Abstract
Box C/D RNAs guide the site-specific formation of 2′-O-methylated nucleotides (Nm) of RNAs in eukaryotes and archaea. Although C/D RNAs have been profiled in several archaea, their targets have not been experimentally determined. Here, we mapped Nm in rRNAs, tRNAs, and abundant small RNAs (sRNAs) and profiled C/D RNAs in the crenarchaeon Sulfolobus islandicus. The targets of C/D RNAs were assigned by analysis of base-pairing interactions, in vitro modification assays, and gene deletion experiments, revealing a complicated landscape of C/D RNA-target interactions. C/D RNAs widely use dual antisense elements to target adjacent sites in rRNAs, enhancing modification at weakly bound sites. Two consecutive sites can be guided with the same antisense element upstream of box D or D′, a phenomenon known as double-specificity that is exclusive to internal box D′ in eukaryotic C/D RNAs. Several C/D RNAs guide modification at a single non-canonical site. This study reveals the global landscape of RNA-guided 2′-O-methylation in an archaeon and unexpected targeting rules employed by C/D RNA.
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Data availability
The raw data of sRNA-seq and RiboMeth-seq have been deposited into the National Genomics Data Center (bigd.big.ac.cn) under GSA accession code CRA011490.
References
Aittaleb, M., Rashid, R., Chen, Q., Palmer, J.R., Daniels, C.J., and Li, H. (2003). Structure and function of archaeal box C/D sRNP core proteins. Nat Struct Mol Biol 10, 256–263.
Benitez-Paez, A., Villarroya, M., Douthwaite, S., Gabaldon, T., and Armengod, M.E. (2010). YibK is the 2′-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNALeu isoacceptors. RNA 16, 2131–2143.
Bernick, D.L., Dennis, P.P., Lui, L.M., and Lowe, T.M. (2012). Diversity of antisense and other non-coding RNAs in archaea revealed by comparative small RNA sequencing in four Pyrobaculum species. Front Microbio 3, 231.
Birkedal, U., Christensen-Dalsgaard, M., Krogh, N., Sabarinathan, R., Gorodkin, J., and Nielsen, H. (2014). Profiling of ribose methylations in RNA by high-throughput sequencing. Angew Chem Int Ed 54, 451–455.
Boccaletto, P., Machnicka, M.A., Purta, E., Piątkowski, P., Bagiński, B., Wirecki, T.K., de Crecy-Lagard, V., Ross, R., Limbach, P.A., Kotter, A., et al. (2018). MODOMICS: a database of RNA modification pathways. 2017 update. Nucleic Acids Res 46, D303–D307.
Bortolin, M.L., Bachellerie, J.P., and Clouet-d’Orval, B. (2003). In vitro RNP assembly and methylation guide activity of an unusual box C/D RNA, cis-acting archaeal pre-tRNATrp. Nucleic Acids Res 31, 6524–6535.
Bruenger, E., Kowalak, J.A., Kuchino, Y., McCloskey, J.A., Mizushima, H., Stetter, K. O., and Crain, P.F. (1993). 5S rRNA modification in the hyperthermophilic archaea Sulfolobus solfataricus and Pyrodictium occultum. FASEB J 7, 196–200.
Cao, Y., Wang, J., Wu, S., Yin, X., Shu, J., Dai, X., Liu, Y., Sun, L., Zhu, D., Deng, X.W., et al. (2022). The small nucleolar RNA SnoR28 regulates plant growth and development by directing rRNA maturation. Plant Cell 34, 4173–4190.
Cavaille, J., and Bachellerie, J.P. (1998). SnoRNA-guided ribose methylation of rRNA: structural features of the guide RNA duplex influencing the extent of the reaction. Nucleic Acids Res 26, 1576–1587.
Cavaille, J., Nicoloso, M., and Bachellerie, J.P. (1996). Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides. Nature 383, 732–735.
Chan, P.P., and Lowe, T.M. (2016). GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucleic Acids Res 44, D184–D189.
Clouet d’Orval, B., Bortolin, M.L., Gaspin, C., and Bachellerie, J.P. (2001). Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp. Nucleic Acids Res 29, 4518–4529.
Daume, M., Uhl, M., Backofen, R., and Randau, L. (2017). RIP-Seq suggests translational regulation by L7Ae in archaea. mBio 8, e00730–17.
Deng, L., Zhu, H., Chen, Z., Liang, Y.X., and She, Q. (2009). Unmarked gene deletion and host-vector system for the hyperthermophilic crenarchaeon Sulfolobus islandicus. Extremophiles 13, 735–746.
Dennis, P.P., Tripp, V., Lui, L., Lowe, T., and Randau, L. (2015). C/D box sRNA-guided 2′-O-methylation patterns of archaeal rRNA molecules. BMC Genomics 16, 632.
Guo, L., Brügger, K., Liu, C., Shah, S.A., Zheng, H., Zhu, Y., Wang, S., Lillestøl, R.K., Chen, L., Frank, J., et al. (2011). Genome analyses of Icelandic strains of Sulfolobus islandicus, model organisms for genetic and virus-host interaction studies. J Bacteriol 193, 1672–1680.
Gupta, R. (1984). Halobacterium volcanii tRNAs. Identification of 41 tRNAs covering all amino acids, and the sequences of 33 class I tRNAs. J Biol Chem 259, 9461–9471.
Hori, H., Kawamura, T., Awai, T., Ochi, A., Yamagami, R., Tomikawa, C., and Hirata, A. (2018). Transfer RNA modification enzymes from thermophiles and their modified nucleosides in tRNA. Microorganisms 6, 110.
Karijolich, J., and Yu, Y.T. (2010). Spliceosomal snRNA modifications and their function. RNA Biol 7, 192–204.
Kim, D., Langmead, B., and Salzberg, S.L. (2015). HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12, 357–360.
Kiss-Laszlo, Z., Henry, Y., Bachellerie, J.P., Caizergues-Ferrer, M., and Kiss, T. (1996). Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85, 1077–1088.
Kiss, T. (2001). Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J 20, 3617–3622.
Lapeyre, B., and Purushothaman, S.K. (2004). Spb1p-directed formation of Gm2922 in the ribosome catalytic center occurs at a late processing stage. Mol Cell 16, 663–669.
Li, Y., Pan, S., Zhang, Y., Ren, M., Feng, M., Peng, N., Chen, L., Liang, Y.X., and She, Q. (2016). Harnessing Type I and Type III CRISPR-Cas systems for genome editing. Nucleic Acids Res 44, e34.
Lin, J., Lai, S., Jia, R., Xu, A., Zhang, L., Lu, J., and Ye, K. (2011). Structural basis for site-specific ribose methylation by box C/D RNA protein complexes. Nature 469, 559–563.
Lorenz, R., Bernhart, S.H., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P. F., and Hofacker, I.L. (2011). ViennaRNA package 2.0. Algorithms Mol Biol 6, 26.
Lowe, T.M., and Eddy, S.R. (1999). A computational screen for methylation guide snoRNAs in yeast. Science 283, 1168–1171.
Marchand, V., Blanloeil-Oillo, F., Helm, M., and Motorin, Y. (2016). Illumina-based RiboMethSeq approach for mapping of 2′-O-Me residues in RNA. Nucleic Acids Res 44, e135.
Marchand, V., Pichot, F., Thüring, K., Ayadi, L., Freund, I., Dalpke, A., Helm, M., and Motorin, Y. (2017). Next-generation sequencing-based RiboMethSeq protocol for analysis of tRNA 2′-O-methylation. Biomolecules 7, 13.
Noon, K.R., Bruenger, E., and McCloskey, J.A. (1998). Posttranscriptional modifications in 16S and 23S rRNAs of the archaeal hyperthermophile Sulfolobus solfataricus. J Bacteriol 180, 2883–2888.
Omer, A.D., Lowe, T.M., Russell, A.G., Ebhardt, H., Eddy, S.R., and Dennis, P.P. (2000). Homologs of small nucleolar RNAs in archaea. Science 288, 517–522.
Omer, A.D., Ziesche, S., Ebhardt, H., and Dennis, P.P. (2002). In vitro reconstitution and activity of a C/D box methylation guide ribonucleoprotein complex. Proc Natl Acad Sci USA 99, 5289–5294.
Peng, N., Han, W., Li, Y., Liang, Y., and She, Q. (2017). Genetic technologies for extremely thermophilic microorganisms of Sulfolobus, the only genetically tractable genus of crenarchaea. Sci China Life Sci 60, 370–385.
Pintard, L., Lecointe, F., Bujnicki, J.M., Bonnerot, C., Grosjean, H., and Lapeyre, B. (2002). Trm7p catalyses the formation of two 2′-O-methylriboses in yeast tRNA anticodon loop. EMBO J 21, 1811–1820.
Quinlan, A.R., and Hall, I.M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842.
Renalier, M.H., Joseph, N., Gaspin, C., Thebault, P., and Mougin, A. (2005). The Cm56 tRNA modification in archaea is catalyzed either by a specific 2′-O-methylase, or a C/D sRNP. RNA 11, 1051–1063.
Robinson, J.T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E.S., Getz, G., and Mesirov, J.P. (2011). Integrative genomics viewer. Nat Biotechnol 29, 24–26.
Roehr, J.T., Dieterich, C., and Reinert, K. (2017). Flexbar 3.0-SIMD and multicore parallelization. Bioinformatics 33, 2941–2942.
Somme, J., Van Laer, B., Roovers, M., Steyaert, J., Versées, W., and Droogmans, L. (2014). Characterization of two homologous 2′-O-methyltransferases showing different specificities for their tRNA substrates. RNA 20, 1257–1271.
Tang, T.H., Polacek, N., Zywicki, M., Huber, H., Brugger, K., Garrett, R., Bachellerie, J. P., and Hüttenhofer, A. (2005). Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus. Mol Microbiol 55, 469–481.
Taoka, M., Nobe, Y., Yamaki, Y., Sato, K., Ishikawa, H., Izumikawa, K., Yamauchi, Y., Hirota, K., Nakayama, H., Takahashi, N., et al. (2018). Landscape of the complete RNA chemical modifications in the human 80S ribosome. Nucleic Acids Res 46, 9289–9298.
Taoka, M., Nobe, Y., Yamaki, Y., Yamauchi, Y., Ishikawa, H., Takahashi, N., Nakayama, H., and Isobe, T. (2016). The complete chemical structure of Saccharomyces cerevisiae rRNA: partial pseudouridylation of U2345 in 25S rRNA by snoRNA snR9. Nucleic Acids Res 44, 8951–8961.
Tran, E.J., Zhang, X., and Maxwell, E.S. (2003). Efficient RNA 2′-O-methylation requires juxtaposed and symmetrically assembled archaeal box C/D and C′/D′ RNPs. EMBO J 22, 3930–3940.
Tycowski, K.T., Smith, C.M., Shu, M.D., and Steitz, J.A. (1996). A small nucleolar RNA requirement for site-specific ribose methylation of rRNA in Xenopus. Proc Natl Acad Sci USA 93, 14480–14485.
van Nues, R.W., Granneman, S., Kudla, G., Sloan, K.E., Chicken, M., Tollervey, D., and Watkins, N.J. (2011). Box C/D snoRNP catalysed methylation is aided by additional pre-rRNA base-pairing. EMBO J 30, 2420–2430.
van Nues, R.W., and Watkins, N.J. (2016). Unusual C′/D′ motifs enable box C/D snoRNPs to modify multiple sites in the same rRNA target region. Nucleic Acids Res 45, 2016–2028.
Watkins, N.J., and Bohnsack, M.T. (2011). The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA. WIREs RNA 3, 397–414.
Wolff, P., Villette, C., Zumsteg, J., Heintz, D., Antoine, L., Chane-Woon-Ming, B., Droogmans, L., Grosjean, H., and Westhof, E. (2020). Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea. RNA 26, 1957–1975.
Wu, S., Wang, Y., Wang, J., Li, X., Li, J., and Ye, K. (2021). Profiling of RNA ribose methylation in Arabidopsis thaliana. Nucleic Acids Res 49, 4104–4119.
Yang, J., Sharma, S., Watzinger, P., Hartmann, J.D., Kotter, P., and Entian, K.D. (2016a). Mapping of complete set of ribose and base modifications of yeast rRNA by RP-HPLC and mung bean nuclease assay. PLoS ONE 11, e0168873.
Yang, Z., Lin, J., and Ye, K. (2016b). Box C/D guide RNAs recognize a maximum of 10 nt of substrates. Proc Natl Acad Sci USA 113, 10878–10883.
Yang, Z., Wang, J., Huang, L., Lilley, D.M.J., and Ye, K. (2020). Functional organization of box C/D RNA-guided RNA methyltransferase. Nucleic Acids Res 48, 5094–5105.
Ye, K., Jia, R., Lin, J., Ju, M., Peng, J., Xu, A., and Zhang, L. (2009). Structural organization of box C/D RNA-guided RNA methyltransferase. Proc Natl Acad Sci USA 106, 13808–13813.
Yu, N., Jora, M., Solivio, B., Thakur, P., Acevedo-Rocha, C.G., Randau, L., de Crecy-Lagard, V., Addepalli, B., and Limbach, P.A. (2019). tRNA modification profiles and codon-decoding strategies in Methanocaldococcus jannaschii. J Bacteriol 201, e00690–18.
Yu, Y.T., and Meier, U.T. (2014). RNA-guided isomerization of uridine to pseudouridine-pseudouridylation. RNA Biol 11, 1483–1494.
Zago, M.A., Dennis, P.P., and Omer, A.D. (2005). The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol Microbiol 55, 1812–1828.
Ziesche, S.M., Omer, A.D., and Dennis, P.P. (2004). RNA-guided nucleotide modification of ribosomal and non-ribosomal RNAs in Archaea. Mol Microbiol 54, 980–993.
Zillig, W., Kletzin, A., Schleper, C., Holz, I., Janekovic, D., Hain, J., Lanzendörfer, M., and Kristjansson, J.K. (1993). Screening for Sulfolobales, their plasmids and their viruses in icelandic solfataras. Syst Appl Microbiol 16, 609–628.
Acknowledgement
This work was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB0570000, XDB37010201), the Basic Research Program Based on Major Scientific Infrastructures of Chinese Academy of Sciences (JZHKYPT-2021-05), the National Natural Science Foundation of China (91940302, 91540201, 31430024, 31325007) and the National Key Research and Development Program of China (2017YFA0504600). We thank Qunxin She for providing S. islandicus strains, Li Huang for help in S. islandicus culturing, Hongjie Zhang for help in radioactivity experiments and Xiuling Gao for technical assistance.
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Wang, J., Wu, S. & Ye, K. Complicated target recognition by archaeal box C/D guide RNAs. Sci. China Life Sci. 67, 631–644 (2024). https://doi.org/10.1007/s11427-022-2412-3
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DOI: https://doi.org/10.1007/s11427-022-2412-3