1
|
Wu Y, Garushyants SK, van den Hurk A, Aparicio-Maldonado C, Kushwaha SK, King CM, Ou Y, Todeschini TC, Clokie MRJ, Millard AD, Gençay YE, Koonin EV, Nobrega FL. Bacterial defense systems exhibit synergistic anti-phage activity. Cell Host Microbe 2024; 32:557-572.e6. [PMID: 38402614 PMCID: PMC11009048 DOI: 10.1016/j.chom.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Bacterial defense against phage predation involves diverse defense systems acting individually and concurrently, yet their interactions remain poorly understood. We investigated >100 defense systems in 42,925 bacterial genomes and identified numerous instances of their non-random co-occurrence and negative association. For several pairs of defense systems significantly co-occurring in Escherichia coli strains, we demonstrate synergistic anti-phage activity. Notably, Zorya II synergizes with Druantia III and ietAS defense systems, while tmn exhibits synergy with co-occurring systems Gabija, Septu I, and PrrC. For Gabija, tmn co-opts the sensory switch ATPase domain, enhancing anti-phage activity. Some defense system pairs that are negatively associated in E. coli show synergy and significantly co-occur in other taxa, demonstrating that bacterial immune repertoires are largely shaped by selection for resistance against host-specific phages rather than negative epistasis. Collectively, these findings demonstrate compatibility and synergy between defense systems, allowing bacteria to adopt flexible strategies for phage defense.
Collapse
Affiliation(s)
- Yi Wu
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sofya K Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Anne van den Hurk
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | | | - Simran Krishnakant Kushwaha
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Claire M King
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Yaqing Ou
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Thomas C Todeschini
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Martha R J Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Andrew D Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Franklin L Nobrega
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
| |
Collapse
|
2
|
Fogarty EC, Schechter MS, Lolans K, Sheahan ML, Veseli I, Moore RM, Kiefl E, Moody T, Rice PA, Yu MK, Mimee M, Chang EB, Ruscheweyh HJ, Sunagawa S, Mclellan SL, Willis AD, Comstock LE, Eren AM. A cryptic plasmid is among the most numerous genetic elements in the human gut. Cell 2024; 187:1206-1222.e16. [PMID: 38428395 DOI: 10.1016/j.cell.2024.01.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 10/03/2023] [Accepted: 01/25/2024] [Indexed: 03/03/2024]
Abstract
Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry "cryptic" plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and is 14 times as numerous as crAssphage, currently established as the most abundant extrachromosomal genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales, and although it does not appear to impact bacterial host fitness in vivo, it can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an alternative approach to track human colonic inflammatory states.
Collapse
Affiliation(s)
- Emily C Fogarty
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
| | - Matthew S Schechter
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Karen Lolans
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Madeline L Sheahan
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Iva Veseli
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Ryan M Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Evan Kiefl
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Thomas Moody
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Phoebe A Rice
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry, University of Chicago, Chicago, IL 60637, USA
| | - Michael K Yu
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Mark Mimee
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA; Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Eugene B Chang
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Sandra L Mclellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53204, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Laurie E Comstock
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA.
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Marine Biological Laboratory, Woods Hole, MA 02543, USA; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany; Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129 Oldenburg, Germany; Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany; Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany.
| |
Collapse
|
3
|
Koonin EV, Kuhn JH, Dolja VV, Krupovic M. Megataxonomy and global ecology of the virosphere. THE ISME JOURNAL 2024; 18:wrad042. [PMID: 38365236 PMCID: PMC10848233 DOI: 10.1093/ismejo/wrad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 02/18/2024]
Abstract
Nearly all organisms are hosts to multiple viruses that collectively appear to be the most abundant biological entities in the biosphere. With recent advances in metagenomics and metatranscriptomics, the known diversity of viruses substantially expanded. Comparative analysis of these viruses using advanced computational methods culminated in the reconstruction of the evolution of major groups of viruses and enabled the construction of a virus megataxonomy, which has been formally adopted by the International Committee on Taxonomy of Viruses. This comprehensive taxonomy consists of six virus realms, which are aspired to be monophyletic and assembled based on the conservation of hallmark proteins involved in capsid structure formation or genome replication. The viruses in different major taxa substantially differ in host range and accordingly in ecological niches. In this review article, we outline the latest developments in virus megataxonomy and the recent discoveries that will likely lead to reassessment of some major taxa, in particular, split of three of the current six realms into two or more independent realms. We then discuss the correspondence between virus taxonomy and the distribution of viruses among hosts and ecological niches, as well as the abundance of viruses versus cells in different habitats. The distribution of viruses across environments appears to be primarily determined by the host ranges, i.e. the virome is shaped by the composition of the biome in a given habitat, which itself is affected by abiotic factors.
Collapse
Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, United States
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, United States
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, 75015 Paris, France
| |
Collapse
|
4
|
Lezcano OM, Fuhrmann L, Ramakrishnan G, Beerenwinkel N, Huynen MA, van Rij RP. Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster. Virus Evol 2023; 9:vead074. [PMID: 38162315 PMCID: PMC10757409 DOI: 10.1093/ve/vead074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/30/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024] Open
Abstract
Virus evolution is strongly affected by antagonistic co-evolution of virus and host. Host immunity positively selects for viruses that evade the immune response, which in turn may drive counter-adaptations in host immune genes. We investigated how host immune pressure shapes virus populations, using the fruit fly Drosophila melanogaster and its natural pathogen Drosophila C virus (DCV), as a model. We performed an experimental evolution study in which DCV was serially passaged for ten generations in three fly genotypes differing in their antiviral RNAi response: wild-type flies and flies in which the endonuclease gene Dicer-2 was either overexpressed or inactivated. All evolved virus populations replicated more efficiently in vivo and were more virulent than the parental stock. The number of polymorphisms increased in all three host genotypes with passage number, which was most pronounced in Dicer-2 knockout flies. Mutational analysis showed strong parallel evolution, as mutations accumulated in a specific region of the VP3 capsid protein in every lineage in a host genotype-independent manner. The parental tyrosine at position ninety-five of VP3 was substituted with either one of five different amino acids in fourteen out of fifteen lineages. However, no consistent amino acid changes were observed in the viral RNAi suppressor gene 1A, nor elsewhere in the genome in any of the host backgrounds. Our study indicates that the RNAi response restricts the sequence space that can be explored by viral populations. Moreover, our study illustrates how evolution towards higher virulence can be a highly reproducible, yet unpredictable process.
Collapse
Affiliation(s)
| | - Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zurich, Klingelbergstrasse 48, Basel 4056, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, Lausanne 1015, Switzerland
| | - Gayatri Ramakrishnan
- Department of Medical BioSciences, Radboud University Medical Center, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Klingelbergstrasse 48, Basel 4056, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, Lausanne 1015, Switzerland
- Department of Medical Microbiology, Radboud University Medical Center, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
| | | | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
- Department of Medical BioSciences, Radboud University Medical Center, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
| |
Collapse
|
5
|
Wagner A, Mutschler H. Design principles and applications of synthetic self-replicating RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1803. [PMID: 37264531 DOI: 10.1002/wrna.1803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/24/2023] [Accepted: 05/11/2023] [Indexed: 06/03/2023]
Abstract
With the advent of ever more sophisticated methods for the in vitro synthesis and the in vivo delivery of RNAs, synthetic mRNAs have gained substantial interest both for medical applications, as well as for biotechnology. However, in most biological systems exogeneous mRNAs possess only a limited half-life, especially in fast dividing cells. In contrast, viral RNAs can extend their lifetime by actively replicating inside their host. As such they may serve as scaffolds for the design of synthetic self-replicating RNAs (srRNA), which can be used to increase both the half-life and intracellular concentration of coding RNAs. Synthetic srRNAs may be used to enhance recombinant protein expression or induce the reprogramming of differentiated cells into pluripotent stem cells but also to create cell-free systems for research based on experimental evolution. In this article, we discuss the applications and design principles of srRNAs used for cellular reprogramming, mRNA-based vaccines and tools for synthetic biology. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
Collapse
Affiliation(s)
- Alexander Wagner
- Biomimetic Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Hannes Mutschler
- Biomimetic Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| |
Collapse
|
6
|
Abad L, Gauthier CH, Florian I, Jacobs-Sera D, Hatfull GF. The heterogenous and diverse population of prophages in Mycobacterium genomes. mSystems 2023; 8:e0044623. [PMID: 37791767 PMCID: PMC10654092 DOI: 10.1128/msystems.00446-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/18/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE Mycobacterium species include several human pathogens and mycobacteriophages show potential for therapeutic use to control Mycobacterium infections. However, phage infection profiles vary greatly among Mycobacterium abscessus clinical isolates and phage therapies must be personalized for individual patients. Mycobacterium phage susceptibility is likely determined primarily by accessory parts of bacterial genomes, and we have identified the prophage and phage-related genomic regions across sequenced Mycobacterium strains. The prophages are numerous and diverse, especially in M. abscessus genomes, and provide a potentially rich reservoir of new viruses that can be propagated lytically and used to expand the repertoire of therapeutically useful phages.
Collapse
Affiliation(s)
- Lawrence Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Christian H. Gauthier
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Isabella Florian
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
7
|
Seoane LF, Solé R. How Turing parasites expand the computational landscape of digital life. Phys Rev E 2023; 108:044407. [PMID: 37978635 DOI: 10.1103/physreve.108.044407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 09/19/2023] [Indexed: 11/19/2023]
Abstract
Why are living systems complex? Why does the biosphere contain living beings with complexity features beyond those of the simplest replicators? What kind of evolutionary pressures result in more complex life forms? These are key questions that pervade the problem of how complexity arises in evolution. One particular way of tackling this is grounded in an algorithmic description of life: living organisms can be seen as systems that extract and process information from their surroundings to reduce uncertainty. Here we take this computational approach using a simple bit string model of coevolving agents and their parasites. While agents try to predict their worlds, parasites do the same with their hosts. The result of this process is that, to escape their parasites, the host agents expand their computational complexity despite the cost of maintaining it. This, in turn, is followed by increasingly complex parasitic counterparts. Such arms races display several qualitative phases, from monotonous to punctuated evolution or even ecological collapse. Our minimal model illustrates the relevance of parasites in providing an active mechanism for expanding living complexity beyond simple replicators, suggesting that parasitic agents are likely to be a major evolutionary driver for biological complexity.
Collapse
Affiliation(s)
- Luís F Seoane
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología (CSIC), C/Darwin 3, 28049 Madrid, Spain
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
| | - Ricard Solé
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra (GRIB), Dr Aiguader 80, 08003 Barcelona, Spain
- Institut de Biologia Evolutiva, CSIC-UPF, Pg Maritim de la Barceloneta 37, 08003 Barcelona, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico 87501, USA
| |
Collapse
|
8
|
Fogarty EC, Schechter MS, Lolans K, Sheahan ML, Veseli I, Moore R, Kiefl E, Moody T, Rice PA, Yu MK, Mimee M, Chang EB, Mclellan SL, Willis AD, Comstock LE, Eren AM. A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.25.534219. [PMID: 36993556 PMCID: PMC10055365 DOI: 10.1101/2023.03.25.534219] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Plasmids are extrachromosomal genetic elements that often encode fitness enhancing features. However, many bacteria carry 'cryptic' plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes, and is 14 times as numerous as crAssphage, currently established as the most abundant genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales and although it does not appear to impact bacterial host fitness in vivo, can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an inexpensive alternative for detecting human colonic inflammatory states.
Collapse
Affiliation(s)
- Emily C Fogarty
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Matthew S Schechter
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Karen Lolans
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Madeline L. Sheahan
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Microbiology, University of Chicago, Chicago, IL, 60637, USA
| | - Iva Veseli
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Ryan Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Evan Kiefl
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Thomas Moody
- Department of Systems Biology, Columbia University, New York, NY, 10032 USA
| | - Phoebe A Rice
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Department of Biochemistry, University of Chicago, Chicago, IL, 60637, USA
| | | | - Mark Mimee
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Department of Microbiology, University of Chicago, Chicago, IL, 60637, USA
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Eugene B Chang
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Sandra L Mclellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53204, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Laurie E Comstock
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Microbiology, University of Chicago, Chicago, IL, 60637, USA
| | - A Murat Eren
- Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129 Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany
| |
Collapse
|
9
|
Conrad B, Iseli C, Pirovino M. Energy-harnessing problem solving of primordial life: Modeling the emergence of catalytic host-nested parasite life cycles. PLoS One 2023; 18:e0281661. [PMID: 36972235 PMCID: PMC10042343 DOI: 10.1371/journal.pone.0281661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/29/2023] [Indexed: 03/29/2023] Open
Abstract
All life forms on earth ultimately descended from a primordial population dubbed the last universal common ancestor or LUCA via Darwinian evolution. Extant living systems share two salient functional features, a metabolism extracting and transforming energy required for survival, and an evolvable, informational polymer-the genome-conferring heredity. Genome replication invariably generates essential and ubiquitous genetic parasites. Here we model the energetic, replicative conditions of LUCA-like organisms and their parasites, as well as adaptive problem solving of host-parasite pairs. We show using an adapted Lotka-Volterra frame-work that three host-parasite pairs-individually a unit of a host and a parasite that is itself parasitized, therefore a nested parasite pair-are sufficient for robust and stable homeostasis, forming a life cycle. This nested parasitism model includes competition and habitat restriction. Its catalytic life cycle efficiently captures, channels and transforms energy, enabling dynamic host survival and adaptation. We propose a Malthusian fitness model for a quasispecies evolving through a host-nested parasite life cycle with two core features, rapid replacement of degenerate parasites and increasing evolutionary stability of host-nested parasite units from one to three pairs.
Collapse
Affiliation(s)
| | - Christian Iseli
- Bioinformatics Competence Center, EPFL and Unil, Lausanne, Switzerland
| | - Magnus Pirovino
- OPIRO Consulting Ltd, Triesen, Principality of Liechtenstein
| |
Collapse
|
10
|
Kamiura R, Mizuuchi R, Ichihashi N. Plausible pathway for a host-parasite molecular replication network to increase its complexity through Darwinian evolution. PLoS Comput Biol 2022; 18:e1010709. [PMID: 36454734 PMCID: PMC9714742 DOI: 10.1371/journal.pcbi.1010709] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 11/04/2022] [Indexed: 12/05/2022] Open
Abstract
How the complexity of primitive self-replication molecules develops through Darwinian evolution remains a mystery with regards to the origin of life. Theoretical studies have proposed that coevolution with parasitic replicators increases network complexity by inducing inter-dependent replication. Particularly, Takeuchi and Hogeweg proposed a complexification process of replicator networks by successive appearance of a parasitic replicator followed by the addition of a new host replicator that is resistant to the parasitic replicator. However, the feasibility of such complexification with biologically relevant molecules is still unknown owing to the lack of an experimental model. Here, we investigated the plausible complexification pathway of host-parasite replicators using both an experimental host-parasite RNA replication system and a theoretical model based on the experimental system. We first analyzed the parameter space that allows for sustainable replication in various replication networks ranging from a single molecule to three-member networks using computer simulation. The analysis shows that the most plausible complexification pathway from a single host replicator is the addition of a parasitic replicator, followed by the addition of a new host replicator that is resistant to the parasite, consistent with the previous study by Takeuchi and Hogeweg. We also provide evidence that the pathway actually occurred in our previous evolutionary experiment. These results provide experimental evidence that a population of a single replicator spontaneously evolves into multi-replicator networks through coevolution with parasitic replicators.
Collapse
Affiliation(s)
- Rikuto Kamiura
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Tokyo, Japan
| | - Ryo Mizuuchi
- JST, PRESTO, Kawaguchi, Saitama, Japan
- Komaba Institute for Science, The University of Tokyo, Tokyo, Japan
| | - Norikazu Ichihashi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Tokyo, Japan
- Komaba Institute for Science, The University of Tokyo, Tokyo, Japan
- Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Tokyo, Japan
- * E-mail:
| |
Collapse
|
11
|
Abstract
Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very close interactions with cells. Although in the short term these relationships may appear to be negative for life, it is evident that they can be beneficial in the long term. Viruses are one of the most powerful selective pressures that exist, accelerating the evolution of defense mechanisms in the cellular world. They can also exchange genetic material with the host during the infection process, providing organisms with capacities that favor the colonization of new ecological niches or confer an advantage over competitors, just to cite a few examples. In addition, viruses have a relevant participation in the biogeochemical cycles of our planet, contributing to the recycling of the matter necessary for the maintenance of life. Therefore, although viruses have traditionally been excluded from the tree of life, the structure of this tree is largely the result of the interactions that have been established throughout the intertwined history of the cellular and the viral worlds. We do not know how other possible biospheres outside our planet could be, but it is clear that viruses play an essential role in the terrestrial one. Therefore, they must be taken into account both to improve our understanding of life that we know, and to understand other possible lives that might exist in the cosmos.
Collapse
Affiliation(s)
- Ignacio de la Higuera
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, OR, United States
| | - Ester Lázaro
- Centro de Astrobiología (CAB), CSIC-INTA, Torrejón de Ardoz, Spain
| |
Collapse
|
12
|
Manrubia S. The simple emergence of complex molecular function. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20200422. [PMID: 35599566 DOI: 10.1098/rsta.2020.0422] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
At odds with a traditional view of molecular evolution that seeks a descent-with-modification relationship between functional sequences, new functions can emerge de novo with relative ease. At early times of molecular evolution, random polymers could have sufficed for the appearance of incipient chemical activity, while the cellular environment harbours a myriad of proto-functional molecules. The emergence of function is facilitated by several mechanisms intrinsic to molecular organization, such as redundant mapping of sequences into structures, phenotypic plasticity, modularity or cooperative associations between genomic sequences. It is the availability of niches in the molecular ecology that filters new potentially functional proposals. New phenotypes and subsequent levels of molecular complexity could be attained through combinatorial explorations of currently available molecular variants. Natural selection does the rest. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.
Collapse
Affiliation(s)
- Susanna Manrubia
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
- Systems Biology Department, National Biotechnology Centre (CSIC), c/Darwin 3, 28049 Madrid, Spain
| |
Collapse
|
13
|
Torri A, Jaeger J, Pradeu T, Saleh MC. The origin of RNA interference: Adaptive or neutral evolution? PLoS Biol 2022; 20:e3001715. [PMID: 35767561 PMCID: PMC9275709 DOI: 10.1371/journal.pbio.3001715] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/12/2022] [Indexed: 11/30/2022] Open
Abstract
The origin of RNA interference (RNAi) is usually explained by a defense-based hypothesis, in which RNAi evolved as a defense against transposable elements (TEs) and RNA viruses and was already present in the last eukaryotic common ancestor (LECA). However, since RNA antisense regulation and double-stranded RNAs (dsRNAs) are ancient and widespread phenomena, the origin of defensive RNAi should have occurred in parallel with its regulative functions to avoid imbalances in gene regulation. Thus, we propose a neutral evolutionary hypothesis for the origin of RNAi in which qualitative system drift from a prokaryotic antisense RNA gene regulation mechanism leads to the formation of RNAi through constructive neutral evolution (CNE). We argue that RNAi was already present in the ancestor of LECA before the need for a new defense system arose and that its presence helped to shape eukaryotic genomic architecture and stability. Where does RNA interference come from? This Essay describes a new step-by-step evolutionary model of how RNA interference might have originated in early eukaryotes through neutral events from the molecular machinery present in prokaryotes.
Collapse
Affiliation(s)
- Alessandro Torri
- Virus & RNA interference Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Université Paris Cité, Paris, France
- * E-mail: (AT); (M-CS)
| | | | - Thomas Pradeu
- ImmunoConcEpT, CNRS UMR 5164, University of Bordeaux, Bordeaux, France
- Institut d’histoire et de philosophie des sciences et des techniques, CNRS UMR 8590, Pantheon-Sorbonne University, Paris, France
| | - Maria-Carla Saleh
- Virus & RNA interference Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Université Paris Cité, Paris, France
- * E-mail: (AT); (M-CS)
| |
Collapse
|
14
|
Bell PJL. Eukaryogenesis: The Rise of an Emergent Superorganism. Front Microbiol 2022; 13:858064. [PMID: 35633668 PMCID: PMC9130767 DOI: 10.3389/fmicb.2022.858064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/15/2022] [Indexed: 12/11/2022] Open
Abstract
Although it is widely taught that all modern life descended via modification from a last universal common ancestor (LUCA), this dominant paradigm is yet to provide a generally accepted explanation for the chasm in design between prokaryotic and eukaryotic cells. Counter to this dominant paradigm, the viral eukaryogenesis (VE) hypothesis proposes that the eukaryotes originated as an emergent superorganism and thus did not evolve from LUCA via descent with incremental modification. According to the VE hypothesis, the eukaryotic nucleus descends from a viral factory, the mitochondrion descends from an enslaved alpha-proteobacteria and the cytoplasm and plasma membrane descend from an archaeal host. A virus initiated the eukaryogenesis process by colonising an archaeal host to create a virocell that had its metabolism reprogrammed to support the viral factory. Subsequently, viral processes facilitated the entry of a bacterium into the archaeal cytoplasm which was also eventually reprogrammed to support the viral factory. As the viral factory increased control of the consortium, the archaeal genome was lost, the bacterial genome was greatly reduced and the viral factory eventually evolved into the nucleus. It is proposed that the interaction between these three simple components generated a superorganism whose emergent properties allowed the evolution of eukaryotic complexity. If the radical tenets of the VE hypothesis are ultimately accepted, current biological paradigms regarding viruses, cell theory, LUCA and the universal Tree of Life (ToL) should be fundamentally altered or completely abandoned.
Collapse
|
15
|
Benler S, Koonin EV. Recruitment of Mobile Genetic Elements for Diverse Cellular Functions in Prokaryotes. Front Mol Biosci 2022; 9:821197. [PMID: 35402511 PMCID: PMC8987985 DOI: 10.3389/fmolb.2022.821197] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/08/2022] [Indexed: 12/15/2022] Open
Abstract
Prokaryotic genomes are replete with mobile genetic elements (MGE) that span a continuum of replication autonomy. On numerous occasions during microbial evolution, diverse MGE lose their autonomy altogether but, rather than being quickly purged from the host genome, assume a new function that benefits the host, rendering the immobilized MGE subject to purifying selection, and resulting in its vertical inheritance. This mini-review highlights the diversity of the repurposed (exapted) MGE as well as the plethora of cellular functions that they perform. The principal contribution of the exaptation of MGE and their components is to the prokaryotic functional systems involved in biological conflicts, and in particular, defense against viruses and other MGE. This evolutionary entanglement between MGE and defense systems appears to stem both from mechanistic similarities and from similar evolutionary predicaments whereby both MGEs and defense systems tend to incur fitness costs to the hosts and thereby evolve mechanisms for survival including horizontal mobility, causing host addiction, and exaptation for functions beneficial to the host. The examples discussed demonstrate that the identity of an MGE, overall mobility and relationship with the host cell (mutualistic, symbiotic, commensal, or parasitic) are all factors that affect exaptation.
Collapse
|
16
|
Furubayashi T, Ichihashi N. How evolution builds up complexity?: In vitro evolution approaches to witness complexification in artificial molecular replication systems. Biophys Physicobiol 2022; 19:1-10. [PMID: 35435608 PMCID: PMC8938154 DOI: 10.2142/biophysico.bppb-v19.0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/10/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Taro Furubayashi
- Department of Applied Chemistry, School of Engineering, The University of Tokyo
| | | |
Collapse
|
17
|
Fagundes NJ, Bisso-Machado R, Figueiredo PI, Varal M, Zani AL. OUP accepted manuscript. Genome Biol Evol 2022; 14:6583081. [PMID: 35535669 PMCID: PMC9086759 DOI: 10.1093/gbe/evac055] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2022] [Indexed: 11/12/2022] Open
Abstract
“Junk DNA” is a popular yet controversial concept that states that organisms carry in their genomes DNA that has no positive impact on their fitness. Nonetheless, biochemical functions have been identified for an increasing fraction of DNA elements traditionally seen as “Junk DNA”. These findings have been interpreted as fundamentally undermining the “Junk DNA” concept. Here, we reinforce previous arguments that this interpretation relies on an inadequate concept of biological function that does not consider the selected effect of a given genomic structure, which is central to the “Junk DNA” concept. Next, we suggest that another (though ignored) confounding factor is that the discussion about biological functions includes two different dimensions: a horizontal, ecological dimension that reflects how a given genomic element affects fitness in a specific time, and a vertical, temporal dimension that reflects how a given genomic element persisted along time. We suggest that “Junk DNA” should be used exclusively relative to the horizontal dimension, while for the vertical dimension, we propose a new term, “Spam DNA”, that reflects the fact that a given genomic element may persist in the genome even if not selected for on their origin. Importantly, these concepts are complementary. An element can be both “Spam DNA” and “Junk DNA”, and “Spam DNA” can also be recruited to perform evolved biological functions, as illustrated in processes of exaptation or constructive neutral evolution.
Collapse
Affiliation(s)
| | - Rafael Bisso-Machado
- Postgraduate Program in Genetics and Molecular Biology, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Pedro I.C.C. Figueiredo
- Postgraduate Program in Genetics and Molecular Biology, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Maikel Varal
- Postgraduate Program in Genetics and Molecular Biology, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - André L.S. Zani
- Postgraduate Program in Genetics and Molecular Biology, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| |
Collapse
|
18
|
Koonin EV, Dolja VV, Krupovic M, Kuhn JH. Viruses Defined by the Position of the Virosphere within the Replicator Space. Microbiol Mol Biol Rev 2021; 85:e0019320. [PMID: 34468181 PMCID: PMC8483706 DOI: 10.1128/mmbr.00193-20] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Originally, viruses were defined as miniscule infectious agents that passed through filters that retain even the smallest cells. Subsequently, viruses were considered obligate intracellular parasites whose reproduction depends on their cellular hosts for energy supply and molecular building blocks. However, these features are insufficient to unambiguously define viruses as they are broadly understood today. We outline possible approaches to define viruses and explore the boundaries of the virosphere within the virtual space of replicators and the relationships between viruses and other types of replicators. Regardless of how, exactly, viruses are defined, viruses clearly have evolved on many occasions from nonviral replicators, such as plasmids, by recruiting host proteins to become virion components. Conversely, other types of replicators have repeatedly evolved from viruses. Thus, the virosphere is a dynamic entity with extensive evolutionary traffic across its boundaries. We argue that the virosphere proper, here termed orthovirosphere, consists of a distinct variety of replicators that encode structural proteins encasing the replicators' genomes, thereby providing protection and facilitating transmission among hosts. Numerous and diverse replicators, such as virus-derived but capsidless RNA and DNA elements, or defective viruses occupy the zone surrounding the orthovirosphere in the virtual replicator space. We define this zone as the perivirosphere. Although intense debates on the nature of certain replicators that adorn the internal and external boundaries of the virosphere will likely continue, we present an operational definition of virus that recently has been accepted by the International Committee on Taxonomy of Viruses.
Collapse
Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Valerian V. Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| |
Collapse
|
19
|
Lee IPA, Eldakar OT, Gogarten JP, Andam CP. Bacterial cooperation through horizontal gene transfer. Trends Ecol Evol 2021; 37:223-232. [PMID: 34815098 DOI: 10.1016/j.tree.2021.11.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/27/2021] [Accepted: 11/01/2021] [Indexed: 11/16/2022]
Abstract
Cooperation exists across all scales of biological organization, from genetic elements to complex human societies. Bacteria cooperate by secreting molecules that benefit all individuals in the population (i.e., public goods). Genes associated with cooperation can spread among strains through horizontal gene transfer (HGT). We discuss recent findings on how HGT mediated by mobile genetic elements promotes bacterial cooperation, how cooperation in turn can facilitate more frequent HGT, and how the act of HGT itself may be considered as a form of cooperation. We propose that HGT is an important enforcement mechanism in bacterial populations, thus creating a positive feedback loop that further maintains cooperation. To enforce cooperation, HGT serves as a homogenizing force by transferring the cooperative trait, effectively eliminating cheaters.
Collapse
Affiliation(s)
- Isaiah Paolo A Lee
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Omar Tonsi Eldakar
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - J Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA.
| |
Collapse
|
20
|
Douglas GM, Shapiro BJ. Genic Selection Within Prokaryotic Pangenomes. Genome Biol Evol 2021; 13:6402011. [PMID: 34665261 PMCID: PMC8598171 DOI: 10.1093/gbe/evab234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the evolutionary forces shaping prokaryotic pangenome structure is a major goal of microbial evolution research. Recent work has highlighted that a substantial proportion of accessory genes appear to confer niche-specific adaptations. This work has primarily focused on selection acting at the level of individual cells. Herein, we discuss a lower level of selection that also contributes to pangenome variation: genic selection. This refers to cases where genetic elements, rather than individual cells, are the entities under selection. The clearest examples of this form of selection are selfish mobile genetic elements, which are those that have either a neutral or a deleterious effect on host fitness. We review the major classes of these and other mobile elements and discuss the characteristic features of such elements that could be under genic selection. We also discuss how genetic elements that are beneficial to hosts can also be under genic selection, a scenario that may be more prevalent but not widely appreciated, because disentangling the effects of selection at different levels (i.e., organisms vs. genes) is challenging. Nonetheless, an appreciation for the potential action and implications of genic selection is important to better understand the evolution of prokaryotic pangenomes.
Collapse
Affiliation(s)
- Gavin M Douglas
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - B Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| |
Collapse
|
21
|
Dissection of Highly Prevalent qnrS1-Carrying IncX Plasmid Types in Commensal Escherichia coli from German Food and Livestock. Antibiotics (Basel) 2021; 10:antibiotics10101236. [PMID: 34680816 PMCID: PMC8532951 DOI: 10.3390/antibiotics10101236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/29/2021] [Accepted: 10/08/2021] [Indexed: 11/16/2022] Open
Abstract
Plasmids are mobile genetic elements, contributing to the spread of resistance determinants by horizontal gene transfer. Plasmid-mediated quinolone resistances (PMQRs) are important determinants able to decrease the antimicrobial susceptibility of bacteria against fluoroquinolones and quinolones. The PMQR gene qnrS1, especially, is broadly present in the livestock and food sector. Thus, it is of interest to understand the characteristics of plasmids able to carry and disseminate this determinant and therewith contribute to the resistance development against this class of high-priority, critically important antimicrobials. Therefore, we investigated all commensal Escherichia (E.) coli isolates, with reduced susceptibility to quinolones, recovered during the annual zoonosis monitoring 2017 in the pork and beef production chain in Germany (n = 2799). Through short-read whole-genome sequencing and bioinformatics analysis, the composition of the plasmids and factors involved in their occurrence were determined. We analysed the presence and structures of predominant plasmids carrying the PMQR qnrS1. This gene was most frequently located on IncX plasmids. Although the E. coli harbouring these IncX plasmids were highly diverse in their sequence types as well as their phenotypic resistance profiles, the IncX plasmids-carrying the qnrS1 gene were rather conserved. Thus, we only detected three distinct IncX plasmids carrying qnrS1 in the investigated isolates. The IncX plasmids were assigned either to IncX1 or to IncX3. All qnrS1-carrying IncX plasmids further harboured a β-lactamase gene (bla). In addition, all investigated IncX plasmids were transmissible. Overall, we found highly heterogenic E. coli harbouring conserved IncX plasmids as vehicles for the most prevalent qnr gene qnrS1. These IncX plasmids may play an important role in the dissemination of those two resistance determinants and their presence, transfer and co-selection properties require a deeper understanding for a thorough risk assessment.
Collapse
|
22
|
Harrow GL, Lees JA, Hanage WP, Lipsitch M, Corander J, Colijn C, Croucher NJ. Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures. THE ISME JOURNAL 2021; 15:1523-1538. [PMID: 33408365 PMCID: PMC8115253 DOI: 10.1038/s41396-020-00867-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
Streptococcus pneumoniae can be divided into many strains, each a distinct set of isolates sharing similar core and accessory genomes, which co-circulate within the same hosts. Previous analyses suggested the short-term vaccine-associated dynamics of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), which maintains accessory loci at equilibrium frequencies. Long-term simulations demonstrated NFDS stabilised clonally-evolving multi-strain populations through preventing the loss of variation through drift, based on polymorphism frequencies, pairwise genetic distances and phylogenies. However, allowing symmetrical recombination between isolates evolving under multi-locus NFDS generated unstructured populations of diverse genotypes. Replication of the observed data improved when multi-locus NFDS was combined with recombination that was instead asymmetrical, favouring deletion of accessory loci over insertion. This combination separated populations into strains through outbreeding depression, resulting from recombinants with reduced accessory genomes having lower fitness than their parental genotypes. Although simplistic modelling of recombination likely limited these simulations' ability to maintain some properties of genomic data as accurately as those lacking recombination, the combination of asymmetrical recombination and multi-locus NFDS could restore multi-strain population structures from randomised initial populations. As many bacteria inhibit insertions into their chromosomes, this combination may commonly underlie the co-existence of strains within a niche.
Collapse
Affiliation(s)
- Gabrielle L Harrow
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Caroline Colijn
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK.
| |
Collapse
|
23
|
Roca Suarez AA, Testoni B, Baumert TF, Lupberger J. Nucleic Acid-Induced Signaling in Chronic Viral Liver Disease. Front Immunol 2021; 11:624034. [PMID: 33613561 PMCID: PMC7892431 DOI: 10.3389/fimmu.2020.624034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
A hallmark for the development and progression of chronic liver diseases is the persistent dysregulation of signaling pathways related to inflammatory responses, which eventually promotes the development of hepatic fibrosis, cirrhosis and hepatocellular carcinoma (HCC). The two major etiological agents associated with these complications in immunocompetent patients are hepatitis B virus (HBV) and hepatitis C virus (HCV), accounting for almost 1.4 million liver disease-associated deaths worldwide. Although both differ significantly from the point of their genomes and viral life cycles, they exert not only individual but also common strategies to divert innate antiviral defenses. Multiple virus-modulated pathways implicated in stress and inflammation illustrate how chronic viral hepatitis persistently tweaks host signaling processes with important consequences for liver pathogenesis. The following review aims to summarize the molecular events implicated in the sensing of viral nucleic acids, the mechanisms employed by HBV and HCV to counter these measures and how the dysregulation of these cellular pathways drives the development of chronic liver disease and the progression toward HCC.
Collapse
MESH Headings
- Carcinoma, Hepatocellular/immunology
- Carcinoma, Hepatocellular/mortality
- Carcinoma, Hepatocellular/pathology
- DNA, Viral/immunology
- Hepacivirus/immunology
- Hepatitis B virus/immunology
- Hepatitis B, Chronic/immunology
- Hepatitis B, Chronic/mortality
- Hepatitis B, Chronic/pathology
- Hepatitis C, Chronic/immunology
- Hepatitis C, Chronic/mortality
- Hepatitis C, Chronic/pathology
- Humans
- Liver Neoplasms/immunology
- Liver Neoplasms/mortality
- Liver Neoplasms/pathology
- RNA, Viral/immunology
- Signal Transduction/immunology
Collapse
Affiliation(s)
- Armando Andres Roca Suarez
- INSERM, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France
- University of Lyon, Université Claude-Bernard (UCBL), Lyon, France
| | - Barbara Testoni
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France
- University of Lyon, Université Claude-Bernard (UCBL), Lyon, France
| | - Thomas F. Baumert
- INSERM, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
| | - Joachim Lupberger
- INSERM, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| |
Collapse
|
24
|
Domingo-Sananes MR, McInerney JO. Mechanisms That Shape Microbial Pangenomes. Trends Microbiol 2021; 29:493-503. [PMID: 33423895 DOI: 10.1016/j.tim.2020.12.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 01/02/2023]
Abstract
Analyses of multiple whole-genome sequences from the same species have revealed that differences in gene content can be substantial, particularly in prokaryotes. Such variation has led to the recognition of pangenomes, the complete set of genes present in a species - consisting of core genes, present in all individuals, and accessory genes whose presence is variable. Questions now arise about how pangenomes originate and evolve. We describe how gene content variation can arise as a result of the combination of several processes, including random drift, selection, gain/loss balance, and the influence of ecological and epistatic interactions. We believe that identifying the contributions of these processes to pangenomes will need novel theoretical approaches and empirical data.
Collapse
Affiliation(s)
- Maria Rosa Domingo-Sananes
- School of Life Sciences, University of Nottingham, Nottingham, UK; School of Science and Technology, Nottingham Trent University, Nottingham, UK.
| | | |
Collapse
|
25
|
Dahiya A. The Phenomenology of Contagion. JOURNAL OF BIOETHICAL INQUIRY 2020; 17:519-523. [PMID: 32840826 PMCID: PMC7445722 DOI: 10.1007/s11673-020-09997-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/17/2020] [Indexed: 06/11/2023]
Abstract
The lived experience of COVID-19 forcibly returns us to our bodies. This essay uses this (for most, sudden) return to embodiment to consider how our senses, as well as our "sense" of space, have been reoriented by this pandemic. It turns to certain strands within feminist philosophy that have questioned the privileged place vision has been accorded in the history of Western thought, as well as to mid-twentieth century phenomenologist Maurice Merleau-Ponty's aim to rediscover the world of perception by philosophically centring the body, as touchstones to put forth a phenomenology of contagion. Contagion makes us confront our phenomenological and embodied experience of tactility. This focus on tactility undermines the philosophical hierarchy of the senses that accords sight as the most "noble" of the senses in Western canonical thought. While COVID-19 results in us rediscovering our bodies through touch in a moment of fear and panic, this essay considers how this rediscovery may be harnessed for different, possibly more just, futures.
Collapse
Affiliation(s)
- Annu Dahiya
- Duke University, Durham, North Carolina, USA.
| |
Collapse
|
26
|
Benler S, Koonin EV. Phage lysis‐lysogeny switches and programmed cell death: Danse macabre. Bioessays 2020; 42:e2000114. [DOI: 10.1002/bies.202000114] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/25/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Sean Benler
- National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda Maryland USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda Maryland USA
| |
Collapse
|
27
|
Bell PJ. Evidence supporting a viral origin of the eukaryotic nucleus. Virus Res 2020; 289:198168. [DOI: 10.1016/j.virusres.2020.198168] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 12/22/2022]
|
28
|
Abstract
The ancestral strain of Bacillus subtilis NCIB3610 (3610) bears a large, low-copy-number plasmid, called pBS32, that was lost during the domestication of laboratory strain derivatives. Selection against pBS32 may have been because it encodes a potent inhibitor of natural genetic competence (ComI), as laboratory strains were selected for high-frequency transformation. Previous studies have shown that pBS32 and its sibling, pLS32 in Bacillus subtilis subsp. natto, encode a replication initiation protein (RepN), a plasmid partitioning system (AlfAB), a biofilm inhibitor (RapP), and an alternative sigma factor (SigN) that can induce plasmid-mediated cell death in response to DNA damage. Here, we review the literature on pBS32/pLS32, the genes found on it, and their associated phenotypes.
Collapse
|
29
|
Hall RJ, Whelan FJ, McInerney JO, Ou Y, Domingo-Sananes MR. Horizontal Gene Transfer as a Source of Conflict and Cooperation in Prokaryotes. Front Microbiol 2020; 11:1569. [PMID: 32849327 PMCID: PMC7396663 DOI: 10.3389/fmicb.2020.01569] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/17/2020] [Indexed: 02/01/2023] Open
Abstract
Horizontal gene transfer (HGT) is one of the most important processes in prokaryote evolution. The sharing of DNA can spread neutral or beneficial genes, as well as genetic parasites across populations and communities, creating a large proportion of the variability acted on by natural selection. Here, we highlight the role of HGT in enhancing the opportunities for conflict and cooperation within and between prokaryote genomes. We discuss how horizontally acquired genes can cooperate or conflict both with each other and with a recipient genome, resulting in signature patterns of gene co-occurrence, avoidance, and dependence. We then describe how interactions involving horizontally transferred genes may influence cooperation and conflict at higher levels (populations, communities, and symbioses). Finally, we consider the benefits and drawbacks of HGT for prokaryotes and its fundamental role in understanding conflict and cooperation from the gene-gene to the microbiome level.
Collapse
Affiliation(s)
- Rebecca J Hall
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Fiona J Whelan
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - James O McInerney
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Yaqing Ou
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | | |
Collapse
|
30
|
Redondo-Salvo S, Fernández-López R, Ruiz R, Vielva L, de Toro M, Rocha EPC, Garcillán-Barcia MP, de la Cruz F. Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids. Nat Commun 2020; 11:3602. [PMID: 32681114 PMCID: PMC7367871 DOI: 10.1038/s41467-020-17278-2] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/19/2020] [Indexed: 01/04/2023] Open
Abstract
Plasmids can mediate horizontal gene transfer of antibiotic resistance, virulence genes, and other adaptive factors across bacterial populations. Here, we analyze genomic composition and pairwise sequence identity for over 10,000 reference plasmids to obtain a global map of the prokaryotic plasmidome. Plasmids in this map organize into discrete clusters, which we call plasmid taxonomic units (PTUs), with high average nucleotide identity between its members. We identify 83 PTUs in the order Enterobacterales, 28 of them corresponding to previously described archetypes. Furthermore, we develop an automated algorithm for PTU identification, and validate its performance using stochastic blockmodeling. The algorithm reveals a total of 276 PTUs in the bacterial domain. Each PTU exhibits a characteristic host distribution, organized into a six-grade scale (I–VI), ranging from plasmids restricted to a single host species (grade I) to plasmids able to colonize species from different phyla (grade VI). More than 60% of the plasmids in the global map are in groups with host ranges beyond the species barrier. Plasmids can mediate gene transfer across bacterial populations. Here, the authors describe a global map of the prokaryotic plasmidome, where plasmids organize into discrete ‘plasmid taxonomic units’ based on their genomic composition and pairwise sequence identity.
Collapse
Affiliation(s)
- Santiago Redondo-Salvo
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011, Santander, Spain
| | - Raúl Fernández-López
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011, Santander, Spain
| | - Raúl Ruiz
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011, Santander, Spain
| | - Luis Vielva
- Departamento de Ingeniería de las Comunicaciones, Universidad de Cantabria, Santander, Spain
| | - María de Toro
- CIBIR, Centro de Investigación Biomédica de La Rioja, Logroño, Spain
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011, Santander, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011, Santander, Spain.
| |
Collapse
|
31
|
Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, Zerbini FM, Kuhn JH. Global Organization and Proposed Megataxonomy of the Virus World. Microbiol Mol Biol Rev 2020; 84:e00061-19. [PMID: 32132243 PMCID: PMC7062200 DOI: 10.1128/mmbr.00061-19] [Citation(s) in RCA: 324] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve with nearly all forms of cellular life. The route of virus replication and protein expression is determined by the viral genome type. Comparison of these routes led to the classification of viruses into seven "Baltimore classes" (BCs) that define the major features of virus reproduction. However, recent phylogenomic studies identified multiple evolutionary connections among viruses within each of the BCs as well as between different classes. Due to the modular organization of virus genomes, these relationships defy simple representation as lines of descent but rather form complex networks. Phylogenetic analyses of virus hallmark genes combined with analyses of gene-sharing networks show that replication modules of five BCs (three classes of RNA viruses and two classes of reverse-transcribing viruses) evolved from a common ancestor that encoded an RNA-directed RNA polymerase or a reverse transcriptase. Bona fide viruses evolved from this ancestor on multiple, independent occasions via the recruitment of distinct cellular proteins as capsid subunits and other structural components of virions. The single-stranded DNA (ssDNA) viruses are a polyphyletic class, with different groups evolving by recombination between rolling-circle-replicating plasmids, which contributed the replication protein, and positive-sense RNA viruses, which contributed the capsid protein. The double-stranded DNA (dsDNA) viruses are distributed among several large monophyletic groups and arose via the combination of distinct structural modules with equally diverse replication modules. Phylogenomic analyses reveal the finer structure of evolutionary connections among RNA viruses and reverse-transcribing viruses, ssDNA viruses, and large subsets of dsDNA viruses. Taken together, these analyses allow us to outline the global organization of the virus world. Here, we describe the key aspects of this organization and propose a comprehensive hierarchical taxonomy of viruses.
Collapse
Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Mart Krupovic
- Institut Pasteur, Archaeal Virology Unit, Department of Microbiology, Paris, France
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - F Murilo Zerbini
- Departamento de Fitopatologia/Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| |
Collapse
|
32
|
Bartlett S, Wong ML. Defining Lyfe in the Universe: From Three Privileged Functions to Four Pillars. Life (Basel) 2020; 10:E42. [PMID: 32316364 PMCID: PMC7235751 DOI: 10.3390/life10040042] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 01/08/2023] Open
Abstract
Motivated by the need to paint a more general picture of what life is-and could be-with respect to the rest of the phenomena of the universe, we propose a new vocabulary for astrobiological research. Lyfe is defined as any system that fulfills all four processes of the living state, namely: dissipation, autocatalysis, homeostasis, and learning. Life is defined as the instance of lyfe that we are familiar with on Earth, one that uses a specific organometallic molecular toolbox to record information about its environment and achieve dynamical order by dissipating certain planetary disequilibria. This new classification system allows the astrobiological community to more clearly define the questions that propel their research-e.g., whether they are developing a historical narrative to explain the origin of life (on Earth), or a universal narrative for the emergence of lyfe, or whether they are seeking signs of life specifically, or lyfe at large across the universe. While the concept of "life as we don't know it" is not new, the four pillars of lyfe offer a novel perspective on the living state that is indifferent to the particular components that might produce it.
Collapse
Affiliation(s)
- Stuart Bartlett
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Michael L. Wong
- Department of Astronomy and Astrobiology Program, University of Washington, Seattle, WA 98195, USA;
- NASA Nexus for Exoplanet System Science’s Virtual Planetary Laboratory, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
33
|
Alba P, Leekitcharoenphon P, Carfora V, Amoruso R, Cordaro G, Di Matteo P, Ianzano A, Iurescia M, Diaconu EL, Study Group EEAN, Pedersen SK, Guerra B, Hendriksen RS, Franco A, Battisti A. Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid. Microb Genom 2020; 6. [PMID: 32271142 PMCID: PMC7371121 DOI: 10.1099/mgen.0.000365] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Salmonella Infantis is one of the five serovars most frequently causing human salmonellosis in Europe, mainly associated with poultry. A clone harbouring a conjugative plasmid of emerging S. Infantis (pESI)-like megaplasmid, carrying multidrug resistant (MDR) and extended-spectrum beta-lactamases (ESBL) genes, has spread in the Italian broiler chicken industry also causing human illness. This work is aimed at elucidating the molecular epidemiology of S. Infantis and pESI-like in Europe using whole-genome sequencing and bioinformatics analysis, and to investigate the genetic relatedness of S. Infantis clones and pESI-like from animals, meat, feed and humans provided by institutions of nine European countries. Two genotyping approaches were used: chromosome or plasmid SNP-based analysis and the minimum spanning tree (MST) algorithm based on core-genome multilocus sequence typing (cgMLST). The European S. Infantis population appeared heterogeneous, with different genetic clusters defined at core-genome level. However, pESI-like variants present in 64.1 % of the isolates were more genetically homogeneous and capable of infecting different clonal lineages in most of the countries. Two different pESI-like with ESBL genes (n=82) were observed: blaCTX-M-1-positive in European isolates and blaCTX-M-65-positive in American isolates (study outgroup). Both variants had toxin-antitoxin systems, resistance genes towards tetracyclines, trimethoprim, sulphonamides and aminoglycosides, heavy metals (merA) and disinfectants (qacEΔ). Worryingly, 66 % of the total isolates studied presented different gyrA chromosomal point mutations associated with (fluoro)quinolone resistance (MIC range 0.125–0.5 mg/L), while 18 % displayed transferable macrolide resistance mediated by mph, mef and erm(B) genes. Proper intervention strategies are needed to prevent further dissemination/transmission of MDR S. Infantis and pESI-like along the food chain in Europe.
Collapse
Affiliation(s)
- Patricia Alba
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Pimlapas Leekitcharoenphon
- European Union Reference Laboratory for Antimicrobial-Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Virginia Carfora
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Roberta Amoruso
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Gessica Cordaro
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Paola Di Matteo
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Angela Ianzano
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Manuela Iurescia
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Elena L Diaconu
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | | | - Susanne K Pedersen
- European Union Reference Laboratory for Antimicrobial-Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Rene S Hendriksen
- European Union Reference Laboratory for Antimicrobial-Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alessia Franco
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Antonio Battisti
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| |
Collapse
|
34
|
Carvalho G, Fouchet D, Danesh G, Godeux AS, Laaberki MH, Pontier D, Charpentier X, Venner S. Bacterial Transformation Buffers Environmental Fluctuations through the Reversible Integration of Mobile Genetic Elements. mBio 2020; 11:mBio.02443-19. [PMID: 32127449 PMCID: PMC7064763 DOI: 10.1128/mbio.02443-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Horizontal gene transfer (HGT) promotes the spread of genes within bacterial communities. Among the HGT mechanisms, natural transformation stands out as being encoded by the bacterial core genome. Natural transformation is often viewed as a way to acquire new genes and to generate genetic mixing within bacterial populations. Another recently proposed function is the curing of bacterial genomes of their infectious parasitic mobile genetic elements (MGEs). Here, we propose that these seemingly opposing theoretical points of view can be unified. Although costly for bacterial cells, MGEs can carry functions that are at points in time beneficial to bacteria under stressful conditions (e.g., antibiotic resistance genes). Using computational modeling, we show that, in stochastic environments, an intermediate transformation rate maximizes bacterial fitness by allowing the reversible integration of MGEs carrying resistance genes, although these MGEs are costly for host cell replication. Based on this dual function (MGE acquisition and removal), transformation would be a key mechanism for stabilizing the bacterial genome in the long term, and this would explain its striking conservation.IMPORTANCE Natural transformation is the acquisition, controlled by bacteria, of extracellular DNA and is one of the most common mechanisms of horizontal gene transfer, promoting the spread of resistance genes. However, its evolutionary function remains elusive, and two main roles have been proposed: (i) the new gene acquisition and genetic mixing within bacterial populations and (ii) the removal of infectious parasitic mobile genetic elements (MGEs). While the first one promotes genetic diversification, the other one promotes the removal of foreign DNA and thus genome stability, making these two functions apparently antagonistic. Using a computational model, we show that intermediate transformation rates, commonly observed in bacteria, allow the acquisition then removal of MGEs. The transient acquisition of costly MGEs with resistance genes maximizes bacterial fitness in environments with stochastic stress exposure. Thus, transformation would ensure both a strong dynamic of the bacterial genome in the short term and its long-term stabilization.
Collapse
Affiliation(s)
- Gabriel Carvalho
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - David Fouchet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Gonché Danesh
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Anne-Sophie Godeux
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, Villeurbanne, France
- CNRS UMR5308, École Normale Supérieure de Lyon, University of Lyon, Villeurbanne, France
| | - Maria-Halima Laaberki
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, Villeurbanne, France
- Université de Lyon, VetAgro Sup, Marcy-l'Étoile, France
- CNRS UMR5308, École Normale Supérieure de Lyon, University of Lyon, Villeurbanne, France
| | - Dominique Pontier
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Xavier Charpentier
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, Villeurbanne, France
- CNRS UMR5308, École Normale Supérieure de Lyon, University of Lyon, Villeurbanne, France
| | - Samuel Venner
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| |
Collapse
|
35
|
Abstract
Viruses are ubiquitous parasites of cellular life and the most abundant biological entities on Earth. It is widely accepted that viruses are polyphyletic, but a consensus scenario for their ultimate origin is still lacking. Traditionally, three scenarios for the origin of viruses have been considered: descent from primordial, precellular genetic elements, reductive evolution from cellular ancestors and escape of genes from cellular hosts, achieving partial replicative autonomy and becoming parasitic genetic elements. These classical scenarios give different timelines for the origin(s) of viruses and do not explain the provenance of the two key functional modules that are responsible, respectively, for viral genome replication and virion morphogenesis. Here, we outline a 'chimeric' scenario under which different types of primordial, selfish replicons gave rise to viruses by recruiting host proteins for virion formation. We also propose that new groups of viruses have repeatedly emerged at all stages of the evolution of life, often through the displacement of ancestral structural and genome replication genes.
Collapse
|
36
|
González R, Butković A, Elena SF. From foes to friends: Viral infections expand the limits of host phenotypic plasticity. Adv Virus Res 2020; 106:85-121. [PMID: 32327149 DOI: 10.1016/bs.aivir.2020.01.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Phenotypic plasticity enables organisms to survive in the face of unpredictable environmental stress. Intimately related to the notion of phenotypic plasticity is the concept of the reaction norm that places phenotypic plasticity in the context of a genotype-specific response to environmental gradients. Whether reaction norms themselves evolve and which factors might affect their shape has been the object of intense debates among evolutionary biologists along the years. Since their discovery, viruses have been considered as pathogens. However, new viromic techniques and a shift in conceptual paradigms are showing that viruses are mostly non-pathogenic ubiquitous entities. Recent studies have shown how viral infections can even be beneficial for their hosts. This may happen especially in the context of stressed hosts, where the virus infection can induce beneficial changes in the host's physiological homeostasis, hence changing the shape of the reaction norm. Despite the fact that underlying physiological mechanisms and evolutionary dynamics are still not well understood, such beneficial interactions are being discovered in a growing number of plant-virus systems. Here, we aim to review these disperse studies and place them into the context of phenotypic plasticity and the evolution of reaction norms. This is an emerging field that is posing many questions that still need to be properly answered. The answers would clearly interest virologists, plant pathologists and evolutionary biologists and likely they will suggest possible future biotechnological applications, including the development of crops with higher survival rates and yield under adverse environmental situations.
Collapse
Affiliation(s)
- Rubén González
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Valencia, Spain.
| | - Anamarija Butković
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Valencia, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Valencia, Spain; The Santa Fe Institute, Santa Fe, NM, United States.
| |
Collapse
|
37
|
Koonin EV, Makarova KS, Wolf YI, Krupovic M. Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire. Nat Rev Genet 2019; 21:119-131. [PMID: 31611667 DOI: 10.1038/s41576-019-0172-9] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2019] [Indexed: 12/12/2022]
Abstract
All cellular life forms are afflicted by diverse genetic parasites, including viruses and other types of mobile genetic elements (MGEs), and have evolved multiple, diverse defence systems that protect them from MGE assault via different mechanisms. Here, we provide our perspectives on how recent evidence points to tight evolutionary connections between MGEs and defence systems that reach far beyond the proverbial arms race. Defence systems incur a fitness cost for the hosts; therefore, at least in prokaryotes, horizontal mobility of defence systems, mediated primarily by MGEs, is essential for their persistence. Moreover, defence systems themselves possess certain features of selfish elements. Common components of MGEs, such as site-specific nucleases, are 'guns for hire' that can also function as parts of defence mechanisms and are often shuttled between MGEs and defence systems. Thus, evolutionary and molecular factors converge to mould the multifaceted, inextricable connection between MGEs and anti-MGE defence systems.
Collapse
Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA.
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, Paris, France.
| |
Collapse
|
38
|
Enforcement is central to the evolution of cooperation. Nat Ecol Evol 2019; 3:1018-1029. [PMID: 31239554 DOI: 10.1038/s41559-019-0907-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 04/26/2019] [Indexed: 01/21/2023]
Abstract
Cooperation occurs at all levels of life, from genomes, complex cells and multicellular organisms to societies and mutualisms between species. A major question for evolutionary biology is what these diverse systems have in common. Here, we review the full breadth of cooperative systems and find that they frequently rely on enforcement mechanisms that suppress selfish behaviour. We discuss many examples, including the suppression of transposable elements, uniparental inheritance of mitochondria and plastids, anti-cancer mechanisms, reciprocation and punishment in humans and other vertebrates, policing in eusocial insects and partner choice in mutualisms between species. To address a lack of accompanying theory, we develop a series of evolutionary models that show that the enforcement of cooperation is widely predicted. We argue that enforcement is an underappreciated, and often critical, ingredient for cooperation across all scales of biological organization.
Collapse
|
39
|
Catalán P, Elena SF, Cuesta JA, Manrubia S. Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo. Viruses 2019; 11:v11050425. [PMID: 31075860 PMCID: PMC6563258 DOI: 10.3390/v11050425] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 01/12/2023] Open
Abstract
Viroids are small, non-coding, circular RNA molecules that infect plants. Different hypotheses for their evolutionary origin have been put forward, such as an early emergence in a precellular RNA World or several de novo independent evolutionary origins in plants. Here, we discuss the plausibility of de novo emergence of viroid-like replicons by giving theoretical support to the likelihood of different steps along a parsimonious evolutionary pathway. While Avsunviroidae-like structures are relatively easy to obtain through evolution of a population of random RNA sequences of fixed length, rod-like structures typical of Pospiviroidae are difficult to fix. Using different quantitative approaches, we evaluated the likelihood that RNA sequences fold into a rod-like structure and bear specific sequence motifs facilitating interactions with other molecules, e.g., RNA polymerases, RNases, and ligases. By means of numerical simulations, we show that circular RNA replicons analogous to Pospiviroidae emerge if evolution is seeded with minimal circular RNAs that grow through the gradual addition of nucleotides. Further, these rod-like replicons often maintain their structure if independent functional modules are acquired that impose selective constraints. The evolutionary scenario we propose here is consistent with the structural and biochemical properties of viroids described to date.
Collapse
Affiliation(s)
- Pablo Catalán
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Paterna, 46980 València, Spain.
- The Santa Fe Institute, Santa Fe, NM 87501, USA.
| | - José A Cuesta
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
- Departamento de Matemáticas, Universidad Carlos III de Madrid, 28911 Leganés, Spain.
- Instituto de Biocomputación y Física de Sistemas Complejos (BiFi), Universidad de Zaragoza, 50018 Zaragoza, Spain.
- Institute of Financial Big Data (IFiBiD), Universidad Carlos III de Madrid⁻Banco de Santander, 28903 Getafe, Spain.
| | - Susanna Manrubia
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
- National Biotechnology Centre (CSIC), 28049 Madrid, Spain.
| |
Collapse
|
40
|
Rosani U, Shapiro M, Venier P, Allam B. A Needle in A Haystack: Tracing Bivalve-Associated Viruses in High-Throughput Transcriptomic Data. Viruses 2019; 11:v11030205. [PMID: 30832203 PMCID: PMC6466128 DOI: 10.3390/v11030205] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 02/08/2023] Open
Abstract
Bivalve mollusks thrive in environments rich in microorganisms, such as estuarine and coastal waters, and they tend to accumulate various particles, including viruses. However, the current knowledge on mollusk viruses is mainly centered on few pathogenic viruses, whereas a general view of bivalve-associated viromes is lacking. This study was designed to explore the viral abundance and diversity in bivalve mollusks using transcriptomic datasets. From analyzing RNA-seq data of 58 bivalve species, we have reconstructed 26 nearly complete and over 413 partial RNA virus genomes. Although 96.4% of the predicted viral proteins refer to new viruses, some sequences belong to viruses associated with bivalve species or other marine invertebrates. We considered short non-coding RNAs (sncRNA) and post-transcriptional modifications occurring specifically on viral RNAs as tools for virus host-assignment. We could not identify virus-derived small RNAs in sncRNA reads obtained from the oyster sample richest in viral reads. Single Nucleotide Polymorphism (SNP) analysis revealed 938 A-to-G substitutions occurring on the 26 identified RNA viruses, preferentially impacting the AA di-nucleotide motif. Under-representation analysis revealed that the AA motif is under-represented in these bivalve-associated viruses. These findings improve our understanding of bivalve viromes, and set the stage for targeted investigations on the specificity and dynamics of identified viruses.
Collapse
Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padua, 35121 Padua, Italy.
| | - Maxwell Shapiro
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794-5000, USA.
| | - Paola Venier
- Department of Biology, University of Padua, 35121 Padua, Italy.
| | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA.
| |
Collapse
|
41
|
Sau S, Ghosh SK, Liu YT, Ma CH, Jayaram M. Hitchhiking on chromosomes: A persistence strategy shared by diverse selfish DNA elements. Plasmid 2019; 102:19-28. [PMID: 30726706 DOI: 10.1016/j.plasmid.2019.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 12/12/2022]
Abstract
An underlying theme in the segregation of low-copy bacterial plasmids is the assembly of a 'segrosome' by DNA-protein and protein-protein interactions, followed by energy-driven directed movement. Analogous partitioning mechanisms drive the segregation of host chromosomes as well. Eukaryotic extra-chromosomal elements, exemplified by budding yeast plasmids and episomes of certain mammalian viruses, harbor partitioning systems that promote their physical association with chromosomes. In doing so, they indirectly take advantage of the spindle force that directs chromosome movement to opposite cell poles. Molecular-genetic, biochemical and cell biological studies have revealed several unsuspected aspects of 'chromosome hitchhiking' by the yeast 2-micron plasmid, including the ability of plasmid sisters to associate symmetrically with sister chromatids. As a result, the plasmid overcomes the 'mother bias' experienced by plasmids lacking a partitioning system, and elevates itself to near chromosome status in equal segregation. Chromosome association for stable propagation, without direct energy expenditure, may also be utilized by a small minority of bacterial plasmids-at least one case has been reported. Given the near perfect accuracy of chromosome segregation, it is not surprising that elements residing in evolutionarily distant host organisms have converged upon the common strategy of gaining passage to daughter cells as passengers on chromosomes.
Collapse
Affiliation(s)
- Soumitra Sau
- Amity Institute of Biotechnology, Amity University Kolkata, Kolkata 700135, India
| | - Santanu Kumar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Yen-Ting Liu
- Department of Molecular Biosciences, UT Austin, Austin, TX TX7 8712, USA
| | - Chien-Hui Ma
- Department of Molecular Biosciences, UT Austin, Austin, TX TX7 8712, USA
| | - Makkuni Jayaram
- Department of Molecular Biosciences, UT Austin, Austin, TX TX7 8712, USA.
| |
Collapse
|
42
|
Koonin EV. CRISPR: a new principle of genome engineering linked to conceptual shifts in evolutionary biology. BIOLOGY & PHILOSOPHY 2019; 34:9. [PMID: 30930513 PMCID: PMC6404382 DOI: 10.1007/s10539-018-9658-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
The CRISPR-Cas systems of bacterial and archaeal adaptive immunity have become a household name among biologists and even the general public thanks to the unprecedented success of the new generation of genome editing tools utilizing Cas proteins. However, the fundamental biological features of CRISPR-Cas are of no lesser interest and have major impacts on our understanding of the evolution of antivirus defense, host-parasite coevolution, self versus non-self discrimination and mechanisms of adaptation. CRISPR-Cas systems present the best known case in point for Lamarckian evolution, i.e. generation of heritable, adaptive genomic changes in response to encounters with external factors, in this case, foreign nucleic acids. CRISPR-Cas systems employ multiple mechanisms of self versus non-self discrimination but, as is the case with immune systems in general, are nevertheless costly because autoimmunity cannot be eliminated completely. In addition to the autoimmunity, the fitness cost of CRISPR-Cas systems appears to be determined by their inhibitory effect on horizontal gene transfer, curtailing evolutionary innovation. Hence the dynamic evolution of CRISPR-Cas loci that are frequently lost and (re)acquired by archaea and bacteria. Another fundamental biological feature of CRISPR-Cas is its intimate connection with programmed cell death and dormancy induction in microbes. In this and, possibly, other immune systems, active immune response appears to be coupled to a different form of defense, namely, "altruistic" shutdown of cellular functions resulting in protection of neighboring cells. Finally, analysis of the evolutionary connections of Cas proteins reveals multiple contributions of mobile genetic elements (MGE) to the origin of various components of CRISPR-Cas systems, furthermore, different biological systems that function by genome manipulation appear to have evolved convergently from unrelated MGE. The shared features of adaptive defense systems and MGE, namely the ability to recognize and cleave unique sites in genomes, make them ideal candidates for genome editing and engineering tools.
Collapse
Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894 USA
| |
Collapse
|
43
|
Berezovskaya F, Karev GP, Katsnelson MI, Wolf YI, Koonin EV. Stable coevolutionary regimes for genetic parasites and their hosts: you must differ to coevolve. Biol Direct 2018; 13:27. [PMID: 30621743 PMCID: PMC6822691 DOI: 10.1186/s13062-018-0230-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/29/2018] [Indexed: 12/19/2022] Open
Abstract
Background Genetic parasites are ubiquitous satellites of cellular life forms most of which host a variety of mobile genetic elements including transposons, plasmids and viruses. Theoretical considerations and computer simulations suggest that emergence of genetic parasites is intrinsic to evolving replicator systems. Results Using methods of bifurcation analysis, we investigated the stability of simple models of replicator-parasite coevolution in a well-mixed environment. We first analyze what appears to be the simplest imaginable system of this type, one in which the parasite evolves during the replication of the host genome through a minimal mutation that renders the genome of the emerging parasite incapable of producing the replicase but able to recognize and recruit it for its own replication. This model has only trivial or “semi-trivial”, parasite-free equilibria: an inefficient parasite is outcompeted by the host and dies off, whereas an efficient one pushes the host out of existence, leading to the collapse of the entire system. We show that stable host-parasite coevolution (a non-trivial equilibrium) is possible in a modified model where the parasite is qualitatively distinct from the host replicator in that the replication of the parasite depends solely on the availability of the host but not on the carrying capacity of the environment. Conclusions We analytically determine the conditions for stable coevolution of genetic parasites and their hosts coevolution in simple mathematical models. It is shown that the evolutionary dynamics of a parasite that initially evolves from the host through the loss of the ability to replicate autonomously must substantially differ from that of the host, for a stable host-parasite coevolution regime to be established. Electronic supplementary material The online version of this article (10.1186/s13062-018-0230-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Faina Berezovskaya
- Department of Mathematics, Howard University, Washington, DC, 20059, USA
| | - Georgy P Karev
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Mikhail I Katsnelson
- Institute for Molecules and Materials, Radboud University, 6525AJ, Nijmegen, Netherlands
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| |
Collapse
|
44
|
Faure G, Makarova KS, Koonin EV. CRISPR-Cas: Complex Functional Networks and Multiple Roles beyond Adaptive Immunity. J Mol Biol 2018; 431:3-20. [PMID: 30193985 DOI: 10.1016/j.jmb.2018.08.030] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 01/26/2023]
Abstract
CRISPR-Cas is a prokaryotic adaptive immune system that functions by incorporating fragments of foreign DNA into CRISPR arrays. The arrays containing spacers derived from foreign DNA are transcribed, and the transcripts are processed to generate spacer-containing mature CRISPR-RNAs that are employed as guides to specifically recognize and cleave the DNA or RNA of the cognate parasitic genetic elements. The CRISPR-Cas systems show remarkable complexity and diversity of molecular organization and appear to be involved in various cellular functions that are distinct from, even if connected to, adaptive immunity. In this review, we discuss some of such functional links of CRISPR-Cas systems including their effect on horizontal gene transfer that can be either inhibitory or stimulatory, connections between CRISPR-Cas and DNA repair systems as well as programmed cell death and signal transduction mechanisms, and potential role of CRISPR-Cas in transposon integration and plasmid maintenance. The interplay between the primary function of CRISPR-Cas as an adaptive immunity mechanism and these other roles defines the richness of the biological effects of these systems and affects their spread among bacteria and archaea.
Collapse
Affiliation(s)
- Guilhem Faure
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| |
Collapse
|
45
|
Koonin EV, Krupovic M. The depths of virus exaptation. Curr Opin Virol 2018; 31:1-8. [PMID: 30071360 DOI: 10.1016/j.coviro.2018.07.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/13/2018] [Accepted: 07/19/2018] [Indexed: 02/07/2023]
Abstract
Viruses are ubiquitous parasites of cellular life forms and the most abundant biological entities on earth. The relationships between viruses and their hosts involve the continuous arms race but are by no account limited to it. Growing evidence shows that, in the course of evolution, viruses and their components are repeatedly recruited (exapted) for host functions. The functions of exapted viruses typically involve either defense from other viruses or cellular competitors or transfer of nucleic acids between cells, or storage functions. Virus exaptation can reach different depths, from recruitment of a fully functional virus to exploitation of defective, partially degraded viruses, to utilization of individual virus proteins.
Collapse
Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States.
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France.
| |
Collapse
|
46
|
Braga LPP, Soucy SM, Amgarten DE, da Silva AM, Setubal JC. Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
|
47
|
Koonin EV, Wolf YI, Katsnelson MI. Inevitability of the emergence and persistence of genetic parasites caused by evolutionary instability of parasite-free states. Biol Direct 2017; 12:31. [PMID: 29202832 PMCID: PMC5715634 DOI: 10.1186/s13062-017-0202-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/22/2017] [Indexed: 01/02/2023] Open
Abstract
Genetic parasites, including viruses and mobile genetic elements, are ubiquitous among cellular life forms, and moreover, are the most abundant biological entities on earth that harbor the bulk of the genetic diversity. Here we examine simple thought experiments to demonstrate that both the emergence of parasites in simple replicator systems and their persistence in evolving life forms are inevitable because the putative parasite-free states are evolutionarily unstable. REVIEWERS This article has been reviewed by Yitzhak Pilpel, Bojan Zagrovic, and Eric van Nimwegen.
Collapse
Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Mikhail I Katsnelson
- Institute for Molecules and Materials, Radboud University, 6525AJ, Nijmegen, Netherlands
| |
Collapse
|
48
|
Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Artem S. Novozhilov
- Department of Mathematics, North Dakota State University, Fargo, North Dakota 58108, USA
| |
Collapse
|
49
|
Recombination-Driven Genome Evolution and Stability of Bacterial Species. Genetics 2017; 207:281-295. [PMID: 28751420 DOI: 10.1534/genetics.117.300061] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 07/18/2017] [Indexed: 01/21/2023] Open
Abstract
While bacteria divide clonally, horizontal gene transfer followed by homologous recombination is now recognized as an important contributor to their evolution. However, the details of how the competition between clonality and recombination shapes genome diversity remains poorly understood. Using a computational model, we find two principal regimes in bacterial evolution and identify two composite parameters that dictate the evolutionary fate of bacterial species. In the divergent regime, characterized by either a low recombination frequency or strict barriers to recombination, cohesion due to recombination is not sufficient to overcome the mutational drift. As a consequence, the divergence between pairs of genomes in the population steadily increases in the course of their evolution. The species lacks genetic coherence with sexually isolated clonal subpopulations continuously formed and dissolved. In contrast, in the metastable regime, characterized by a high recombination frequency combined with low barriers to recombination, genomes continuously recombine with the rest of the population. The population remains genetically cohesive and temporally stable. Notably, the transition between these two regimes can be affected by relatively small changes in evolutionary parameters. Using the Multi Locus Sequence Typing (MLST) data, we classify a number of bacterial species to be either the divergent or the metastable type. Generalizations of our framework to include selection, ecologically structured populations, and horizontal gene transfer of nonhomologous regions are discussed as well.
Collapse
|
50
|
Abstract
Evolution of bacteria and archaea involves an incessant arms race against an enormous diversity of genetic parasites. Accordingly, a substantial fraction of the genes in most bacteria and archaea are dedicated to antiparasite defense. The functions of these defense systems follow several distinct strategies, including innate immunity; adaptive immunity; and dormancy induction, or programmed cell death. Recent comparative genomic studies taking advantage of the expanding database of microbial genomes and metagenomes, combined with direct experiments, resulted in the discovery of several previously unknown defense systems, including innate immunity centered on Argonaute proteins, bacteriophage exclusion, and new types of CRISPR-Cas systems of adaptive immunity. Some general principles of function and evolution of defense systems are starting to crystallize, in particular, extensive gain and loss of defense genes during the evolution of prokaryotes; formation of genomic defense islands; evolutionary connections between mobile genetic elements and defense, whereby genes of mobile elements are repeatedly recruited for defense functions; the partially selfish and addictive behavior of the defense systems; and coupling between immunity and dormancy induction/programmed cell death.
Collapse
Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894;
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894;
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894;
| |
Collapse
|