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Mobile Genetic Elements in Streptococci
Curr. Issues Mol. Biol. (2019) 32: 123-166. DOI: https://dx.doi.org/10.21775/cimb.032.123 Mobile Genetic Elements in Streptococci Miao Lu#, Tao Gong#, Anqi Zhang, Boyu Tang, Jiamin Chen, Zhong Zhang, Yuqing Li*, Xuedong Zhou* State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China. #Miao Lu and Tao Gong contributed equally to this work. *Address correspondence to: [email protected], [email protected] Abstract Streptococci are a group of Gram-positive bacteria belonging to the family Streptococcaceae, which are responsible of multiple diseases. Some of these species can cause invasive infection that may result in life-threatening illness. Moreover, antibiotic-resistant bacteria are considerably increasing, thus imposing a global consideration. One of the main causes of this resistance is the horizontal gene transfer (HGT), associated to gene transfer agents including transposons, integrons, plasmids and bacteriophages. These agents, which are called mobile genetic elements (MGEs), encode proteins able to mediate DNA movements. This review briefly describes MGEs in streptococci, focusing on their structure and properties related to HGT and antibiotic resistance. caister.com/cimb 123 Curr. Issues Mol. Biol. (2019) Vol. 32 Mobile Genetic Elements Lu et al Introduction Streptococci are a group of Gram-positive bacteria widely distributed across human and animals. Unlike the Staphylococcus species, streptococci are catalase negative and are subclassified into the three subspecies alpha, beta and gamma according to the partial, complete or absent hemolysis induced, respectively. The beta hemolytic streptococci species are further classified by the cell wall carbohydrate composition (Lancefield, 1933) and according to human diseases in Lancefield groups A, B, C and G. -
Imaging, Tracking and Computational Analyses of Virus Entry and Egress
1 Review 2 Imaging, Tracking and Computational Analyses of 3 Virus Entry and Egress with the Cytoskeleton 4 I-Hsuan Wang 1,†, Christoph J. Burckhardt 2,†, A. Yakimovich 3 and Urs F. Greber 4,* 5 1 Division of Virology, Institute of Medical Science, tHe University of ToKyo, ToKyo 108-8639, Japan 6 2 UT SoutHwestern Medical Center, Lyda Hill Department of Bioinformatics, Dallas TX 75390, USA 7 3 MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom 8 4 Department of Molecular Life Sciences, University of ZuricH, WintertHurerstrasse 190, CH-8057 ZuricH, 9 Switzerland 10 * Correspondence: [email protected], Telephone: +41 44 635 4841, Fax: +41 44 635 6817 11 † These autHors contributed equally to tHis work. 12 Received: date; Accepted: date; PublisHed: date 13 Abstract: Viruses Have a dual nature - particles are ‘passive substances’ lacKing chemical energy 14 transformation, wHereas infected cells are ‘active substances’ turning-over energy. How passive 15 viral substances convert to active substances, comprising viral replication and assembly 16 compartments Has been of intense interest to virologists, cell and molecular biologists and 17 immunologists. Infection starts witH virus entry into a susceptible cell and delivers tHe viral 18 genome to the replication site. THis is a multi-step process, and involves tHe cytosKeleton and 19 associated motor proteins. LiKewise, the egress of progeny virus particles from the replication site 20 to the extracellular space is enHanced by tHe cytosKeleton and associated motor proteins. THis 21 overcomes tHe limitation of tHermal diffusion, and transports virions and virion components, 22 often in association witH cellular organelles. -
Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification
ORIGINAL RESEARCH published: 10 March 2017 doi: 10.3389/fmicb.2017.00380 Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification Arshan Nasir 1, 2 and Gustavo Caetano-Anollés 1* 1 Department of Crop Sciences, Evolutionary Bioinformatics Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA, 2 Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan The viral supergroup includes the entire collection of known and unknown viruses that roam our planet and infect life forms. The supergroup is remarkably diverse both in its genetics and morphology and has historically remained difficult to study and classify. The accumulation of protein structure data in the past few years now provides an excellent opportunity to re-examine the classification and evolution of viruses. Here we scan completely sequenced viral proteomes from all genome types and identify protein folds involved in the formation of viral capsids and virion architectures. Viruses encoding similar capsid/coat related folds were pooled into lineages, after benchmarking against published literature. Remarkably, the in silico exercise reproduced all previously described members of known structure-based viral lineages, along with several proposals for new Edited by: additions, suggesting it could be a useful supplement to experimental approaches and Ricardo Flores, to aid qualitative assessment of viral diversity in metagenome samples. Polytechnic University of Valencia, Spain Keywords: capsid, virion, protein structure, virus taxonomy, SCOP, fold superfamily Reviewed by: Mario A. Fares, Consejo Superior de Investigaciones INTRODUCTION Científicas(CSIC), Spain Janne J. Ravantti, The last few years have dramatically increased our knowledge about viral systematics and University of Helsinki, Finland evolution. -
An Expanded View of Viruses
An Expanded View of Viruses Urs F. Greber 1) & Ralf Bartenschlager 2) 1) Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland 2) Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69198 Heidelberg, Germany Correspondence to: [email protected] [email protected] 1 figure Keywords: Zoonosis; Pandemics; Dengue, Ebola; Influenza; Entry; Endocytosis; Uncoating; Transport; Filovirus; Comparative genomics; Computational analyses; Virus-host interactions; Filamentous virus; Bacterial biofilm; Phage; Bacteriophage; Glycan; Immunity; Infection; Disease; Evolution; Variability; Giant virus; Ferret; Guinea pig; Emerging disease; Pandemic; Host range; Enveloped virus; 1 Viruses are ubiquitous, and are important in medicine, biology, biotechnology and ecology. All kinds of cells can be infected with viruses, and sometimes, a particular cell is infected with different viruses at the same time. The virus particle, ‘virion’ is composed of the viral coat proteins sheltering the viral genome, and is often surrounded by a lipid “envelope”. A virion is small compared to cells, and when it enters cells gives rise to infection distinct from an intracellular bacterial pathogen (Lwoff, 1957). A virus-infected cell has a profoundly altered homeostasis due to numerous interactions between cellular and viral components. This leads to evolutionary pressure on both virus and host, and argues that viruses are a part of life (Ludmir & Enquist, 2009). Our cells can be infected by viruses causing acute disease, such as respiratory disease by Influenza virus or rhinoviruses, or chronic disease, such as hepatitis or immune deficiency. However, most viral attacks on cells are fend off, or the spread of viruses in an infected organism is restricted, and infection abrogated. -
A Persistent Giant Algal Virus, with a Unique Morphology, Encodes An
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.30.228163; this version posted January 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 A persistent giant algal virus, with a unique morphology, encodes an 2 unprecedented number of genes involved in energy metabolism 3 4 Romain Blanc-Mathieu1,2, Håkon Dahle3, Antje Hofgaard4, David Brandt5, Hiroki 5 Ban1, Jörn Kalinowski5, Hiroyuki Ogata1 and Ruth-Anne Sandaa6* 6 7 1: Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan 8 2: Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, 9 CNRS, INRA, IRIG, Grenoble, France 10 3: Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, 11 University of Bergen, Bergen, Norway 12 4: Department of Biosciences, University of Oslo, Norway 13 5: Center for Biotechnology, Universität Bielefeld, Bielefeld, 33615, Germany 14 6: Department of Biological Sciences, University of Bergen, Bergen, Norway 15 *Corresponding author: Ruth-Anne Sandaa, +47 55584646, [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.30.228163; this version posted January 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 16 Abstract 17 Viruses have long been viewed as entities possessing extremely limited metabolic 18 capacities. -
The LUCA and Its Complex Virome in Another Recent Synthesis, We Examined the Origins of the Replication and Structural Mart Krupovic , Valerian V
PERSPECTIVES archaea that form several distinct, seemingly unrelated groups16–18. The LUCA and its complex virome In another recent synthesis, we examined the origins of the replication and structural Mart Krupovic , Valerian V. Dolja and Eugene V. Koonin modules of viruses and posited a ‘chimeric’ scenario of virus evolution19. Under this Abstract | The last universal cellular ancestor (LUCA) is the most recent population model, the replication machineries of each of of organisms from which all cellular life on Earth descends. The reconstruction of the four realms derive from the primordial the genome and phenotype of the LUCA is a major challenge in evolutionary pool of genetic elements, whereas the major biology. Given that all life forms are associated with viruses and/or other mobile virion structural proteins were acquired genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by from cellular hosts at different stages of evolution giving rise to bona fide viruses. projecting back in time using the extant distribution of viruses across the two In this Perspective article, we combine primary domains of life, bacteria and archaea, and tracing the evolutionary this recent work with observations on the histories of some key virus genes, we attempt a reconstruction of the LUCA virome. host ranges of viruses in each of the four Even a conservative version of this reconstruction suggests a remarkably complex realms, along with deeper reconstructions virome that already included the main groups of extant viruses of bacteria and of virus evolution, to tentatively infer archaea. We further present evidence of extensive virus evolution antedating the the composition of the virome of the last universal cellular ancestor (LUCA; also LUCA. -
Persistent Virus and Addiction Modules: an Engine of Symbiosis
UC Irvine UC Irvine Previously Published Works Title Persistent virus and addiction modules: an engine of symbiosis. Permalink https://escholarship.org/uc/item/5ck1g026 Journal Current opinion in microbiology, 31 ISSN 1369-5274 Author Villarreal, Luis P Publication Date 2016-06-01 DOI 10.1016/j.mib.2016.03.005 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Available online at www.sciencedirect.com ScienceDirect Persistent virus and addiction modules: an engine of symbiosis Luis P Villarreal The giant DNA viruses are highly prevalent and have a particular host would occasionally survive but still retain a bit of affinity for the lytic infection of unicellular eukaryotic host. The the selfish virus DNA. Thus although parasitic selfish giant viruses can also be infected by inhibitory virophage which (virus-like) information is common in the genomes of all can provide lysis protection to their host. The combined life forms, its presence was explained as mostly defective protective and destructive action of such viruses can define a remnants of past plague sweeps that provides no func- general model (PD) of virus-mediated host survival. Here, I tional benefit to the host (e.g. junk). Until recently, this present a general model for role such viruses play in the explanation seemed satisfactory. In the last twenty years, evolution of host symbiosis. By considering how virus mixtures however, various observation-based developments have can participate in addiction modules, I provide a functional compelled us to re-evaluate this stance. Both comparative explanation for persistence of virus derived genetic ‘junk’ in genomics and metagenomics (sequencing habitats) has their host genomic habitats. -
On the Biological Success of Viruses
MI67CH25-Turner ARI 19 June 2013 8:14 V I E E W R S Review in Advance first posted online on June 28, 2013. (Changes may still occur before final publication E online and in print.) I N C N A D V A On the Biological Success of Viruses Brian R. Wasik and Paul E. Turner Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520-8106; email: [email protected], [email protected] Annu. Rev. Microbiol. 2013. 67:519–41 Keywords The Annual Review of Microbiology is online at adaptation, biodiversity, environmental change, evolvability, extinction, micro.annualreviews.org robustness This article’s doi: 10.1146/annurev-micro-090110-102833 Abstract Copyright c 2013 by Annual Reviews. Are viruses more biologically successful than cellular life? Here we exam- All rights reserved ine many ways of gauging biological success, including numerical abun- dance, environmental tolerance, type biodiversity, reproductive potential, and widespread impact on other organisms. We especially focus on suc- cessful ability to evolutionarily adapt in the face of environmental change. Viruses are often challenged by dynamic environments, such as host immune function and evolved resistance as well as abiotic fluctuations in temperature, moisture, and other stressors that reduce virion stability. Despite these chal- lenges, our experimental evolution studies show that viruses can often readily adapt, and novel virus emergence in humans and other hosts is increasingly problematic. We additionally consider whether viruses are advantaged in evolvability—the capacity to evolve—and in avoidance of extinction. On the basis of these different ways of gauging biological success, we conclude that viruses are the most successful inhabitants of the biosphere. -
Tiny Giants | Maxplanckresearch 3/2019
BIOLOGY & MEDICINE_Viruses Tiny giants Viruses are usually incredibly small, but some deviate from the norm and reach sizes greater than that of a bacterial cell. Matthias Fischer from the Max Planck Institute for Medical Research in Heidelberg is one of a small number of scientists working on giant viruses of this kind. TEXT STEFANIE REINBERGER Photo: Wolfram Scheible 58 MaxPlanckResearch 3 | 19 n the laboratory of Matthias Fischer Although they look like nothing more As giant viruses are about at the Max Planck Institute in Hei- than vials of water to the naked eye, the the same size as bacteria, delberg, vials containing water samples are actually teeming with it is almost impossible to purify them by filtration samples are lined up against one life, which only becomes visible when only. However, as viruses another, each containing a whole viewed through a microscope: countless and bacteria have different I world of aquatic single-celled organ- tiny dots are scurrying back and forth. densities, they form layers isms and viruses. The labels reveal the “The smaller ones are bacteria, which when spun in an ultracen- trifuge. Scientists can then origins of the samples: Guenzburg, are devoured by larger cells that have a extract the viral band using Kiel, but also more exotic locations nucleus. These so-called protists are the a syringe and needle. such as Tallinn or the British Virgin reason we created the collection in the Islands. “The collection is the result of first place,” Fischer explains. Indeed, many years of work,” the microbiolo- these protists are susceptible to attack Photo: Wolfram Scheible gist explains. -
An Update on Self-Amplifying Mrna Vaccine Development
Review An Update on Self-Amplifying mRNA Vaccine Development Anna K. Blakney 1,* , Shell Ip 2 and Andrew J. Geall 2 1 Michael Smith Laboratories, School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z4, Canada 2 Precision NanoSystems Inc., Vancouver, BC V6P 6T7, Canada; [email protected] (S.I.); [email protected] (A.J.G.) * Correspondence: [email protected] Abstract: This review will explore the four major pillars required for design and development of an saRNA vaccine: Antigen design, vector design, non-viral delivery systems, and manufacturing (both saRNA and lipid nanoparticles (LNP)). We report on the major innovations, preclinical and clinical data reported in the last five years and will discuss future prospects. Keywords: RNA; self-amplifying RNA; replicon; vaccine; drug delivery 1. Introduction: The Four Pillars of saRNA Vaccines In December 2019, the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) virus emerged, causing a respiratory illness, coronavirus disease 2019 (COVID-19), in Hubei province, China [1,2]. The virus has spread globally, with the World Health Organization (WHO) declaring it a Public Health Emergency of International concern on 30 January 2020 and a pandemic officially on 7 March 2020 [3]. There is a strong consensus globally that a COVID-19 vaccine is likely the most effective approach to sustainably controlling the COVID-19 pandemic [4]. There has been an unprecedented research effort and global Citation: Blakney, A.K.; Ip, S.; Geall, coordination which has resulted in the rapid development of vaccine candidates and A.J. An Update on Self-Amplifying initiation of human clinical trials. -
Multiple Replicons Constituting the Genome of Pseudomonas Cepacia 17616 HAI-PING Chengt and THOMAS G
JOURNAL OF BACrERIOLOGY, JUlY 1994, p. 4034-4042 Vol. 176, No. 13 0021-9193/94/$04.00+0 Copyright © 1994, American Society for Microbiology Multiple Replicons Constituting the Genome of Pseudomonas cepacia 17616 HAI-PING CHENGt AND THOMAS G. LESSIE* Department ofMicrobiology, University ofMassachusetts, Amherst, Massachusetts 01002 Received 4 February 1994/Accepted 25 April 1994 Macrorestriction fragment analysis of DNA from Pseudomonas cepacia 17616, in conjunction with Southern hybridization experiments using junction fragments containing rare restriction enzyme sites as probes, indicated that this bacterium contains three large circular replicons of 3.4, 2.5, and 0.9 megabases (Mb). Inclusion of the 170-kb cryptic plasmid present in this strain gave an overall estimate of genome size of 7 Mb. Other Southern hybridization experiments indicated that the three large replicons contained rRNA genes as well as insertion sequence elements identified previously in this strain. The distribution of Swal, PacI, and Pmel sites on the three replicons was determined. A derivative of TnS-751 carrying a SwaI site was used to inactivate and map genes on the 2.5- and 3.4-Mb replicons. Mutants were isolated in which the 2.5- and 0.9-Mb replicons had been reduced in size to 1.8 and 0.65 Mb, respectively. The loss of DNA from the 2.5-Mb replicon was associated with lysine auxotrophy, P-lactamase deficiency, and failure to utilize ribitol and trehalose as carbon and energy sources. DNA fragments corresponding in size to randomly linearized forms of the different replicons were detected in unrestricted DNA by pulsed-field gel electrophoresis. -
Giant Virus with a Remarkable Complement of Genes Infects Marine Zooplankton
Giant virus with a remarkable complement of genes infects marine zooplankton Matthias G. Fischera, Michael J. Allenb, William H. Wilsonc, and Curtis A. Suttlea,d,e,1 Departments of aMicrobiology and Immunology, dBotany, and eEarth and Ocean Sciences, University of British Columbia, Vancouver, BC, Canada V6T 1Z4; bPlymouth Marine Laboratory, Plymouth PL1 3DH, United Kingdom; and cBigelow Laboratory for Ocean Sciences, West Boothbay Harbor, ME 04575-0475 Edited* by James L. Van Etten, University of Nebraska, Lincoln, NE, and approved October 4, 2010 (received for review June 2, 2010) As major consumers of heterotrophic bacteria and phytoplankton, viruses (13), was originally misidentified as Bodo sp. (12). It is a 2- microzooplankton are a critical link in aquatic foodwebs. Here, we μm– to 6-μm–long bicosoecid heterokont phagotrophic flagellate show that a major marine microflagellate grazer is infected by (Stramenopiles) that is widespread in marine environments and is a giant virus, Cafeteria roenbergensis virus (CroV), which has the found in various habitats such as surface waters, deep sea sedi- largest genome of any described marine virus (≈730 kb of double- ments, and hydrothermal vents (14, 15). Populations of C. roen- stranded DNA). The central 618-kb coding part of this AT-rich ge- bergensis may be regulated by viruses in nature (16). nome contains 544 predicted protein-coding genes; putative early and late promoter motifs have been detected and assigned to 191 Results and Discussion and 72 of them, respectively, and at least 274 genes were expressed General Genome Features. The genome of CroV is a linear double- during infection.