic genes implicate genetic exchange in the early evolution and diversification of eukaryotes, particularly through viral-derived glycosyltransferases, which have impacted structures as diverse as algal cell walls, trypanosome mitochondria and animal tissues. These findings illuminate the nature of viral-eukaryotic gene exchange and its impact on the evolution of viruses and their eukaryotic hosts.
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Affiliation(s)
- Nicholas A T Irwin
- Merton College, University of Oxford, Oxford, UK. .,Department of Zoology, University of Oxford, Oxford, UK. .,Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Alexandros A Pittis
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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34
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McKenna V, Archibald JM, Beinart R, Dawson MN, Hentschel U, Keeling PJ, Lopez JV, Martín-Durán JM, Petersen JM, Sigwart JD, Simakov O, Sutherland KR, Sweet M, Talbot N, Thompson AW, Bender S, Harrison PW, Rajan J, Cochrane G, Berriman M, Lawniczak M, Blaxter M. The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.17222.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present the Aquatic Symbiosis Genomics Project, a global collaboration to generate high quality genome sequences for a wide range of eukaryotes and their microbial symbionts. Launched under the Symbiosis in Aquatic Systems Initiative of the Gordon and Betty Moore Foundation, the ASG Project brings together researchers from across the globe who hope to use these reference genomes to augment and extend their analyses of the dynamics, mechanisms and environmental importance of symbiosis. Applying large-scale, high-throughput sequencing and assembly technologies, the ASG collaboration will assemble and annotate the genomes of 500 symbiotic organisms – both the “hosts” and the microbial symbionts with which they associate. These data will be released openly to benefit all who work on symbiosis, from conservation geneticists to those interested in the origin of the eukaryotic cell.
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35
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Cooney EC, Okamoto N, Cho A, Hehenberger E, Richards TA, Santoro AE, Worden AZ, Leander BS, Keeling PJ. Single-Cell Transcriptomics of Abedinium Reveals a New Early-Branching Dinoflagellate Lineage. Genome Biol Evol 2021; 12:2417-2428. [PMID: 33045041 DOI: 10.1093/gbe/evaa196] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
Dinoflagellates possess many cellular characteristics with unresolved evolutionary histories. These include nuclei with greatly expanded genomes and chromatin packaged using histone-like proteins and dinoflagellate-viral nucleoproteins instead of histones, highly reduced mitochondrial genomes with extensive RNA editing, a mix of photosynthetic and cryptic secondary plastids, and tertiary plastids. Resolving the evolutionary origin of these traits requires understanding their ancestral states and early intermediates. Several early-branching dinoflagellate lineages are good candidates for such reconstruction, however these cells tend to be delicate and environmentally sparse, complicating such analyses. Here, we employ transcriptome sequencing from manually isolated and microscopically documented cells to resolve the placement of two cells of one such genus, Abedinium, collected by remotely operated vehicle in deep waters off the coast of Monterey Bay, CA. One cell corresponds to the only described species, Abedinium dasypus, whereas the second cell is distinct and formally described as Abedinium folium, sp. nov. Abedinium has classically been assigned to the early-branching dinoflagellate subgroup Noctilucales, which is weakly supported by phylogenetic analyses of small subunit ribosomal RNA, the single characterized gene from any member of the order. However, an analysis based on 221 proteins from the transcriptome places Abedinium as a distinct lineage, separate from and basal to Noctilucales and the rest of the core dinoflagellates. The transcriptome also contains evidence of a cryptic plastid functioning in the biosynthesis of isoprenoids, iron-sulfur clusters, and heme, a mitochondrial genome with all three expected protein-coding genes (cob, cox1, and cox3), and the presence of some but not all dinoflagellate-specific chromatin packaging proteins.
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Affiliation(s)
- Elizabeth C Cooney
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Noriko Okamoto
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anna Cho
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elisabeth Hehenberger
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Ocean Ecosystems Biology Unit, GEOMAR-Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara
| | - Alexandra Z Worden
- Ocean Ecosystems Biology Unit, GEOMAR-Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Kiel University, Germany
| | - Brian S Leander
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Abstract
Most of the genetic, cellular, and biochemical diversity of life rests within single-celled organisms - the prokaryotes (bacteria and archaea) and microbial eukaryotes (protists). Very close interactions, or symbioses, between protists and prokaryotes are ubiquitous, ecologically significant, and date back at least two billion years ago to the origin of mitochondria. However, most of our knowledge about the evolution and functions of eukaryotic symbioses comes from the study of animal hosts, which represent only a small subset of eukaryotic diversity. Here, we take a broad view of bacterial and archaeal symbioses with protist hosts, focusing on their evolution, ecology, and cell biology, and also explore what functions (if any) the symbionts provide to their hosts. With the immense diversity of protist symbioses starting to come into focus, we can now begin to see how these systems will impact symbiosis theory more broadly.
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Affiliation(s)
- Filip Husnik
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Daria Tashyreva
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Emma E George
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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Mathur V, Wakeman KC, Keeling PJ. Parallel functional reduction in the mitochondria of apicomplexan parasites. Curr Biol 2021; 31:2920-2928.e4. [PMID: 33974849 DOI: 10.1016/j.cub.2021.04.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/18/2021] [Accepted: 04/12/2021] [Indexed: 12/20/2022]
Abstract
Gregarines are an early-diverging lineage of apicomplexan parasites that hold many clues into the origin and evolution of the group, a remarkable transition from free-living phototrophic algae into obligate parasites of animals.1 Using single-cell transcriptomics targeting understudied lineages to complement available sequencing data, we characterized the mitochondrial metabolic repertoire across the tree of apicomplexans. In contrast to the large suite of proteins involved in aerobic respiration in well-studied parasites like Toxoplasma or Plasmodium,2 we find that gregarine trophozoites have significantly reduced energy metabolism: most lack respiratory complexes III and IV, and some lack the electron transport chains (ETCs) and tricarboxylic acid (TCA) cycle entirely. Phylogenomic analyses show that these reductions took place several times in parallel, resulting in a functional range from fully aerobic organelles to extremely reduced "mitosomes" restricted to Fe-S cluster biosynthesis. The mitochondrial genome has also been lost repeatedly: in species with severe functional reduction simply by gene loss but in one species with a complete ETC by relocating cox1 to the nuclear genome. Severe functional reduction of mitochondria is generally associated with structural reduction, resulting in small, nondescript mitochondrial-related organelles (MROs).3 By contrast, gregarines retain distinctive mitochondria with tubular cristae, even the most functionally reduced cases that also lack genes associated with cristae formation. Overall, the parallel, severe reduction of gregarine mitochondria expands the diversity of organisms that contain MROs and further emphasizes the role of parallel transitions in apicomplexan evolution.
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Affiliation(s)
- Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Kevin C Wakeman
- Institute for the Advancement of Higher Education, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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Kwong WK, Irwin NAT, Mathur V, Na I, Okamoto N, Vermeij MJA, Keeling PJ. Taxonomy of the Apicomplexan Symbionts of Coral, including Corallicolida ord. nov., Reassignment of the Genus Gemmocystis, and Description of New Species Corallicola aquarius gen. nov. sp. nov. and Anthozoaphila gnarlus gen. nov. sp. nov. J Eukaryot Microbiol 2021; 68:e12852. [PMID: 33768669 DOI: 10.1111/jeu.12852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/27/2021] [Accepted: 03/12/2021] [Indexed: 11/30/2022]
Abstract
Corals (Metazoa; Cnidaria; Anthozoa) have recently been shown to play host to a widespread and diverse group of intracellular symbionts of the phylum Apicomplexa. These symbionts, colloquially called "corallicolids", are mostly known through molecular analyses, and no formal taxonomy has been proposed. Another apicomplexan, Gemmocystis cylindrus (described from the coral Dendrogyra cylindrus), may be related to corallicolids, but lacks molecular data. Here, we isolate and describe motile trophozoite (feeding) corallicolids cells using microscopic (light, SEM, and TEM) and molecular phylogenetic analysis to provide the basis for a formal description. Phylogenetic analyses using nuclear and plastid rRNA operons, and three mitochondrial protein sequences derived from single cell transcriptomes, all confirm that these organisms fall into a discrete deep-branching clade within the Apicomplexa not closely related to any known species or major subgroup. As a result, we assign this clade to a new order, Corallicolida ord. nov., and family, Corallicolidae fam. nov. We describe a type species, Corallicola aquarius gen. nov. sp. nov. from its Rhodactis sp. host, and also describe a second species, Anthozoaphila gnarlus gen. nov. sp. nov., from the coral host Madracis mirabilis. Finally, we propose reassigning the incertae sedis taxon G. cylindrus from the order Agamococcidiorida to the Corallicolida, based on similarities in morphology and host localization to that of the corallicolids.
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Affiliation(s)
- Waldan K Kwong
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Ina Na
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Noriko Okamoto
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Mark J A Vermeij
- Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 700, Amsterdam, 1098 XH, The Netherlands
- CARMABI Foundation, PO Box 2090, Piscaderabaai z/n, Willemstad, Curaçao
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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Irwin NAT, Twynstra CS, Mathur V, Keeling PJ. The molecular phylogeny of Chionaster nivalis reveals a novel order of psychrophilic and globally distributed Tremellomycetes (Fungi, Basidiomycota). PLoS One 2021; 16:e0247594. [PMID: 33760841 PMCID: PMC7990227 DOI: 10.1371/journal.pone.0247594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/09/2021] [Indexed: 12/04/2022] Open
Abstract
Snow and ice present challenging substrates for cellular growth, yet microbial snow communities not only exist, but are diverse and ecologically impactful. These communities are dominated by green algae, but additional organisms, such as fungi, are also abundant and may be important for nutrient cycling, syntrophic interactions, and community structure in general. However, little is known about these non-algal community members, including their taxonomic affiliations. An example of this is Chionaster nivalis, a unicellular fungus that is morphologically enigmatic and frequently observed in snow communities globally. Despite being described over one hundred years ago, the phylogeny and higher-level taxonomic classifications of C. nivalis remain unknown. Here, we isolated and sequenced the internal transcribed spacer (ITS) and the D1-D2 region of the large subunit ribosomal RNA gene of C. nivalis, providing a molecular barcode for future studies. Phylogenetic analyses using the ITS and D1-D2 region revealed that C. nivalis is part of a novel lineage in the class Tremellomycetes (Basidiomycota, Agaricomycotina) for which a new order Chionasterales ord. nov. (MB838717) and family Chionasteraceae fam. nov. (MB838718) are proposed. Comparisons between C. nivalis and sequences generated from environmental surveys revealed that the Chionasterales are globally distributed and probably psychrophilic, as they appear to be limited to the high alpine and arctic regions. These results highlight the unexplored diversity that exists within these extreme habitats and emphasize the utility of single-cell approaches in characterizing these complex algal-dominated communities.
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Affiliation(s)
- Nicholas A. T. Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Merton College, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Chantelle S. Twynstra
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J. Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Mathur V, Kwong WK, Husnik F, Irwin NAT, Kristmundsson Á, Gestal C, Freeman M, Keeling PJ. Phylogenomics Identifies a New Major Subgroup of Apicomplexans, Marosporida class nov., with Extreme Apicoplast Genome Reduction. Genome Biol Evol 2021; 13:evaa244. [PMID: 33566096 PMCID: PMC7875001 DOI: 10.1093/gbe/evaa244] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2020] [Indexed: 12/16/2022] Open
Abstract
The phylum Apicomplexa consists largely of obligate animal parasites that include the causative agents of human diseases such as malaria. Apicomplexans have also emerged as models to study the evolution of nonphotosynthetic plastids, as they contain a relict chloroplast known as the apicoplast. The apicoplast offers important clues into how apicomplexan parasites evolved from free-living ancestors and can provide insights into reductive organelle evolution. Here, we sequenced the transcriptomes and apicoplast genomes of three deep-branching apicomplexans, Margolisiella islandica, Aggregata octopiana, and Merocystis kathae. Phylogenomic analyses show that these taxa, together with Rhytidocystis, form a new lineage of apicomplexans that is sister to the Coccidia and Hematozoa (the lineages including most medically significant taxa). Members of this clade retain plastid genomes and the canonical apicomplexan plastid metabolism. However, the apicoplast genomes of Margolisiella and Rhytidocystis are the most reduced of any apicoplast, are extremely GC-poor, and have even lost genes for the canonical plastidial RNA polymerase. This new lineage of apicomplexans, for which we propose the class Marosporida class nov., occupies a key intermediate position in the apicomplexan phylogeny, and adds a new complexity to the models of stepwise reductive evolution of genome structure and organelle function in these parasites.
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Affiliation(s)
- Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Waldan K Kwong
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Filip Husnik
- Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Árni Kristmundsson
- Fish Disease Laboratory, Institute for Experimental Pathology, University of Iceland, Reykjavík, Iceland
| | - Camino Gestal
- Institute of Marine Research (IIM-CSIC), Vigo, Spain
| | - Mark Freeman
- Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis, West Indies
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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41
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Tikhonenkov DV, Gawryluk RMR, Mylnikov AP, Keeling PJ. First finding of free-living representatives of Prokinetoplastina and their nuclear and mitochondrial genomes. Sci Rep 2021; 11:2946. [PMID: 33536456 PMCID: PMC7859406 DOI: 10.1038/s41598-021-82369-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/19/2021] [Indexed: 01/30/2023] Open
Abstract
Kinetoplastids are heterotrophic flagellated protists, including important parasites of humans and animals (trypanosomatids), and ecologically important free-living bacterial consumers (bodonids). Phylogenies have shown that the earliest-branching kinetoplastids are all parasites or obligate endosymbionts, whose highly-derived state makes reconstructing the ancestral state of the group challenging. We have isolated new strains of unusual free-living flagellates that molecular phylogeny shows to be most closely related to endosymbiotic and parasitic Perkinsela and Ichthyobodo species that, together with unidentified environmental sequences, form the clade at the base of kinetoplastids. These strains are therefore the first described free-living prokinetoplastids, and potentially very informative in understanding the evolution and ancestral states of morphological and molecular characteristics described in other kinetoplastids. Overall, we find that these organisms morphologically and ultrastructurally resemble some free-living bodonids and diplonemids, and possess nuclear genomes with few introns, polycistronic mRNA expression, high coding density, and derived traits shared with other kinetoplastids. Their genetic repertoires are more diverse than the best-studied free-living kinetoplastids, which is likely a reflection of their higher metabolic potential. Mitochondrial RNAs of these new species undergo the most extensive U insertion/deletion editing reported so far, and limited deaminative C-to-U and A-to-I editing, but we find no evidence for mitochondrial trans-splicing.
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Affiliation(s)
- Denis V. Tikhonenkov
- grid.4886.20000 0001 2192 9124Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, 152742 Russia ,grid.446209.d0000 0000 9203 3563AquaBioSafe Laboratory, University of Tyumen, 625003 Tyumen, Russia
| | - Ryan M. R. Gawryluk
- grid.143640.40000 0004 1936 9465Department of Biology, University of Victoria, Victoria, British Columbia V8W 2Y2 Canada
| | - Alexander P. Mylnikov
- grid.4886.20000 0001 2192 9124Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, 152742 Russia
| | - Patrick J. Keeling
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada
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42
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Lax G, Kolisko M, Eglit Y, Lee WJ, Yubuki N, Karnkowska A, Leander BS, Burger G, Keeling PJ, Simpson AGB. Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs. Mol Phylogenet Evol 2021; 159:107088. [PMID: 33545276 DOI: 10.1016/j.ympev.2021.107088] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/24/2021] [Accepted: 01/26/2021] [Indexed: 12/22/2022]
Abstract
Euglenids are a well-known group of single-celled eukaryotes, with phototrophic, osmotrophic and phagotrophic members. Phagotrophs represent most of the phylogenetic diversity of euglenids, and gave rise to the phototrophs and osmotrophs, but their evolutionary relationships are poorly understood. Symbiontids, in contrast, are anaerobes that are alternatively inferred to be derived euglenids, or a separate euglenozoan group. Most phylogenetic studies of euglenids have examined the SSU rDNA only, which is often highly divergent. Also, many phagotrophic euglenids (and symbiontids) are uncultured, restricting collection of other molecular data. We generated transcriptome data for 28 taxa, mostly using a single-cell approach, and conducted the first multigene phylogenetic analyses of euglenids to include phagotrophs and symbiontids. Euglenids are recovered as monophyletic, with symbiontids forming an independent branch within Euglenozoa. Spirocuta, the clade of flexible euglenids that contains both the phototrophs (Euglenophyceae) and osmotrophs (Aphagea), is robustly resolved, with the ploeotid Olkasia as its sister group, forming the new taxon Olkaspira. Ploeotids are paraphyletic, although Ploeotiidae (represented by Ploeotia spp.), Lentomonas, and Keelungia form a robust clade (new taxon Alistosa). Petalomonadida branches robustly as sister to other euglenids in outgroup-rooted analyses. Within Spirocuta, Euglenophyceae is a robust clade that includes Rapaza, and Anisonemia is a well-supported monophyletic group containing Anisonemidae (Anisonema and Dinema spp.), 'Heteronema II' (represented by H. vittatum), and a clade of Neometanema plus Aphagea. Among 'peranemid' phagotrophs, Chasmostoma branches with included Urceolus, and Peranema with the undescribed 'Jenningsia II', while other relationships are weakly supported and consequently the closest sister group to Euglenophyceae remains unresolved. Our results are inconsistent with recent inferences that Entosiphon is the evolutionarily pivotal sister either to other euglenids, or to Spirocuta. At least three transitions between posterior and anterior flagellar gliding occurred in euglenids, with the phylogenetic positions and directions of those transitions remaining ambiguous.
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Affiliation(s)
- G Lax
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada; Department of Botany, University of British Columbia, Vancouver, Canada(1)
| | - M Kolisko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Y Eglit
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
| | - W J Lee
- Department of Environment and Energy Engineering, Kyungnam University, Changwon, Republic of Korea
| | - N Yubuki
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, Orsay, France; Department of Zoology, University of British Columbia, Vancouver, Canada
| | - A Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw, Poland
| | - B S Leander
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - G Burger
- Robert-Cedergren Centre for Bioinformatics and Genomics, Biochemistry Department, Université de Montréal, Montréal, Canada
| | - P J Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada(1)
| | - A G B Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada.
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Irwin NAT, Pittis AA, Mathur V, Howe LJ, Keeling PJ, Lynn DH, Bourland WA. The Function and Evolution of Motile DNA Replication Systems in Ciliates. Curr Biol 2020; 31:66-76.e6. [PMID: 33125869 DOI: 10.1016/j.cub.2020.09.077] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/09/2020] [Accepted: 09/25/2020] [Indexed: 01/31/2023]
Abstract
DNA replication is a ubiquitous and conserved cellular process. However, regulation of DNA replication is only understood in a small fraction of organisms that poorly represent the diversity of genetic systems in nature. Here we used computational and experimental approaches to examine the function and evolution of one such system, the replication band (RB) in spirotrich ciliates, which is a localized, motile hub that traverses the macronucleus while replicating DNA. We show that the RB can take unique forms in different species, from polar bands to a "replication envelope," where replication initiates at the nuclear periphery before advancing inward. Furthermore, we identify genes involved in cellular transport, including calcium transporters and cytoskeletal regulators, that are associated with the RB and may be involved in its function and translocation. These findings highlight the evolution and diversity of DNA replication systems and provide insights into the regulation of nuclear organization and processes.
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Affiliation(s)
- Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Alexandros A Pittis
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - LeAnn J Howe
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Denis H Lynn
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - William A Bourland
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA.
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Del Campo J, Heger TJ, Rodríguez-Martínez R, Worden AZ, Richards TA, Massana R, Keeling PJ. Corrigendum: Assessing the Diversity and Distribution of Apicomplexans in Host and Free-Living Environments Using High-Throughput Amplicon Data and a Phylogenetically Informed Reference Framework. Front Microbiol 2020; 11:576322. [PMID: 33133045 PMCID: PMC7578665 DOI: 10.3389/fmicb.2020.576322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/31/2020] [Indexed: 11/26/2022] Open
Affiliation(s)
- Javier Del Campo
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.,Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Thierry J Heger
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.,Soil Science Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Nyon, Switzerland
| | - Raquel Rodríguez-Martínez
- Department of Biosciences, Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | | | - Thomas A Richards
- Department of Biosciences, Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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45
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Tikhonenkov DV, Mikhailov KV, Hehenberger E, Karpov SA, Prokina KI, Esaulov AS, Belyakova OI, Mazei YA, Mylnikov AP, Aleoshin VV, Keeling PJ. New Lineage of Microbial Predators Adds Complexity to Reconstructing the Evolutionary Origin of Animals. Curr Biol 2020; 30:4500-4509.e5. [PMID: 32976804 DOI: 10.1016/j.cub.2020.08.061] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/20/2020] [Accepted: 08/17/2020] [Indexed: 02/05/2023]
Abstract
The origin of animals is one of the most intensely studied evolutionary events, and our understanding of this transition was greatly advanced by analyses of unicellular relatives of animals, which have shown many "animal-specific" genes actually arose in protistan ancestors long before the emergence of animals [1-3]. These genes have complex distributions, and the protists have diverse lifestyles, so understanding their evolutionary significance requires both a robust phylogeny of animal relatives and a detailed understanding of their biology [4, 5]. But discoveries of new animal-related lineages are rare and historically biased to bacteriovores and parasites. Here, we characterize the morphology and transcriptome content of a new animal-related lineage, predatory flagellate Tunicaraptor unikontum. Tunicaraptor is an extremely small (3-5 μm) and morphologically simple cell superficially resembling some fungal zoospores, but it survives by preying on other eukaryotes, possibly using a dedicated but transient "mouth," which is unique for unicellular opisthokonts. The Tunicaraptor transcriptome encodes a full complement of flagellar genes and the flagella-associated calcium channel, which is only common to predatory animal relatives and missing in microbial parasites and grazers. Tunicaraptor also encodes several major classes of animal cell adhesion molecules, as well as transcription factors and homologs of proteins involved in neurodevelopment that have not been found in other animal-related lineages. Phylogenomics, including Tunicaraptor, challenges the existing framework used to reconstruct the evolution of animal-specific genes and emphasizes that the diversity of animal-related lineages may be better understood only once the smaller, more inconspicuous animal-related lineages are better studied. VIDEO ABSTRACT.
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Affiliation(s)
- Denis V Tikhonenkov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Kirill V Mikhailov
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia.
| | - Elisabeth Hehenberger
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Duesternbrookerweg 20, 24105 Kiel, Germany
| | - Sergei A Karpov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg 199034, Russia; Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg 199034, Russia
| | - Kristina I Prokina
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia; Zoological Institute, Russian Academy of Sciences, Saint Petersburg 199034, Russia
| | - Anton S Esaulov
- Department of Zoology and Ecology, Penza State University, Penza 440026, Russia
| | - Olga I Belyakova
- Department of Zoology and Ecology, Penza State University, Penza 440026, Russia
| | - Yuri A Mazei
- Department of General Ecology and Hydrobiology, Lomonosov Moscow State University, Moscow 119991, Russia; A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia
| | - Alexander P Mylnikov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia
| | - Vladimir V Aleoshin
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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Massana R, Labarre A, López-Escardó D, Obiol A, Bucchini F, Hackl T, Fischer MG, Vandepoele K, Tikhonenkov DV, Husnik F, Keeling PJ. Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate. ISME J 2020; 15:154-167. [PMID: 32920602 PMCID: PMC7852580 DOI: 10.1038/s41396-020-00770-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 08/19/2020] [Accepted: 09/02/2020] [Indexed: 11/17/2022]
Abstract
Phagocytosis is a fundamental process in marine ecosystems by which prey organisms are consumed and their biomass incorporated in food webs or remineralized. However, studies searching for the genes underlying this key ecological process in free-living phagocytizing protists are still scarce, in part due to the lack of appropriate ecological models. Our reanalysis of recent molecular datasets revealed that the cultured heterotrophic flagellate Cafeteria burkhardae is widespread in the global oceans, which prompted us to design a transcriptomics study with this species, grown with the cultured flavobacterium Dokdonia sp. We compared the gene expression between exponential and stationary phases, which were complemented with three starvation by dilution phases that appeared as intermediate states. We found distinct expression profiles in each condition and identified 2056 differentially expressed genes between exponential and stationary samples. Upregulated genes at the exponential phase were related to DNA duplication, transcription and translational machinery, protein remodeling, respiration and phagocytosis, whereas upregulated genes in the stationary phase were involved in signal transduction, cell adhesion, and lipid metabolism. We identified a few highly expressed phagocytosis genes, like peptidases and proton pumps, which could be used to target this ecologically relevant process in marine ecosystems.
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Affiliation(s)
- Ramon Massana
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta 37-49, ES-08003, Barcelona, Catalonia, Spain.
| | - Aurelie Labarre
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - David López-Escardó
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - Aleix Obiol
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - François Bucchini
- Department of Plant Systems Biology, VIB, B-9052, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Thomas Hackl
- Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
| | | | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, B-9052, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Denis V Tikhonenkov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, 152742, Russia
| | - Filip Husnik
- University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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47
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Abstract
Developing a detailed understanding of how all known forms of life are related to one another in the tree of life has been a major preoccupation of biology since the idea of tree-like evolution first took hold. Since most life is microbial, our intuitive use of morphological comparisons to infer relatedness only goes so far, and molecular sequence data, most recently from genomes and transcriptomes, has been the primary means to infer these relationships. For prokaryotes this presented new challenges, since the degree of horizontal gene transfer led some to question the tree-like depiction of evolution altogether. Most eukaryotes are also microbial, but in contrast to prokaryotic life, the application of large-scale molecular data to the tree of eukaryotes has largely been a constructive process, leading to a small number of very diverse lineages, or 'supergroups'. The tree is not completely resolved, and contentious problems remain, but many well-established supergroups now encompass much more diversity than the traditional kingdoms. Some of the most exciting recent developments come from the discovery of branches in the tree that we previously had no inkling even existed, many of which are of great ecological or evolutionary interest. These new branches highlight the need for more exploration, by high-throughput molecular surveys, but also more traditional means of observations and cultivation.
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Affiliation(s)
- Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada.
| | - Fabien Burki
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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48
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Faktorová D, Nisbet RER, Fernández Robledo JA, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget FY, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano JC, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Novák Vanclová AMG, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Jason Smith G, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, von Dassow P, von der Haar T, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J. Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nat Methods 2020; 17:551. [PMID: 32296171 PMCID: PMC7200595 DOI: 10.1038/s41592-020-0828-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
| | - R Ellen R Nisbet
- Department of Biochemistry, University of Cambridge, Cambridge, UK.,School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | | | - Elena Casacuberta
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Lisa Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Andrew E Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.,Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Manuel Ares
- Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Cristina Aresté
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Cecilia Balestreri
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | | | - Patrick Beardslee
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Sara Bender
- Gordon and Betty Moore Foundation, Palo Alto, CA, USA
| | - David S Booth
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - François-Yves Bouget
- Sorbonne Université, CNRS UMR7621, Observatoire Océanologique, Banyuls sur Mer, France
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Susana A Breglia
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Colin Brownlee
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Heriberto Cerutti
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Rachele Cesaroni
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Miguel A Chiurillo
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Thomas Clemente
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Duncan B Coles
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Jackie L Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Elizabeth C Cooney
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathryn Coyne
- University of Delaware College of Earth, Ocean and Environment, Lewes, DE, USA
| | - Roberto Docampo
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Christopher L Dupont
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | | | - Elin Einarsson
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Pía A Elustondo
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada.,AGADA Biosciences Inc., Halifax, Nova Scotia, Canada
| | - Fernan Federici
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Veronica Freire-Beneitez
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Laboratory of Molecular and Evolutionary Parasitology, University of Kent, Kent, UK
| | | | - Kodai Fukuda
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Paulo A García
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Boston, MA, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Fatma Gomaa
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Sebastian G Gornik
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Jian Guo
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Yutaka Hanawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Esteban R Haro-Contreras
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Elisabeth Hehenberger
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrea Highfield
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Yoshihisa Hirakawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | | | - Ian Hu
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jorge Ibañez
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yuu Ishii
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Natalia Ewa Janowicz
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Adam C Jones
- Gordon and Betty Moore Foundation, Palo Alto, CA, USA
| | - Ambar Kachale
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | - Konomi Fujimura-Kamada
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Binnypreet Kaur
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | | | - Eleanna Kazana
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Laboratory of Molecular and Evolutionary Parasitology, University of Kent, Kent, UK
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicole King
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Noelia Lander
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Zhuhong Li
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Jean-Claude Lozano
- Sorbonne Université, CNRS UMR7621, Observatoire Océanologique, Banyuls sur Mer, France
| | - Fulei Luan
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | | | - Tamara Matute
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Jun Minagawa
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Aichi, Japan.,Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki, Aichi, Japan
| | - Mark Moosburner
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.,Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Sebastián R Najle
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.,Instituto de Biología Molecular y Celular, CONICET, and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Deepak Nanjappa
- University of Delaware College of Earth, Ocean and Environment, Lewes, DE, USA
| | - Isabel C Nimmo
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Luke Noble
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.,Institute de Biologie de l'ENS, Département de biologie, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Anna M G Novák Vanclová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Isaac Nuñez
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Arnab Pain
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Center for Zoonosis Control, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Angela Piersanti
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Jan Pyrih
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Joshua S Rest
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Mariana Rius
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | | | - Albane Ruaud
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.,Departament de Genètica Microbiologia i Estadıśtica, Universitat de Barcelona, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Monika A Sigg
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Claudio H Slamovits
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - G Jason Smith
- Department of Environmental Biotechnology, Moss Landing Marine Laboratories, Moss Landing, CA, USA
| | | | - Rowena Stern
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Estienne C Swart
- Institute of Cell Biology, University of Bern, Bern, Switzerland.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Anastasios D Tsaousis
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Laboratory of Molecular and Evolutionary Parasitology, University of Kent, Kent, UK
| | - Lev Tsypin
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA.,Department of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Aaron Turkewitz
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - Jernej Turnšek
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.,Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Valérie Vergé
- Sorbonne Université, CNRS UMR7621, Observatoire Océanologique, Banyuls sur Mer, France
| | - Peter von Dassow
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile.,Instituto Milenio de Oceanografia de Chile, Concepción, Chile
| | | | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Lu Wang
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Xiaoxue Wen
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Glen Wheeler
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - April Woods
- Department of Environmental Biotechnology, Moss Landing Marine Laboratories, Moss Landing, CA, USA
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, UK.
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA. .,Ocean EcoSystems Biology Unit, Marine Ecology Division, Helmholtz Centre for Ocean Research, Kiel, Germany.
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
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49
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Tikhonenkov DV, Hehenberger E, Esaulov AS, Belyakova OI, Mazei YA, Mylnikov AP, Keeling PJ. Insights into the origin of metazoan multicellularity from predatory unicellular relatives of animals. BMC Biol 2020; 18:39. [PMID: 32272915 PMCID: PMC7147346 DOI: 10.1186/s12915-020-0762-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 03/02/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The origin of animals from their unicellular ancestor was one of the most important events in evolutionary history, but the nature and the order of events leading up to the emergence of multicellular animals are still highly uncertain. The diversity and biology of unicellular relatives of animals have strongly informed our understanding of the transition from single-celled organisms to the multicellular Metazoa. Here, we analyze the cellular structures and complex life cycles of the novel unicellular holozoans Pigoraptor and Syssomonas (Opisthokonta), and their implications for the origin of animals. RESULTS Syssomonas and Pigoraptor are characterized by complex life cycles with a variety of cell types including flagellates, amoeboflagellates, amoeboid non-flagellar cells, and spherical cysts. The life cycles also include the formation of multicellular aggregations and syncytium-like structures, and an unusual diet for single-celled opisthokonts (partial cell fusion and joint sucking of a large eukaryotic prey), all of which provide new insights into the origin of multicellularity in Metazoa. Several existing models explaining the origin of multicellular animals have been put forward, but these data are interestingly consistent with one, the "synzoospore hypothesis." CONCLUSIONS The feeding modes of the ancestral metazoan may have been more complex than previously thought, including not only bacterial prey, but also larger eukaryotic cells and organic structures. The ability to feed on large eukaryotic prey could have been a powerful trigger in the formation and development of both aggregative (e.g., joint feeding, which also implies signaling) and clonal (e.g., hypertrophic growth followed by palintomy) multicellular stages that played important roles in the emergence of multicellular animals.
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Affiliation(s)
- Denis V Tikhonenkov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia, 152742.
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
| | - Elisabeth Hehenberger
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Duesternbrookerweg 20, 24105, Kiel, Germany
| | | | | | | | - Alexander P Mylnikov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia, 152742
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
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Hehenberger E, Eitel M, Fortunato SAV, Miller DJ, Keeling PJ, Cahill MA. Early eukaryotic origins and metazoan elaboration of MAPR family proteins. Mol Phylogenet Evol 2020; 148:106814. [PMID: 32278076 DOI: 10.1016/j.ympev.2020.106814] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 03/24/2020] [Accepted: 04/01/2020] [Indexed: 01/01/2023]
Abstract
The membrane-associated progesterone receptor (MAPR) family consists of heme-binding proteins containing a cytochrome b5 (cytb5) domain characterized by the presence of a MAPR-specific interhelical insert region (MIHIR) between helices 3 and 4 of the canonical cytb5-domain fold. Animals possess three MAPR genes (PGRMC-like, Neuferricin and Neudesin). Here we show that all three animal MAPR genes were already present in the common ancestor of the opisthokonts (comprising animals and fungi as well as related single-celled taxa). All three MAPR genes acquired extensions C-terminal to the cytb5 domain, either before or with the evolution of animals. The archetypical MAPR protein, progesterone receptor membrane component 1 (PGRMC1), contains phosphorylated tyrosines Y139 and Y180. The combination of Y139/Y180 appeared in the common ancestor of cnidarians and bilaterians, along with an early embryological organizer and synapsed neurons, and is strongly conserved in all bilaterian animals. A predicted protein interaction motif in the PGRMC1 MIHIR is potentially regulated by Y139 phosphorylation. A multilayered model of animal MAPR function acquisition includes some pre-metazoan functions (e.g., heme binding and cytochrome P450 interactions) and some acquired animal-specific functions that involve regulation of strongly conserved protein interaction motifs acquired by animals (Metazoa). This study provides a conceptual framework for future studies, against which especially PGRMC1's multiple functions can perhaps be stratified and functionally dissected.
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Affiliation(s)
- Elisabeth Hehenberger
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Michael Eitel
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sofia A V Fortunato
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Michael A Cahill
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia; ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Canberra, ACT 2601, Australia.
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