Landscape of RNA pseudouridylation in archaeon Sulfolobus islandicus

Abstract Pseudouridine, one of the most abundant RNA modifications, is synthesized by stand-alone or RNA-guided pseudouridine synthases. Here, we comprehensively mapped pseudouridines in rRNAs, tRNAs and small RNAs in the archaeon Sulfolobus islandicus and identified Cbf5-associated H/ACA RNAs. Through genetic deletion and in vitro modification assays, we determined the responsible enzymes for these modifications. The pseudouridylation machinery in S. islandicus consists of the stand-alone enzymes aPus7 and aPus10, and six H/ACA RNA-guided enzymes that account for all identified pseudouridines. These H/ACA RNAs guide the modification of all eleven sites in rRNAs, two sites in tRNAs, and two sites in CRISPR RNAs. One H/ACA RNA shows exceptional versatility by targeting eight different sites. aPus7 and aPus10 are responsible for modifying positions 13, 54 and 55 in tRNAs. We identified four atypical H/ACA RNAs that lack the lower stem and the ACA motif and confirmed their function both in vivo and in vitro. Intriguingly, atypical H/ACA RNAs can be modified by Cbf5 in a guide-independent manner. Our data provide the first global view of pseudouridylation in archaea and reveal unexpected structures, substrates, and activities of archaeal H/ACA RNPs.

[1]  K. Ye,et al.  Complicated target recognition by archaeal box C/D guide RNAs. , 2023, Science China. Life sciences.

[2]  T. Pan,et al.  Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution , 2022, Nature Biotechnology.

[3]  C. Yi,et al.  Quantitative profiling of pseudouridylation landscape in the human transcriptome , 2022, bioRxiv.

[4]  K. Ye,et al.  Profiling of RNA ribose methylation in Arabidopsis thaliana , 2021, Nucleic acids research.

[5]  E. Westhof,et al.  Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea , 2020, RNA.

[6]  P. Kharel,et al.  The presence of the ACA box in archaeal H/ACA guide RNAs promotes atypical pseudouridylation , 2020, RNA.

[7]  Tsutomu Suzuki,et al.  Biogenesis and functions of aminocarboxypropyluridine in tRNA , 2019, Nature Communications.

[8]  Xiaohong Zhu,et al.  Transcriptome-wide analysis of pseudouridylation of mRNA and non-coding RNAs in Arabidopsis , 2019, Journal of experimental botany.

[9]  V. de Crécy-Lagard,et al.  tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii , 2019, Journal of bacteriology.

[10]  P. Forterre,et al.  Contribution of protein Gar1 to the RNA-guided and RNA-independent rRNA:Ψ-synthase activities of the archaeal Cbf5 protein , 2018, Scientific Reports.

[11]  G. Olsen,et al.  The essential genome of the crenarchaeal model Sulfolobus islandicus , 2018, Nature Communications.

[12]  L. Montanaro,et al.  RNA Pseudouridylation in Physiology and Medicine: For Better and for Worse , 2017, Genes.

[13]  Knut Reinert,et al.  Flexbar 3.0 ‐ SIMD and multicore parallelization , 2017, Bioinform..

[14]  Margaret A. Nakamoto,et al.  mRNA pseudouridylation affects RNA metabolism in the parasite Toxoplasma gondii , 2017, RNA.

[15]  Q. She,et al.  Genetic technologies for extremely thermophilic microorganisms of Sulfolobus, the only genetically tractable genus of crenarchaea , 2017, Science China Life Sciences.

[16]  Masato Taoka,et al.  The complete chemical structure of Saccharomyces cerevisiae rRNA: partial pseudouridylation of U2345 in 25S rRNA by snoRNA snR9 , 2016, Nucleic acids research.

[17]  K. Entian,et al.  Ribosome biogenesis factor Tsr3 is the aminocarboxypropyl transferase responsible for 18S rRNA hypermodification in yeast and humans , 2016, Nucleic acids research.

[18]  Yan Zhang,et al.  Harnessing Type I and Type III CRISPR-Cas systems for genome editing , 2015, Nucleic acids research.

[19]  P. Sergiev,et al.  What do we know about ribosomal RNA methylation in Escherichia coli? , 2015, Biochimie.

[20]  Shiqing Ma,et al.  Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. , 2015, Nature chemical biology.

[21]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[22]  Yi-Tao Yu,et al.  RNA-guided isomerization of uridine to pseudouridine—pseudouridylation , 2014, RNA biology.

[23]  P. Brown,et al.  Transcriptome-Wide Mapping of Pseudouridines: Pseudouridine Synthases Modify Specific mRNAs in S. cerevisiae , 2014, PloS one.

[24]  W. Gilbert,et al.  Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells , 2014, Nature.

[25]  Maxwell R. Mumbach,et al.  Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA , 2014, Cell.

[26]  T. Lowe,et al.  Discovery of Pyrobaculum small RNA families with atypical pseudouridine guide RNA features. , 2012, RNA.

[27]  Shuang Li,et al.  Reconstitution and structural analysis of the yeast box H/ACA RNA-guided pseudouridine synthase. , 2011, Genes & development.

[28]  Ian K. Blaby,et al.  Pseudouridine formation in archaeal RNAs: The case of Haloferax volcanii. , 2011, RNA.

[29]  Shiraz A. Shah,et al.  Genome Analyses of Icelandic Strains of Sulfolobus islandicus, Model Organisms for Genetic and Virus-Host Interaction Studies , 2011, Journal of bacteriology.

[30]  K. Entian,et al.  The Bowen–Conradi syndrome protein Nep1 (Emg1) has a dual role in eukaryotic ribosome biogenesis, as an essential assembly factor and in the methylation of Ψ1191 in yeast 18S rRNA , 2010, Nucleic acids research.

[31]  T. Kiss,et al.  Box H/ACA small ribonucleoproteins. , 2010, Molecular cell.

[32]  John Karijolich,et al.  Spliceosomal snRNA modifications and their function , 2010, RNA biology.

[33]  K. Entian,et al.  The ribosome assembly factor Nep1 responsible for Bowen–Conradi syndrome is a pseudouridine-N1-specific methyltransferase , 2010, Nucleic acids research.

[34]  R. Terns,et al.  Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA , 2009, Nature Structural &Molecular Biology.

[35]  Q. She,et al.  Unmarked gene deletion and host–vector system for the hyperthermophilic crenarchaeon Sulfolobus islandicus , 2009, Extremophiles.

[36]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[37]  K. Ye,et al.  Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase. , 2009, Molecular cell.

[38]  Y. Motorin,et al.  Deficiency of the tRNATyr:Ψ35-synthase aPus7 in Archaea of the Sulfolobales order might be rescued by the H/ACA sRNA-guided machinery , 2009, Nucleic acids research.

[39]  Priyatansh Gurha,et al.  Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA. , 2008, RNA.

[40]  Henri Grosjean,et al.  RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes , 2008, BMC Genomics.

[41]  Wayne A. Decatur,et al.  Different Mechanisms for Pseudouridine Formation in Yeast 5S and 5.8S rRNAs , 2008, Molecular and Cellular Biology.

[42]  I. Behm-Ansmant,et al.  Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in ribosomal RNAs , 2008, Nucleic acids research.

[43]  Glen Spraggon,et al.  Crystal structure of human Pus10, a novel pseudouridine synthase. , 2007, Journal of molecular biology.

[44]  C. Branlant,et al.  Identification of determinants in the protein partners aCBF5 and aNOP10 necessary for the tRNA:Ψ55-synthase and RNA-guided RNA:Ψ-synthase activities , 2007, Nucleic acids research.

[45]  K. Ye,et al.  Crystal structure of an H/ACA box ribonucleoprotein particle , 2006, Nature.

[46]  R. Terns,et al.  Formation of the conserved pseudouridine at position 55 in archaeal tRNA , 2006, Nucleic Acids Research.

[47]  Gabriele Varani,et al.  The Cbf5–Nop10 complex is a molecular bracket that organizes box H/ACA RNPs , 2005, Nature Structural &Molecular Biology.

[48]  C. Branlant,et al.  Reconstitution of archaeal H/ACA small ribonucleoprotein complexes active in pseudouridylation , 2005, Nucleic acids research.

[49]  Gwenael Badis,et al.  The complete set of H/ACA snoRNAs that guide rRNA pseudouridylations in Saccharomyces cerevisiae. , 2005, RNA.

[50]  Daniel L Baker,et al.  RNA-guided RNA modification: functional organization of the archaeal H/ACA RNP. , 2005, Genes & development.

[51]  L. H. Hansen,et al.  The archaeon Haloarcula marismortui has few modifications in the central parts of its 23S ribosomal RNA. , 2005, Journal of molecular biology.

[52]  A. Omer,et al.  The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus , 2005, Molecular microbiology.

[53]  J. Ofengand,et al.  Number, position, and significance of the pseudouridines in the large subunit ribosomal RNA of Haloarcula marismortui and Deinococcus radiodurans. , 2005, RNA.

[54]  Christiane Branlant,et al.  The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Psi-synthase also acting on tRNAs. , 2003, RNA.

[55]  A. Hüttenhofer,et al.  Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea. , 2003, Nucleic acids research.

[56]  A. Hüttenhofer,et al.  Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[57]  J. Ofengand.  Ribosomal RNA pseudouridines and pseudouridine synthases , 2002, FEBS letters.

[58]  M. Hansen,et al.  Posttranscriptional modifications in the A-loop of 23S rRNAs from selected archaea and eubacteria. , 2002, RNA.

[59]  S. Eddy,et al.  Homologs of small nucleolar RNAs in Archaea. , 2000, Science.

[60]  Y. Motorin,et al.  The first determination of pseudouridine residues in 23S ribosomal RNA from hyperthermophilic Archaea Sulfolobus acidocaldarius , 1999, FEBS letters.

[61]  Kathleen R. Noon,et al.  Posttranscriptional Modifications in 16S and 23S rRNAs of the Archaeal Hyperthermophile Sulfolobus solfataricus , 1998, Journal of bacteriology.

[62]  Tamás Kiss,et al.  Site-Specific Pseudouridine Formation in Preribosomal RNA Is Guided by Small Nucleolar RNAs , 1997, Cell.

[63]  T. Kiss,et al.  The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. , 1997, Genes & development.

[64]  J Ofengand,et al.  Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts. , 1997, Journal of molecular biology.

[65]  J Ofengand,et al.  Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: analysis by the application of a new sequencing technique. , 1993, Biochemistry.

[66]  Ramesh C. Gupta.  Transfer RNAs of Halobacterium volcanii: Sequences of five leucine and three serine tRNAs* , 1986 .

[67]  R. Gupta.  Halobacterium volcanii tRNAs. Identification of 41 tRNAs covering all amino acids, and the sequences of 33 class I tRNAs. , 1984, The Journal of biological chemistry.

[68]  C. Branlant,et al.  A dedicated computational approach for the identification of archaeal H/ACA sRNAs. , 2007, Methods in enzymology.

[69]  A. Ferré-D’Amaré,et al.  Pseudouridine synthases. , 2006, Chemistry & biology.

[70]  Wayne A. Decatur,et al.  Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome. , 2004, Nucleic acids research.