Searching genomes for ribozymes and riboswitches

New regulatory RNAs with complex structures have recently been discovered, among them the first catalytic riboswitch, a gene-regulatory RNA sequence with catalytic activity. Here we discuss some of the experimental approaches and theoretical difficulties attached to the identification of new ribozymes in genomes.

[1]  T. Steitz,et al.  The structural basis of ribosome activity in peptide bond synthesis. , 2000, Science.

[2]  E. Westhof,et al.  Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity , 2003, Nature Structural Biology.

[3]  J. Daròs,et al.  Identification of a retroviroid-like element from plants. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[4]  D. Haussler,et al.  Ultraconserved Elements in the Human Genome , 2004, Science.

[5]  N. Proudfoot,et al.  Autocatalytic RNA cleavage in the human β-globin pre-mRNA promotes transcription termination , 2004, Nature.

[6]  Sean R. Eddy,et al.  Rfam: an RNA family database , 2003, Nucleic Acids Res..

[7]  D. Lilley.  The Varkud satellite ribozyme. , 2004, RNA.

[8]  J. Perreault,et al.  Natural 2′,5′-Phosphodiester Bonds Found at the Ligation Sites of Peach Latent Mosaic Viroid , 2001, Journal of Virology.

[9]  I. Shih,et al.  Ribozyme cleavage of a 2,5-phosphodiester linkage: mechanism and a restricted divalent metal-ion requirement. , 1999, RNA.

[10]  E. Westhof,et al.  Geometric nomenclature and classification of RNA base pairs. , 2001, RNA.

[11]  Hong Li,et al.  RNA Recognition and Cleavage by a Splicing Endonuclease , 2006, Science.

[12]  R. Breaker,et al.  Riboswitches as versatile gene control elements. , 2005, Current opinion in structural biology.

[13]  Bjarne Knudsen,et al.  Pfold: RNA Secondary Structure Prediction Using Stochastic Context-Free Grammars , 2003 .

[14]  Quentin Vicens,et al.  Atomic level architecture of group I introns revealed. , 2006, Trends in biochemical sciences.

[15]  F. Michel,et al.  Multiple tertiary interactions involving domain II of group II self-splicing introns. , 1997, Journal of molecular biology.

[16]  S. Silverman,et al.  Parallel Selections In Vitro Reveal a Preference for 2′–5′ RNA Ligation upon Deoxyribozyme-Mediated Opening of a 2′,3′-Cyclic Phosphate , 2005, Journal of Molecular Evolution.

[17]  K. Umesono,et al.  Comparative and functional anatomy of group II catalytic introns--a review. , 1989, Gene.

[18]  P. Schuster,et al.  IR-98-039 / April Continuity in Evolution : On the Nature of Transitions , 1998 .

[19]  Eduardo A. Groisman,et al.  An RNA Sensor for Intracellular Mg2+ , 2006, Cell.

[20]  J. Mattick,et al.  Small regulatory RNAs in mammals. , 2005, Human molecular genetics.

[21]  James W. Brown,et al.  RNase P RNAs from some Archaea are catalytically active. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[22]  M. Gelfand,et al.  A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes. , 1999, Trends in genetics : TIG.

[23]  E. Westhof.  A tale in molecular recognition: the hammerhead ribozyme , 2007, Journal of molecular recognition : JMR.

[24]  Vitaly Epshtein,et al.  The riboswitch-mediated control of sulfur metabolism in bacteria , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[25]  A. Ferré-D’Amaré,et al.  Crystal structure of a hairpin ribozyme–inhibitor complex with implications for catalysis , 2001, Nature.

[26]  Klaudia Walter,et al.  Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development , 2004, PLoS biology.

[27]  W. Scott,et al.  Tertiary Contacts Distant from the Active Site Prime a Ribozyme for Catalysis , 2006, Cell.

[28]  C. Trotta,et al.  Crystal structure and evolution of a transfer RNA splicing enzyme. , 1998, Science.

[29]  Thomas A. Steitz,et al.  RNA tertiary interactions in the large ribosomal subunit: The A-minor motif , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[30]  M. Famulok,et al.  Novel RNA catalysts for the Michael reaction. , 2001, Chemistry & biology.

[31]  J. Mattick.  The Functional Genomics of Noncoding RNA , 2005, Science.

[32]  Eric Westhof,et al.  The non-Watson-Crick base pairs and their associated isostericity matrices. , 2002, Nucleic acids research.

[33]  Zasha Weinberg,et al.  A Glycine-Dependent Riboswitch That Uses Cooperative Binding to Control Gene Expression , 2004, Science.

[34]  Margaret S. Ebert,et al.  An mRNA structure in bacteria that controls gene expression by binding lysine. , 2003, Genes & development.

[35]  A. Ferré-D’Amaré,et al.  Crystal structure of a hepatitis delta virus ribozyme , 1998, Nature.

[36]  R. Collins,et al.  A site-specific self-cleavage reaction performed by a novel RNA in neurospora mitochondria , 1990, Cell.

[37]  I. Hofacker,et al.  Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. , 2004, Journal of molecular biology.

[38]  Ali Nahvi,et al.  Genetic control by a metabolite binding mRNA. , 2002, Chemistry & biology.

[39]  J. M. Buzayan,et al.  Autolytic Processing of Dimeric Plant Virus Satellite RNA , 1986, Science.

[40]  J. Gall,et al.  Self-cleaving transcripts of satellite DNA from the newt , 1987, Cell.

[41]  Ricardo Flores,et al.  Peripheral regions of natural hammerhead ribozymes greatly increase their self‐cleavage activity , 2003, The EMBO journal.

[42]  R. Breaker,et al.  Adenine riboswitches and gene activation by disruption of a transcription terminator , 2004, Nature Structural &Molecular Biology.

[43]  T. Cech,et al.  In vitro splicing of the ribosomal RNA precursor of tetrahymena: Involvement of a guanosine nucleotide in the excision of the intervening sequence , 1981, Cell.

[44]  Ronald R. Breaker,et al.  Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression , 2002, Nature.

[45]  Ali Nahvi,et al.  An mRNA structure that controls gene expression by binding S-adenosylmethionine , 2003, Nature Structural Biology.

[46]  T. Cech,et al.  Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site. , 2004, Molecular cell.

[47]  E. Westhof,et al.  Topology of three-way junctions in folded RNAs. , 2006, RNA.

[48]  R. Overbeek,et al.  Searching for patterns in genomic data. , 1997, Trends in genetics : TIG.

[49]  David Haussler,et al.  Identification and Classification of Conserved RNA Secondary Structures in the Human Genome , 2006, PLoS Comput. Biol..

[50]  Daniel Gautheret,et al.  An RNA pattern matching program with enhanced performance and portability , 1994, Comput. Appl. Biosci..

[51]  Ricardo Flores,et al.  Viroids: the minimal non‐coding RNAs with autonomous replication , 2004, FEBS letters.

[52]  E. Westhof,et al.  The interaction networks of structured RNAs. , 2006, Nucleic acids research.

[53]  Jennifer A. Doudna,et al.  The chemical repertoire of natural ribozymes , 2002, Nature.

[54]  Scott A Strobel,et al.  Crystal structure of a group I intron splicing intermediate. , 2004, RNA.

[55]  S. Gräf,et al.  A database search for hammerhead ribozyme motifs. , 2005, Biochemical Society transactions.

[56]  D. Meadows,et al.  The mechanism of action of ribonuclease. , 1969, Proceedings of the National Academy of Sciences of the United States of America.

[57]  R Cedergren,et al.  Hammerhead-mediated processing of satellite pDo500 family transcripts from Dolichopoda cave crickets. , 2000, Nucleic acids research.

[58]  R. Gutell,et al.  Representation of the secondary and tertiary structure of group I introns , 1994, Nature Structural Biology.

[59]  D. Haussler,et al.  An RNA gene expressed during cortical development evolved rapidly in humans , 2006, Nature.

[60]  Ivo L. Hofacker,et al.  Vienna RNA secondary structure server , 2003, Nucleic Acids Res..

[61]  M. Lai,et al.  Human hepatitis delta virus RNA subfragments contain an autocleavage activity. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[62]  Tao Pan,et al.  A small metalloribozyme with a two-step mechanism , 1992, Nature.

[63]  Zasha Weinberg,et al.  Sequence-based heuristics for faster annotation of non-coding RNA families , 2006, Bioinform..

[64]  P. Schuster,et al.  From sequences to shapes and back: a case study in RNA secondary structures , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[65]  Arnold E. Hampel,et al.  Catalytic properties of hairpin ribozymes derived from Chicory yellow mottle virus and arabis mosaic virus satellite RNAs. , 1995, Biochemistry.

[66]  E. Westhof,et al.  Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. , 1990, Journal of molecular biology.

[67]  David H Mathews,et al.  Prediction of RNA secondary structure by free energy minimization. , 2006, Current opinion in structural biology.

[68]  E Westhof,et al.  Group I-like ribozymes with a novel core organization perform obligate sequential hydrolytic cleavages at two processing sites. , 1998, RNA.

[69]  Robert Cedergren,et al.  Schistosome Satellite DNA Encodes Active Hammerhead Ribozymes , 1998, Molecular and Cellular Biology.

[70]  D. Haussler,et al.  A distal enhancer and an ultraconserved exon are derived from a novel retroposon , 2006, Nature.

[71]  J. Mattick,et al.  Non-coding RNA. , 2006, Human molecular genetics.

[72]  R. Nielsen.  A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes , 2022 .

[73]  T. Henkin,et al.  Transcription termination control of the S box system: Direct measurement of S-adenosylmethionine by the leader RNA , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[74]  R. Breaker,et al.  Control of gene expression by a natural metabolite-responsive ribozyme , 2004, Nature.

[75]  J. Szostak,et al.  Evolution of aptamers with a new specificity and new secondary structures from an ATP aptamer. , 2003, RNA.

[76]  Zasha Weinberg,et al.  CMfinder - a covariance model based RNA motif finding algorithm , 2006, Bioinform..

[77]  Evgeny Nudler,et al.  Sensing Small Molecules by Nascent RNA A Mechanism to Control Transcription in Bacteria , 2002, Cell.

[78]  L. Grivell,et al.  Excised group II introns in yeast mitochondria are lariats and can be formed by self-splicing in vitro , 1986, Cell.

[79]  Jeffrey E. Barrick,et al.  New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[80]  James W. Brown.  The ribonuclease P database , 1998, Nucleic Acids Res..

[81]  A. Ferré-D’Amaré,et al.  Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module. , 2000, Journal of molecular biology.

[82]  Eric Westhof,et al.  Functional Hammerhead Ribozymes Naturally Encoded in the Genome of Arabidopsis thalianaw⃞ , 2005, The Plant Cell Online.

[83]  Eric Westhof,et al.  An mRNA Is Capped by a 2', 5' Lariat Catalyzed by a Group I-Like Ribozyme , 2005, Science.

[84]  Donald H. Burke,et al.  Evolutionary Landscapes for the Acquisition of New Ligand Recognition by RNA Aptamers , 2003, Journal of Molecular Evolution.

[85]  Eric Westhof,et al.  Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure , 2005, Bioinform..

[86]  Jack W. Szostak,et al.  In vitro evolution suggests multiple origins for the hammerhead ribozyme , 2001, Nature.

[87]  N. Pace,et al.  The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme , 1983, Cell.

[88]  Robert Giegerich,et al.  A comprehensive comparison of comparative RNA structure prediction approaches , 2004, BMC Bioinformatics.

[89]  J. Perreault,et al.  Peach latent mosaic viroid is locked by a 2',5'-phosphodiester bond produced by in vitro self-ligation. , 1997, Journal of molecular biology.

[90]  Piero Carninci,et al.  Tagging mammalian transcription complexity. , 2006, Trends in genetics : TIG.

[91]  Jeffrey E. Barrick,et al.  Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria , 2005, Genome Biology.

[92]  M. Gelfand,et al.  Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? , 2003, Nucleic acids research.

[93]  D. Lilley,et al.  Structure, folding and mechanisms of ribozymes. , 2005, Current opinion in structural biology.

[94]  E. Westhof,et al.  The building blocks and motifs of RNA architecture. , 2006, Current opinion in structural biology.

[95]  F. Lisacek,et al.  Automatic identification of group I intron cores in genomic DNA sequences. , 1994, Journal of molecular biology.

[96]  R R Breaker,et al.  Structural diversity of self-cleaving ribozymes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[97]  Jeffrey E. Barrick,et al.  Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria , 2003, Cell.

[98]  T. Henkin,et al.  The L box regulon: Lysine sensing by leader RNAs of bacterial lysine biosynthesis genes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[99]  A. Ferré-D’Amaré,et al.  Structural Basis of glmS Ribozyme Activation by Glucosamine-6-Phosphate , 2006, Science.

[100]  T. Tarasow,et al.  RNA-catalysed carbon–carbon bond formation , 1997, Nature.

[101]  B. Dujon,et al.  Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. , 1982, Biochimie.

[102]  H. Noller,et al.  Unusual resistance of peptidyl transferase to protein extraction procedures. , 1992, Science.

[103]  B. Golden,et al.  Crystal structure of a phage Twort group I ribozyme–product complex , 2005, Nature Structural &Molecular Biology.

[104]  Martin Tabler,et al.  Viroids: petite RNA pathogens with distinguished talents. , 2004, Trends in plant science.

[105]  Hong Li,et al.  tRNA Splicing* , 1998, The Journal of Biological Chemistry.

[106]  P. Perlman,et al.  A self-splicing RNA excises an intron lariat , 1986, Cell.

[107]  E. Kool,et al.  Generation of catalytic RNAs by rolling transcription of synthetic DNA nanocircles , 1997, Nature Biotechnology.

[108]  Jennifer A. Doudna,et al.  A universal mode of helix packing in RNA , 2001, Nature Structural Biology.

[109]  E Westhof,et al.  The A-minor motifs in the decoding recognition process. , 2006, Biochimie.

[110]  R. Durbin,et al.  RNA sequence analysis using covariance models. , 1994, Nucleic acids research.

[111]  Eric Westhof,et al.  Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments , 2005, Nucleic acids research.

[112]  Adam Roth,et al.  Identification of a large noncoding RNA in extremophilic eubacteria , 2006, Proceedings of the National Academy of Sciences.

[113]  J. Miranda-Ríos,et al.  A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[114]  L. M. Epstein,et al.  Cloning and characterization of extended hammerheads from a diverse set of caudate amphibians. , 1996, Gene.

[115]  Andrej Lupták,et al.  A Genomewide Search for Ribozymes Reveals an HDV-Like Sequence in the Human CPEB3 Gene , 2006, Science.

[116]  J. M. Buzayan,et al.  Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA , 1986, Nature.

[117]  D. Bartel,et al.  One sequence, two ribozymes: implications for the emergence of new ribozyme folds. , 2000, Science.

[118]  R. Symons,et al.  Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites , 1987, Cell.