Distinct characteristics of putative archaeal 5-methylcytosine RNA methyltransferases unveil their substrate specificities and evolutionary ancestries

Abstract

5-Methylcytosine methyltransferases (m⁵C MTases) are known to be involved in the modification of RNA. Although these enzymes have been relatively well characterized in bacteria and eukarya, a complete understanding of the archaeal counterparts is lacking. In this study, the identification and characterization of archaeal RNA m⁵C MTases were performed. As a case study, a hyperthermophilic archaeon, Pyrococcus horikoshii OT3, which possesses five putative RNA m⁵C MTases, was chosen. Among the five putative RNA m⁵C MTases, two proteins (PH0851 and PH1991) have been characterized as homologs of a bacterial rRNA MTase (RsmB) and eukaryal tRNA MTase (NSUN6), respectively. The in-depth characterization of the remaining three putative RNA m⁵C MTases (PH1078, PH1374, and PH1537) in this study suggests the presence of the signature architecture and catalytic residues plausibly involved in the binding of their cognate RNA substrates. Additionally, the results also suggest the existence of two RsmB-like proteins (PH0851 and PH1078) belonging to the same subfamily IV of m⁵C RNA MTase. However, the proteins PH1374 and PH1537 belong to the same subfamily V but bind to different substrates, rRNA and tRNA, respectively. The findings further indicate that archaeal RNA m⁵C MTases link those from bacteria and eukarya.

Communicated by Ramaswamy H. Sarma

Keywords:

• Archease
• bicistronic operon
• NSUN
• RNA m⁵C subfamilies
• RsmB
• RsmF

Acknowledgments

The authors acknowledge the facilities provided by the Indian Institute of Technology Guwahati, Assam, India. SS acknowledges the Ministry of Education, Government of India, for providing the research fellowship.

Authors contributions

SPK conceived the project and guided the research. SS performed the analysis. SS, SKM, and SPK wrote the manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.