DOCSLIB.ORG

The Distribution of Genes Associated with Regulated Cell Death Is

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Distribution of Genes Associated with Regulated Cell Death Is The Distribution of Genes Associated With Regulated Cell Death Is Decoupled From the Mitochondrial Phenotypes Within Unicellular Eukaryotic Hosts Jérôme Teulière, Guillaume Bernard, Eric Bapteste To cite this version: Jérôme Teulière, Guillaume Bernard, Eric Bapteste. The Distribution of Genes Associated With Regulated Cell Death Is Decoupled From the Mitochondrial Phenotypes Within Unicellu- lar Eukaryotic Hosts. Frontiers in Cell and Developmental Biology, Frontiers media, 2020, 8, 10.3389/fcell.2020.536389. hal-02947759 HAL Id: hal-02947759 https://hal.archives-ouvertes.fr/hal-02947759 Submitted on 24 Sep 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. fcell-08-536389 September 23, 2020 Time: 11:36 # 1 BRIEF RESEARCH REPORT published: 23 September 2020 doi: 10.3389/fcell.2020.536389 The Distribution of Genes Associated With Regulated Cell Death Is Decoupled From the Mitochondrial Phenotypes Within Unicellular Eukaryotic Hosts Jérôme Teulière*, Guillaume Bernard and Eric Bapteste Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université des Antilles, Paris, France Genetically regulated cell death (RCD) occurs in all domains of life. In eukaryotes, the evolutionary origin of the mitochondrion and of certain forms of RCD, in particular apoptosis, are thought to coincide, suggesting a central general role for mitochondria in cellular suicide. We tested this mitochondrial centrality hypothesis across a dataset Edited by: of 67 species of protists, presenting 5 classes of mitochondrial phenotypes, including Binfeng Lu, University of Pittsburgh, United States functional mitochondria, metabolically diversified mitochondria, functionally reduced Reviewed by: mitochondria (Mitochondrion Related Organelle or MRO) and even complete absence of Marek Eliáš, mitochondria. We investigated the distribution of genes associated with various forms University of Ostrava, Czechia Javier del Campo, of RCD. No homologs for described mammalian regulators of regulated necrosis could University of Miami, United States be identified in our set of 67 unicellular taxa. Protists with MRO and the secondarily *Correspondence: a mitochondriate Monocercomonoides exilis display heterogeneous reductions of Jérôme Teulière apoptosis gene sets with respect to typical mitochondriate protists. Remarkably, despite [email protected] the total lack of mitochondria in M. exilis, apoptosis-associated genes could still be Specialty section: identified. These same species of protists with MRO and M. exilis harbored non- This article was submitted to reduced autophagic cell death gene sets. Moreover, transiently multicellular protist Cell Death and Survival, a section of the journal taxa appeared enriched in apoptotic and autophagy associated genes compared to Frontiers in Cell and Developmental free-living protists. This analysis suggests that genes associated with apoptosis in Biology animals and the presence of the mitochondria are significant yet non-essential biological Received: 19 February 2020 Accepted: 07 September 2020 components for RCD in protists. More generally, our results support the hypothesis Published: 23 September 2020 of a selection for RCD, including both apoptosis and autophagy, as a developmental Citation: mechanism linked to multicellularity. Teulière J, Bernard G and Bapteste E (2020) The Distribution Keywords: regulated cell death, unicellular eukaryotes, mitochondria, mitochondrion-related organelle, of Genes Associated With Regulated apoptosis, autophagy Cell Death Is Decoupled From the Mitochondrial Phenotypes Within Unicellular Eukaryotic Hosts. Abbreviations: RCD, regulated cell death; MRO, mitochondrion-related organelle; AMO, Amorphea; SAR, Stramenopiles- Front. Cell Dev. Biol. 8:536389. Alveolates-Rhizaria; ARC, Archaeplastida; EXC, Excavata; HAP,Haptophyta; CRYP,Cryptista; P,parasitic, S, (ecto)symbiotic; doi: 10.3389/fcell.2020.536389 F, free-living; M, transiently multicellular; Mit., mitochondria. Frontiers in Cell and Developmental Biology| www.frontiersin.org 1 September 2020| Volume 8| Article 536389 fcell-08-536389 September 23, 2020 Time: 11:36 # 2 Teulière et al. Testing the Centrality of Mitochondria in Cell Death INTRODUCTION genes associated with various forms of RCD can be tested, because these unicellular eukaryotes undergo RCD and exhibit a Regulated cell death (RCD) is a central, ancient, and widespread range of diversified mitochondria. Indeed, whereas many protists phenotype of life, displayed by prokaryotes and eukaryotes, harbor “typical” mitochondria, several independent anaerobic be they multicellular or unicellular (Ameisen, 2002; Koonin protists lineages exhibit various degrees of mitochondrial and Aravind, 2002; Van Hautegem et al., 2015; Bidle, 2016; metabolic diversification and electron-transport chain (ETC) Gonçalves et al., 2017; Peeters and de Jonge, 2018; Durand and reduction. Despite heterogeneity in metabolic functions Ramsey, 2019). Yet, the origins and evolution of RCD and of associated to these organelles, mitochondrial phenotypes its associated molecular mechanisms remain poorly understood. have been classified into five types depending on common A broader evolutionary explanation for the evolution of RCD, characteristics in their energy metabolism: first, fully aerobic including, but not limited to apoptosis, is still lacking. This is mitochondria; second, anaerobic mitochondria (ETC using an partly because the focus of the research on RCD has indeed endogenous electron acceptor instead of O2); third, hydrogen- largely been restricted to animal apoptosis. When broader producing mitochondria (with a reduced ETC); fourth, the taxonomic scales are considered, two main hypotheses are more functionally reduced hydrogenosomes (lacking ETC) and commonly discussed to explain the evolutionary origin of mitosomes (only retaining Fe/S cluster assembly function), that apoptosis. These hypotheses give distinct roles to mitochondria. retained the mitochondrial membranes but lost the mtDNA The “Original Sin” hypothesis proposes that apoptosis emerged (Muller et al., 2012; Roger et al., 2017). The three latter as a consequence of the evolution of multicellularity, providing classes of mitochondria-derived organelles are referred to as a social control of cell survival (Ameisen, 1996), hence possibly Mitochondrion-Related Organelles (MRO). Furthermore, in one independently from the mitochondrial acquisition. By contrast, secondarily amitochondriate lineage, the Monocercomonoides the endosymbiotic hypothesis posits that the evolution of spp., mitochondria were entirely lost (Karnkowska et al., apoptosis was a consequence of the mitochondrial acquisition 2016), defining a fifth mitochondrial phenotype (i.e., complete (Ameisen, 1996; Kroemer, 1997; Kaczanowski, 2016), and gives a secondary loss). Former studies, conducted in protists with central role to this organelle in the origin of apoptosis. Moreover, MRO before the sequencing of Monocercomonoides exilis, many hypotheses have been proposed to explain why RCD started to question the connection between apoptosis-like is maintained in unicellular eukaryotes despite its high cost RCD and the presence of a mitochondrion (Chose et al., on individual fitness. Thus, kin-selected altruistic death could 2003; Sarde and Roseto, 2008; Taylor-Brown and Hurd, 2013). provide an evolutionary advantage to a population of protists as These studies concluded that RCD could be performed by (i) a mechanism of immunity against viruses, (ii) a response to mitochondria-independent apoptosis-like death, resulting from starvation and stress, (iii) a developmental process in transiently extensive mitochondrial gene transfer to the nuclear genome multicellular species, or (iv) as a way to control parasite density in (Taylor-Brown and Hurd, 2013). an infected host (Durand and Ramsey, 2019). These hypotheses Here, we further investigated the presence of characteristic suggest that a selective pressure exists to drive the evolution of genes associated with various forms of RCD, as defined in RCD, but they do not specify whether mitochondria are required multicellular organisms, across a broad taxonomic diversity of for various forms of RCD to occur. mitochondriate protists, protists with MRO and M. exilis, with Beyond apoptosis, many forms of RCD, such as autophagic publicly available whole-genome sequencing data. cell death, parthanatos and several types of regulated necrosis such as ferroptosis, pyroptosis, necroptosis, or Mitochondrial Permeability Transition (MPT)-driven necrosis have been METHODS characterized in metazoans and, for some forms, proposed in some protists (Calvo-Garrido et al., 2010; van Zandbergen Proteome Data Mining et al., 2010; Reece et al., 2011; Galluzzi et al., 2018; Tang Whole-proteome assemblies (Supplementary Table S1) were et al., 2019). Mitochondria have been consistently implicated searched for proteins or domains defined as RCD-associated in apoptosis, parthanatos and MPT-driven necrosis.
Load more

Recommended publications
  • Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life
    Smith ScholarWorks Biological Sciences: Faculty Publications Biological Sciences 10-1-2010 Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life Laura Wegener Parfrey University of Massachusetts Amherst Jessica Grant Smith College Yonas I. Tekle Smith College Erica Lasek-Nesselquist Marine Biological Laboratory Hilary G. Morrison Marine Biological Laboratory See next page for additional authors Follow this and additional works at: https://scholarworks.smith.edu/bio_facpubs Part of the Biology Commons Recommended Citation Parfrey, Laura Wegener; Grant, Jessica; Tekle, Yonas I.; Lasek-Nesselquist, Erica; Morrison, Hilary G.; Sogin, Mitchell L.; Patterson, David J.; and Katz, Laura A., "Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life" (2010). Biological Sciences: Faculty Publications, Smith College, Northampton, MA. https://scholarworks.smith.edu/bio_facpubs/126 This Article has been accepted for inclusion in Biological Sciences: Faculty Publications by an authorized administrator of Smith ScholarWorks. For more information, please contact [email protected] Authors Laura Wegener Parfrey, Jessica Grant, Yonas I. Tekle, Erica Lasek-Nesselquist, Hilary G. Morrison, Mitchell L. Sogin, David J. Patterson, and Laura A. Katz This article is available at Smith ScholarWorks: https://scholarworks.smith.edu/bio_facpubs/126 Syst. Biol. 59(5):518–533, 2010 c The Author(s) 2010. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: [email protected] DOI:10.1093/sysbio/syq037 Advance Access publication on July 23, 2010 Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life LAURA WEGENER PARFREY1,JESSICA GRANT2,YONAS I. TEKLE2,6,ERICA LASEK-NESSELQUIST3,4, 3 3 5 1,2, HILARY G.
    [Show full text]
  • The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion Anna Karnkowska,*,1,2 Sebastian C
    The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion Anna Karnkowska,*,1,2 Sebastian C. Treitli,1 Ondrej Brzon, 1 Lukas Novak,1 Vojtech Vacek,1 Petr Soukal,1 Lael D. Barlow,3 Emily K. Herman,3 Shweta V. Pipaliya,3 TomasPanek,4 David Zihala, 4 Romana Petrzelkova,4 Anzhelika Butenko,4 Laura Eme,5,6 Courtney W. Stairs,5,6 Andrew J. Roger,5 Marek Elias,4,7 Joel B. Dacks,3 and Vladimır Hampl*,1 1Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic 2Department of Molecular Phylogenetics and Evolution, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland 3Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada 4Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic Downloaded from https://academic.oup.com/mbe/article-abstract/36/10/2292/5525708 by guest on 13 January 2020 5Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada 6Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden 7Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic *Corresponding authors: E-mails: [email protected]; [email protected]. Associate editor: Fabia Ursula Battistuzzi Abstract The discovery that the protist Monocercomonoides exilis completely lacks mitochondria demonstrates that these organ- elles are not absolutely essential to eukaryotic cells. However, the degree to which the metabolism and cellular systems of this organism have adapted to the loss of mitochondria is unknown. Here, we report an extensive analysis of the M.
    [Show full text]
  • Prokaryotic and Eukaryotic Organisms Pdf
    Prokaryotic and eukaryotic organisms pdf Continue There are two types of cells: prokaryotic and eukaryotic. In this section, we will examine the similarities and differences between the two types. The objectives of the training to identify features common to all cells contrast the composition and size of prokaryotic and eukaryotic cells fall into one of two broad categories: prokaryotic and eukaryotic. Single-celled organisms of the domains Of Bacteria and Archaea are classified as prokaryotes (pro - before; carion - core). Animal cells, plant cells, fungi and proteanists are eukaryotes (eu - truth). Components of prokaryotic cells All cells have four common components: (1) plasma membrane, external coating separating the inner part of the cell from the environment; (2) cytoplasm, consisting of a jelly-like area inside the cell in which other cellular components are located; (3) DNA, the genetic material of the cell; and (4) ribosomes, particles that synthesize proteins. However, prokaryotes differ from eukaryotic cells in several ways. Figure 1. This image shows the generalized structure of the prokaryotic cell. A prokaryotic cell is a simple single-celled organism that lacks a nucleus or any other membrane organella. Soon we will see that this is significantly different in eukaryotes. Prokaryotic DNA is found in the central part of the cell: a darkened area called a nucleoid (Figure 1). Unlike archaea and eukaryote, bacteria have a cell wall of peptidoglycan consisting of sugars and amino acids, and many of them have a polysaccharide capsule (Figure 1). The cell wall acts as an additional layer of protection, helps the cell maintain its shape and prevents dehydration.
    [Show full text]
  • Biosystems, 10 (1978) 67--89 67 © Elsevier/North-Holland Scientific Publishers Ltd. PROBLEMS in the DEVELOPMENT of an EXPLICIT
    BioSystems, 10 (1978) 67--89 67 © Elsevier/North-Holland Scientific Publishers Ltd. PROBLEMS IN THE DEVELOPMENT OF AN EXPLICIT HYPOTHETICAL PHYLOGENY OF THE LOWER EUKARYOTES F.J.R. TAYLOR Department of Botany and Institute of Oceanography, The University of British Columbia, Vancouver, B.C., Canada V6T 1 W5 A semi-explicit arrangement of the lower eukaryotes is provided to serve as a basis for phyletic discussions. No single character is used to determine the position of all the groups. The tree provides no ready separation of protozoa, algae and fungi, groups assigned to these traditional assemblages being considered to be for the most part inextricably interwoven. Photosynthetic forms, whose relationships seem to be more readily discernable, are considered to have given rise repeatedly to nonphotosynthetic forms. The assumption that there are primitive "preflagellar" eukaryotes (red algae, non-flagellated fungi) is adopted. The potential value of mitochondrial features as indicators of broad affinities is emphasised, particularly in determining the probable affinities of non-photosynthetic forms, and this criterion is contra-indicative of a ciliate ancestry for the Metazoa. In the arrangement provided the distributions of chloroplast, mitochondrial and flagellar features match one another well, suggesting their probable co-evolution. 1. Introduction view of the relations of the algae, his "tree" contained numerous, not strictly representa- At the start of a paper of this type it is tional "twigs". Dodge {1974) was even less often appropriate to begin with an apt, but explicit, preferring to comment more on not very serious quotation to set the right taxonomic consequences. Leedale (1974) tone. In this instmace, the only quotation preferred to ignore the details of origin of which sprang readily to mind was "..
    [Show full text]
  • Novel Lineages of Oxymonad Flagellates from the Termite Porotermes Adamsoni (Stolotermitidae): the Genera Oxynympha and Termitim
    Protist, Vol. 170, 125683, December 2019 http://www.elsevier.de/protis Published online date 21 October 2019 ORIGINAL PAPER Novel Lineages of Oxymonad Flagellates from the Termite Porotermes adamsoni (Stolotermitidae): the Genera Oxynympha and Termitimonas a,1 b a c b,1 Renate Radek , Katja Meuser , Samet Altinay , Nathan Lo , and Andreas Brune a Evolutionary Biology, Institute for Biology/Zoology, Freie Universität Berlin, 14195 Berlin, Germany b Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany c School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia Submitted January 21, 2019; Accepted October 9, 2019 Monitoring Editor: Alastair Simpson The symbiotic gut flagellates of lower termites form host-specific consortia composed of Parabasalia and Oxymonadida. The analysis of their coevolution with termites is hampered by a lack of informa- tion, particularly on the flagellates colonizing the basal host lineages. To date, there are no reports on the presence of oxymonads in termites of the family Stolotermitidae. We discovered three novel, deep-branching lineages of oxymonads in a member of this family, the damp-wood termite Porotermes adamsoni. One tiny species (6–10 ␮m), Termitimonas travisi, morphologically resembles members of the genus Monocercomonoides, but its SSU rRNA genes are highly dissimilar to recently published sequences of Polymastigidae from cockroaches and vertebrates. A second small species (9–13 ␮m), Oxynympha loricata, has a slight phylogenetic affinity to members of the Saccinobaculidae, which are found exclusively in wood-feeding cockroaches of the genus Cryptocercus, the closest relatives of termites, but shows a combination of morphological features that is unprecedented in any oxymonad family.
    [Show full text]
  • The Amoeboid Parabasalid Flagellate Gigantomonas Herculeaof
    Acta Protozool. (2005) 44: 189 - 199 The Amoeboid Parabasalid Flagellate Gigantomonas herculea of the African Termite Hodotermes mossambicus Reinvestigated Using Immunological and Ultrastructural Techniques Guy BRUGEROLLE Biologie des Protistes, UMR 6023, CNRS and Université Blaise Pascal de Clermont-Ferrand, Aubière Cedex, France Summary. The amoeboid form of Gigantomonas herculea (Dogiel 1916, Kirby 1946), a symbiotic flagellate of the grass-eating subterranean termite Hodotermes mossambicus from East Africa, is observed by light, immunofluorescence and transmission electron microscopy. Amoeboid cells display a hyaline margin and a central granular area containing the nucleus, the internalized flagellar apparatus, and organelles such as Golgi bodies, hydrogenosomes, and food vacuoles with bacteria or wood particles. Immunofluorescence microscopy using monoclonal antibodies raised against Trichomonas vaginalis cytoskeleton, such as the anti-tubulin IG10, reveals the three long anteriorly-directed flagella, and the axostyle folded into the cytoplasm. A second antibody, 4E5, decorates the conspicuous crescent-shaped structure or cresta bordered by the adhering recurrent flagellum. Transmission electron micrographs show a microfibrillar network in the cytoplasmic margin and internal bundles of microfilaments similar to those of lobose amoebae that are indicative of cytoplasmic streaming. They also confirm the internalization of the flagella. The arrangement of basal bodies and fibre appendages, and the axostyle composed of a rolled sheet of microtubules are very close to that of the devescovinids Foaina and Devescovina. The very large microfibrillar cresta supporting an enlarged recurrent flagellum resembles that of Macrotrichomonas. The parabasal apparatus attached to the basal bodies is small in comparison to the cell size; this is probably related to the presence of many Golgi bodies supported by a striated fibre that are spread throughout the central cytoplasm in a similar way to Placojoenia and Mixotricha.
    [Show full text]
  • Author's Manuscript (764.7Kb)
    1 BROADLY SAMPLED TREE OF EUKARYOTIC LIFE Broadly Sampled Multigene Analyses Yield a Well-resolved Eukaryotic Tree of Life Laura Wegener Parfrey1†, Jessica Grant2†, Yonas I. Tekle2,6, Erica Lasek-Nesselquist3,4, Hilary G. Morrison3, Mitchell L. Sogin3, David J. Patterson5, Laura A. Katz1,2,* 1Program in Organismic and Evolutionary Biology, University of Massachusetts, 611 North Pleasant Street, Amherst, Massachusetts 01003, USA 2Department of Biological Sciences, Smith College, 44 College Lane, Northampton, Massachusetts 01063, USA 3Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA 4Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Providence, Rhode Island 02912, USA 5Biodiversity Informatics Group, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA 6Current address: Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut 06520, USA †These authors contributed equally *Corresponding author: L.A.K - [email protected] Phone: 413-585-3825, Fax: 413-585-3786 Keywords: Microbial eukaryotes, supergroups, taxon sampling, Rhizaria, systematic error, Excavata 2 An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g. plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level ‘supergroups’, many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Further, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduces power to evaluate hypotheses.
    [Show full text]
  • Patterns of Conservation of Spliceosomal Intron Structures and Spliceosome Divergence in Representatives of the Diplomonad and Parabasalid Lineages Andrew J
    Hudson et al. BMC Evolutionary Biology (2019) 19:162 https://doi.org/10.1186/s12862-019-1488-y RESEARCH ARTICLE Open Access Patterns of conservation of spliceosomal intron structures and spliceosome divergence in representatives of the diplomonad and parabasalid lineages Andrew J. Hudson1,2†, David C. McWatters1,2†, Bradley A. Bowser3, Ashley N. Moore1,2, Graham E. Larue3, Scott W. Roy3,4 and Anthony G. Russell1,2* Abstract Background: Two spliceosomal intron types co-exist in eukaryotic precursor mRNAs and are excised by distinct U2- dependent and U12-dependent spliceosomes. In the diplomonad Giardia lamblia, small nuclear (sn) RNAs show hybrid characteristics of U2- and U12-dependent spliceosomal snRNAs and 5 of 11 identified remaining spliceosomal introns are trans-spliced. It is unknown whether unusual intron and spliceosome features are conserved in other diplomonads. Results: We have identified spliceosomal introns, snRNAs and proteins from two additional diplomonads for which genome information is currently available, Spironucleus vortens and Spironucleus salmonicida, as well as relatives, including 6 verified cis-spliceosomal introns in S. vortens. Intron splicing signals are mostly conserved between the Spironucleus species and G. lamblia. Similar to ‘long’ G. lamblia introns, RNA secondary structural potential is evident for ‘long’ (> 50 nt) Spironucleus introns as well as introns identified in the parabasalid Trichomonas vaginalis. Base pairing within these introns is predicted to constrain spatial distances between splice junctions to similar distances seen in the shorter and uniformly-sized introns in these organisms. We find that several remaining Spironucleus spliceosomal introns are ancient. We identified a candidate U2 snRNA from S. vortens, and U2 and U5 snRNAs in S.
    [Show full text]
  • A Free-Living Protist That Lacks Canonical Eukaryotic DNA Replication and Segregation Systems
    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.14.435266; this version posted March 15, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 A free-living protist that lacks canonical eukaryotic DNA replication and segregation systems 2 Dayana E. Salas-Leiva1, Eelco C. Tromer2,3, Bruce A. Curtis1, Jon Jerlström-Hultqvist1, Martin 3 Kolisko4, Zhenzhen Yi5, Joan S. Salas-Leiva6, Lucie Gallot-Lavallée1, Geert J. P. L. Kops3, John M. 4 Archibald1, Alastair G. B. Simpson7 and Andrew J. Roger1* 5 1Centre for Comparative Genomics and Evolutionary Bioinformatics (CGEB), Department of 6 Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada, B3H 4R2 2 7 Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom 8 3Oncode Institute, Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences) 9 and University Medical Centre Utrecht, Utrecht, The Netherlands 10 4Institute of Parasitology Biology Centre, Czech Acad. Sci, České Budějovice, Czech Republic 11 5Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, 12 South China Normal University, Guangzhou 510631, China 13 6CONACyT-Centro de Investigación en Materiales Avanzados, Departamento de medio ambiente y 14 energía, Miguel de Cervantes 120, Complejo Industrial Chihuahua, 31136 Chihuahua, Chih., México 15 7Centre for Comparative Genomics and Evolutionary Bioinformatics (CGEB), Department of 16 Biology, Dalhousie University, Halifax, NS, Canada, B3H 4R2 17 *corresponding author: [email protected] 18 D.E.S-L ORCID iD: 0000-0003-2356-3351 19 E.C.T.
    [Show full text]
  • Revealing the Metabolic Capacity of Streblomastix Strix and Its Bacterial Symbionts Using Single- Cell Metagenomics
    Revealing the metabolic capacity of Streblomastix strix and its bacterial symbionts using single- cell metagenomics Sebastian C. Treitlia, Martin Koliskob, Filip Husníkc, Patrick J. Keelingc, and Vladimír Hampla,1 aDepartment of Parasitology, Faculty of Science, Charles University, BIOCEV, 252 42 Vestec, Czech Republic; bInstitute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 Cˇeské Budeˇ jovice, Czech Republic; and cDepartment of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada Edited by Nancy A. Moran, University of Texas at Austin, Austin, TX, and approved August 14, 2019 (received for review June 26, 2019) Lower termites harbor in their hindgut complex microbial commu- Besides partial ribosomal (r)RNA genes used for diversity studies, nities that are involved in the digestion of cellulose. Among these are there are almost no molecular or biochemical data available for protists, which are usually associated with specific bacterial symbi- any of these protists. Early studies showed that Trichomitopsis onts found on their surface or inside their cells. While these form the termopsidis and several Trichonympha species, from the hindgut of foundations of a classic system in symbiosis research, we still know Zootermopsis (13–16), have the capacity to degrade cellulose (17, little about the functional basis for most of these relationships. Here, 18), but for other flagellates, including all oxymonads, the in- we describe the complex functional relationship between one pro- volvement in cellulose digestion remains unclear. Recent results tist, the oxymonad Streblomastix strix, and its ectosymbiotic bacte- have shown that the bacterial symbionts of oxymonads have the rial community using single-cell genomics.
    [Show full text]
  • Phylogenomic Analyses Support the Monophyly of Excavata and Resolve Relationships Among Eukaryotic ‘‘Supergroups’’
    Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic ‘‘supergroups’’ Vladimir Hampla,b,c, Laura Huga, Jessica W. Leigha, Joel B. Dacksd,e, B. Franz Langf, Alastair G. B. Simpsonb, and Andrew J. Rogera,1 aDepartment of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 1X5; bDepartment of Biology, Dalhousie University, Halifax, NS, Canada B3H 4J1; cDepartment of Parasitology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; dDepartment of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; eDepartment of Cell Biology, University of Alberta, Edmonton, AB, Canada T6G 2H7; and fDepartement de Biochimie, Universite´de Montre´al, Montre´al, QC, Canada H3T 1J4 Edited by Jeffrey D. Palmer, Indiana University, Bloomington, IN, and approved January 22, 2009 (received for review August 12, 2008) Nearly all of eukaryotic diversity has been classified into 6 strong support for an incorrect phylogeny (16, 19, 24). Some recent suprakingdom-level groups (supergroups) based on molecular and analyses employ objective data filtering approaches that isolate and morphological/cell-biological evidence; these are Opisthokonta, remove the sites or taxa that contribute most to these systematic Amoebozoa, Archaeplastida, Rhizaria, Chromalveolata, and Exca- errors (19, 24). vata. However, molecular phylogeny has not provided clear evi- The prevailing model of eukaryotic phylogeny posits 6 major dence that either Chromalveolata or Excavata is monophyletic, nor supergroups (25–28): Opisthokonta, Amoebozoa, Archaeplastida, has it resolved the relationships among the supergroups. To Rhizaria, Chromalveolata, and Excavata. With some caveats, solid establish the affinities of Excavata, which contains parasites of molecular phylogenetic evidence supports the monophyly of each of global importance and organisms regarded previously as primitive Rhizaria, Archaeplastida, Opisthokonta, and Amoebozoa (16, 18, eukaryotes, we conducted a phylogenomic analysis of a dataset of 29–34).
    [Show full text]
  • Mitochondrial Respiratory States and Rates
    MitoFit Preprint Arch (2019) doi:10.26124/mitofit:190001 Posted online 2019-02-12 Open Access Freely available online Mitochondrial respiratory states and rates Gnaiger E, Aasander Frostner E, Abdul Karim N, Abumrad NA, Acuna-Castroviejo D, Adiele RC, Ahn B, Ali SS, Alton L, Alves MG, Amati F, Amoedo ND, Andreadou I, Aragó M, Aragones J, Aral C, Arandarčikaitė O, Armand AS, Arnould T, Avram VF, Bailey DM, Bajpeyi S, Bajzikova M, Bakker BM, Barlow J, Bastos Sant'Anna Silva AC, Batterson P, Battino M, Bazil J, Beard DA, Bednarczyk P, Bello F, Ben-Shachar D, Bergdahl A, Berge RK, Bergmeister L, Bernardi P, Berridge MV, Bettinazzi S, Bishop D, Blier PU, Blindheim DF, Boardman NT, Boetker HE, Borchard S, Boros M, Børsheim E, Borutaite V, Botella J, Bouillaud F, Bouitbir J, Boushel RC, Bovard J, Breton S, Brown DA, Brown GC, Brown RA, Brozinick JT, Buettner GR, Burtscher J, Calabria E, Calbet JA, Calzia E, Cannon DT, Cano Sanchez M, Canto AC, Cardoso LHD, Carvalho E, Casado Pinna M, Cassar S, Cassina AM, Castelo MP, Castro L, Cavalcanti-de-Albuquerque JP, Cervinkova Z, Chabi B, Chakrabarti L, Chakrabarti S, Chaurasia B, Chen Q, Chicco AJ, Chinopoulos C, Chowdhury SK, Cizmarova B, Clementi E, Coen PM, Cohen BH, Coker RH, Collin A, Crisóstomo L, Dahdah N, Dalgaard LT, Dambrova M, Danhelovska T, Darveau CA, Das AM, Dash RK, Davidova E, Davis MS, De Goede P, De Palma C, Dembinska-Kiec A, Detraux D, Devaux Y, Di Marcello M, Dias TR, Distefano G, Doermann N, Doerrier C, Dong L, Donnelly C, Drahota Z, Duarte FV, Dubouchaud H, Duchen MR, Dumas JF,
    [Show full text]