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https://www.readbyqxmd.com/read/28928211/the-crispr-spacer-space-is-dominated-by-sequences-from-species-specific-mobilomes
#1
Sergey A Shmakov, Vassilii Sitnik, Kira S Makarova, Yuri I Wolf, Konstantin V Severinov, Eugene V Koonin
Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR "dark matter." We performed a comprehensive analysis of the spacers from all CRISPR-cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average)...
September 19, 2017: MBio
https://www.readbyqxmd.com/read/28853922/origin-and-evolution-of-the-universal-genetic-code
#2
Eugene V Koonin, Artem S Novozhilov
The standard genetic code (SGC) is virtually universal among extant life forms. Although many deviations from the universal code exist, particularly in organelles and prokaryotes with small genomes, they are limited in scope and obviously secondary. The universality of the code likely results from the combination of a frozen accident, i.e., the deleterious effect of codon reassignment in the SGC, and the inhibitory effect of changes in the code on horizontal gene transfer. The structure of the SGC is nonrandom and ensures high robustness of the code to mutational and translational errors...
August 30, 2017: Annual Review of Genetics
https://www.readbyqxmd.com/read/28851439/on-the-global-crispr-array-behavior-in-class-i-systems
#3
Alice Toms, Rodolphe Barrangou
BACKGROUND: Much effort is underway to build and upgrade databases and tools related to occurrence, diversity, and characterization of CRISPR-Cas systems. As microbial communities and their genome complements are unearthed, much emphasis has been placed on details of individual strains and model systems within the CRISPR-Cas classification, and that collection of information as a whole affords the opportunity to analyze CRISPR-Cas systems from a quantitative perspective to gain insight into distribution of CRISPR array sizes across the different classes, types and subtypes...
August 29, 2017: Biology Direct
https://www.readbyqxmd.com/read/28811374/recruitment-of-crispr-cas-systems-by-tn7-like-transposons
#4
Joseph E Peters, Kira S Makarova, Sergey Shmakov, Eugene V Koonin
A survey of bacterial and archaeal genomes shows that many Tn7-like transposons contain minimal type I-F CRISPR-Cas systems that consist of fused cas8f and cas5f, cas7f, and cas6f genes and a short CRISPR array. Several small groups of Tn7-like transposons encompass similarly truncated type I-B CRISPR-Cas. This minimal gene complement of the transposon-associated CRISPR-Cas systems implies that they are competent for pre-CRISPR RNA (precrRNA) processing yielding mature crRNAs and target binding but not target cleavage that is required for interference...
August 29, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28722509/adaptation-of-mrna-structure-to-control-protein-folding
#5
Guilhem Faure, Aleksey Y Ogurtsov, Svetlana A Shabalina, Eugene V Koonin
Comparison of mRNA and protein structures shows that highly structured mRNAs typically encode compact protein domains suggesting that mRNA structure controls protein folding. This function is apparently performed by distinct structural elements in the mRNA, which implies 'fine tuning' of mRNA structure under selection for optimal protein folding. We find that, during evolution, changes in the mRNA folding energy follow amino acid replacements, reinforcing the notion of an intimate connection between the structures of a mRNA and the protein it encodes, and the double encoding of protein sequence and folding in the mRNA...
July 19, 2017: RNA Biology
https://www.readbyqxmd.com/read/28698278/on-the-origin-of-reverse-transcriptase-using-crispr-cas-systems-and-their-hyperdiverse-enigmatic-spacer-repertoires
#6
Sukrit Silas, Kira S Makarova, Sergey Shmakov, David Páez-Espino, Georg Mohr, Yi Liu, Michelle Davison, Simon Roux, Siddharth R Krishnamurthy, Becky Xu Hua Fu, Loren L Hansen, David Wang, Matthew B Sullivan, Andrew Millard, Martha R Clokie, Devaki Bhaya, Alan M Lambowitz, Nikos C Kyrpides, Eugene V Koonin, Andrew Z Fire
Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains...
July 11, 2017: MBio
https://www.readbyqxmd.com/read/28672161/polintons-virophages-and-transpovirons-a-tangled-web-linking-viruses-transposons-and-immunity
#7
REVIEW
Eugene V Koonin, Mart Krupovic
Virophages are satellite DNA viruses that depend for their replication on giant viruses of the family Mimiviridae. An evolutionary relationship exists between the virophages and Polintons, large self-synthesizing transposons that are wide spread in the genomes of diverse eukaryotes. Most of the Polintons encode homologs of major and minor icosahedral virus capsid proteins and accordingly are predicted to form virions. Additionally, metagenome analysis has led to the discovery of an expansive family of Polinton-like viruses (PLV) that are more distantly related to bona fide Polintons and virophages...
June 30, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/28657885/evolutionary-genomics-of-defense-systems-in-archaea-and-bacteria
#8
Eugene V Koonin, Kira S Makarova, Yuri I Wolf
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...
June 28, 2017: Annual Review of Microbiology
https://www.readbyqxmd.com/read/28652353/disentangling-the-effects-of-selection-and-loss-bias-on-gene-dynamics
#9
Jaime Iranzo, José A Cuesta, Susanna Manrubia, Mikhail I Katsnelson, Eugene V Koonin
We combine mathematical modeling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different functional classes of genes and mobile genetic elements (MGE). An exact solution for the dynamics of gene family size was obtained under a linear duplication-transfer-loss model with selection. With the exception of genes involved in information processing, particularly translation, which are maintained by strong selection, the average selection coefficient for most nonparasitic genes is low albeit positive, compatible with observed positive correlation between genome size and effective population size...
July 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28605718/diversity-classification-and-evolution-of-crispr-cas-systems
#10
REVIEW
Eugene V Koonin, Kira S Makarova, Feng Zhang
The bacterial and archaeal CRISPR-Cas systems of adaptive immunity show remarkable diversity of protein composition, effector complex structure, genome locus architecture and mechanisms of adaptation, pre-CRISPR (cr)RNA processing and interference. The CRISPR-Cas systems belong to two classes, with multi-subunit effector complexes in Class 1 and single-protein effector modules in Class 2. Concerted genomic and experimental efforts on comprehensive characterization of Class 2 CRISPR-Cas systems led to the identification of two new types and several subtypes...
June 9, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28572664/mapping-refrigerant-gases-in-the-new-york-city-skyline
#11
Masoud Ghandehari, Milad Aghamohamadnia, Gregory Dobler, Andreas Karpf, Kerry Buckland, Jun Qian, Steven Koonin
Cities are now home to more than 50% of the world's population and emit large quantities of pollutants from sources such as fossil fuel combustion and the leakage of refrigerants. We demonstrate the utility of persistent synoptic longwave hyperspectral imaging to study the ongoing leakage of refrigerant gases in New York City, compounds that either deplete the stratosphere ozone or have significant global warming potential. In contrast to current monitoring programs that are based on country-level reporting or aggregate measures of emissions, we present the identification of gaseous plumes with high spatial and temporal granularity in real-time over the skyline of Manhattan...
June 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28555626/discovery-of-extremely-halophilic-methyl-reducing-euryarchaea-provides-insights-into-the-evolutionary-origin-of-methanogenesis
#12
Dimitry Y Sorokin, Kira S Makarova, Ben Abbas, Manuel Ferrer, Peter N Golyshin, Erwin A Galinski, Sergio Ciordia, María Carmen Mena, Alexander Y Merkel, Yuri I Wolf, Mark C M van Loosdrecht, Eugene V Koonin
Methanogenic archaea are major players in the global carbon cycle and in the biotechnology of anaerobic digestion. The phylum Euryarchaeota includes diverse groups of methanogens that are interspersed with non-methanogenic lineages. So far, methanogens inhabiting hypersaline environments have been identified only within the order Methanosarcinales. We report the discovery of a deep phylogenetic lineage of extremophilic methanogens in hypersaline lakes and present analysis of two nearly complete genomes from this group...
May 30, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28545555/the-complex-domain-architecture-of-samd9-family-proteins-predicted-stand-like-ntpases-suggests-new-links-to-inflammation-and-apoptosis
#13
Sergei L Mekhedov, Kira S Makarova, Eugene V Koonin
We report a comprehensive computational dissection of the domain architecture of the SAMD9 family proteins that are involved in antivirus and antitumor response in humans. We show that the SAMD9 protein family is represented in most animals and also, unexpectedly, in bacteria, in particular actinomycetes. From the N to C terminus, the core SAMD9 family architecture includes DNA/RNA-binding AlbA domain, a variant Sir2-like domain, a STAND-like P-loop NTPase, an array of TPR repeats and an OB-fold domain with predicted RNA-binding properties...
May 25, 2017: Biology Direct
https://www.readbyqxmd.com/read/28545255/frozen-accident-pushing-50-stereochemistry-expansion-and-chance-in-the-evolution-of-the-genetic-code
#14
Eugene V Koonin
Nearly 50 years ago, Francis Crick propounded the frozen accident scenario for the evolution of the genetic code along with the hypothesis that the early translation system consisted primarily of RNA. Under the frozen accident perspective, the code is universal among modern life forms because any change in codon assignment would be highly deleterious. The frozen accident can be considered the default theory of code evolution because it does not imply any specific interactions between amino acids and the cognate codons or anticodons, or any particular properties of the code...
May 23, 2017: Life
https://www.readbyqxmd.com/read/28544876/principles-of-systems-biology-no-17
#15
(no author information available yet)
This month: understanding spatial arrangements (Süel/Laue/Schweisguth/de Lorenzo), a giant virus sheds light on evolution (Koonin), synthetic systems (Comtet, Wang, Pósfai), and omics tools (Siuzdak, Kim).
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28514948/demystification-of-animal-symmetry-symmetry-is-a-response-to-mechanical-forces
#16
Gábor Holló
ᅟ: Symmetry is an eye-catching feature of animal body plans, yet its causes are not well enough understood. The evolution of animal form is mainly due to changes in gene regulatory networks (GRNs). Based on theoretical considerations regarding fundamental GRN properties, it has recently been proposed that the animal genome, on large time scales, should be regarded as a system which can construct both the main symmetries - radial and bilateral - simultaneously; and that the expression of any of these depends on functional constraints...
May 17, 2017: Biology Direct
https://www.readbyqxmd.com/read/28472712/casposons-mobile-genetic-elements-that-gave-rise-to-the-crispr-cas-adaptation-machinery
#17
REVIEW
Mart Krupovic, Pierre Béguin, Eugene V Koonin
A casposon, a member of a distinct superfamily of archaeal and bacterial self-synthesizing transposons that employ a recombinase (casposase) homologous to the Cas1 endonuclease, appears to have given rise to the adaptation module of CRISPR-Cas systems as well as the CRISPR repeats themselves. Comparison of the mechanistic features of the reactions catalyzed by the casposase and the Cas1-Cas2 heterohexamer, the CRISPR integrase, reveals close similarity but also important differences that explain the requirement of Cas2 for integration of short DNA fragments, the CRISPR spacers...
May 1, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28457865/novel-abundant-oceanic-viruses-of-uncultured-marine-group-ii-euryarchaeota
#18
Alon Philosof, Natalya Yutin, José Flores-Uribe, Itai Sharon, Eugene V Koonin, Oded Béjà
Marine group II Euryarchaeota (MG-II) are among the most abundant microbes in oceanic surface waters [1-4]. So far, however, representatives of MG-II have not been cultivated, and no viruses infecting these organisms have been described. Here, we present complete genomes for three distinct groups of viruses assembled from metagenomic sequence datasets highly enriched for MG-II. These novel viruses, which we denote magroviruses, possess double-stranded DNA genomes of 65 to 100 kilobases in size that encode a structural module characteristic of head-tailed viruses and, unusually for archaeal and bacterial viruses, a nearly complete replication apparatus of apparent archaeal origin...
May 8, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28451057/a-network-perspective-on-the-virus-world
#19
COMMENT
Jaime Iranzo, Mart Krupovic, Eugene V Koonin
Viral evolution is characterized by high rates of horizontal gene transfer and fast sequence divergence. Furthermore, there are no universal genes shared by all viruses. As a result, distant relationships among viruses are better represented by a network than by a tree. Here we discuss 3 network representations of the virus world with decreasing levels of complexity, from a multilayer network that integrates sequence conservation and patterns of gene sharing to a classic genome similarity network. As new tools for network analysis are developed, we expect that novel insights into virus evolution will result from the study of more complex representations of the virus world...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28408723/nucleic-acid-detection-with-crispr-cas13a-c2c2
#20
Jonathan S Gootenberg, Omar O Abudayyeh, Jeong Wook Lee, Patrick Essletzbichler, Aaron J Dy, Julia Joung, Vanessa Verdine, Nina Donghia, Nichole M Daringer, Catherine A Freije, Cameron Myhrvold, Roby P Bhattacharyya, Jonathan Livny, Aviv Regev, Eugene V Koonin, Deborah T Hung, Pardis C Sabeti, James J Collins, Feng Zhang
Rapid, inexpensive, and sensitive nucleic acid detection may aid point-of-care pathogen detection, genotyping, and disease monitoring. The RNA-guided, RNA-targeting clustered regularly interspaced short palindromic repeats (CRISPR) effector Cas13a (previously known as C2c2) exhibits a "collateral effect" of promiscuous ribonuclease activity upon target recognition. We combine the collateral effect of Cas13a with isothermal amplification to establish a CRISPR-based diagnostic (CRISPR-Dx), providing rapid DNA or RNA detection with attomolar sensitivity and single-base mismatch specificity...
April 28, 2017: Science
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