Skip to main content
SpringerLink
Log in

Complicated target recognition by archaeal box C/D guide RNAs

  • Cover Article
  • Published:
Science China Life Sciences Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • Daume, M., Uhl, M., Backofen, R., and Randau, L. (2017). RIP-Seq suggests translational regulation by L7Ae in archaea. mBio 8, e00730–17.

    Article  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Karijolich, J., and Yu, Y.T. (2010). Spliceosomal snRNA modifications and their function. RNA Biol 7, 192–204.

    Article  CAS  PubMed  Google Scholar 

  • Kim, D., Langmead, B., and Salzberg, S.L. (2015). HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12, 357–360.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • Kiss, T. (2001). Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J 20, 3617–3622.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  PubMed  PubMed Central  Google Scholar 

  • Lowe, T.M., and Eddy, S.R. (1999). A computational screen for methylation guide snoRNAs in yeast. Science 283, 1168–1171.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Quinlan, A.R., and Hall, I.M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roehr, J.T., Dieterich, C., and Reinert, K. (2017). Flexbar 3.0-SIMD and multicore parallelization. Bioinformatics 33, 2941–2942.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    PubMed Central  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yu, Y.T., and Meier, U.T. (2014). RNA-guided isomerization of uridine to pseudouridine-pseudouridylation. RNA Biol 11, 1483–1494.

    Article  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  Google Scholar 

Download references

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.

Author information

Author notes

  1. Contributed equally to this work

Authors and Affiliations

  1. Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China

    Jiayin Wang, Songlin Wu & Keqiong Ye

  2. University of Chinese Academy of Sciences, Beijing, 100049, China

    Jiayin Wang, Songlin Wu & Keqiong Ye

Authors
  1. Jiayin Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Songlin Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Keqiong Ye
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Keqiong Ye.

Ethics declarations

The author(s) declare that they have no conflict of interest.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11427-022-2412-3

Search

Navigation