Recoding: translational bifurcations in gene expression.

During the expression of a certain genes standard decoding is over-ridden in a site or mRNA specific manner. This recoding occurs in response to special signals in mRNA and probably occurs in all organisms. This review deals with the function and distribution of recoding with a focus on the ribosomal frameshifting used for gene expression in bacteria.

[1]  J. F. Atkins,et al.  Structural studies of the RNA pseudoknot required for readthrough of the gag-termination codon of murine leukemia virus. , 1999, Journal of molecular biology.

[2]  M. Chandler,et al.  Insertion Sequences , 1998, Microbiology and Molecular Biology Reviews.

[3]  A. Flower,et al.  The gamma subunit of DNA polymerase III holoenzyme of Escherichia coli is produced by ribosomal frameshifting. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[4]  A Danchin,et al.  SubtiList: a relational database for the Bacillus subtilis genome. , 1995, Microbiology.

[5]  B. Barrell,et al.  The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences , 2000, Nature.

[6]  Igor P. Ivanov,et al.  Antizyme expression: a subversion of triplet decoding, which is remarkably conserved by evolution, is a sensor for an autoregulatory circuit , 2000, Nucleic acids research.

[7]  Seymour S. Cohen.  A Guide to the Polyamines , 1998 .

[8]  S. Matsufuji,et al.  Analyses of ornithine decarboxylase antizyme mRNA with a cDNA cloned from rat liver. , 1990, Journal of biochemistry.

[9]  E. Westhof,et al.  A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs. , 1996, RNA.

[10]  A. Böck,et al.  Heterologous expression of archaeal selenoprotein genes directed by the SECIS element located in the 3′ non‐translated region , 2001, Molecular microbiology.

[11]  L. Shapiro,et al.  tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[12]  C. Kahana,et al.  Polyamines regulate the expression of ornithine decarboxylase antizyme in vitro by inducing ribosomal frame-shifting. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Philip J. Farabaugh,et al.  Programmed Alternative Reading of the Genetic Code , 1997, Springer US.

[14]  J. F. Atkins,et al.  Pseudoknot‐dependent read‐through of retroviral gag termination codons: importance of sequences in the spacer and loop 2. , 1994, The EMBO journal.

[15]  Igor P. Ivanov,et al.  A second mammalian antizyme: conservation of programmed ribosomal frameshifting. , 1998, Genomics.

[16]  R. Weiss,et al.  E. coli ribosomes re-phase on retroviral frameshift signals at rates ranging from 2 to 50 percent. , 1989, The New biologist.

[17]  R. Wickner,et al.  Ribosomal frameshifting efficiency and gag/gag-pol ratio are critical for yeast M1 double-stranded RNA virus propagation , 1992, Journal of virology.

[18]  W P Tate,et al.  UGA: a dual signal for 'stop' and for recoding in protein synthesis. , 1999, Biochemistry. Biokhimiia.

[19]  P. Coffino.  Ubiquitin and proteasomes: Regulation of cellular polyamines by antizyme , 2001, Nature Reviews Molecular Cell Biology.

[20]  P. Farabaugh,et al.  A novel programed frameshift expresses the POL3 gene of retrotransposon Ty3 of yeast: Frameshifting without tRNA slippage , 1993, Cell.

[21]  J. Wootton,et al.  Selenocysteine-containing thioredoxin reductase in C. elegans. , 1999, Biochemical and biophysical research communications.

[22]  D. Giedroc,et al.  Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting1 , 2000, Journal of Molecular Biology.

[23]  P. Farabaugh,et al.  Programmed +1 frameshifting stimulated by complementarity between a downstream mRNA sequence and an error-correcting region of rRNA. , 2001, RNA.

[24]  J. F. Curran,et al.  Analyses of frameshifting at UUU-pyrimidine sites. , 1997, Nucleic acids research.

[25]  S. Peltz,et al.  Identification of putative programmed -1 ribosomal frameshift signals in large DNA databases. , 1999, Genome research.

[26]  R. Weiss,et al.  A nascent peptide is required for ribosomal bypass of the coding gap in bacteriophage T4 gene 60 , 1990, Cell.

[27]  R. Weiss,et al.  Slippery runs, shifty stops, backward steps, and forward hops: -2, -1, +1, +2, +5, and +6 ribosomal frameshifting. , 1987, Cold Spring Harbor symposia on quantitative biology.

[28]  R. Sauer,et al.  Identification of Endogenous SsrA-tagged Proteins Reveals Tagging at Positions Corresponding to Stop Codons* , 2001, The Journal of Biological Chemistry.

[29]  J. F. Atkins,et al.  Autoregulatory frameshifting in decoding mammalian ornithine decarboxylase antizyme , 1995, Cell.

[30]  C S McHenry,et al.  tau binds and organizes Escherichia coli replication proteins through distinct domains. Domain IV, located within the unique C terminus of tau, binds the replication fork, helicase, DnaB. , 2001, The Journal of biological chemistry.

[31]  I. Brierley,et al.  Mutational analysis of the “slippery-sequence” component of a coronavirus ribosomal frameshifting signal , 1992, Journal of Molecular Biology.

[32]  S. Osawa,et al.  Codon recognition patterns as deduced from sequences of the complete set of transfer RNA species in Mycoplasma capricolum. Resemblance to mitochondria. , 1989, Journal of molecular biology.

[33]  Y. Takai,et al.  Isolation and characterization of a novel actin filament-binding protein from Saccharomyces cerevisiae , 1998, Oncogene.

[34]  J. F. Atkins,et al.  Does Disparate Occurrence of Autoregulatory Programmed Frameshifting in Decoding the Release Factor 2 Gene Reflect an Ancient Origin with Loss in Independent Lineages? , 1998, Journal of bacteriology.

[35]  A. Kyriakopoulos,et al.  Mammalian selenium-containing proteins. , 2003, Annual review of nutrition.

[36]  H. Okamoto,et al.  Two zebrafish (Danio rerio) antizymes with different expression and activities. , 2000, The Biochemical journal.

[37]  T. Hughes,et al.  The role of the EST genes in yeast telomere replication. , 1997, Ciba Foundation symposium.

[38]  P. G. Wilson,et al.  Sequence requirements for efficient translational frameshifting in the Escherichia coli dnaX gene and the role of an unstable interaction between tRNA(Lys) and an AAG lysine codon. , 1992, Genes & development.

[39]  W. Craigen,et al.  Bacterial peptide chain release factors: conserved primary structure and possible frameshift regulation of release factor 2. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[40]  J. London,et al.  Expression of the Prevotella loescheii adhesin gene (plaA) is mediated by a programmed frameshifting hop , 1994, Journal of bacteriology.

[41]  R. Weiss,et al.  Recoding: reprogrammed genetic decoding. , 1992, Science.

[42]  M. Berry,et al.  Ultraviolet-induced cell death blocked by a selenoprotein from a human dermatotropic poxvirus. , 1998, Science.

[43]  F. Studier,et al.  Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. , 1983, Journal of molecular biology.

[44]  F. Repoila,et al.  Genomic polymorphism in the T‐even bacteriophages. , 1994, The EMBO journal.

[45]  D. M. Ivey,et al.  A 1.6 kb region of Bacillus firmus OF4 DNA encodes a homolog of Escherichia coli and yeast DNA topoisomerases and may contain a translational readthrough of UGA. , 1992, Nucleic acids research.

[46]  J. Harney,et al.  The Caenorhabditis elegans Homologue of Thioredoxin Reductase Contains a Selenocysteine Insertion Sequence (SECIS) Element That Differs from Mammalian SECIS Elements but Directs Selenocysteine Incorporation* , 1999, The Journal of Biological Chemistry.

[47]  D. Wilson,et al.  A Bacteroides ruminicola 1,4-beta-D-endoglucanase is encoded in two reading frames , 1991, Journal of bacteriology.

[48]  August Böck,et al.  RNA Structures Involved in Selenoprotein Synthesis , 1998 .

[49]  M. Wolfgang,et al.  Charged tmRNA but not tmRNA‐mediated proteolysis is essential for Neisseria gonorrhoeae viability , 2000, The EMBO journal.

[50]  C. James,et al.  The Amber Codon in the Gene Encoding the Monomethylamine Methyltransferase Isolated from Methanosarcina barkeri Is Translated as a Sense Codon* , 2001, The Journal of Biological Chemistry.

[51]  J. F. Atkins,et al.  Overriding standard decoding: implications of recoding for ribosome function and enrichment of gene expression. , 2001, Cold Spring Harbor symposia on quantitative biology.

[52]  P. Coffino,et al.  Antizyme2 Is a Negative Regulator of Ornithine Decarboxylase and Polyamine Transport* , 1999, The Journal of Biological Chemistry.

[53]  P. Farabaugh.  Translational frameshifting: implications for the mechanism of translational frame maintenance. , 2000, Progress in nucleic acid research and molecular biology.

[54]  O. Fayet,et al.  Translational frameshifting in the control of transposition in bacteria , 1993, Molecular microbiology.

[55]  J. F. Atkins,et al.  Nonlinearity in genetic decoding: homologous DNA replicase genes use alternatives of transcriptional slippage or translational frameshifting. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[56]  J. Rousset,et al.  Versatile vectors to study recoding: conservation of rules between yeast and mammalian cells. , 1995, Nucleic acids research.

[57]  A J Herr,et al.  Coupling of open reading frames by translational bypassing. , 2000, Annual review of biochemistry.

[58]  H. Varmus,et al.  A characteristic bent conformation of RNA pseudoknots promotes -1 frameshifting during translation of retroviral RNA. , 1996, Journal of molecular biology.

[59]  A. Shevchenko,et al.  Euplotes telomerase contains an La motif protein produced by apparent translational frameshifting , 2000, The EMBO journal.

[60]  R. Weiss,et al.  Ribosomal frameshifting from -2 to +50 nucleotides. , 1990, Progress in nucleic acid research and molecular biology.

[61]  E. Ohtsubo,et al.  Bacterial insertion sequences. , 1996, Current topics in microbiology and immunology.

[62]  R. Simons,et al.  RNA structure and function , 1998 .

[63]  S. Dinesh-Kumar,et al.  A sequence required for -1 ribosomal frameshifting located four kilobases downstream of the frameshift site. , 2001, Journal of molecular biology.

[64]  E. Ohtsubo,et al.  DNA sequences required for translational frameshifting in production of the transposase encoded by IS 1 , 1992, Molecular and General Genetics MGG.

[65]  D. J. Lewandowski,et al.  Complete sequence of the citrus tristeza virus RNA genome. , 1995, Virology.

[66]  J. F. Atkins,et al.  Recoding: dynamic reprogramming of translation. , 1996, Annual review of biochemistry.

[67]  K.,et al.  Regulatory autonomy and molecular characterization of the Drosophila out at first gene. , 1995, Genetics.

[68]  Igor P. Ivanov,et al.  Conservation of polyamine regulation by translational frameshifting from yeast to mammals , 2000, The EMBO journal.

[69]  J. F. Atkins,et al.  Reading two bases twice: mammalian antizyme frameshifting in yeast. , 1996, The EMBO journal.

[70]  W. Tate,et al.  Competition between frameshifting, termination and suppression at the frameshift site in the Escherichia coli release factor-2 mRNA. , 1993, Nucleic acids research.

[71]  H. Hauser,et al.  Translational Recoding Induced by G-Rich mRNA Sequences That Form Unusual Structures , 1996, Cell.

[72]  P. Manning,et al.  Genes for biosynthesis and assembly of CS3 pili of CFA/II enterotoxigenic Escherichia coli: novel regulation of pilus production by bypassing an amber codon , 1989, Molecular microbiology.

[73]  J. Allen,et al.  The gene encoding a Prevotella loescheii lectin-like adhesin contains an interrupted sequence which causes a frameshift , 1992, Journal of bacteriology.

[74]  I. Brierley,et al.  Characterization of an efficient coronavirus ribosomal frameshifting signal: Requirement for an RNA pseudoknot , 1989, Cell.

[75]  S. Casjens,et al.  A programmed translational frameshift is required for the synthesis of a bacteriophage lambda tail assembly protein. , 1993, Journal of molecular biology.

[76]  J. F. Atkins,et al.  Structure of human ornithine decarboxylase antizyme 2 gene. , 1999, Gene.

[77]  P. Rigby,et al.  Identification and characterisation of a developmentally regulated mammalian gene that utilises -1 programmed ribosomal frameshifting. , 2001, Nucleic acids research.

[78]  S. Matsufuji,et al.  Cloning and characterization of a rat gene encoding ornithine decarboxylase antizyme. , 1992, Gene.

[79]  J. Geiselmann,et al.  The tRNA function of SsrA contributes to controlling repression of bacteriophage Mu prophage , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[80]  J. Parker,et al.  A ribosomal frameshifting error during translation of the argl mRNA of Escherichla coli , 1994, Molecular and General Genetics MGG.

[81]  K. Wise,et al.  Multiple translational products from a Mycoplasma hyorhinis gene expressed in Escherichia coli , 1990, Journal of bacteriology.

[82]  S. Casjens,et al.  A Programmed Translational Frameshift is Required for the Synthesis of a Bacteriophage λ Tail Assembly Protein , 1993 .

[83]  L. Grivell,et al.  Sequence comparison of new prokaryotic and mitochondrial members of the polypeptide chain release factor family predicts a five-domain model for release factor structure. , 1992, Nucleic acids research.

[84]  J. Manch-Citron,et al.  The Translational Hop Junction and the 5′ Transcriptional Start Site for the Prevotella loescheii Adhesin Encoded by plaA , 1999, Current Microbiology.

[85]  E. Koonin,et al.  Beet yellows closterovirus: complete genome structure and identification of a leader papain-like thiol protease. , 1994, Virology.

[86]  William Arbuthnot Sir Lane,et al.  Rabbit beta-globin is extended beyond its UGA stop codon by multiple suppressions and translational reading gaps. , 1998, Biochemistry.

[87]  C. Samakovlis,et al.  Translational readthrough in the hdc mRNA generates a novel branching inhibitor in the drosophila trachea. , 1998, Genes & development.

[88]  C. W. Pleij,et al.  RNA pseudoknots: Translational frameshifting and readthrough on viral RNAs , 1990, Virus Genes.

[89]  D. Voytas,et al.  Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. , 1998, Genome research.

[90]  J. F. Atkins,et al.  Uninterrupted translation through putative 12-nucleotide coding gap in sequence of carA: business as usual , 1994, Journal of bacteriology.

[91]  A. Weiner,et al.  A single UGA codon functions as a natural termination signal in the coliphage q beta coat protein cistron. , 1973, Journal of molecular biology.

[92]  R. Moritz,et al.  C-terminal Extension of Truncated Recombinant Proteins in Escherichia coli with a 10Sa RNA Decapeptide(*) , 1995, The Journal of Biological Chemistry.

[93]  J. F. Atkins,et al.  Analysis of the roles of tRNA structure, ribosomal protein L9, and the bacteriophage T4 gene 60 bypassing signals during ribosome slippage on mRNA. , 2001, Journal of molecular biology.

[94]  J. F. Atkins,et al.  Frameshifting in gene 10 of bacteriophage T7 , 1991, Journal of bacteriology.

[95]  H. Himeno,et al.  Structure and function of 10Sa RNA: trans-translation system. , 1996, Biochimie.

[96]  H. Nojima,et al.  Identi®cation and characterization of testis speci®c ornithine decarboxylase antizyme (OAZ-t) gene: expression in haploid germ cells and polyamine-induced frameshifting , 2000 .

[97]  Reported translational bypass in a trpR'-lacZ' fusion is accounted for by unusual initiation and +1 frameshifting. , 1997, Journal of molecular biology.

[98]  H. Varmus,et al.  Structural and functional studies of retroviral RNA pseudoknots involved in ribosomal frameshifting: nucleotides at the junction of the two stems are important for efficient ribosomal frameshifting. , 1995, The EMBO journal.

[99]  I. Moszer.  The complete genome of Bacillus subtilis: from sequence annotation to data management and analysis , 1998, FEBS letters.

[100]  A Kornberg,et al.  Translational frameshifting generates the gamma subunit of DNA polymerase III holoenzyme. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[101]  K. Wise,et al.  IS1630 of Mycoplasma fermentans, a Novel IS30-Type Insertion Element That Targets and Duplicates Inverted Repeats of Variable Length and Sequence during Insertion , 1999, Journal of bacteriology.

[102]  S. Ao,et al.  A persistent untranslated sequence within bacteriophage T4 DNA topoisomerase gene 60. , 1988, Science.

[103]  J. F. Atkins,et al.  The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons. , 1991, Journal of molecular biology.

[104]  James R. Cole,et al.  A new version of the RDP (Ribosomal Database Project) , 1999, Nucleic Acids Res..

[105]  D. Davis,et al.  Hypermodified nucleosides in the anticodon of tRNALys stabilize a canonical U-turn structure. , 2000, Biochemistry.

[106]  D. Hatfield,et al.  Translational Suppression in Retroviral GENE Expression , 1992, Advances in Virus Research.

[107]  Chris M. Brown,et al.  New Punctuation for the Genetic Code: Luteovirus Gene Expression☆ , 1997 .

[108]  P. Farabaugh,et al.  Near-cognate peptidyl-tRNAs promote +1 programmed translational frameshifting in yeast. , 1999, Molecular cell.

[109]  M. Mcintosh,et al.  Characterization of IS1221 from Mycoplasma hyorhinis: expression of its putative transposase in Escherichia coli incorporates a ribosomal frameshift mechanism , 1995, Molecular microbiology.

[110]  Philip J. Farabaugh,et al.  25 Programmed Translational Frameshifting, Hopping, and Readthrough of Termination Codons , 2000 .

[111]  D. Morris,et al.  Programmed translational frameshifting in a gene required for yeast telomere replication , 1997, Current Biology.

[112]  S. Matsufuji,et al.  Antizyme Regulates the Degradation of Ornithine Decarboxylase in Fission Yeast Schizosaccharomyces pombe , 2001, The Journal of Biological Chemistry.

[113]  Y. Nakamura,et al.  Sequence and functional analysis of mutations in the gene encoding peptide-chain-release factor 2 of Escherichia coli. , 1991, Biochimie.

[114]  Raymond F. Gesteland,et al.  RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression , 2001, Nucleic Acids Res..

[115]  M. Tan,et al.  Programmed Translational Frameshifting Is Likely Required for Expressions of Genes Encoding Putative Nuclear Protein Kinases of the Ciliate Euplotes octocarinatus , 2001, The Journal of eukaryotic microbiology.

[116]  J. Berger,et al.  Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot , 1999, Nature Structural Biology.

[117]  W. Craigen,et al.  Expression of peptide chain release factor 2 requires high-efficiency frameshift , 1986, Nature.

[118]  Isabelle Hatin,et al.  Impact of the six nucleotides downstream of the stop codon on translation termination , 2001, EMBO reports.

[119]  A. Abdelal,et al.  Structure and regulation of the carAB operon in Pseudomonas aeruginosa and Pseudomonas stutzeri: no untranslated region exists , 1994, Journal of bacteriology.

[120]  J. Andreesen,et al.  A selDABC cluster for selenocysteine incorporation in Eubacterium acidaminophilum , 2000, Archives of Microbiology.

[121]  M. Yarus,et al.  Use of tRNA suppressors to probe regulation of Escherichia coli release factor 2. , 1988, Journal of molecular biology.

[122]  M. Berry,et al.  Functional characterization of the eukaryotic SECIS elements which direct selenocysteine insertion at UGA codons. , 1993, The EMBO journal.

[123]  R. Sauer,et al.  Role of a Peptide Tagging System in Degradation of Proteins Synthesized from Damaged Messenger RNA , 1996, Science.

[124]  N. Nguyen,et al.  Mutant analysis of Prevotella sp. plaA-lacZ fusion protein expression in Escherichia coli: support for an essential role of the stem-loop. , 1999, Canadian journal of microbiology.

[125]  J. Walker,et al.  Conservation of the Escherichia coli dnaX programmed ribosomal frameshift signal in Salmonella typhimurium , 1997, Journal of bacteriology.

[126]  T. Abo,et al.  SsrA‐mediated tagging and proteolysis of LacI and its role in the regulation of lac operon , 2000, The EMBO journal.

[127]  Johnson Mak,et al.  Maintenance of the Gag/Gag-Pol Ratio Is Important for Human Immunodeficiency Virus Type 1 RNA Dimerization and Viral Infectivity , 2001, Journal of Virology.

[128]  Chris M. Brown,et al.  Local and distant sequences are required for efficient readthrough of the barley yellow dwarf virus PAV coat protein gene stop codon , 1996, Journal of virology.

[129]  Igor P. Ivanov,et al.  Discovery of a spermatogenesis stage-specific ornithine decarboxylase antizyme: antizyme 3. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[130]  John F. Atkins,et al.  Ribosomal −1 Frameshifting during Decoding ofBacillus subtilis cdd Occurs at the Sequence CGA AAG , 1999, Journal of bacteriology.

[131]  H. Varmus,et al.  Characterization of ribosomal frameshifting in HIV-1 gag-pol expression , 1988, Nature.

[132]  J. F. Curran,et al.  Effects of the nucleotide 3' to an amber codon on ribosomal selection rates of suppressor tRNA and release factor-1. , 1991, Journal of molecular biology.

[133]  L. Cooley,et al.  Kelch encodes a component of intercellular bridges in Drosophila egg chambers , 1993, Cell.

[134]  V. L. Spitsberg,et al.  A new version , 1977 .

[135]  C. Weissmann,et al.  The readthrough protein A1 is essential for the formation of viable Qβ particles , 1974 .

[136]  L. Cooley,et al.  Examination of the function of two kelch proteins generated by stop codon suppression. , 1997, Development.

[137]  A Danchin,et al.  Colibri: a functional data base for the Escherichia coli genome. , 1993, Microbiological reviews.

[138]  J. Walker,et al.  Programmed ribosomal frameshifting generates the Escherichia coli DNA polymerase III gamma subunit from within the tau subunit reading frame. , 1990, Nucleic acids research.

[139]  Peter W. J. Rigby,et al.  Shigemoto, K. et al. Identification and characterisation of a developmentally regulated mammalian gene that utilises -1 programmed ribosomal frameshifting. Nucleic Acids Res. 29, 4079-4088 , 2001 .

[140]  S Commans,et al.  Selenocysteine inserting tRNAs: an overview. , 1999, FEMS microbiology reviews.

[141]  M. Pardue,et al.  Unusual features of the Drosophila melanogaster telomere transposable element HeT-A are conserved in Drosophila yakuba telomere elements. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[142]  Philip J. Farabaugh,et al.  Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site , 1990, Cell.

[143]  E. Ohtsubo,et al.  Translational control in production of transposase and in transposition of insertion sequence IS3. , 1994, Journal of molecular biology.

[144]  S. Matsufuji,et al.  Cell culture analysis of the regulatory frameshift event required for the expression of mammalian antizymes , 2001, Genes to cells : devoted to molecular & cellular mechanisms.

[145]  D Gani,et al.  Analysis of the aphthovirus 2A/2B polyprotein 'cleavage' mechanism indicates not a proteolytic reaction, but a novel translational effect: a putative ribosomal 'skip'. , 2001, The Journal of general virology.

[146]  Davis,et al.  Hypermodified nucleosides in the anticodon of tRNA(Lys) stabilize a canonical U-turn structure , 2000, Biochemistry.