{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T06:35:46Z","timestamp":1773297346638,"version":"3.50.1"},"reference-count":71,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2011,5,5]],"date-time":"2011-05-05T00:00:00Z","timestamp":1304553600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1002031","type":"journal-article","created":{"date-parts":[[2011,5,5]],"date-time":"2011-05-05T20:41:29Z","timestamp":1304628089000},"page":"e1002031","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":141,"title":["Identification of Hammerhead Ribozymes in All Domains of Life Reveals Novel Structural Variations"],"prefix":"10.1371","volume":"7","author":[{"given":"Jonathan","family":"Perreault","sequence":"first","affiliation":[]},{"given":"Zasha","family":"Weinberg","sequence":"additional","affiliation":[]},{"given":"Adam","family":"Roth","sequence":"additional","affiliation":[]},{"given":"Olivia","family":"Popescu","sequence":"additional","affiliation":[]},{"given":"Pascal","family":"Chartrand","sequence":"additional","affiliation":[]},{"given":"Gerardo","family":"Ferbeyre","sequence":"additional","affiliation":[]},{"given":"Ronald R.","family":"Breaker","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2011,5,5]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/0092-8674(87)90562-9","article-title":"Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites.","volume":"49","author":"AC Forster","year":"1987","journal-title":"Cell"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1021\/ar800050c","article-title":"Catalytic Strategies of Self-Cleaving Ribozymes.","volume":"41","author":"JC Cochrane","year":"2008","journal-title":"Acc Chem Res"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"3627","DOI":"10.1093\/nar\/14.9.3627","article-title":"Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid.","volume":"14","author":"CJ Hutchins","year":"1986","journal-title":"Nucleic Acids Res"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1126\/science.231.4745.1577","article-title":"Autolytic Processing of Dimeric Plant Virus Satellite RNA.","volume":"231","author":"GA Prody","year":"1986","journal-title":"Science"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1261\/rna.912608","article-title":"Hammerhead redux: does the new structure fit the old biochemical data?","volume":"14","author":"JA Nelson","year":"2008","journal-title":"RNA"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"5561","DOI":"10.1093\/emboj\/cdg530","article-title":"Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity.","volume":"22","author":"M De la Pena","year":"2003","journal-title":"EMBO J"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1038\/nsb959","article-title":"Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity.","volume":"10","author":"A Khvorova","year":"2003","journal-title":"Nat Struct Biol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1016\/j.cell.2006.06.036","article-title":"Tertiary contacts distant from the active site prime a ribozyme for catalysis.","volume":"126","author":"M Martick","year":"2006","journal-title":"Cell"},{"key":"ref9","first-page":"211","article-title":"An RNA pattern matching program with enhanced performance and portability.","volume":"10","author":"A Laferriere","year":"1994","journal-title":"Comput Appl Biosci"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1101\/gr.10.7.1011","article-title":"Distribution of hammerhead and hammerhead-like RNA motifs through the GenBank.","volume":"10","author":"G Ferbeyre","year":"2000","journal-title":"Genome Res"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1042\/BST0330477","article-title":"A database search for hammerhead ribozyme motifs.","volume":"33","author":"S Graf","year":"2005","journal-title":"Biochem Soc Trans"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"3880","DOI":"10.1128\/MCB.18.7.3880","article-title":"Schistosome satellite DNA encodes active hammerhead ribozymes.","volume":"18","author":"G Ferbeyre","year":"1998","journal-title":"Mol Cell Biol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1877","DOI":"10.1105\/tpc.105.032730","article-title":"Functional hammerhead ribozymes naturally encoded in the genome of Arabidopsis thaliana.","volume":"17","author":"R Przybilski","year":"2005","journal-title":"Plant Cell"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1038\/nature07117","article-title":"A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA.","volume":"454","author":"M Martick","year":"2008","journal-title":"Nature"},{"key":"ref15","article-title":"Intronic hammerhead ribozymes are ultraconserved in the human genome.","author":"M De la Pena","year":"2010","journal-title":"EMBO rep"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1943","DOI":"10.1261\/rna.2130310","article-title":"Ubiquitous presence of the hammerhead ribozyme along the tree of life.","volume":"16","author":"M De la Pena","year":"2010","journal-title":"RNA"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1126\/science.1178084","article-title":"Widespread occurrence of self-cleaving ribozymes.","volume":"326","author":"CH Webb","year":"2009","journal-title":"Science"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1788","DOI":"10.1126\/science.1129308","article-title":"A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene.","volume":"313","author":"K Salehi-Ashtiani","year":"2006","journal-title":"Science"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1038\/nature02362","article-title":"Control of gene expression by a natural metabolite-responsive ribozyme.","volume":"428","author":"WC Winkler","year":"2004","journal-title":"Nature"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/gb-2010-11-3-r31","article-title":"Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes.","volume":"11","author":"Z Weinberg","year":"2010","journal-title":"Genome Biol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1093\/bioinformatics\/bti743","article-title":"Sequence-based heuristics for faster annotation of non-coding RNA families.","volume":"22","author":"Z Weinberg","year":"2006","journal-title":"Bioinformatics"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"4724","DOI":"10.1093\/nar\/29.22.4724","article-title":"RNAMotif, an RNA secondary structure definition and search algorithm.","volume":"29","author":"TJ Macke","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1093\/bioinformatics\/btk008","article-title":"CMfinder\u2013a covariance model based RNA motif finding algorithm.","volume":"22","author":"Z Yao","year":"2006","journal-title":"Bioinformatics"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1471-2148-10-3","article-title":"Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae).","volume":"10","author":"L Martinsen","year":"2010","journal-title":"BMC Evol Biol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"4037","DOI":"10.1093\/nar\/28.20.4037","article-title":"Hammerhead-mediated processing of satellite pDo500 family transcripts from Dolichopoda cave crickets.","volume":"15","author":"AA Rojas","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1007\/978-1-59745-033-1_4","article-title":"In-line probing analysis of riboswitches.","volume":"419","author":"EE Regulski","year":"2008","journal-title":"Methods Mol Biol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"10695","DOI":"10.1021\/bi00499a018","article-title":"Sequence requirements of the hammerhead RNA self-cleavage reaction.","volume":"29","author":"DE Ruffner","year":"1990","journal-title":"Biochemistry"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1002\/1439-7633(20010903)2:9<629::AID-CBIC629>3.0.CO;2-3","article-title":"In vitro selection of hammerhead ribozyme sequence variants.","volume":"2","author":"F Eckstein","year":"2001","journal-title":"Chembiochem"},{"key":"ref29","first-page":"914","article-title":"Examination of the catalytic fitness of the hammerhead ribozyme by in vitro selection.","volume":"3","author":"J Tang","year":"1997","journal-title":"RNA"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1877","DOI":"10.1093\/nar\/26.8.1877","article-title":"In vitro and in vivo self-cleavage of a viroid RNA with a mutation in the hammerhead catalytic pocket.","volume":"26","author":"S Ambros","year":"1998","journal-title":"Nucleic Acids Res"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1515\/BC.2007.065","article-title":"Idiosyncratic cleavage and ligation activity of individual hammerhead ribozymes and core sequence variants thereof.","volume":"388","author":"R Przybilski","year":"2007","journal-title":"Biol Chem"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1625","DOI":"10.1261\/rna.631207","article-title":"The tolerance to exchanges of the Watson Crick base pair in the hammerhead ribozyme core is determined by surrounding elements.","volume":"13","author":"R Przybilski","year":"2007","journal-title":"RNA"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"4116","DOI":"10.1093\/nar\/26.18.4116","article-title":"Sequence specificity of the hammerhead ribozyme revisited; the NHH rule.","volume":"26","author":"AR Kore","year":"1998","journal-title":"Nucleic Acids Res"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1016\/0006-3002(62)90453-5","article-title":"Solute concentrations within cells of halophilic and non-halophilic bacteria.","volume":"65","author":"JH Christian","year":"1962","journal-title":"Biochim Biophys Acta"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1016\/S1074-5521(98)90116-8","article-title":"The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone.","volume":"5","author":"JB Murray","year":"1998","journal-title":"Chem Biol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"10848","DOI":"10.1021\/ja046848v","article-title":"Fast cleavage kinetics of a natural hammerhead ribozyme.","volume":"126","author":"MD Canny","year":"2004","journal-title":"J Am Chem Soc"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1261\/rna.5205404","article-title":"A guide to ions and RNA structure.","volume":"10","author":"DE Draper","year":"2004","journal-title":"RNA"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1146\/annurev.biophys.34.040204.144511","article-title":"Ions and RNA folding.","volume":"34","author":"DE Draper","year":"2005","journal-title":"Annu Rev Biophys Biomol Struct"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"D46","DOI":"10.1093\/nar\/gkp1024","article-title":"GenBank.","volume":"38","author":"DA Benson","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"D142","DOI":"10.1093\/nar\/gkg050","article-title":"Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE.","volume":"31","author":"M Safran","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1002\/jor.20323","article-title":"RECK expression in osteosarcoma: correlation with matrix metalloproteinases activation and tumor invasiveness.","volume":"25","author":"HG Kang","year":"2007","journal-title":"J Orthop Res"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1006\/geno.1996.0177","article-title":"The I.M.A.G.E. Consortium: an integrated molecular analysis of genomes and their expression.","volume":"33","author":"G Lennon","year":"1996","journal-title":"Genomics"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1261\/rna.2429911","article-title":"From alpaca to zebrafish: hammerhead ribozymes wherever you look.","volume":"17","author":"C Seehafer","year":"2011","journal-title":"RNA"},{"key":"ref44","article-title":"Structure-based search reveals hammerhead ribozymes in the human microbiome.","author":"RM Jimenez","year":"2011","journal-title":"J Biol Chem"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1038\/35102081","article-title":"In vitro evolution suggests multiple origins for the hammerhead ribozyme.","volume":"414","author":"K Salehi-Ashtiani","year":"2001","journal-title":"Nature"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"5784","DOI":"10.1073\/pnas.97.11.5784","article-title":"Structural diversity of self-cleaving ribozymes.","volume":"97","author":"J Tang","year":"2000","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"1308","DOI":"10.1126\/science.1169202","article-title":"Extremely high mutation rate of a hammerhead viroid.","volume":"323","author":"S Gago","year":"2009","journal-title":"Science"},{"key":"ref48","first-page":"21","article-title":"RNA-RNA and RNA-DNA ligation with the sTobRV(+) hammerhead ribozyme.","author":"Y Tokumoto","year":"1992","journal-title":"Nucleic Acids Symp Ser"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/978-1-60327-853-9_2","article-title":"Defining the mobilome.","volume":"532","author":"JL Siefert","year":"2009","journal-title":"Methods Mol Biol"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"3142","DOI":"10.1128\/MCB.00300-10","article-title":"R2 retrotransposons encode a self-cleaving ribozyme for processing from an rRNA co-transcript.","volume":"30","author":"DG Eickbush","year":"2010","journal-title":"Mol Cell Biol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1016\/j.bbagrm.2009.09.006","article-title":"Structure and function of regulatory RNA elements: ribozymes that regulate gene expression.","volume":"1789","author":"WG Scott","year":"2009","journal-title":"Biochim Biophys Acta"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1099\/00207713-33-2-381","article-title":"Halobacterium sodomense sp. nov., a Dead Sea halobacterium with extremely high magnesium requirement and tolerance.","volume":"33","author":"A Oren","year":"1983","journal-title":"Int J Syst Bacteriol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"1287","DOI":"10.1111\/j.1462-2920.2004.00692.x","article-title":"Isolation and cultivation of Walsby&apos;s square archaeon.","volume":"6","author":"H Bolhuis","year":"2004","journal-title":"Environ Microbiol"},{"key":"ref54","article-title":"Relationships of extremely halophilic bacteria towards divalent cations.","author":"A Oren","year":"1986"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1006\/viro.1993.1643","article-title":"HF1 and HF2: novel bacteriophages of halophilic archaea.","volume":"197","author":"SD Nuttall","year":"1993","journal-title":"Virology"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1046\/j.1365-2958.2002.02890.x","article-title":"HF2: a double-stranded DNA tailed haloarchaeal virus with a mosaic genome.","volume":"44","author":"SL Tang","year":"2002","journal-title":"Mol Microbiol"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1099\/0022-1317-47-1-29","article-title":"Persisting phage infection in Halobacterium salinarium str. 1.","volume":"47","author":"T Torsvik","year":"1980","journal-title":"J Gen Virol"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"3605","DOI":"10.1128\/AEM.56.11.3605-3608.1990","article-title":"Ecophysiology of bacteriophage S5100 infecting Halobacterium cutirubrum.","volume":"56","author":"LL Daniels","year":"1990","journal-title":"Appl Env Microbiol"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1038\/nature03195","article-title":"Natural and engineered nucleic acids as tools to explore biology.","volume":"432","author":"RR Breaker","year":"2004","journal-title":"Nature"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1038\/nchembio846","article-title":"Synthetic RNA circuits.","volume":"3","author":"EA Davidson","year":"2007","journal-title":"Nat Chem Biol"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"3252","DOI":"10.1093\/nar\/20.12.3252","article-title":"Numbering system for the hammerhead.","volume":"20","author":"KJ Hertel","year":"1992","journal-title":"Nucleic Acids Res"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"D136","DOI":"10.1093\/nar\/gkn766","article-title":"Rfam: updates to the RNA families database.","volume":"37","author":"PP Gardner","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/1471-2180-6-24","article-title":"The Subviral RNA Database: a toolbox for viroids, the hepatitis delta virus and satellite RNAs research.","volume":"6","author":"L Rocheleau","year":"2006","journal-title":"BMC Microbiol"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/0092-8674(87)90204-2","article-title":"Self-cleaving transcripts of satellite DNA from the newt.","volume":"48","author":"LM Epstein","year":"1987","journal-title":"Cell"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1017\/S1355838201002515","article-title":"Geometric nomenclature and classification of RNA base pairs.","volume":"7","author":"NB Leontis","year":"2001","journal-title":"RNA"},{"key":"ref66","article-title":"The PyMOL Molecular Graphics System","author":"WL DeLano","year":"2002"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1038\/nature08586","article-title":"Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis.","volume":"462","author":"Z Weinberg","year":"2009","journal-title":"Nature"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1093\/bioinformatics\/btp157","article-title":"Infernal 1.0: inference of RNA alignments.","volume":"25","author":"EP Nawrocki","year":"2009","journal-title":"Bioinformatics"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1111\/j.1462-5822.2006.00804.x","article-title":"Whole genome sequencing of a novel temperate bacteriophage of P. aeruginosa: evidence of tRNA gene mediating integration of the phage genome into the host bacterial chromosome.","volume":"9","author":"Y Tan","year":"2007","journal-title":"Cell Microbiol"},{"key":"ref70","first-page":"6091","article-title":"Proc Natl Acad Sci USA","volume":"95","author":"JA Esteban","year":"1998","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/334265a0","article-title":"Self-cleaving viroid and newt RNAs may only be active as dimers.","volume":"334","author":"AC Forster","year":"1988","journal-title":"Nature"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002031","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,18]],"date-time":"2020-06-18T23:04:49Z","timestamp":1592521489000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002031"}},"subtitle":[],"editor":[{"given":"Wyeth W.","family":"Wasserman","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2011,5,5]]},"references-count":71,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2011,5,5]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1002031","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,5,5]]}}}