Exploring the influence of hyperthermophilic protein Ssh10b on the stability and conformation of RNA by molecular dynamics simulation

Zhang, Xue; Zheng, Qing‐Chuan

doi:10.1002/bip.23068

Cited by 3 publications

(1 citation statement)

References 47 publications

(69 reference statements)

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“…Sa . shibatae itself also served as a valuable model for investigating different aspects of adaptation to high‐temperature environments, such as DNA relaxation by topoisomerases (Bergerat et al ., 1994; Jaxel et al ., 1996), RNA stability (Zhang and Zheng, 2018) and served as a source for discovery of thermostable proteins with potential industrial applications (Van et al ., 2007; Boyce and Walsh, 2018). However, the application of these models has been strongly limited by the lack of the complete genome sequence for any of the Sa .…”

Section: Introductionmentioning

confidence: 99%

New insights into the diversity and evolution of the archaeal mobilome from three complete genomes of Saccharolobus shibatae

Medvedeva

Brandt

Cvirkaitė-Krupovič

et al. 2021

Environmental Microbiology

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Summary 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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Section: Introductionmentioning

confidence: 99%

New insights into the diversity and evolution of the archaeal mobilome from three complete genomes of Saccharolobus shibatae

Medvedeva

Brandt

Cvirkaitė-Krupovič

et al. 2021

Environmental Microbiology

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How DNA affects the hyperthermophilic protein Ape10b2 for oligomerization: an investigation using multiple short molecular dynamics simulations

Zhang

Zheng

2021

Phys. Chem. Chem. Phys.

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Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples

Ruszkowska

Ruszkowski

Hulewicz

et al. 2020

Nucleic Acids Research

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Three-dimensional structures have been solved for several naturally occurring RNA triple helices, although all are limited to six or fewer consecutive base triples, hindering accurate estimation of global and local structural parameters. We present an X-ray crystal structure of a right-handed, U•A-U-rich RNA triple helix with 11 continuous base triples. Due to helical unwinding, the RNA triple helix spans an average of 12 base triples per turn. The double helix portion of the RNA triple helix is more similar to both the helical and base step structural parameters of A′-RNA rather than A-RNA. Its most striking features are its wide and deep major groove, a smaller inclination angle and all three strands favoring a C3′-endo sugar pucker. Despite the presence of a third strand, the diameter of an RNA triple helix remains nearly identical to those of DNA and RNA double helices. Contrary to our previous modeling predictions, this structure demonstrates that an RNA triple helix is not limited in length to six consecutive base triples and that longer RNA triple helices may exist in nature. Our structure provides a starting point to establish structural parameters of the so-called ‘ideal’ RNA triple helix, analogous to A-RNA and B-DNA double helices.

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Exploring the influence of hyperthermophilic protein Ssh10b on the stability and conformation of RNA by molecular dynamics simulation

Cited by 3 publications

References 47 publications

New insights into the diversity and evolution of the archaeal mobilome from three complete genomes of Saccharolobus shibatae

New insights into the diversity and evolution of the archaeal mobilome from three complete genomes of Saccharolobus shibatae

How DNA affects the hyperthermophilic protein Ape10b2 for oligomerization: an investigation using multiple short molecular dynamics simulations

Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples

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