DOCSLIB.ORG

Advancements of Microbiology 2019

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

POLSKIE TOWARZYSTWO MIKROBIOLOGÓW Kwartalnik Tom 58 Zeszyt 4•2019 PAèDZIERNIK – GRUDZIE¡ CODEN: PMKMAV 58 (4) Advancements of Microbiology 2019 Index Copernicus ICV = 101,48 (2017) Impact Factor ISI = 0,298 (2018) Punktacja MNiSW = 20,00 (2019) http://www.pm.microbiology.plhttp://www.pm.microbiology.pl RADA REDAKCYJNA JACEK BARDOWSKI (Instytut Biochemii i Biofizyki PAN), DARIUSZ BARTOSIK (Uniwersytet Warszawski), JACEK BIELECKI (Uniwersytet Warszawski), RYSZARD CHRÓST (Uniwersytet Warszawski), JERZY DŁUGOŃSKI (Uniwersytet Łódzki), NADZIEJA DRELA (Uniwersytet Warszawski), EUGENIA GOSPODAREK-KOMKOWSKA (Collegium Medicum w Bydgoszczy, Uniwersytet Mikołaja Kopernika w Toruniu), JERZY HREBENDA (Uniwersytet Warszawski), WALERIA HRYNIEWICZ (Narodowy Instytut Leków), MAREK JAKÓBISIAK (Warszawski Uniwersytet Medyczny), JACEK MIĘDZOBRODZKI (Uniwersytet Jagielloński), ANDRZEJ PIEKAROWICZ (Uniwersytet Warszawski), ANTONI RÓŻALSKI (Uniwersytet Łódzki), ALEKSANDRA SKŁODOWSKA (Uniwersytet Warszawski), RADOSŁAW STACHOWIAK (Uniwersytet Warszawski), BOGUSŁAW SZEWCZYK (Uniwersytet Gdański), ELŻBIETA TRAFNY (Wojskowa Akademia Techniczna), STANISŁAWA TYLEWSKA-WIERZBANOWSKA (Narodowy Instytut Zdrowia Publicznego), GRZEGORZ WĘGRZYN (Uniwersytet Gdański), PIOTR ZIELENKIEWICZ (Uniwersytet Warszawski) REDAKCJA JACEK BIELECKI (Redaktor Naczelny) Instytut Mikrobiologii, Wydział Biologii, Uniwersytet Warszawski, ul. Miecznikowa 1, 02-096 Warszawa; tel. 22 5541304; e-mail: [email protected] RADOSŁAW STACHOWIAK (Zastępca) Instytut Mikrobiologii, Wydział Biologii, Uniwersytet Warszawski, ul. Miecznikowa 1, 02-096 Warszawa; tel. 22 5541312; e-mail: [email protected] AGNIESZKA SOBOLEWSKA-RUTA (Sekretarz) Instytut Biotechnologii i Antybiotyków, ul. Starościńska 5, 02-516 Warszawa tel. 22 3786229, e-mail: [email protected] MARTA THOMSEN (korekta tekstów angielskich) ADRES REDAKCJI Instytut Mikrobiologii, Wydział Biologii, Uniwersytet Warszawski ul. Miecznikowa 1, 02-096 Warszawa; tel.: 22 3786229, 22 5541312 e-mail: [email protected] REDAKTORZY MONIKA ADAMCZYK-POPŁAWSKA (Uniwersytet Warszawski) ALEKSANDER DEPTUŁA (Uniwersytet Mikołaja Kopernika w Toruniu), HENRYK KRUKOWSKI (Uniwersytet Przyrodniczy w Lublinie), BOŻENA NEJMAN-FALEŃCZYK (Uniwersytet Gdański) RENATA MATLAKOWSKA (Uniwersytet Warszawski), ADRIANNA RACZKOWSKA (Uniwersytet Warszawski) AGATA GORYLUK-SALMONOWICZ (Szkoła Główna Gospodarstwa Wiejskiego w Warszawie) AGNIESZKA KWIATEK (Uniwersytet Warszawski), AGNIESZKA SZCZEPANKOWSKA (Instytut Biochemii i Biofizyki PAN) BOHDAN STAROŚCIAK (Warszawski Uniwersytet Medyczny), PIOTR ZALESKI (Instytut Biotechnologii i Antybiotyków) PUBLIKACJE METODYCZNE I STANDARDY Redaktor odpowiedzialny: STEFANIA GIEDRYS-KALEMBA (Pomorski Uniwersytet Medyczny w Szczecinie) Adres Redaktora działu Publikacje Metodyczne i Standardy ul. Malinowa 11, 72-003 Wołczkowo tel. 605031324; fax 91 3113186; e-mail: [email protected] STALI RECENZENCI: JERZY DŁUGOŃSKI (Uniwersytet Łódzki), WALERIA HRYNIEWICZ (Narodowy Instytut Leków), EUGENIUSZ MAŁAFIEJ (Instytut Centrum Zdrowia Matki Polki), ANNA PRZONDO-MORDARSKA (Akademia Medyczna we Wrocławiu) ISBN 978 - 83 - 923731 - 3 - 1 Informacja o zdjęciu na okładce: Komórki Neisseria gonorrhoeae, mutant szczepu FA1090. Preparatyka: dr Agnieszka Kwiatek, Zakład Wirusologii, Instytut Mikrobiologii, Uniwersytet Warszawski. Zdjęcie: dr Paweł Bącal, Pracownia Inżynierii Nanohybrydowych Biosystemów Regulacji, Instytut Biocybernetyki i Inżynierii Biome- dycznej im. M. Nałęcza Polskiej Akademii Nauk. Obraz SEM uzyskano przy użyciu aparatury zakupionej w ramach projektu CePT POIG.02.02.00-14-024/08-00. POLSKIE TOWARZYSTWO MIKROBIOLOGÓW Skład i druk: Zakład Wydawniczy Letter Quality, tel.: 22 115 38 10, 607 217 879 e-mail: [email protected]; projekt okładki: Jerzy Grzegorkiewicz Podziękowania Redakcja Postępów Mikrobiologii składa serdeczne podziękowania dla Recenzentów spoza Rady Redakcyjnej, którzy przyczynili się do utrzymania i polepszania standardów naszego czasopisma. Poniżej przedstawiamy listę recenzentów prac w 2019 roku: Dr hab. Tamara Aleksandrzak-Piekarczyk Dr hab. Daria Augustyniak Dr Jadwiga Baj Dr hab. inż. Maria Balcerek, prof. ITFiM Prof. dr hab. inż. Wiesława Barabasz Dr Małgorzata Biegańska Prof. dr hab. Marian Binek Prof. dr hab. inż. Elżbieta Daczkowska-Kozon Dr hab. Łukasz Drewniak, prof. ucz. Dr hab. Bożena Dworecka-Kaszak Dr hab. Tomasz Dzieciątkowski Prof. dr hab. Jan Fiedurek Dr hab. inż. Karol Fijałkowski Dr hab. Magdalena Florek, prof. UEP Prof. dr hab. Mariusz Gagoś Dr hab. Anna Goc, prof. UMK Dr hab. inż. Ewa Górska, prof. SGGW Prof. dr hab. Anna Goździcka-Józefiak Dr hab. n. med. Adam Junka Prof. dr hab. Ewa Karwowska Dr hab. Monika Kordowska-Wiater Dr hab. inż. Alina Kunicka-Styczyńska, prof. ITFiM Dr hab. n. o zdr. Cecylia Łukaszuk Prof. dr hab. Wanda Małek Dr hab. Aneta Nowakiewicz Dr hab. Egbert Piasecki Dr hab. n. med. Aldona Pietrzak Prof. dr hab. inż. Elżbieta Pląskowska Dr hab. n. med. Edyta Podsiadły dr hab. Katarzyna Potrykus, prof. UG Lek. Leszek Rudzki Prof. dr hab. Danuta Sosnowska Prof. dr hab. Zdzisław Targoński Dr hab. Beata Tokarz-Deptuła Dr hab. Agnieszka Tokarzewska, prof. UŁ Prof. dr hab. Stefan Tyski Mgr Paweł Urbanowicz Dr hab. Maciej Walczak Dr hab. Dariusz Wasyl, prof. nadz. Prof. dr hab. Grzegorz Węgrzyn Dr n. med. Iwona Wojciechowska-Koszko Dr hab. Agnieszka Wolna-Maruwka Dr Tomasz Wołkowicz Dr hab. Wiktoria Wróblewska, prof. SGH Dr Patrycja Zalas-Wiecek Dr Magdalena Zalewska Dr n. med. Dorota Żabicka Zakup numerów DOI dla publikowanych artykułów oraz profesjonalne tłumaczenie artykułów z języka polskiego na angielski – zadania finansowane w ramach umowy 659/P-DUN/2018 ze środków Ministerstwa Nauki i Szkolnictwa Wyższego przeznaczonych na działalność upowszechniających naukę. Wersja elektroniczna wydrukowanych w bieżącym zeszycie artykułów jest dostępna w archiwum internetowym czasopisma pod adresem: https://www.exeley.com/journal/advancements_of_microbiology ADVANCEMENTS OF MICROBIOLOGY – POSTĘPY MIKROBIOLOGII 2019, 58, 4, 367–373 DOI: 10.21307/PM–2019.58.4.367 AVOIDANCE OF MECHANISMS OF INNATE IMMUNE RESPONSE BY NEISSERIA GONORRHOEAE Jagoda Płaczkiewicz* Department of Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw Submitted in July, accepted in October 2019 Abstract: Neisseria gonorrhoeae (gonococcus) is a Gram-negative bacteria and an etiological agent of the sexually transmitted disease – gonorrhea. N. gonorrhoeae possesses many mechanism to evade the innate immune response of the human host. Most are related to serum resistance and avoidance of complement killing. However the clinical symptoms of gonorrhea are correlated with a significant pres- ence of neutrophils, whose response is also insufficient and modulated by gonococci. 1. Introduction. 2. Adherence ability. 3. Serum resistance and complement system. 4. Neutrophils. 4.1. Phagocytosis. 4.1.1. Oxygen- dependent intracellular killing. 4.1.2. Oxygen-independent intracellular killing. 4.2. Neutrophil extracellular traps. 4.3. Degranulation. 4.4. Apoptosis. 5. Summary UNIKANIE MECHANIZMÓW WRODZONEJ ODPOWIEDZI IMMUNOLOGICZNEJ PRZEZ NEISSERIA GONORRHOEAE Streszczenie: Neisseria gonorrhoeae (gonokok) to Gram-ujemna dwoinka będąca czynnikiem etiologicznym choroby przenoszonej drogą płciową – rzeżączki. N. gonorrhoeae posiada liczne mechanizmy umożliwiające jej unikanie wrodzonej odpowiedzi immunologicznej gospodarza. Większość z nich związana jest ze zdolnością gonokoków do manipulowania układem dopełniacza gospodarza oraz odpor- nością tej bakterii na surowicę. Jednakże symptomy infekcji N. gonorrhoeae wynikają między innymi z obecności licznych neutrofili, których aktywność jest modulowana przez gonokoki. 1. Wprowadzenie. 2. Zdolność adherencji. 3. Surowica i układ dopełniacza. 4. Neutrofile. 4.1. Fagocytoza. 4.1.1. Wewnątrzkomórkowe zabijanie zależne od tlenu. 4.1.2. Wewnątrzkomórkowe zabijanie niezależne od tlenu. 4.2. Neutrofilowe sieci zewnątrzkomórkowe. 4.3. Degranulacja. 4.4. Apoptoza. 5. Podsumowanie Key words: bacterial pathogenesis, inflammation, innate immune response Słowa kluczowe: bakteryjna patogeneza, stan zapalny, wrodzona odpowiedź immunologiczna 1. Introduction The crucial challenge related to gonorrhea treatment is increased multi-drug resistance of N. gonorrhoeae Nowadays, sexually transmitted infections (STIs) still [54]. What is more, there are problems with construct- remain a major global health problem with about 1 mil- ing an effective vaccine due to the highly antigenically lion of new cases of chlamydia, gonorrhea, trichomo- variable surface of these bacteria and lack of appro- niasis or syphilis daily [55]. However, in 2017 the World priate animal model of this disease, with the exception Health Organization qualified Neisseria gonorrhoeae, as of chimpanzees [20, 26]. Additionally, infection with the only etiological agent of STIs, among the “priority N. gonorrhoeae does not induce protective immunity pathogens” that pose the greatest threat to human health [12]. Hence it is crucial to understand the mechanisms because of antibiotic resistance [54]. In 2012, an esti- underlying the ability of gonococci to avoid the first mated 78 million new cases of gonorrhea caused by an line defence in the human host, which is the innate obligatory human pathogen N. gonorrhoeae (gonococ- immune response [26]. cus), occurred among 15–45 year-old patients world- wide [16, 55]. Gonococci infect a diverse array of human 2. Adherence ability mucosal surfaces,
Recommended publications
  • Novel Sulfolobus Virus with an Exceptional Capsid Architecture

    Novel Sulfolobus Virus with an Exceptional Capsid Architecture

    GENETIC DIVERSITY AND EVOLUTION crossm Novel Sulfolobus Virus with an Exceptional Capsid Architecture Haina Wang,a Zhenqian Guo,b Hongli Feng,b Yufei Chen,c Xiuqiang Chen,a Zhimeng Li,a Walter Hernández-Ascencio,d Xin Dai,a,f Zhenfeng Zhang,a Xiaowei Zheng,a Marielos Mora-López,d Yu Fu,a Chuanlun Zhang,e Ping Zhu,b,f Li Huanga,f aState Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China bNational Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China cState Key Laboratory of Marine Geology, Tongji University, Shanghai, China dCenter for Research in Cell and Molecular Biology, Universidad de Costa Rica, San José, Costa Rica eDepartment of Ocean Science and Engineering, South University of Science and Technology, Shenzhen, China fCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing, China ABSTRACT A novel archaeal virus, denoted Sulfolobus ellipsoid virus 1 (SEV1), was isolated from an acidic hot spring in Costa Rica. The morphologically unique virion of SEV1 contains a protein capsid with 16 regularly spaced striations and an 11-nm- thick envelope. The capsid exhibits an unusual architecture in which the viral DNA, probably in the form of a nucleoprotein filament, wraps around the longitudinal axis of the virion in a plane to form a multilayered disk-like structure with a central hole, and 16 of these structures are stacked to generate a spool-like capsid. SEV1 harbors a linear double-stranded DNA genome of ϳ23 kb, which encodes 38 predicted open reading frames (ORFs).
  • Elisabeth Mendes Martins De Moura Diversidade De Vírus DNA

    Elisabeth Mendes Martins De Moura Diversidade De Vírus DNA

    Elisabeth Mendes Martins de Moura Diversidade de vírus DNA autóctones e alóctones de mananciais e de esgoto da região metropolitana de São Paulo Tese apresentada ao Programa de Pós- Graduação em Microbiologia do Instituto de Ciências Biomédicas da Universidade de São Paulo, para obtenção do Titulo de Doutor em Ciências. Área de concentração: Microbiologia Orienta: Prof (a). Dr (a). Dolores Ursula Mehnert versão original São Paulo 2017 RESUMO MOURA, E. M. M. Diversidade de vírus DNA autóctones e alóctones de mananciais e de esgoto da região metropolitana de São Paulo. 2017. 134f. Tese (Doutorado em Microbiologia) - Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, 2017. A água doce no Brasil, assim como o seu consumo é extremamente importante para as diversas atividades criadas pelo ser humano. Por esta razão o consumo deste bem é muito grande e consequentemente, provocando o seu impacto. Os mananciais são normalmente usados para abastecimento doméstico, comercial, industrial e outros fins. Os estudos na área de ecologia de micro-organismos nos ecossistemas aquáticos (mananciais) e em esgotos vêm sendo realizados com mais intensidade nos últimos anos. Nas últimas décadas foi introduzido o conceito de virioplâncton com base na abundância e diversidade de partículas virais presentes no ambiente aquático. O virioplâncton influencia muitos processos ecológicos e biogeoquímicos, como ciclagem de nutriente, taxa de sedimentação de partículas, diversidade e distribuição de espécies de algas e bactérias, controle de florações de fitoplâncton e transferência genética horizontal. Os estudos nesta área da virologia molecular ainda estão muito restritos no país, bem como muito pouco se conhece sobre a diversidade viral na água no Brasil.
  • Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification

    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.
  • The LUCA and Its Complex Virome in Another Recent Synthesis, We Examined the Origins of the Replication and Structural Mart Krupovic , Valerian V

    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.
  • The Isolation of Viruses Infecting Archaea

    The Isolation of Viruses Infecting Archaea

    Portland State University PDXScholar Biology Faculty Publications and Presentations Biology 2010 The Isolation of Viruses Infecting Archaea Kenneth M. Stedman Portland State University Kate Porter Mike L. Dyall-Smith Follow this and additional works at: https://pdxscholar.library.pdx.edu/bio_fac Part of the Bacteria Commons, Biology Commons, and the Viruses Commons Let us know how access to this document benefits ou.y Citation Details Stedman, Kenneth M., Kate Porter, and Mike L. Dyall-Smith. "The isolation of viruses infecting Archaea." Manual of aquatic viral ecology. American Society for Limnology and Oceanography (ASLO) (2010): 57-64. This Article is brought to you for free and open access. It has been accepted for inclusion in Biology Faculty Publications and Presentations by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. MANUAL of MAVE Chapter 6, 2010, 57–64 AQUATIC VIRAL ECOLOGY © 2010, by the American Society of Limnology and Oceanography, Inc. The isolation of viruses infecting Archaea Kenneth M. Stedman1, Kate Porter2, and Mike L. Dyall-Smith3 1Department of Biology, Center for Life in Extreme Environments, Portland State University, P.O. Box 751, Portland, OR 97207, USA 2Biota Holdings Limited, 10/585 Blackburn Road, Notting Hill Victoria 3168, Australia 3Max Planck Institute of Biochemistry, Department of Membrane Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany Abstract A mere 50 viruses of Archaea have been reported to date; these have been investigated mostly by adapting methods used to isolate bacteriophages to the unique growth conditions of their archaeal hosts. The most numer- ous are viruses of thermophilic Archaea.
  • Virus–Host Interactions and Their Roles in Coral Reef Health and Disease

    Virus–Host Interactions and Their Roles in Coral Reef Health and Disease

    !"#$"%& Virus–host interactions and their roles in coral reef health and disease Rebecca Vega Thurber1, Jérôme P. Payet1,2, Andrew R. Thurber1,2 and Adrienne M. S. Correa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cycling. Last, we outline how marine viruses are an integral part of the reef system and suggest $4&$($4-(01.,/-1'-(+.(80%/#-#(+1(%--.(./1'$0+1(0#(&1(-##-1$0&,('+>3+1-1$(+.($4-#-(:,+"&,,9( 0>3+%$&1$(-180%+1>-1$#; To p - d ow n e f f e c t s Viruses infect all cellular life, including bacteria and evidence that macroorganisms play important parts in The ecological concept that eukaryotes, and contain ~200 megatonnes of carbon the dynamics of viroplankton; for example, sponges can organismal growth and globally1 — thus, they are integral parts of marine eco- filter and consume viruses6,7.
  • Supplementary Text S1

    Supplementary Text S1

    1 Supplementary Text S1 2 Dataset of reference viral genomes Viral genome sequences and taxonomic 3 information of viruses and their hosts are based on the GenomeNet/Virus-Host DB 4 (Mihara, et al., 2016). The Virus-Host DB covers viruses with complete genomes stored 5 in RefSeq/viral and GenBank. The sequence and taxonomic data are downloadable at 6 http://www.genome.jp/virushostdb/. Viral genome sequences and taxonomic 7 information used in ViPTree will be updated every few months following Virus-Host 8 DB updates. 9 Calculation of genomic similarity (SG) and proteomic tree The original Phage 10 Proteomic Tree (Rohwer and Edwards, 2002) tested multiple approaches and 11 parameters to calculate genomic distance for evaluation of compatibility between the 12 Phage Proteomic Tree and taxonomical system of the International Committee on 13 Taxonomy of Viruses. In contrast, ViPTree performs proteomic tree calculation based 14 on tBLASTx as reported previously by other several studies (Bellas, et al., 2015; 15 Bhunchoth, et al., 2016; Mizuno, et al., 2013). Specifically, normalized tBLASTx scores 16 (SG; 0 ≤ SG ≤ 1) between viral genomes are calculated as described (Bhunchoth, et al., 17 2016). For simple calculation of SG of segmented viruses, sequences of each segmented 18 viral genome were concatenated into one sequence by inserting a sequence of 100 19 ambiguous nucleotides (N) at each concatenation site. In addition, genome sequences 20 longer than 100 kb are split into each 100 kb fragment just for faster tBLASTx 21 calculation. Genomic distance is calculated as 1−SG. Proteomic tree generation is 22 performed by BIONJ (Gascuel, 1997) based on the genomic distance, using the R 23 package ‘Ape’.
  • On the Biological Success of Viruses

    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.
  • A Virus of Hyperthermophilic Archaea with a Unique Architecture Among DNA Viruses

    A Virus of Hyperthermophilic Archaea with a Unique Architecture Among DNA Viruses

    A virus of hyperthermophilic archaea with a unique architecture among DNA viruses Elena Ilka Rensena,1, Tomohiro Mochizukia,b,1, Emmanuelle Quemina, Stefan Schoutenc, Mart Krupovica,2, and David Prangishvilia,2 aDepartment of Microbiology, Institut Pasteur, 75015 Paris, France; bEarth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan; and cDepartment of Marine Organic Biogeochemistry, Royal Netherlands Institute for Sea Research, 1790 AB Den Burg, The Netherlands Edited by James L. Van Etten, University of Nebraska-Lincoln, Lincoln, NE, and approved January 19, 2016 (received for review September 23, 2015) Viruses package their genetic material in diverse ways. Most known shell consisting of two protein layers and an external envelope. strategies include encapsulation of nucleic acids into spherical or Our results provide new insights into the diversity of architec- filamentous virions with icosahedral or helical symmetry, respec- tural solutions used by filamentous viruses. tively. Filamentous viruses with dsDNA genomes are currently as- sociated exclusively with Archaea. Here, we describe a filamentous Results hyperthermophilic archaeal virus, Pyrobaculum filamentous virus 1 Virus and Host Isolation. From the environmental sample collected (PFV1), with a type of virion organization not previously observed at the Pozzuoli Solfatara, Italy, enrichment cultures were estab- in DNA viruses. The PFV1 virion, 400 ± 20 × 32 ± 3 nm, contains an lished in conditions known to favor the growth of aerobic mem- envelope and an inner core consisting of two structural units: a rod- bers of the archaeal genus Pyrobaculum (14). The virus-like particles shaped helical nucleocapsid formed of two 14-kDa major virion pro- (VLPs) were detected in the enrichment culture by transmission teins and a nucleocapsid-encompassing protein sheath composed electron microscopy (TEM).
  • Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements

    Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements

    Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280
  • Survey of High-Resolution Archaeal Virus Structures

    Survey of High-Resolution Archaeal Virus Structures

    Available online at www.sciencedirect.com ScienceDirect Survey of high-resolution archaeal virus structures 1 2 3,4 Ross Hartman , Jacob Munson-McGee , Mark J Young and 1,4 Charles Martin Lawrence Archaeal viruses exhibit diverse morphologies whose folds [5]. Of these, only 20 folds are known for the major structures are just beginning to be explored at high-resolution. capsid proteins (MCPs) of viruses [6,7]. Despite the genetic In this review, we update recent findings on archaeal structural diversity of viruses, their structural proteins, and especially proteins and virion architectures and place them in the their MCPs, fit within a limited number of groups. This biological context in which these viruses replicate. We limited number of common structural themes unite viruses conclude that many of the unusual structural features and across all three domains of life (Eukarya, Bacteria, and dynamics of archaeal viruses aid their replication and survival in Archaea) and evolutionary history [8]. Virion structure also the chemically harsh environments, in which they replicate. allows for insights into viral assembly, release, attachment, Furthermore, we should expect to find more novel features and entry by comparing well-characterized members of a from examining the high-resolution structures of additional structural lineage with less characterized members [9–11]. archaeal viruses. Our understanding of viruses that infect Archaea Addresses (archaeal viruses), lags far behind those infecting Bacte- 1 Department of Chemistry and Biochemistry, Montana State University, ria and Eukaryotes and we refer the reader to several Bozeman, MT, USA 2 excellent reviews on archaeal viruses [12–14]. Many Department of Microbiology and Immunology, Montana State archaeal viruses have unique morphologies [12,15–18].
  • Astrovirology: Viral Diversity and Ecology in Extreme Environments

    Astrovirology: Viral Diversity and Ecology in Extreme Environments

    Astrobiology Science Conference 2010 (2010) 5514.pdf ASTROVIROLOGY: VIRAL DIVERSITY AND ECOLOGY IN EXTREME ENVIRONMENTS. Geoffrey S. Diemer, Jennifer Kyle and Kenneth M. Stedman, Biology Department, Center for Life in Extreme Environments, Portland State University, P.O. Box 751, Portland, OR 97207-0751. [email protected]. We are investigating virus-host relationships and virus diversity in extreme-environment microbial eco- systems to understand the importance of viruses on primordial Earth. Boiling Springs Lake (BSL), located in Lassen Volcanic National Park, CA, U.S.A. is a large, acidic hotspring (pH 2.5, 55C-95C) supporting a microbial ecosystem comprised of Archaea, Bacteria and several species of unicellular Eukarya [1], [2]. BSL is thus an ideal environment for discovering viruses that infect extremophilic microorganisms from the major groups of cellular life. As no viruses of extremophilic eu- karyotes have yet been identified, study of BSL offers a unique opportunity for their discovery. BSL exhibits low pH and is predicted to precipitate the iron-bearing minerals jarosite and goethite. Both minerals have recently been detected in Martian soil by the Opportunity rover [3]. These minerals are posi- tively correlated with increased virus precipitation and binding to inorganic substrates. Thus, virus biosigna- tures may be present in BSL sediments. Recent bioinformatics research has identified so- called “virus hallmark genes” that are prevalent in large groups of viruses but have few, if any, cellular homologues. Analysis of this group of viral genes sug- gests that viruses have ancient, possibly pre-cellular origins [4]. In conjunction with the Broad Institute, we are generating a metavirome of ca.