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4. Multi-layered genome defences in bacteria

Author

Agapov, Aleksei, Baker, Kate S, Bedekar, Paritosh, Bhatia, Rama P, Blower, Tim R, Brockhurst, Michael A, Brown, Cooper, Chong, Charlotte E, Fothergill, Joanne L, Graham, Shirley, Hall, James PJ, Maestri, Alice, McQuarrie, Stuart, Olina, Anna, Pagliara, Stefano, Recker, Mario, Richmond, Anna, Shaw, Steven J, Szczelkun, Mark D, Taylor, Tiffany B, van Houte, Stineke, Went, Sam C, Westra, Edze R, White, Malcolm F, and Wright, Rosanna

Published
2024
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5. IAPT chromosome data 33

Author

Marhold, Karol, Kučera, Jaromír, Acuña, Carlos Alberto, Akopian, Janna A., de Almeida, Erton M., Alves, Marccus V., Amorim, Bruno S., An'kova, Tatyana V., Arora, Jaya, Aytaç, Zeki, Baez, Mariana, Cavalcanti, Taciana Barbosa, Calvente, Alice, Catalan, Pilar, Chernyagina, Olga A., Chernysheva, Olga A., Cordeiro, Joel M.P., Daviña, Julio Rubén, Deanna, Rocío, Delgado, Luis, Silva, Yhanndra K. Dias, Elliott, Tammy L., Erst, Andrey S., Felix, Leonardo P., Forni-Martins, Eliana R., Gallego, Francisca, Facco, Marlon Garlet, Aquino, Analía Cecilia Gianini, de Andrade, Maria J. Gomes, Graham, Shirley A., Hojsgaard, Diego Hernán, Honfi, Ana Isabel, Houben, Andreas, Ikeda, Hiroshi, Khalbekova, Khulkar U., Krivenko, Denis A., Lakhanpaul, Suman, Peñas, M. Laura Las, Lavia, Graciela Inés, Leonova, Tatiana V., Lian, Lian, Lomonosova, Maria N., López-González, Beatriz, Martínez, Eric Javier, Matos, Samara S., Melo, André L., Torres, Esteban Meza, Mitrenina, Elizaveta Yu., El Mokni, Ridha, Valls, José Francisco Montenegro, Morero, Rita Ema, de Moura, Clapton Olimpio, de Oliveira, Regina Célia, de Oliveira Maekawa, Vanessa, Olonova, Marina V., Pandit, Maharaj K., Pedrosa-Harand, Andrea, Peruzzi, Lorenzo, Pinzani, Lorenzo, Potseluev, Oleg M., Probatova, Nina S., Pulkina, Svetlana V., Reutemann, Anna Verena, Rico, Enrique, Rua, Gabriel Hugo, Santos, Fabiano J., Santos, Géssica S., dos Santos Sousa, Mayco Werllen, Silva, Marcos C., Silva, Rhuan C., da Silva Santos, Angeline Maria, Silvestri, María Celeste, Singh, Jaswant, Singhal, Vijay Kumar, Souza, Pamela C.S.S., Tashev, Alexander, Thomas, Wayt W., Pozzobon, Marisa Toniolo, Turginov, Orzimat T., Vanzela, André L.L., Berto, Ana Catarina Vasconcelos, Veklich, Tatiana N., and Wang, Wei

Published
2020

9. An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity

Author

Athukoralage, Januka S., McMahon, Stephen A., Zhang, Changyi, Grüschow, Sabine, Graham, Shirley, Krupovic, Mart, and Whitaker, Rachel J.

Subjects
Genetic research, Nucleases -- Genetic aspects, Immunity -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The CRISPR system in bacteria and archaea provides adaptive immunity against mobile genetic elements. Type III CRISPR systems detect viral RNA, resulting in the activation of two regions of the Cas10 protein: an HD nuclease domain (which degrades viral DNA).sup.1,2 and a cyclase domain (which synthesizes cyclic oligoadenylates from ATP).sup.3-5. Cyclic oligoadenylates in turn activate defence enzymes with a CRISPR-associated Rossmann fold domain.sup.6, sculpting a powerful antiviral response.sup.7-10 that can drive viruses to extinction.sup.7,8. Cyclic nucleotides are increasingly implicated in host-pathogen interactions.sup.11-13. Here we identify a new family of viral anti-CRISPR (Acr) enzymes that rapidly degrade cyclic tetra-adenylate (cA.sub.4). The viral ring nuclease AcrIII-1 is widely distributed in archaeal and bacterial viruses and in proviruses. The enzyme uses a previously unknown fold to bind cA.sub.4 specifically, and a conserved active site to rapidly cleave this signalling molecule, allowing viruses to neutralize the type III CRISPR defence system. The AcrIII-1 family has a broad host range, as it targets cA.sub.4 signalling molecules rather than specific CRISPR effector proteins. Our findings highlight the crucial role of cyclic nucleotide signalling in the conflict between viruses and their hosts. Bacteria and archaea use cyclic oligoadenylate molecules as part of the CRISPR system for antiviral defence; here, a family of viral enzymes that rapidly degrades cyclic oligoadenylates is identified and biochemically and structurally described., Author(s): Januka S. Athukoralage [sup.1] , Stephen A. McMahon [sup.1] , Changyi Zhang [sup.3] [sup.4] , Sabine Grüschow [sup.1] , Shirley Graham [sup.1] , Mart Krupovic [sup.2] , Rachel J. [...]

Published
2020
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25. A comprehensive genus-level phylogeny and biogeographical history of the Lythraceae based on whole plastome sequences.

Author

Inglis, Peter W, Cavalcanti, Taciana B, Facco, Marlon G, Bakker, Freek T, and Graham, Shirley A

Subjects
PHYLOGENY, PARSIMONIOUS models, BAYESIAN analysis, CONTINENTS, EOCENE Epoch, VICARIANCE
Abstract

Background and Aims The Lythraceae are a mainly subtropical to tropical family of the order Myrtales with 28 currently accepted genera and approximately 600 species. There is currently no well-supported phylogenetic and biogeographical hypothesis of the Lythraceae incorporating all currently accepted genera, which we sought to provide. Methods Plastomes of representative species of 18 distinct Lythraceae genera were sequenced and annotated. Together with existing sequences, plastomes of all 28 currently accepted genera in the Lythraceae were brought together for the first time. The plastomes were aligned and a Bayesian phylogenetic hypothesis was produced. We then conducted a time-calibrated Bayesian analysis and a biogeographical analysis. Key Results Plastome-based Bayesian and maximum-likelihood phylogenetic trees are generally congruent with recent nuclear phylogenomic data and resolve two deeply branching major clades in the Lythraceae. One major clade concentrates shrubby and arboreal South American and African genera that inhabit seasonally dry environments, with larger, often winged seeds, adapted to dispersal by the wind. The second major clade concentrates North American, Asian, African and several near-cosmopolitan herbaceous, shrubby and arboreal genera, often inhabiting humid or aquatic environments, with smaller seeds possessing structures that facilitate dispersal by water. Conclusions We hypothesize that the Lythraceae dispersed early in the Late Cretaceous from South American to North American continents, with subsequent expansion in the Late Cretaceous of a North American lineage through Laurasia to Africa via a boreotropical route. Two later expansions of South American clades to Africa in the Palaeocene and Eocene, respectively, are also hypothesized. Transoceanic dispersal in the family is possibly facilitated by adaptations to aquatic environments that are common to many extant genera of the Lythraceae, where long-distance dispersal and vicariance may be invoked to explain several remarkable disjunct distributions in Lythraceae clades. [ABSTRACT FROM AUTHOR]

Published
2023
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