A novel N 4, N 4-dimethylcytidine in the archaeal ribosome enhances hyperthermophily

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 121; no. 45; p. e2405999121
• Main Authors: Fluke, Kristin A, Dai, Nan, Wolf, Eric J, Fuchs, Ryan T, Ho, P Shing, Talbott, Victoria, Elkins, Liam, Tsai, Yueh-Lin, Schiltz, Jackson, Febvre, Hallie P, Czarny, Ryan, Robb, G Brett, Corrêa, Jr, Ivan R, Santangelo, Thomas J
• Format: Journal Article
• Language: English
• Published: United States 05-11-2024
• Subjects: Archaea - genetics; Archaea - metabolism; Archaeal Proteins - chemistry; Archaeal Proteins - genetics; Archaeal Proteins - metabolism; Cytidine - analogs & derivatives; Cytidine - chemistry; Cytidine - metabolism; Methyltransferases - chemistry; Methyltransferases - genetics; Methyltransferases - metabolism; Phylogeny; Ribosomes - metabolism; RNA, Archaeal - chemistry; RNA, Archaeal - genetics; RNA, Archaeal - metabolism; RNA, Ribosomal, 16S - genetics; RNA, Ribosomal, 16S - metabolism; epitranscriptome; N4,N4-dimethylcytidine; RNA modifications; hyperthermophile; archaea
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.2405999121

Ribosome structure and activity are challenged at high temperatures, often demanding modifications to ribosomal RNAs (rRNAs) to retain translation fidelity. LC-MS/MS, bisulfite-sequencing, and high-resolution cryo-EM structures of the archaeal ribosome identified an RNA modification,
4,
4-dimethylcytidine (m
C), at the universally conserved C918 in the 16S rRNA helix 31 loop. Here, we characterize and structurally resolve a class of RNA methyltransferase that generates m
C whose function is critical for hyperthermophilic growth. m
C is synthesized by the activity of a unique family of RNA methyltransferase containing a Rossman-fold that targets only intact ribosomes. The phylogenetic distribution of the newly identified m
C synthase family implies that m
C is biologically relevant in each domain. Resistance of m
C to bisulfite-driven deamination suggests that efforts to capture m
C profiles via bisulfite sequencing are also capturing m
C.