Search

Your search keyword '"Yutin, Natalya"' showing total 325 results
Start Over Author "Yutin, Natalya"
325 results on '"Yutin, Natalya"'

2. Updated Virophage Taxonomy and Distinction from Polinton-like Viruses.

Author

Roux, Simon, Fischer, Matthias G, Hackl, Thomas, Katz, Laura A, Schulz, Frederik, and Yutin, Natalya

Subjects
Humans, Viruses, Phylogeny, Genome, Viral, Eukaryota, Virophages, giant virus, polinton, polintovirus, virophage, virus taxonomy, Genetics, Human Genome, Biotechnology, Infectious Diseases, Aetiology, 2.2 Factors relating to the physical environment, Infection, Biochemistry and Cell Biology
Abstract

Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of "hyperparasitism" in the viral world. While only a handful of virophages have been isolated, a vast diversity of virophage-like sequences have been uncovered from diverse metagenomes. Their wide ecological distribution, idiosyncratic infection and replication strategy, ability to integrate into protist and giant virus genomes and potential role in antiviral defense have made virophages a topic of broad interest. However, one limitation for further studies is the lack of clarity regarding the nomenclature and taxonomy of this group of viruses. Specifically, virophages have been linked in the literature to other "virophage-like" mobile genetic elements and viruses, including polinton-like viruses (PLVs), but there are no formal demarcation criteria and proper nomenclature for either group, i.e., virophage or PLVs. Here, as part of the ICTV Virophage Study Group, we leverage a large set of genomes gathered from published datasets as well as newly generated protist genomes to propose delineation criteria and classification methods at multiple taxonomic ranks for virophages 'sensu stricto', i.e., genomes related to the prototype isolates Sputnik and mavirus. Based on a combination of comparative genomics and phylogenetic analyses, we show that this group of virophages forms a cohesive taxon that we propose to establish at the class level and suggest a subdivision into four orders and seven families with distinctive ecogenomic features. Finally, to illustrate how the proposed delineation criteria and classification method would be used, we apply these to two recently published datasets, which we show include both virophages and other virophage-related elements. Overall, we see this proposed classification as a necessary first step to provide a robust taxonomic framework in this area of the virosphere, which will need to be expanded in the future to cover other virophage-related viruses such as PLVs.

Published
2023

7. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author

Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-Bum, Malmstrom, Rex R, Martinez-Garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-Espino, David, Petit, Marie-Agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-Valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, and Eloe-Fadrosh, Emiley A

Subjects
Microbiology, Biological Sciences, Genetics, Human Genome, Databases, Genetic, Genome, Viral, Genomics, Virus Cultivation, Viruses
Abstract

We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.

Published
2019

8. Giant viruses with an expanded complement of translation system components

Author

Schulz, Frederik, Yutin, Natalya, Ivanova, Natalia N, Ortega, Davi R, Lee, Tae Kwon, Vierheilig, Julia, Daims, Holger, Horn, Matthias, Wagner, Michael, Jensen, Grant J, Kyrpides, Nikos C, Koonin, Eugene V, and Woyke, Tanja

Subjects
Microbiology, Biological Sciences, Genetics, 2.2 Factors relating to the physical environment, Amino Acyl-tRNA Synthetases, Austria, Genome, Viral, Giant Viruses, Metagenomics, Phylogeny, Protein Biosynthesis, Wastewater, General Science & Technology
Abstract

The discovery of giant viruses blurred the sharp division between viruses and cellular life. Giant virus genomes encode proteins considered as signatures of cellular organisms, particularly translation system components, prompting hypotheses that these viruses derived from a fourth domain of cellular life. Here we report the discovery of a group of giant viruses (Klosneuviruses) in metagenomic data. Compared with other giant viruses, the Klosneuviruses encode an expanded translation machinery, including aminoacyl transfer RNA synthetases with specificities for all 20 amino acids. Notwithstanding the prevalence of translation system components, comprehensive phylogenomic analysis of these genes indicates that Klosneuviruses did not evolve from a cellular ancestor but rather are derived from a much smaller virus through extensive gain of host genes.

Published
2017

11. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, Jens H., Adkins, Scott, Alioto, Daniela, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Anthony, Simon J., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Bartonička, Tomáš, Basler, Christopher, Bavari, Sina, Beer, Martin, Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol, Blasdell, Kim R., Bradfute, Steven B., Breyta, Rachel, Briese, Thomas, Brown, Paul A., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Buzkan, Nihal, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chamberlain, John, Chandran, Kartik, Charrel, Rémi N., Chen, Biao, Chiumenti, Michela, Choi, Il-Ryong, Clegg, J. Christopher S., Crozier, Ian, da Graça, John V., Dal Bó, Elena, Dávila, Alberto M. R., de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L., Di Bello, Patrick L., Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Dolja, Valerian V., Dolnik, Olga, Drebot, Michael A., Drexler, Jan Felix, Dürrwald, Ralf, Dufkova, Lucie, Dundon, William G., Duprex, W. Paul, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Fernandes, Jorlan, Fooks, Anthony R., Formenty, Pierre B. H., Forth, Leonie F., Fouchier, Ron A. M., Freitas-Astúa, Juliana, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gbakima, Aiah, Goldstein, Tracey, Gonzalez, Jean-Paul J., Griffiths, Anthony, Groschup, Martin H., Günther, Stephan, Guterres, Alexandro, Hall, Roy A., Hammond, John, Hassan, Mohamed, Hepojoki, Jussi, Hepojoki, Satu, Hetzel, Udo, Hewson, Roger, Hoffmann, Bernd, Hongo, Seiji, Höper, Dirk, Horie, Masayuki, Hughes, Holly R., Hyndman, Timothy H., Jambai, Amara, Jardim, Rodrigo, Jiāng, Dàohóng, Jin, Qi, Jonson, Gilda B., Junglen, Sandra, Karadağ, Serpil, Keller, Karen E., Klempa, Boris, Klingström, Jonas, Kobinger, Gary, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kurath, Gael, Kuzmin, Ivan V., Laenen, Lies, Lamb, Robert A., Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lemos, Elba R. S., Leroy, Eric M., Li, Dexin, Lǐ, Jiànróng, Liang, Mifang, Liú, Wénwén, Liú, Yàn, Lukashevich, Igor S., Maes, Piet, Marciel de Souza, William, Marklewitz, Marco, Marshall, Sergio H., Martelli, Giovanni P., Martin, Robert R., Marzano, Shin-Yi L., Massart, Sébastien, McCauley, John W., Mielke-Ehret, Nicole, Minafra, Angelantonio, Minutolo, Maria, Mirazimi, Ali, Mühlbach, Hans-Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, Beatriz, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio R. T., Nylund, Are, Økland, Arnfinn L., Oliveira, Renata C., Palacios, Gustavo, Pallas, Vicente, Pályi, Bernadett, Papa, Anna, Parrish, Colin R., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Pérez, Daniel R., Pfaff, Florian, Radoshitzky, Sheli R., Rahman, Aziz-ul, Ramos-González, Pedro L., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Romanowski, Víctor, Robles Luna, Gabriel, Rota, Paul, Rubbenstroth, Dennis, Runstadler, Jonathan A., Ruzek, Daniel, Sabanadzovic, Sead, Salát, Jiří, Sall, Amadou Alpha, Salvato, Maria S., Sarpkaya, Kamil, Sasaya, Takahide, Schwemmle, Martin, Shabbir, Muhammad Z., Shí, Xiǎohóng, Shí, Zhènglì, Shirako, Yukio, Simmonds, Peter, Širmarová, Jana, Sironi, Manuela, Smither, Sophie, Smura, Teemu, Song, Jin-Won, Spann, Kirsten M., Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Straková, Petra, Takada, Ayato, Tesh, Robert B., Thornburg, Natalie J., Tomonaga, Keizō, Tordo, Noël, Towner, Jonathan S., Turina, Massimo, Tzanetakis, Ioannis, Ulrich, Rainer G., Vaira, Anna Maria, van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, Wahl, Victoria, Walker, Peter J., Wang, Hui, Wang, Jianwei, Wang, Xifeng, Wang, Lin-Fa, Wèi, Tàiyún, Wells, Heather, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wú, Zhìqiáng, Yang, Xin, Yáng, Xīnglóu, Yu, Xuejie, Yutin, Natalya, Zerbini, F. Murilo, Zhang, Tong, Zhang, Yong-Zhen, Zhou, Guohui, and Zhou, Xueping

Published
2020
Full Text
View/download PDF

15. Unique structure and function of viral rhodopsins

Author

Bratanov, Dmitry, Kovalev, Kirill, Machtens, Jan-Philipp, Astashkin, Roman, Chizhov, Igor, Soloviov, Dmytro, Volkov, Dmytro, Polovinkin, Vitaly, Zabelskii, Dmitrii, Mager, Thomas, Gushchin, Ivan, Rokitskaya, Tatyana, Antonenko, Yuri, Alekseev, Alexey, Shevchenko, Vitaly, Yutin, Natalya, Rosselli, Riccardo, Baeken, Christian, Borshchevskiy, Valentin, Bourenkov, Gleb, Popov, Alexander, Balandin, Taras, Büldt, Georg, Manstein, Dietmar J., Rodriguez-Valera, Francisco, Fahlke, Christoph, Bamberg, Ernst, Koonin, Eugene, and Gordeliy, Valentin

Published
2019
Full Text
View/download PDF

17. Programmable RNA-guided endonucleases are widespread in eukaryotes and their viruses

Author

Jiang, Kaiyi, Lim, Justin, Sgrizzi, Samantha, Trinh, Michael, Kayabolen, Alisan, Yutin, Natalya, Koonin, Eugene V., Abudayyeh, Omar O., and Gootenberg, Jonathan S.

Subjects
Article
Abstract

TnpB proteins are RNA-guided nucleases that are broadly associated with IS200/605 family transposons in prokaryotes. TnpB homologs, named Fanzors, have been detected in genomes of some eukaryotes and large viruses, but their activity and functions in eukaryotes remain unknown. We searched genomes of diverse eukaryotes and their viruses for TnpB homologs and identified numerous putative RNA-guided nucleases that are often associated with various transposases, suggesting they are encoded in mobile genetic elements. Reconstruction of the evolution of these nucleases, which we rename Horizontally-transferred Eukaryotic RNA-guided Mobile Element Systems (HERMES), revealed multiple acquisitions of TnpBs by eukaryotes and subsequent diversification. In their adaptation and spread in eukaryotes, HERMES proteins acquired nuclear localization signals, and genes captured introns, indicating extensive, long term adaptation to functioning in eukaryotic cells. Biochemical and cellular evidence show that HERMES employ non-coding RNAs encoded adjacent to the nuclease for RNA-guided cleavage of double-stranded DNA. HERMES nucleases contain a re-arranged catalytic site of the RuvC domain, similar to a distinct subset of TnpBs, and lack collateral cleavage activity. We demonstrate that HERMES can be harnessed for genome editing in human cells, highlighting the potential of these widespread eukaryotic RNA-guided nucleases for biotechnology applications.

Published
2023

20. Structural atlas of the most abundant human gut virus

Author

Bayfield, Oliver, Shkoporov, Andrey, Yutin, Natalya, Khokhlova, Ekaterina, Smith, Jake, Hawkins, Dorothy, Koonin, Eugene, Hill, Colin, and Antson, Alfred

Abstract

Bacteriophages of the order Crassvirales (crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant viruses in the human gut, are found in the majority of individual gut viromes and account for up to ~95% of the viral sequences in some individuals(1–4). Crassviruses are likely to play major roles in shaping the composition and functionality of the human microbiome, but the structures and roles of most of the phage-encoded proteins are unknown, with only generic predictions resulting from bioinformatic analyses(4,5). Here we present a cryo-electron microscopy structure of Bacteroides intestinalis bacteriophage ΦcrAss001(6), providing the structural basis for the functional assignment of most of its virion proteins. The muzzle protein forms a ~1 MDa assembly at the end of the tail and exhibits a previously unknown fold that we designate “crAss fold”, that likely serves as a gatekeeper to control ejection of cargoes. In addition to packing the ~103 kb virus DNA, the ΦcrAss001 virion encompasses extensive storage space for cargo proteins in the capsid and, most unusually, within the tail. One of the cargo proteins is present in both the capsid and the tail, suggesting a general mechanism for protein ejection, which involves partial unfolding of proteins during their extrusion through the tail. These findings provide the structural basis for understanding the mechanisms of assembly and infection of these hugely abundant crassviruses.

Published
2022

21. Structural atlas of the most abundant human gut virus

Author

Bayfield, Oliver, primary, Shkoporov, Andrey, additional, Yutin, Natalya, additional, Khokhlova, Ekaterina, additional, Smith, Jake, additional, Hawkins, Dorothy, additional, Koonin, Eugene, additional, Hill, Colin, additional, and Antson, Alfred, additional

Published
2022
Full Text
View/download PDF

29. Viruses of Asgard archaea

Author

Medvedeva, Sofia, primary, Sun, Jiarui, additional, Yutin, Natalya, additional, Koonin, Eugene V., additional, Nunoura, Takuro, additional, Rinke, Christian, additional, and Krupovic, Mart, additional

Published
2021
Full Text
View/download PDF

31. Additional file 10 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes

Author

Benler, Sean, Yutin, Natalya, Antipov, Dmitry, Rayko, Mikhail, Shmakov, Sergey, Gussow, Ayal B., Pevzner, Pavel, and Koonin, Eugene V.

Abstract

Additional file 9. Alignment of the template and variable repeats from the Quimbyvirus DGRs. The template repeat (TR) from Quimbyvirus is the first listed sequence and is followed by the variable repeats from either ORF80 (VR1) or ORF 47 (VR2) encoded in phage genomes that are nearly identical to Quimbyvirus (> 95 % average nucleotide identity). A total of 21 adenine residues (green) in the template repeat exhibit a least one substitution in a corresponding variable repeat.

Published
2021
Full Text
View/download PDF

33. Additional file 7 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes

Author

Benler, Sean, Yutin, Natalya, Antipov, Dmitry, Rayko, Mikhail, Shmakov, Sergey, Gussow, Ayal B., Pevzner, Pavel, and Koonin, Eugene V.

Subjects
musculoskeletal diseases
Abstract

Additional file 6. Genome maps of predicted anti-CRISPR proteins (Acrs) in uncharacterized Bifidobacteria phages. Open reading frames are colored according to function: large terminase subunit (red), structural components (blue), replication (orange), integrase (pink), general function (green) and unknown (grey). The candidate Acrs are indicated with a dashed box.

Published
2021
Full Text
View/download PDF

34. Additional file 8 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes

Author

Benler, Sean, Yutin, Natalya, Antipov, Dmitry, Rayko, Mikhail, Shmakov, Sergey, Gussow, Ayal B., Pevzner, Pavel, and Koonin, Eugene V.

Abstract

Additional file 7. Coverage heatmap of a “Quimbyviridae” genome across human gut viromes. The coverage of the most abundant “Quimbyviridae” phage genome (accession OMAC01000147.1) is plotted as a heatmap, scaled from 0 – 100x per 100 bp window.

Published
2021
Full Text
View/download PDF

35. Additional file 4 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes

Author

Benler, Sean, Yutin, Natalya, Antipov, Dmitry, Rayko, Mikhail, Shmakov, Sergey, Gussow, Ayal B., Pevzner, Pavel, and Koonin, Eugene V.

Subjects
viruses
Abstract

Additional file 3. Distribution of the marker profiles identified on each phage genome and pie chart representation of the gut phage taxonomy. (A) Histogram of marker proteins detected on each phage genome recovered from human gut metagenomes. Abbreviations are as follows: M, major capsid protein; P, portal, T, terminase large subunit. (B) Taxonomic assignments of the dereplicated contigs (n = 1,886), with the outermost ring corresponding to ICTV families.

Published
2021
Full Text
View/download PDF

39. Novel primers reveal wider diversity among marine aerobic anoxygenic phototrophs

Author

Yutin, Natalya, Suzuki, Marcelino T., and Beja, Oded

Subjects
Bacteria, Photosynthetic -- Genetic aspects, Planktonic bacteria -- Genetic aspects, Photosynthesis -- Analysis, Biological sciences
Abstract

A new set of pufM (M subunit of anoxygenic photosyntheic reaction center genes)-specific primers are designed and tested. These new primers have revealed several new aerobic anoxygenic phototrophic bacteria (AAnP) variants in environmental DNA samples and genomic libraries.

Published
2005

40. Structure and function of virion RNA polymerase of a crAss-like phage

Author

Drobysheva, Arina V., primary, Panafidina, Sofia A., additional, Kolesnik, Matvei V., additional, Klimuk, Evgeny I., additional, Minakhin, Leonid, additional, Yakunina, Maria V., additional, Borukhov, Sergei, additional, Nilsson, Emelie, additional, Holmfeldt, Karin, additional, Yutin, Natalya, additional, Makarova, Kira S., additional, Koonin, Eugene V., additional, Severinov, Konstantin V., additional, Leiman, Petr G., additional, and Sokolova, Maria L., additional

Published
2020
Full Text
View/download PDF

44. Cressdnaviricota : a Virus Phylum Unifying Seven Families of Rep-Encoding Viruses with Single-Stranded, Circular DNA Genomes

Author

Krupovic, Mart, primary, Varsani, Arvind, additional, Kazlauskas, Darius, additional, Breitbart, Mya, additional, Delwart, Eric, additional, Rosario, Karyna, additional, Yutin, Natalya, additional, Wolf, Yuri I., additional, Harrach, Balázs, additional, Zerbini, F. Murilo, additional, Dolja, Valerian V., additional, Kuhn, Jens H., additional, and Koonin, Eugene V., additional

Published
2020
Full Text
View/download PDF

46. Structure and function of virion RNA polymerase of crAss-like phage

Author

Drobysheva, Arina V., primary, Panafidina, Sofia A., additional, Kolesnik, Matvei V., additional, Klimuk, Evgeny I., additional, Minakhin, Leonid, additional, Yakunina, Maria V., additional, Borukhov, Sergei, additional, Nilsson, Emelie, additional, Holmfeldt, Karin, additional, Yutin, Natalya, additional, Makarova, Kira S., additional, Koonin, Eugene V., additional, Severinov, Konstantin V., additional, Leiman, Petr G., additional, and Sokolova, Maria L., additional

Published
2020
Full Text
View/download PDF

47. A New Family of DNA Viruses Causing Disease in Crustaceans from Diverse Aquatic Biomes

Author

Subramaniam, Kuttichantran, primary, Behringer, Donald C., additional, Bojko, Jamie, additional, Yutin, Natalya, additional, Clark, Abigail S., additional, Bateman, Kelly S., additional, van Aerle, Ronny, additional, Bass, David, additional, Kerr, Rose C., additional, Koonin, Eugene V., additional, Stentiford, Grant D., additional, and Waltzek, Thomas B., additional

Published
2020
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results