A research group led by Prof. YE Keqiong at the Institute of Biophysics, Chinese Academy of Sciences, revealed a first global map of RNA pseudouridine distribution and synthesis in the model archaeon Sulfolobus islandicus, which is published in Nucleic Acids Research.

Pseudouridine is one of the most common modifications in RNA, found in tRNA, rRNA, snRNA, as well as in eukaryotic mRNA and snoRNA, modulating their structure and function. Pseudouridine is enzymatically synthesized through post-transcriptional conversion of uridine by pseudouridine synthases (PUSs). Among them, Cbf5 is a special PUS belonging to the TruB family, which recognizes substrates guided by H/ACA RNA.

To comprehensively understand the RNA pseudouridylation of S. islandicus, the researchers profiled pseudouridine in rRNA, tRNA, and abundant sRNA, and analyzed potential PUSs. All high-confidence pseudouridines detected in the study were assigned to H/ACA-guided or independent PUSs, most of which were validated by genetic or biochemical methods.

The researchers identified 11 pseudouridines in S. islandicus rRNA, all of which are modified by enzymes guided by H/ACA RNA. They also fully characterized the pseudouridines in S. islandicus tRNA and assigned the corresponding PUSs.

In addition to rRNA and tRNA, pseudouridines in crRNA were identified, revealing that their formation is guided by H/ACA RNA. This is the first evidence of pseudouridines in crRNA, suggesting that archaeal H/ACA RNA is involved in guiding the modification of RNAs other than rRNA and tRNA.

The researchers found 6 H/ACA RNAs in S.islandicus, four of which are atypical H/ACA RNAs. These atypical H/ACA RNAs lack the lower stem and ACA motif. They also found that two atypical H/ACA RNAs can be modified by Cbf5 in a non-guided manner.

This study reveals a landscape of pseudouridylation in archaea. The discovery that archaeal H/ACA RNA can target new types of substrates with atypical structures and exhibit great substrate recognition versatility significantly enhances understanding of the distribution and formation of pseudouridines in archaea, as well as the structure and function of H/ACA RNA.

Figure. Distribution and synthesis of pseudouridine in Sulfolobus islandicus

(Image by YE Keqiong's group)

Article link: https://doi.org/10.1093/nar/gkae096

Contact: YE Keqiong

Institute of Biophysics, Chinese Academy of Sciences

Beijing 100101, China

Email: yekeqiong@ibp.ac.cn