Introns in protein‐coding genes in Archaea

Introns in protein‐coding genes are ubiquitous in eukaryotic cells, but pre‐mRNA splicing has yet to be reported in archaeal and its viral genomes. We present evidence of introns in genes encoding a homolog of eukaryotic Cbf5p (centromere‐binding factor 5; a subunit of a small nucleolar ribonucleoprotein) in three Archaea; Aeropyrum pernix, Sulfolobus solfataricus and Sulfolobus tokodaii. Splicing of pre‐mRNAs in vivo was demonstrated by reverse transcriptase‐mediated polymerase chain reaction. The exon–intron boundaries of these genes are predicted to be folded into a structure similar to the bulge–helix–bulge motif, suggesting that splicing of these pre‐mRNAs probably depends on the splicing system elucidated for archaeal pre‐tRNAs and rRNAs.

[1]  R. Garrett,et al.  Archaeal rRNA operons. , 1991, Trends in biochemical sciences.

[2]  N. Nomura,et al.  Molecular Characterization and Postsplicing Fate of Three Introns within the Single rRNA Operon of the Hyperthermophilic ArchaeonAeropyrum pernix K1 , 1998, Journal of bacteriology.

[3]  W. Doolittle,et al.  Transcription and excision of a large intron in the tRNATrp gene of an archaebacterium, Halobacterium volcanii. , 1985, The Journal of biological chemistry.

[4]  Y. Watanabe,et al.  Evolutionary appearance of genes encoding proteins associated with box H/ACA snoRNAs: cbf5p in Euglena gracilis, an early diverging eukaryote, and candidate Gar1p and Nop10p homologs in archaebacteria. , 2000, Nucleic acids research.

[5]  T. D. Brock,et al.  Sulfolobus: A new genus of sulfur-oxidizing bacteria living at low pH and high temperature , 2004, Archiv für Mikrobiologie.

[6]  V. Thorsson,et al.  Genome sequence of Halobacterium species NRC-1. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[7]  J. Sabina,et al.  Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.

[8]  R. Garrett,et al.  An intron in the 23S ribosomal RNA gene of the archaebacterium Desulfurococcus mobilis , 1985, Nature.

[9]  M. Belfort,et al.  Barriers to Intron Promiscuity in Bacteria , 2000, Journal of bacteriology.

[10]  G. Church,et al.  Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics , 1997, Journal of bacteriology.

[11]  K. Kanehori,et al.  Determination of the complete genomic DNA sequence of Thermoplasma volcanium GSS1 , 1999 .

[12]  D. Armbruster,et al.  Splicing of Intron-containing tRNATrp by the ArchaeonHaloferax volcanii Occurs Independent of Mature tRNA Structure* , 1997, The Journal of Biological Chemistry.

[13]  Y. Kawarabayasi,et al.  Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. , 1999, DNA research : an international journal for rapid publication of reports on genes and genomes.

[14]  Dmitrij Frishman,et al.  The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum , 2000, Nature.

[15]  Maurille J. Fournier,et al.  Point Mutations in Yeast CBF5 Can Abolish In Vivo Pseudouridylation of rRNA , 1999, Molecular and Cellular Biology.

[16]  R. Garrett,et al.  Comparison of transfer RNA and ribosomal RNA intron splicing in the extreme thermophile and archaebacterium Desulfurococcus mobilis. , 1989, Canadian journal of microbiology.

[17]  R. Garrett,et al.  RNA–protein interactions of an archaeal homotetrameric splicing endoribonuclease with an exceptional evolutionary history , 1997, The EMBO journal.

[18]  C. Daniels,et al.  Recognition of exon-intron boundaries by the Halobacterium volcanii tRNA intron endonuclease. , 1990, The Journal of biological chemistry.

[19]  C J Daniels,et al.  A tRNA(Trp) intron endonuclease from Halobacterium volcanii. Unique substrate recognition properties. , 1988, The Journal of biological chemistry.

[20]  R. Garrett,et al.  Archaeal introns: splicing, intercellular mobility and evolution. , 1997, Trends in biochemical sciences.

[21]  Y. Kawarabayasi,et al.  Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7. , 2001, DNA research : an international journal for rapid publication of reports on genes and genomes.

[22]  F. Robb,et al.  Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. , 1998, DNA research : an international journal for rapid publication of reports on genes and genomes.

[23]  R. Fleischmann,et al.  The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus , 1997, Nature.

[24]  D. Armbruster,et al.  Properties of H. volcanii tRNA Intron Endonuclease Reveal a Relationship between the Archaeal and Eucaryal tRNA Intron Processing Systems , 1997, Cell.

[25]  R A Garrett,et al.  Ribosomal RNA introns in archaea and evidence for RNA conformational changes associated with splicing. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Tadashi Maruyama,et al.  Aeropyrum pernix gen. nov., sp. nov., a Novel Aerobic Hyperthermophilic Archaeon Growing at Temperatures up to 100°C , 1996 .

[27]  E V Koonin,et al.  Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases. , 1996, Nucleic acids research.

[28]  Mark Gerstein,et al.  Structural proteomics of an archaeon , 2000, Nature Structural Biology.

[29]  Mark A. Ragan,et al.  The complete genome of the crenarchaeon Sulfolobus solfataricus P2 , 2001, Proceedings of the National Academy of Sciences of the United States of America.