Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Insight/Outlook Slip-Sliding the Frame: Programmed −1 Frameshifting on Eukaryotic Transcripts Gerald M. Wilson and Gary Brewer1 Department of Microbiology and Immunology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157-1064 USA -frameshifting Database searches using this com 1מ The basic mechanisms of mRNA tems, some bacterial frameshift sites 1מ translation are ubiquitous among all or- events have also been documented pound algorithm for ganisms, in that the accurate decoding (Blinkowa and Walker 1990; Tsuchiha- yielded a host of potential signals in all of triplet codon sequences programs se- shi and Brown 1992; Chandler and databases tested, including eukaryotic rial amide linkages of amino acid resi- Fayet 1993; Engelberg-Kulka and Schou- sequences, with frequencies signifi- dues by ribosomal complexes. In gen- laker-Schwarz 1994). At present, no ex- cantly higher than found in random se- eral, the fidelity of this process is depen- amples of eukaryotic mRNAs exhibiting quence populations. In a number of frameshift activity have been re- cases, frameshift signals were conserved 1מ dent on both accurate recognition of mRNA codons by aminoacyl tRNAs and ported. However, a number of viruses in- in homologous mRNAs from different maintenance of the corresponding open fecting eukaryotic cells utilize pro- species. A convincing argument for the ribosomal frameshifts, validity of these searches was provided 1מ reading frame. However, in a growing grammed 1מ number of cases, deviations from this demonstrating that the cis elements in- by the functional demonstration of triplet codon rule are observed, indicat- volved in the frameshifting process are frameshifting activity for two selected ing that the information content of an operational in eukaryotes. In viral sys- signals (from Saccharomyces cerevisiae mRNA to encode protein may extend tems, the efficiency of frameshifting is RAS1 and human CCR5 mRNAs) in a re- beyond its primary structure. These an essential determinant of the stoichi- combinant assay system. Furthermore, frameshift 1מ cases, collectively referred to as transla- ometry of synthesized viral protein in four cases, potential tional recoding (for review, see Geste- products, which must be rigidly main- signals colocalized to sites of mutation land and Atkins 1996), present excep- tained for efficient propagation of the linked to heritable diseases in humans, -frame 1מ tions to the venerable genetic code and virus (Brierly 1995 and references raising the possibility that are typically subdivided among three therein; Dinman and Wickner 1995). shift activity may be a physiologically primary mechanisms: (1) frameshifting, In work presented in this issue, relevant component of regulated gene in which translating ribosomes are in- (Hammell et al. 1999), a bioinformatic expression in humans. Modifications of duced to slide one nucleotide forward or approach was used to screen prokaryotic the parameters employed in this search backward at a distinct point in the tran- and eukaryotic DNA sequence databases algorithm may yet reveal additional can- -frameshift signals. Be- didate frameshift signals, as the poten 1מ script, with protein synthesis then con- for potential frame- tial for 3Ј-RNA pseudoknot formation 1מ reading frame, cause of the complexity of 1מ tinuing in the +1 or respectively; (2) alternative codon usage, shift sites and the sequence variability was a constraint placed upon their selec- where stop codons are not interpreted as observed among these elements in na- tion in this study. An RNA pseudoknot frameshifting at 1מ sites of translational termination but, ture, a multicomponent search algo- is not requisite for rather, encode an amino acid residue; rithm was required to identify candidate the gag–pol overlap of HIV-1 (Jacks et al. and (3) translational bypassing, where sites from bulk database entries. This 1988), for example, which only contains the translational machinery traverses a was made possible in part by the a weak 3Ј-stem–loop structure in vivo gap in the mRNA coding sequence yet plethora of information available de- (Parkin et al. 1992). 1מ yields a single polypeptide chain. scribing structural features of frameshift The identification of functional -ribosomal frame- signals, much of which is described in frameshift signals in chromosomally en 1מ Programmed shift signals are among the most exten- Hammell et al. (1999) and elsewhere coded eukaryotic mRNAs raises several sively characterized of these transla- (Brierly 1995; Chen et al. 1996; Marcz- interesting questions for further investi- tional recoding phenomena (for review, inke et al. 1998). This strategy represents gation. First, it will be important to de- see Brierly 1995; Dinman 1995; Far- a marked contrast to many examples of termine if ribosomal frameshifting oc- abaugh 1996). Although current ex- database searching, which typically in- curs in vivo in the context of these tran- amples are largely limited to viral sys- volve a single motif or are limited to pri- scripts. If so, what is the function of the mary structure parameters (Fickett 1996; frameshift event? A ribosomal frame- 1Corresponding author. E-MAIL [email protected]; FAX (336) 716- Altschul et al. 1997; Aravind and Lands- shift may serve to generate alternate 9928. man 1998; O’Neill 1998). protein isoforms, with common amino- 9:393–394 ©1999 by Cold Spring Harbor Laboratory Press ISSN 1054-9803/99 $5.00; www.genome.org Genome Research 393 www.genome.org Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Insight/Outlook terminal sequences but distinct carboxy- Despite the identification of pro- Brierly, I. 1995. J. Gen. Virol. 76: 1885– .ribosomal frameshifting 1892 1מ terminal regions. Protein products con- grammed taining alternatively framed moieties activity associated with human mRNA Chandler, M. and O. Fayet. 1993. Mol. Microbiol. 7: 497–503. may present unique functional features sequences, the possibility of developing Chen, X., H. Kang, L.X. Shen, M. or may be subject to different modes of antiviral therapeutic strategies targeting Chamorro, H.E. Varmus, and I. Tinoco, regulatory control. In other cases, frame- this mechanism remains an intriguing Jr. 1996. J. Mol. Biol. 260: 479–483. shifting events may have more direct possibility (Dinman et al. 1997, 1998; Cui, Y., J.D. Dinman, and S.W. Peltz. 1996. regulatory roles. For example, frame- Hung et al. 1998). For example, com- EMBO J. 15: 5726–5736. shifts could result in premature termina- pounds that modulate the stability of ei- Cui, Y., J.D. Dinman, T.G. Kinzy, and S.W. tion of protein synthesis if the frame- ther the downstream RNA structural Peltz. 1998. Mol. Cell. Biol. 18: 1506–1516. .motif or codon/anticodon interactions Dinman, J.D. 1995. Yeast 11: 1115–1127 1מ shift generates a stop codon in the open reading frame. In this case, the may alter the efficiency of frameshifting Dinman, J.D. and R.B. Wickner. 1995. mRNA may be subject to accelerated events, leading to a change in the ratio Genetics 141: 95–105. turnover by the nonsense-mediated of frameshifted/nonshifted viral pro- Dinman, J.D., M.J. Ruiz-Echevarria, K. mRNA decay pathway (for review, see teins. Because the function of the RNA Czaplinski, and S.W. Peltz. 1997. Proc. Maquat 1995; Jacobson and Peltz 1996; pseudoknot structure may involve re- Natl. Acad. Sci. 94: 6606–6611. Dinman, J.D., M.J. Ruiz-Echevarria, and Ruiz-Echevarria et al. 1996). Another tarding translating ribosomes at the S.W. Peltz. 1998. Trends Biotechnol. question regarding eukaryotic frame- frameshift site (for review, see Brierly 16: 190–196. shifting events is whether their effi- 1995; Farabaugh 1996), compounds Engelberg-Kulka, H. and R. ciency may be regulated in response to modulating the kinetics of translational Schoulaker-Schwarz. 1994. Mol. Microbiol. signaling pathways or other stimuli. elongation may similarly influence 11: 3–8. This is particularly applicable in the con- frameshit efficiency. Obviously, the im- Farabaugh, P.J. 1996. Annu. Rev. Genet. text of multicellular organisms, whose plications for modulation of host gene 30: 507–528. Fickett, J.W. 1996. Trends Genet. control of gene expression is often sub- expression must also be considered in 12: 316–320. ject to a host of endocrine and develop- the development of such therapies, but Gesteland, R.F. and J.F. Atkins. 1996. Annu. mental effects. even modest changes in viral frameshift- Rev. Biochem. 65: 741–768. ribosomal ing efficiency may be sufficient to confer Hammell, A.B., R.C. Taylor, S.W. Peltz, and 1מ If programmed frameshifting does not occur with eu- significant host benefit. This was dem- J.D. Dinman. 1999. Genome Res. (this karyotic mRNAs, it is possible that flank- onstrated using LA virus infection of issue). ing sequences may have evolved to re- yeast, where up- or down-regulation of Hung, M., P. Patel, S. Davis, and S.R. Green. 1998. J. Virol. 72: 4819-4824. press this activity. Alternatively, specific frameshifting efficiency by more than Jacks, T., M.D. Power, F.R. Masiarz, P.A. trans-acting factors may participate in twofold prevented viral propagation Luciw, P.J. Barr, and H.E. Varmus. 1988. the repression of frameshifting events (Dinman and Wickner 1995). Extrapo- Nature 331: 280–283. on eukaryotic transcripts. For example, lating to the possibility that alterations Jacobson, A. and S.W. Peltz. 1996. Annu. .frameshifting may Rev. Biochem. 65: 693–739 1מ the MOF2/SUI1 gene product of S. cerevi- in programmed siae functions as an inhibitor of viral also contribute to human genetic disor- Maquat, L.E. 1995. RNA 1: 453–465. Marczinke, B., R. Fisher, M. Vidakovic, A.J. RNA frameshifting in infected yeast cells ders, similar strategies aimed at modu- Bloys, and I. Brierly. 1998. J. Mol. Biol. (Cui et al. 1998). This function is well lating the frameshift efficiencies of en- 284: 205–225.