TY - JOUR
T1 - New insights into the diversity and evolution of the archaeal mobilome from three complete genomes of Saccharolobus shibatae
AU - Medvedeva, Sofia
AU - Brandt, David
AU - Cvirkaite-Krupovic, Virginija
AU - Liu, Ying
AU - Severinov, Konstantin
AU - Ishino, Sonoko
AU - Ishino, Yoshizumi
AU - Prangishvili, David
AU - Kalinowski, Jörn
AU - Krupovic, Mart
N1 - Funding Information:
This work was supported by l'Agence Nationale de la Recherche (Grant ENVIRA, ANR-17-CE15-0005-01) and the Emergence(s) project MEMREMA from Ville de Paris (to M.K.); the European Union's Horizon 2020 research and innovation program under grant agreement 685778, project VIRUS-X (to D.P. and J.K.). Y.L. was a recipient of the Pasteur-Roux-Cantarini Fellowship from Institut Pasteur. S.M. was partly supported by the Metchnikov fellowship from Campus France.
Funding Information:
This work was supported by l'Agence Nationale de la Recherche (Grant ENVIRA, ANR‐17‐CE15‐0005‐01) and the Emergence(s) project MEMREMA from Ville de Paris (to M.K.); the European Union's Horizon 2020 research and innovation program under grant agreement 685778, project VIRUS‐X (to D.P. and J.K.). Y.L. was a recipient of the Pasteur‐Roux‐Cantarini Fellowship from Institut Pasteur. S.M. was partly supported by the Metchnikov fellowship from Campus France.
Publisher Copyright:
© 2021 Society for Applied Microbiology and John Wiley & Sons Ltd.
PY - 2021/8
Y1 - 2021/8
N2 - Saccharolobus (formerly Sulfolobus) shibatae B12, isolated from a hot spring in Beppu, Japan in 1982, is one of the first hyperthermophilic and acidophilic archaeal species to be discovered. It serves as a natural host to the extensively studied spindle-shaped virus SSV1, a prototype of the Fuselloviridae family. Two additional Sa. shibatae strains, BEU9 and S38A, sensitive to viruses of the families Lipothrixviridae and Portogloboviridae, respectively, have been isolated more recently. However, none of the strains has been fully sequenced, limiting their utility for studies on archaeal biology and virus–host interactions. Here, we present the complete genome sequences of all three Sa. shibatae strains and explore the rich diversity of their integrated mobile genetic elements (MGE), including transposable insertion sequences, integrative and conjugative elements, plasmids, and viruses, some of which were also detected in the extrachromosomal form. Analysis of related MGEs in other Sulfolobales species and patterns of CRISPR spacer targeting revealed a complex network of MGE distributions, involving horizontal spread and relatively frequent host switching by MGEs over large phylogenetic distances, involving species of the genera Saccharolobus, Sulfurisphaera and Acidianus. Furthermore, we characterize a remarkable case of a virus-to-plasmid transition, whereby a fusellovirus has lost the genes encoding for the capsid proteins, while retaining the replication module, effectively becoming a plasmid.
AB - Saccharolobus (formerly Sulfolobus) shibatae B12, isolated from a hot spring in Beppu, Japan in 1982, is one of the first hyperthermophilic and acidophilic archaeal species to be discovered. It serves as a natural host to the extensively studied spindle-shaped virus SSV1, a prototype of the Fuselloviridae family. Two additional Sa. shibatae strains, BEU9 and S38A, sensitive to viruses of the families Lipothrixviridae and Portogloboviridae, respectively, have been isolated more recently. However, none of the strains has been fully sequenced, limiting their utility for studies on archaeal biology and virus–host interactions. Here, we present the complete genome sequences of all three Sa. shibatae strains and explore the rich diversity of their integrated mobile genetic elements (MGE), including transposable insertion sequences, integrative and conjugative elements, plasmids, and viruses, some of which were also detected in the extrachromosomal form. Analysis of related MGEs in other Sulfolobales species and patterns of CRISPR spacer targeting revealed a complex network of MGE distributions, involving horizontal spread and relatively frequent host switching by MGEs over large phylogenetic distances, involving species of the genera Saccharolobus, Sulfurisphaera and Acidianus. Furthermore, we characterize a remarkable case of a virus-to-plasmid transition, whereby a fusellovirus has lost the genes encoding for the capsid proteins, while retaining the replication module, effectively becoming a plasmid.
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U2 - 10.1111/1462-2920.15654
DO - 10.1111/1462-2920.15654
M3 - Article
C2 - 34190379
AN - SCOPUS:85109603068
VL - 23
SP - 4612
EP - 4630
JO - Environmental Microbiology
JF - Environmental Microbiology
SN - 1462-2912
IS - 8
ER -