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https://www.readbyqxmd.com/read/29784811/systematic-prediction-of-genes-functionally-linked-to-crispr-cas-systems-by-gene-neighborhood-analysis
#1
Sergey A Shmakov, Kira S Makarova, Yuri I Wolf, Konstantin V Severinov, Eugene V Koonin
The CRISPR-Cas systems of bacterial and archaeal adaptive immunity consist of direct repeat arrays separated by unique spacers and multiple CRISPR-associated ( cas ) genes encoding proteins that mediate all stages of the CRISPR response. In addition to the relatively small set of core cas genes that are typically present in all CRISPR-Cas systems of a given (sub)type and are essential for the defense function, numerous genes occur in CRISPR- cas loci only sporadically. Some of these have been shown to perform various ancillary roles in CRISPR response, but the functional relevance of most remains unknown...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29781801/methanonatronarchaeum-thermophilum-gen-nov-sp-nov-and-candidatus-methanohalarchaeum-thermophilum-extremely-halo-natrono-philic-methyl-reducing-methanogens-from-hypersaline-lakes-comprising-a-new-euryarchaeal-class-methanonatronarchaeia-classis-nov
#2
Dimitry Y Sorokin, Alexander Y Merkel, Ben Abbas, Kira S Makarova, W Irene C Rijpstra, M Koenen, Jaap S Sinninghe Damsté, Erwin A Galinski, Eugene V Koonin, Mark C M van Loosdrecht
Methanogenic enrichments from hypersaline lakes at moderate thermophilic conditions have resulted in the cultivation of an unknown deep lineage of euryarchaeota related to the class Halobacteria. Eleven soda lake isolates and three salt lake enrichment cultures were methyl-reducing methanogens that utilize C1 methylated compounds as electron acceptors and H2 or formate as electron donors, but they were unable to grow on either substrates alone or to form methane from acetate. They are extreme halophiles, growing optimally at 4 M total Na+ and the first representatives of methanogens employing the 'salt-in' osmoprotective mechanism...
May 21, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29757994/bioinformatics-meets-virology-the-european-virus-bioinformatics-center-s-second-annual-meeting
#3
Bashar Ibrahim, Ksenia Arkhipova, Arno C Andeweg, Susana Posada-Céspedes, François Enault, Arthur Gruber, Eugene V Koonin, Anne Kupczok, Philippe Lemey, Alice C McHardy, Dino P McMahon, Brett E Pickett, David L Robertson, Richard H Scheuermann, Alexandra Zhernakova, Mark P Zwart, Alexander Schönhuth, Bas E Dutilh, Manja Marz
The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions...
May 14, 2018: Viruses
https://www.readbyqxmd.com/read/29680923/taxonomy-of-the-family-arenaviridae-and-the-order-bunyavirales-update-2018
#4
Piet Maes, Sergey V Alkhovsky, Yīmíng Bào, Martin Beer, Monica Birkhead, Thomas Briese, Michael J Buchmeier, Charles H Calisher, Rémi N Charrel, Il Ryong Choi, Christopher S Clegg, Juan Carlos de la Torre, Eric Delwart, Joseph L DeRisi, Patrick L Di Bello, Francesco Di Serio, Michele Digiaro, Valerian V Dolja, Christian Drosten, Tobiasz Z Druciarek, Jiang Du, Hideki Ebihara, Toufic Elbeaino, Rose C Gergerich, Amethyst N Gillis, Jean-Paul J Gonzalez, Anne-Lise Haenni, Jussi Hepojoki, Udo Hetzel, Thiện Hồ, Ní Hóng, Rakesh K Jain, Petrus Jansen van Vuren, Qi Jin, Miranda Gilda Jonson, Sandra Junglen, Karen E Keller, Alan Kemp, Anja Kipar, Nikola O Kondov, Eugene V Koonin, Richard Kormelink, Yegor Korzyukov, Mart Krupovic, Amy J Lambert, Alma G Laney, Matthew LeBreton, Igor S Lukashevich, Marco Marklewitz, Wanda Markotter, Giovanni P Martelli, Robert R Martin, Nicole Mielke-Ehret, Hans-Peter Mühlbach, Beatriz Navarro, Terry Fei Fan Ng, Márcio Roberto Teixeira Nunes, Gustavo Palacios, Janusz T Pawęska, Clarence J Peters, Alexander Plyusnin, Sheli R Radoshitzky, Víctor Romanowski, Pertteli Salmenperä, Maria S Salvato, Hélène Sanfaçon, Takahide Sasaya, Connie Schmaljohn, Bradley S Schneider, Yukio Shirako, Stuart Siddell, Tarja A Sironen, Mark D Stenglein, Nadia Storm, Harikishan Sudini, Robert B Tesh, Ioannis E Tzanetakis, Mangala Uppala, Olli Vapalahti, Nikos Vasilakis, Peter J Walker, Guópíng Wáng, Lìpíng Wáng, Yànxiăng Wáng, Tàiyún Wèi, Michael R Wiley, Yuri I Wolf, Nathan D Wolfe, Zhìqiáng Wú, Wénxìng Xú, Li Yang, Zuòkūn Yāng, Shyi-Dong Yeh, Yǒng-Zhèn Zhāng, Yàzhōu Zhèng, Xueping Zhou, Chénxī Zhū, Florian Zirkel, Jens H Kuhn
In 2018, the family Arenaviridae was expanded by inclusion of 1 new genus and 5 novel species. At the same time, the recently established order Bunyavirales was expanded by 3 species. This article presents the updated taxonomy of the family Arenaviridae and the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.
April 21, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29668953/evolution-of-genome-architecture-in-archaea-spontaneous-generation-of-a-new-chromosome-in-haloferax-volcanii
#5
Darya Ausiannikava, Laura Mitchell, Hannah Marriott, Victoria Smith, Michelle Hawkins, Kira S Makarova, Eugene V Koonin, Conrad A Nieduszynski, Thorsten Allers
The common ancestry of archaea and eukaryotes is evident in their genome architecture. All eukaryotic and several archaeal genomes consist of multiple chromosomes, each replicated from multiple origins. Three scenarios have been proposed for the evolution of this genome architecture: (1) mutational diversification of a multi-copy chromosome; (2) capture of a new chromosome by horizontal transfer; (3) acquisition of new origins and splitting into two replication-competent chromosomes. We report an example of the third scenario: the multi-origin chromosome of the archaeon Haloferax volcanii has split into two elements via homologous recombination...
April 16, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29652909/estimation-of-universal-and-taxon-specific-parameters-of-prokaryotic-genome-evolution
#6
Itamar Sela, Yuri I Wolf, Eugene V Koonin
The results of our recent study on mathematical modeling of microbial genome evolution indicate that, on average, genomes of bacteria and archaea evolve in the regime of mutation-selection balance defined by positive selection coefficients associated with gene acquisition that is counter-acted by the intrinsic deletion bias. This analysis was based on the strong assumption that parameters of genome evolution are universal across the diversity of bacteria and archaea, and yielded extremely low values of the selection coefficient...
2018: PloS One
https://www.readbyqxmd.com/read/29618642/-ortervirales-a-new-viral-order-unifying-five-families-of-reverse-transcribing-viruses
#7
Mart Krupovic, Jonas Blomberg, John M Coffin, Indranil Dasgupta, Hung Fan, Andrew D Geering, Robert Gifford, Balázs Harrach, Roger Hull, Welkin Johnson, Jan F Kreuze, Dirk Lindemann, Carlos Llorens, Ben Lockhart, Jens Mayer, Emmanuelle Muller, Neil Olszewski, Hanu R Pappu, Mikhail Pooggin, Katja R Richert-Pöggeler, Sead Sabanadzovic, Hélène Sanfaçon, James E Schoelz, Susan Seal, Livia Stavolone, Jonathan P Stoye, Pierre-Yves Teycheney, Michael Tristem, Eugene V Koonin, Jens H Kuhn
Reverse-transcribing viruses, which synthesize a copy of genomic DNA from an RNA template, are widespread in animals, plants, algae and fungi (1, 2).….
April 4, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29570363/pharmacist-views-on-alternative-methods-for-antiviral-distribution-and-dispensing-during-an-influenza-pandemic
#8
Gillian K SteelFisher, John M Benson, Hannah Caporello, Lisa M Koonin, Anita Patel, Eran Ben-Porath, Robert J Blendon
Antiviral drugs are likely to be a frontline countermeasure needed to minimize disease impact during an influenza pandemic. As part of pandemic influenza preparedness efforts, the Centers for Disease Control and Prevention, in coordination with state health departments, has plans in place to distribute and dispense antiviral drugs from public stockpiles. These plans are currently under review and include evaluation of the benefits of commercial distribution and dispensing through community pharmacies. To ensure this alternative distribution and dispensing system is viable, it is critical to assess pharmacist acceptability and to understand the pharmacist perspective on dispensing these antivirals during a response...
March 23, 2018: Health Security
https://www.readbyqxmd.com/read/29551514/cas13d-is-a-compact-rna-targeting-type-vi-crispr-effector-positively-modulated-by-a-wyl-domain-containing-accessory-protein
#9
Winston X Yan, Shaorong Chong, Huaibin Zhang, Kira S Makarova, Eugene V Koonin, David R Cheng, David A Scott
Bacterial class 2 CRISPR-Cas systems utilize a single RNA-guided protein effector to mitigate viral infection. We aggregated genomic data from multiple sources and constructed an expanded database of predicted class 2 CRISPR-Cas systems. A search for novel RNA-targeting systems identified subtype VI-D, encoding dual HEPN domain-containing Cas13d effectors and putative WYL-domain-containing accessory proteins (WYL1 and WYL-b1 through WYL-b5). The median size of Cas13d proteins is 190 to 300 aa smaller than that of Cas13a-Cas13c...
April 19, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29507349/anti-crispr-proteins-encoded-by-archaeal-lytic-viruses-inhibit-subtype-i-d-immunity
#10
Fei He, Yuvaraj Bhoobalan-Chitty, Lan B Van, Anders L Kjeldsen, Matteo Dedola, Kira S Makarova, Eugene V Koonin, Ditlev E Brodersen, Xu Peng
Viruses employ a range of strategies to counteract the prokaryotic adaptive immune system, clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas), including mutational escape and physical blocking of enzymatic function using anti-CRISPR proteins (Acrs). Acrs have been found in many bacteriophages but so far not in archaeal viruses, despite the near ubiquity of CRISPR-Cas systems in archaea. Here, we report the functional and structural characterization of two archaeal Acrs from the lytic rudiviruses, SIRV2 and SIRV3...
April 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29433650/metaviromics-a-tectonic-shift-in-understanding-virus-evolution
#11
EDITORIAL
Eugene V Koonin, Valerian V Dolja
No abstract text is available yet for this article.
February 15, 2018: Virus Research
https://www.readbyqxmd.com/read/29360740/proteomic-analysis-of-methanonatronarchaeum-thermophilum-amet1-a-representative-of-a-putative-new-class-of-euryarchaeota-methanonatronarchaeia
#12
Manuel Ferrer, Dimitry Y Sorokin, Yuri I Wolf, Sergio Ciordia, María C Mena, Rafael Bargiela, Eugene V Koonin, Kira S Makarova
The recently discovered Methanonatronarchaeia are extremely halophilic and moderately thermophilic methyl-reducing methanogens representing a novel class-level lineage in the phylum Euryarchaeota related to the class Halobacteria. Here we present a detailed analysis of 1D-nano liquid chromatography-electrospray ionization tandem mass spectrometry data obtained for "Methanonatronarchaeum thermophilum" AMET1 grown in different physiological conditions, including variation of the growth temperature and substrates...
January 23, 2018: Genes
https://www.readbyqxmd.com/read/29208747/proposed-role-for-kaic-like-atpases-as-major-signal-transduction-hubs-in-archaea
#13
Kira S Makarova, Michael Y Galperin, Eugene V Koonin
All organisms must adapt to ever-changing environmental conditions and accordingly have evolved diverse signal transduction systems. In bacteria, the most abundant networks are built around the two-component signal transduction systems that include histidine kinases and receiver domains. In contrast, eukaryotic signal transduction is dominated by serine/threonine/tyrosine protein kinases. Both of these systems are also found in archaea, but they are not as common and diversified as their bacterial and eukaryotic counterparts, suggesting the possibility that archaea have evolved other, still uncharacterized signal transduction networks...
December 5, 2017: MBio
https://www.readbyqxmd.com/read/29202832/inevitability-of-the-emergence-and-persistence-of-genetic-parasites-caused-by-evolutionary-instability-of-parasite-free-states
#14
Eugene V Koonin, Yuri I Wolf, Mikhail I Katsnelson
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...
December 4, 2017: Biology Direct
https://www.readbyqxmd.com/read/29191215/domestication-of-self-splicing-introns-during-eukaryogenesis-the-rise-of-the-complex-spliceosomal-machinery
#15
REVIEW
Julian Vosseberg, Berend Snel
ᅟ: The spliceosome is a eukaryote-specific complex that is essential for the removal of introns from pre-mRNA. It consists of five small nuclear RNAs (snRNAs) and over a hundred proteins, making it one of the most complex molecular machineries. Most of this complexity has emerged during eukaryogenesis, a period that is characterised by a drastic increase in cellular and genomic complexity. Although not fully resolved, recent findings have started to shed some light on how and why the spliceosome originated...
December 1, 2017: Biology Direct
https://www.readbyqxmd.com/read/29179671/phylogenomics-of-cas4-family-nucleases
#16
Sanjarbek Hudaiberdiev, Sergey Shmakov, Yuri I Wolf, Michael P Terns, Kira S Makarova, Eugene V Koonin
BACKGROUND: The Cas4 family endonuclease is a component of the adaptation module in many variants of CRISPR-Cas adaptive immunity systems. Unlike most of the other Cas proteins, Cas4 is often encoded outside CRISPR-cas loci (solo-Cas4) and is also found in mobile genetic elements (MGE-Cas4). RESULTS: As part of our ongoing investigation of CRISPR-Cas evolution, we explored the phylogenomics of the Cas4 family. About 90% of the archaeal genomes encode Cas4 compared to only about 20% of the bacterial genomes...
November 28, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29175107/viruses-of-archaea-structural-functional-environmental-and-evolutionary-genomics
#17
REVIEW
Mart Krupovic, Virginija Cvirkaite-Krupovic, Jaime Iranzo, David Prangishvili, Eugene V Koonin
Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among viruses of bacteria or eukaryotes. The uniqueness of the virion morphologies is matched by the distinctiveness of the genomes of these viruses, with ∼75% of genes encoding unique proteins, refractory to functional annotation based on sequence analyses. In this review, we summarize the state-of-the-art knowledge on various aspects of archaeal virus genomics...
January 15, 2018: Virus Research
https://www.readbyqxmd.com/read/29133882/discovery-of-an-expansive-bacteriophage-family-that-includes-the-most-abundant-viruses-from-the-human-gut
#18
Natalya Yutin, Kira S Makarova, Ayal B Gussow, Mart Krupovic, Anca Segall, Robert A Edwards, Eugene V Koonin
Metagenomic sequence analysis is rapidly becoming the primary source of virus discovery1-3 . A substantial majority of the currently available virus genomes come from metagenomics, and some of these represent extremely abundant viruses, even if never grown in the laboratory. A particularly striking case of a virus discovered via metagenomics is crAssphage, which is by far the most abundant human-associated virus known, comprising up to 90% of sequences in the gut virome4 . Over 80% of the predicted proteins encoded in the approximately 100 kilobase crAssphage genome showed no significant similarity to available protein sequences, precluding classification of this virus and hampering further study...
January 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29132422/cellular-origin-of-the-viral-capsid-like-bacterial-microcompartments
#19
Mart Krupovic, Eugene V Koonin
ᅟ: Bacterial microcompartments (BMC) are proteinaceous organelles that structurally resemble viral capsids, but encapsulate enzymes that perform various specialized biochemical reactions in the cell cytoplasm. The BMC are constructed from two major shell proteins, BMC-H and BMC-P, which form the facets and vertices of the icosahedral assembly, and are functionally equivalent to the major and minor capsid proteins of viruses, respectively. This equivalence notwithstanding, neither of the BMC proteins displays structural similarity to known capsid proteins, rendering the origins of the BMC enigmatic...
November 13, 2017: Biology Direct
https://www.readbyqxmd.com/read/29123227/the-enigmatic-archaeal-virosphere
#20
REVIEW
David Prangishvili, Dennis H Bamford, Patrick Forterre, Jaime Iranzo, Eugene V Koonin, Mart Krupovic
One of the most prominent features of archaea is the extraordinary diversity of their DNA viruses. Many archaeal viruses differ substantially in morphology from bacterial and eukaryotic viruses and represent unique virus families. The distinct nature of archaeal viruses also extends to the gene composition and architectures of their genomes and the properties of the proteins that they encode. Environmental research has revealed prominent roles of archaeal viruses in influencing microbial communities in ocean ecosystems, and recent metagenomic studies have uncovered new groups of archaeal viruses that infect extremophiles and mesophiles in diverse habitats...
November 10, 2017: Nature Reviews. Microbiology
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