RNA stabilization in hyperthermophilic archaea

Abstract

Analyses of the RNA metabolism of hyperthermophilic archaea highlight the efficiency of regulatory RNAs and RNA‐guided processes at extreme temperatures. These organisms must overcome the intrinsic thermolability of RNAs. Elevated levels of RNA modifications and structured GC‐rich regions are observed for many universal noncoding RNA families. Guide RNAs are often protected from degradation by their presence within ribonucleoprotein complexes. Modification and ligation of RNA termini can be employed to impair exonucleolytic degradation. Finally, antisense strand transcription promotes the formation of RNA duplexes and can be used to stabilize RNA regions. In our review, we provide examples of these RNA stabilization mechanisms that have been observed in hyperthermophilic archaeal model organisms.

Exploring prokaryotic transcription, operon structures, rRNA maturation and modifications using Nanopore-based native RNA sequencing

“…Moreover, our sample-compare approach also suggests an increased amount of rRNA modifications in the hyperthermophile P. furiosus , and a decrease amount of predicted rRNA modifications in halophile H. volcanii in comparison to E. coli . These differential modification patterns across archaea are in good agreement with previous studies and may reflect adaptation to the environmental conditions that these extremophilic archaea encounter 49,87,88 . Unfortunately, the exact nature of these modifications can not be unveiled yet.…”

“…6g), better accuracy of the sample-compare model could be confirmed. Moreover, these data support the long-standing hypothesis that hyperthermophilic organisms might stabilize their rRNAs by a higher degree of RNA modifications 87,88 .…”

Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea

“…In particular, reverse transcription is a crucial step that can be optimised by using other reverse transcriptases and reaction conditions. In our experiments, differences in RT efficiency leading to shortened RNA molecules and non-stoichiometric amounts of 16S and 23S rRNA could not be explained by GC content and could be due to more stable RNA structures in the (hyper)-thermophilic model organisms (Gomes-Filho et al 2019;Sas-Chen et al 2020). This conclusion is supported by the observation that in Sulfolobus, and to a greater extent in Pyrococcus, there is a significant proportion of reads considered full-length sequenced that are notably short.…”

Exponentially few RNA structures are designable

“…or as a direct performer of a large collection of enzymatic activities (ncRNAs) [28]. For a large subset of ncRNA family, the adoption of a predefined structure is instrumental to the function(s) of individual molecules [45], and even, at times, the survival of its hosts organisms [20]. Accordingly, the evolutionary pressure on RNA families induced by RNA structure, at the secondary structure level, is at the core of most approaches for the identification of novel ncRNA families [46].…”