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The Neomuran Revolution and Phagotrophic Origin of Eukaryotes and Cilia in the Light of Intracellular Coevolution and a Revised Tree of Life

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Downloaded from http://cshperspectives.cshlp.org/ on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press The Neomuran Revolution and Phagotrophic Origin of Eukaryotes and Cilia in the Light of Intracellular Coevolution and a Revised Tree of Life Thomas Cavalier-Smith Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom Correspondence: [email protected] Three kinds of cells exist with increasingly complex membrane-protein targeting: Uni- bacteria (Archaebacteria, Posibacteria) with one cytoplasmic membrane (CM); Negibacte- ria with a two-membrane envelope (inner CM; outer membrane [OM]); eukaryotes with a plasma membrane and topologically distinct endomembranes and peroxisomes. I combine evidence from multigene trees, palaeontology, and cell biology to show that eukaryotes and archaebacteria are sisters, forming the clade neomura that evolved 1.2 Gy ago from a posibacterium, whose DNA segregation and cell division were destabilized by murein wall loss and rescued by the evolving novel neomuran endoskeleton, histones, cytokinesis, and glycoproteins. Phagotrophy then induced coevolving serial major changes making eu- karyote cells, culminating in two dissimilar cilia via a novel gliding–fishing–swimming scenario. I transfer Chloroflexi to Posibacteria, root the universal tree between them and Heliobacteria, and argue that Negibacteria are a clade whose OM, evolving in a green posibacterium, was never lost. THE FIVE KINDS OF CELLS mechanisms of the radical transitions between them. Figure 1 highlights three fundamentally he eukaryotic cell originated by the most different kinds of prokaryote differing great- Tcomplex set of evolutionary changes since ly in membrane topology and membrane and life began: eukaryogenesis. Their complexity wall chemistry. In all cells, the major membrane and mechanistic difficulty explain why eukary- lipids are glycerophospholipids having two hy- otes evolved 2 billion years or more after pro- drophobic hydrocarbon tails attached to a hy- karyotes (Cavalier-Smith 2006a). To under- drophilic phosphorylated glycerol head, but stand these changes, we must consider the cell glycerol-phosphate stereochemistry differs in biology of all five major kinds of cells (Fig. 1); archaebacteria (sn-glycerol-1-phosphate) from determine their correct phylogenetic relation- that in all other cells (sn-glycerol-3-phosphate). ships; and explain the causes, steps, and detailed Negibacteria and posibacteria (collectively called Editors: Patrick J. Keeling and Eugene V. Koonin Additional Perspectives on The Origin and Evolution of Eukaryotes available at www.cshperspectives.org. Copyright # 2014 Cold Spring Harbor Laboratory Press; all rights reserved; doi: 10.1101/cshperspect.a016006 Cite this article as Cold Spring Harb Perspect Biol 2014;6:a016006 1 Downloaded from http://cshperspectives.cshlp.org/ on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press T. Cavalier-Smith nucleus cytopharynx 2 cilia, centrioles microtubules OM neokaryotes TFs IIA, F; Smc Euglenozoa mitochondrion 5/6, CENPA, 1-haem reticulin cytochrome c murein ventral feeding mRNA SL trans-splicing; loss of loss groove, split right transcriptional control root eukaryogenesis: endomembranes, peroxisomes, EUKARYOTA endoskeleton, nucleus, centrioles, cilia, cyclins, mitosis, sex BACTERIA phagotrophy type IV secretion lost (=prokaryotes) hyperthermophily: 1.2 Gy ago isoprenoid ether CM phospholipds; reverse gyrase Archaebacteria loss of PI, ACP, CL, sterols, and many genes neomura neomuran eubacteria revolution N-linked glycoprotein histones, Cdc6, MCM, PCNA; OM murein ESCRT III GTPase; SRP arrest; CM periplasmic losses of Xer termination, space loss DnaA, G, DNA gyrase, SecA murein peptidoglycan OM Omp85 Negibacteria porins Posibacteria CM murein peptidoglycan flagellum acyl ester phospholipids; SRP protein-targeting to CM ; cell division by FtsZ and divisome DnaA replication initiator; Xer DNA replication terminator; anoxygenic green bacterial photosynthesis; Smc condensins; parABS origin segregation; DNA translocases; conjugation via type IV secretion; 3.5 Gy ago Figure 1. Relationships between the five major cell types, showing key evolutionary innovations in the transitions making them. Rigid murein cell walls originated before the cenancestor of all life using both D- and L-amino acids in the first cell, a posibacterium with acyl ester glycerophospholipids that divided using FtsZ, possibly a photoheterotroph similar to Heliobacterium. Negibacteria evolved by acquiring an outer membrane (OM) with complex targeting of porins and other b-barrel proteins inserted by Omp85-dependent machinery never lost in the history of life, being retained when eukaryotes enslaved phagocytosed negibacteria to make mitochondria and subsequently chloroplasts (even kept in secondarily anaerobic DNA-free hydrogenosomes and mitosomes that evolved by drastically modifying aerobic mitochondria). The neomuran revolution was arguably a stabi- lizing response to traumatic loss of murein. Histones H3/4 ensured passive negative DNA supercoiling (making nucleosomes) to replace eubacterial ATP-driven supercoiling by DNA gyrase; this stabler DNA coiling forced drastic coevolutionary changes in RNA polymerase and especially DNA replication machinery: repair polymer- ase d replaced DNA polymerase III, the b-clamp became PCNA, the replication fork helicase Mcm replaced DnaB, the unrelated Pol primase replaced DnaG primase, and Cdc6 replaced the replication initiator DnaA; Cdc6 possibly evolved from a gene duplicate of the eubacterial clamp loader DnaX, itself undergoing minor modification to neomuran RFC. (Legend continues on following page.) 2 Cite this article as Cold Spring Harb Perspect Biol 2014;6:a016006 Downloaded from http://cshperspectives.cshlp.org/ on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press The Neomuran Revolution and Origin of Eukaryotes “eubacteria”) are mutually closer in cell enve- non-cross-linked globular glycoproteins con- lope chemistry and informational machinery taining hydrophilic oligosaccharides covalently than either is to archaebacteria, whose basic linked to asparagine (N) residues. N-linked gly- informational machinery is eukaryote-like de- coproteins are made cotranslationally, oligosac- spite their cells being fully prokaryotic in struc- charides being attached during trans-membrane ture and DNA segregation machinery. Eubac- protein secretion by membrane-associated ri- teria, unlike eukaryotes and archaebacteria, bosomes. I argued that this shared character generally have cell walls of the peptidoglycan evolved in the last common ancestor (cenances- murein that forms a covalently cross-linked tor) of eukaryotes and archaebacteria, which bag (sacculus) completely surrounding the cy- jointly constitute the putative clade neomura. toplasmic membrane (CM). Murein hydrolase The neomuran theory of eukaryote origins (Ca- enzymes must repeatedly cleave, and other en- valier-Smith 1987c; revised and updated: Ca- zymes reseal, murein covalent bonds so that eu- valier-Smith 2002c, 2009, 2010c) has a phylo- bacteria can grow without bursting under high genetic part and a causal mechanistic part, as internal osmotic pressure (Egan and Vollmer should any scientific explanation of megaevo- 2013). lutionary events. Many inadequate “theories” of Some derived methanogenic archaebacte- eukaryote origin focus exclusively on phylogeny ria have covalently cross-linked walls of pseudo- and have no explanatory part or only a cursory, murein, a different peptidoglycan with similar unconvincing one. Phylogenetically, the neo- cleavage-resealing growth. However, other arch- muran theory asserts that (1) eubacteria are aebacteria and all eukaryotes have cell surfaces of substantially older than and ancestors of neo- Figure 1. (Continued) Novel TATA-box-binding transcription factors (TBP and others) (Ouhammouch et al. 2009) replaced the eubacterial transcription regulator CrtA. Murein loss freed MreB filaments that maintain eubacterial rod shape (or related ParM filaments that segregate some plasmids) to become the actin endoskel- eton, conferring osmotic stability; new ESCRT-III filaments helped membrane division, allowing loss of FtsZ in eukaryotes and some archaebacteria. Novel cotranslationally made N-linked glycoprotein enabled archaebac- teria to make rigid S-layer-like walls and eukaryotes a flexible cell surface coat, allowing phagotrophy and ingestion of prey cells to evolve, triggering a cascade of eukaryogenic changes associated with coated vesicle origins. These mediated endomembrane differentiation, internal digestion, targeted vesicle fusion, and nuclear envelope evolution to protect chromatin internalized by phagocytosis (see Fig. 2); a-tubulin, b-tubulin, and g- tubulin evolved from posibacterial plasmid-segregating TubZ GTPase, enabling DNA segregation by mitosis, drastically changing chromosome organization; cohesins enabling mitosis and eukaryotic cell-cycle controls evolved from duplicated Smc condensins. Archaebacteria replaced acyl ester lipids by heat-stable isoprenoid tetraethers to become the first extremophiles, but lost so many lipids and proteins that they could never have evolved directly into eukaryotes, as did the transient neomuran ancestor, retaining far more eubacterial char- acters. Archaebacteria kept fatty acid (FA) synthesis (Lombard et al. 2012a) but lost acyl-carrier protein (ACP), which enables rapid bulk FA synthesis in eubacteria and eukaryotes, no longer needed
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    Universidade Nova de Lisboa Osmo- andInstituto thermo de Tecnologia-adaptation Química e Biológica in hyperthermophilic Archaea: Subtitle Subtitle Luís Pedro Gafeira Gonçalves Osmo- and thermo-adaptation in hyperthermophilic Archaea: identification of compatible solutes, accumulation profiles, and biosynthetic routes in Archaeoglobus spp. OH OH OH CDP c c c - CMP O O - PPi O3P P CTP O O O OH OH OH OH OH OH O- C C C O P O O P i Dissertation presented to obtain the Ph.D degree in BiochemistryO O- Instituto de Tecnologia Química e Biológica | Universidade Nova de LisboaP OH O O OH OH OH Oeiras, Luís Pedro Gafeira Gonçalves January, 2008 2008 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica Osmo- and thermo-adaptation in hyperthermophilic Archaea: identification of compatible solutes, accumulation profiles, and biosynthetic routes in Archaeoglobus spp. This dissertation was presented to obtain a Ph. D. degree in Biochemistry at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. By Luís Pedro Gafeira Gonçalves Supervised by Prof. Dr. Helena Santos Oeiras, January, 2008 Apoio financeiro da Fundação para a Ciência e Tecnologia (POCI 2010 – Formação Avançada para a Ciência – Medida IV.3) e FSE no âmbito do Quadro Comunitário de apoio, Bolsa de Doutoramento com a referência SFRH / BD / 5076 / 2001. ii ACKNOWNLEDGMENTS The work presented in this thesis, would not have been possible without the help, in terms of time and knowledge, of many people, to whom I am extremely grateful. Firstly and mostly, I need to thank my supervisor, Prof. Helena Santos, for her way of thinking science, her knowledge, her rigorous criticism, and her commitment to science.