# Circularization of 23S rRNA but not 16S rRNA within archaeal ribosomes

## TL;DR

This study shows that archaeal ribosomes contain circular 23S rRNA, but not 16S rRNA, revealing new insights into rRNA processing in archaea.

## Contribution

The study reveals that circular 23S rRNA is a common feature in archaeal ribosomes, while 16S rRNA circularization varies among archaeal groups.

## Key findings

- Circular 23S rRNA is abundant in archaeal ribosomes across diverse species.
- Circular 16S rRNA intermediates are present in most archaea but not all.
- Structural modeling supports the circular conformation of 23S rRNA via a GNRA tetraloop.

## Abstract

Processing of archaeal 16S and 23S rRNAs is believed to involve excision of individual rRNAs from polycistronic precursors, circularization of excised rRNAs, and re-linearization before the incorporation into ribosomes. However, all the knowledge is derived from several isolated species, leaving open the possibility that different processes may occur in other archaeal groups.

Here, we investigate rRNAs from diverse and mostly uncultivated archaea. Sequencing of total cellular RNA from eight phylum-level lineages indicates that archaeal circular 23S rRNA transcript abundances vastly exceed those of linear counterparts, and linear versions are often undetectable. As the majority of rRNAs derive from mature ribosomes, the data suggest that ribosomes contain circular 23S rRNAs. Thus, we directly sequence RNA extracted from isolated ribosomes of a model archaeon, Methanosarcina acetivorans, and confirm that the 23S rRNAs in the ribosomes are circular. Structural modeling places the 5′ and 3′ ends of the linear precursors of archaeal 23S rRNAs in close proximity to form a GNRA tetraloop (in which N is A, C, G, or U and R is A or G), consistent with their existence as circular molecules. We also confirm the existence of circular 16S rRNA intermediates in transcriptomes of most archaea, yet a circular form is not evident in some distinct archaeal groups, suggesting that certain archaea do not circularize 16S rRNA during processing.

Our findings uncover unexpected variations in the processing required to generate mature rRNAs and the conformation of functional molecules in archaeal ribosomes.

The online version contains supplementary material available at 10.1186/s13059-025-03903-0.