Architecture of the U5 small nuclear RNA

We have used comparative sequence analysis and deletion analysis to examine the secondary structure of the U5 small nuclear RNA (snRNA), an essential component of the pre-mRNA splicing apparatus. The secondary structure of Saccharomyces cerevisiae U5 snRNA was studied in detail, while sequences from six other fungal species were included in the phylogenetic analysis. Our results indicate that fungal U5 snRNAs, like their counterparts from other taxa, can be folded into a secondary structure characterized by a highly conserved stem-loop (stem-loop 1) that is flanked by a moderately conserved internal loop (internal loop 1). In addition, several of the fungal U5 snRNAs include a novel stem-loop structure (ca. 30 nucleotides) that is adjacent to stem-loop 1. By deletion analysis of the S. cerevisiae snRNA, we have demonstrated that the minimal U5 snRNA that can complement the lethal phenotype of a U5 gene disruption consists of (i) stem-loop 1, (ii) internal loop 1, (iii) a stem-closing internal loop 1, and (iv) the conserved Sm protein binding site. Remarkably, all essential, U5-specific primary sequence elements are encoded by a 39-nucleotide domain consisting of stem-loop 1 and internal loop 1. This domain must, therefore, contain all U5-specific sequences that are essential for splicing activity, including binding sites for U5-specific proteins.

[1]  I. Mattaj,et al.  The determinants for Sm protein binding to Xenopus U1 and U5 snRNAs are complex and non‐identical. , 1993, The EMBO journal.

[2]  J. Steitz,et al.  Site-specific cross-linking of mammalian U5 snRNP to the 5' splice site before the first step of pre-mRNA splicing. , 1992, Genes & development.

[3]  C. Guthrie,et al.  Synthetic lethal mutations suggest interactions between U5 small nuclear RNA and four proteins required for the second step of splicing , 1992, Molecular and cellular biology.

[4]  C. Guthrie,et al.  An essential splicing factor, SLU7, mediates 3' splice site choice in yeast. , 1992, Genes & development.

[5]  J. Steitz,et al.  Interactions of small nuclear RNA's with precursor messenger RNA during in vitro splicing. , 1992, Science.

[6]  C. Norman,et al.  U5 snRNA interacts with exon sequences at 5′ and 3′ splice sites , 1992, Cell.

[7]  C. Guthrie,et al.  More than half of yeast U1 snRNA is dispensable for growth. , 1991, Nucleic acids research.

[8]  H. Nielsen,et al.  Spliceosomal small nuclear RNAs of Tetrahymena thermophila and some possible snRNA-snRNA base-pairing interactions. , 1991, Journal of molecular biology.

[9]  M. Schuler,et al.  cDNA cloning of U1, U2, U4 and U5 snRNA families expressed in pea nuclei. , 1991, Nucleic acids research.

[10]  R. Lührmann,et al.  Protein-RNA interactions in 20S U5 snRNPs. , 1991, Biochimica et biophysica acta.

[11]  Thomas D. Bruns,et al.  Fungal Molecular Systematics , 1991 .

[12]  J. Wise,et al.  Preparation and analysis of low molecular weight RNAs and small ribonucleoproteins. , 1991, Methods in enzymology.

[13]  Janina Maier,et al.  Guide to yeast genetics and molecular biology. , 1991, Methods in enzymology.

[14]  B. Séraphin,et al.  Universally conserved and yeast-specific U1 snRNA sequences are important but not essential for U1 snRNP function. , 1990, Genes & development.

[15]  C. Guthrie,et al.  Unexpected flexibility in an evolutionarily conserved protein‐RNA interaction: genetic analysis of the Sm binding site. , 1990, The EMBO journal.

[16]  J. Thomas,et al.  The spliceosomal snRNAs of Caenorhabditis elegans. , 1990, Nucleic acids research.

[17]  J. Wise,et al.  Sequence and structure of U5 snRNA from Schizosaccharomyces pombe. , 1989, Nucleic acids research.

[18]  C. Guthrie,et al.  Small nuclear RNAs from budding yeasts: phylogenetic comparisons reveal extensive size variation. , 1989, Gene.

[19]  N. Pace,et al.  Phylogenetic comparative analysis and the secondary structure of ribonuclease P RNA--a review. , 1989, Gene.

[20]  D. Black,et al.  U5 small nuclear ribonucleoprotein: RNA structure analysis and ATP-dependent interaction with U4/U6 , 1989, Molecular and cellular biology.

[21]  R. Lührmann,et al.  20S small nuclear ribonucleoprotein U5 shows a surprisingly complex protein composition. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[22]  N. Pace,et al.  The design and catalytic properties of a simplified ribonuclease P RNA. , 1989, Science.

[23]  F. Witney,et al.  Efficient site-directed in vitro mutagenesis using phagemid vectors. , 1989, BioTechniques.

[24]  O. Uhlenbeck,et al.  Synthesis of small RNAs using T7 RNA polymerase. , 1989, Methods in enzymology.

[25]  W. Filipowicz,et al.  Structure and expression of the U5 snRNA gene of Arabidopsis thaliana. Conserved upstream sequence elements in plant U-RNA genes. , 1988, Nucleic acids research.

[26]  C. Guthrie,et al.  Two conserved domains of yeast U2 snRNA are separated by 945 nonessential nucleotides , 1988, Cell.

[27]  M. Birnstiel,et al.  Structure and Function of Major and Minor Small Nuclear Ribonucleoprotein Particles , 1988, Springer Berlin Heidelberg.

[28]  I. Mattaj.  UsnRNP Assembly and Transport , 1988 .

[29]  C. Guthrie,et al.  Spliceosomal snRNAs. , 1988, Annual review of genetics.

[30]  J. Beggs,et al.  Identification of a yeast snRNP protein and detection of snRNP-snRNP interactions , 1987, Cell.

[31]  G. Tebb,et al.  Functional characterization of X. laevis U5 snRNA genes. , 1987, The EMBO journal.

[32]  C. Guthrie,et al.  An essential yeast snRNA with a U5-like domain is required for splicing in vivo , 1987, Cell.

[33]  C. Guthrie,et al.  A subset of yeast snRNA's contains functional binding sites for the highly conserved Sm antigen. , 1987, Science.

[34]  R. Parker.  9 – Architecture of Fungal Introns: Implications for Spliceosome Assembly , 1987 .

[35]  J. Tazi,et al.  A protein that specifically recognizes the 3′ splice site of mammalian pre-mRNA introns is associated with a small nuclear ribonucleoprotein , 1986, Cell.

[36]  M. Rosbash,et al.  Electrophoresis of ribonucleoproteins reveals an ordered assembly pathway of yeast splicing complexes , 1986, Nature.

[37]  J. Steitz,et al.  The 3' splice site of pre-messenger RNA is recognized by a small nuclear ribonucleoprotein. , 1985, Science.

[38]  R. Gutell,et al.  Comparative anatomy of 16-S-like ribosomal RNA. , 1985, Progress in nucleic acid research and molecular biology.

[39]  E. Wieben,et al.  The small nuclear RNAs of Drosophila. , 1984, Journal of molecular biology.

[40]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[41]  A. Krol,et al.  High evolutionary conservation of the secondary structure and of certain nucleotide sequences of U5 RNA. , 1983, Nucleic acids research.

[42]  D. Spector,et al.  Isolation and partial characterization of dinoflagellate U1-U6 small RNAs homologous to rat U small nuclear RNAs. , 1983, The Journal of biological chemistry.

[43]  F. Harada,et al.  Nucleotide sequence of nuclear 5S RNA of mouse cells. , 1981, Biochemical and biophysical research communications.

[44]  C. Branlant,et al.  The nuclear 5S RNAs from chicken, rat and man. U5 RNAs are encoded by multiple genes. , 1981, Nucleic acids research.

[45]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.