RNA Structure: Pseudoknots

Abstract

An RNA pseudoknot results from Watson–Crick base pairing of a single‐stranded segment, located between two regions, paired to each other, with a sequence that is not located between these paired regions. This leads to a structure with at least two helical stems and two loops crossing the grooves of the helices. Pseudoknots are further stabilised by coaxial stacking between stems and the formation of triple ribonucleic acid (RNA) interactions between stems and loops. RNA pseudoknots adopt different folding topologies and are an essential part of various functional RNA molecules, including ribosomal RNAs, ribozymes and riboswitches. In this review, the thermodynamics and main structural features of pseudoknots, important for their function, are discussed: amongst others, viral tRNA‐like structures, ribosomal frameshifter pseudoknots and pseudoknots formed by S‐adenosylmethionine and pre‐queuosine riboswitches upon binding of their respective ligands.

Key Concepts:

  • The simplest RNA pseudoknot is formed by base‐pairing of nucleotides within a hairpin loop to a complementary sequence outside the hairpin (H‐pseudoknot).

  • Classical H‐pseudoknots consist of two coaxially stacked helical stems and two loops that cross one deep groove of one helix and the shallow groove of the other helical stem.

  • Pseudoknots are usually stabilised by coaxial stacking between stems and triple base pairs formed between the bases of the stems and loops.

  • Many complex pseudoknots may be interpreted as classical pseudoknots containing additional structural elements inserted in the pseudoknot loops.

  • Pseudoknots are folded in various types of RNA molecules and have diverse functions.

  • Limited information is available on thermodynamic stability of pseudoknots.

  • Computer‐assisted prediction of pseudoknots is partially hampered by a lack of knowledge about the thermodynamics of pseudoknot folding.

Keywords: RNA folding; RNA secondary structure; RNA tertiary structure; ribozyme; ribosome; reprogramming; frameshifting

Figure 1.

Formation of the H‐pseudoknot from two alternative hairpins. The equilibria in the shown model oligonucleotide were studied by UV‐melting and NMR spectroscopy (Puglisi et al., ).

Figure 2.

Three different topologies of two stems stacked coaxially in the H‐pseudoknots. In classical pseudoknot (with no loop L2), loop L3 is frequently named L2.

Figure 3.

Examples of triple helices (dotted lines) in H‐pseudoknots with different functions. (a) The pseudoknot of the tRNA‐like structure from TYMV (Kolk et al., ); (b) Frameshifting pseudoknot from BWYV (Su et al., ; Nixon et al., ); (c) Modified SRV‐1 frameshifting pseudoknot (Michiels et al., ; Olsthoorn et al., ); (d) the Kluyveromyces lactis telomerase pseudoknot (Shefer et al., ).

Figure 4.

Examples of complex pseudoknot topologies. (a) A ‘nonclassical’ stacking topology in the pseudoknot from influenza A virus (Gultyaev et al., ); (b) additional hairpin inserted in loop L2 of the HIV‐1 group O frameshifting pseudoknot (Baril et al., ); (c) additional hairpin insertion in L1 of the pseudoknot from PYVV (Livieratos et al., ); (d) formation of a pseudoknot by the pairing of the loop in branched structure with a downstream region in yellow fever virus (YFV) (Olsthoorn and Bol, ).

Figure 5.

Pseudoknot formation in the riboswitches, induced by a ligand binding. (a) SAM‐II riboswitch from the metX gene in the Sargasso Sea metagenome (Gilbert et al., ); (b) Bacillus subtilisqueC PreQ1 riboswitch (Klein et al., ). Ligands are shown in red, triple interactions are shown by dotted lines. Non‐Watson–Crick edge‐to‐edge base pairs are depicted by symbols according to their nomenclature (Leontis and Westhof, ).

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References

Baril M, Dulude D, Steinberg SV and Brakier‐Gingras L (2003) The frameshift stimulatory signal of human immunodeficiency virus type 1 group O is a pseudoknot. Journal of Molecular Biology 331: 571–583.

Brierley I, Pennell S and Gilbert RJC (2007) Viral RNA pseudoknots: versatile motifs in gene expression and replication. Nature Reviews Microbiology 5: 598–610.

Brion P and Westhof E (1997) Hierarchy and dynamics of RNA folding. Annual Reviews of Biophysics and Biomolecular Structure 26: 113–137.

Cao S and Chen SJ (2006) Predicting RNA pseudoknot folding thermodynamics. Nucleic Acids Research 34: 2634–2652.

Chen G, Chang KY, Chou MY et al. (2009) Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of −1 ribosomal frameshifting. Proceedings of the National Academy of Sciences of the USA 106: 12706–12711.

Cochrane JC, Lipchock SV and Strobel SA (2007) Structural investigation of the GlmS ribozyme bound to its catalytic cofactor. Chemical Biology 14: 97–105.

Dirks RM and Pierce NA (2003) A partition function algorithm for nucleic acid secondary structure including pseudoknots. Journal of Computational Chemistry 24: 1664–1677.

Ehresmann C, Ehresmann B, Ennifar E et al. (2004) Molecular mimicry in translational regulation: the case of ribosomal protein S15. RNA Biology 1: 66–73.

Ferre‐D'Amare AR, Zhou K and Doudna JA (1998) Crystal structure of a hepatitis delta virus ribozyme. Nature 395: 567–574.

Giedroc DP, Theimer CA and Nixon PL (2000) Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting. Journal of Molecular Biology 298: 167–185.

Gilbert SD, Rambo RP, Van Tyne D and Batey RT (2008) Structure of the SAM‐II riboswitch bound to S‐adenosylmethionine. Nature Structural & Molecular Biology 15: 177–182.

Gultyaev AP (1991) The computer simulation of RNA folding involving pseudoknot formation. Nucleic Acids Research 19: 2489–2494.

Gultyaev AP, van Batenburg FHD and Pleij CWA (1995) The computer simulation of RNA folding pathways using a genetic algorithm. Journal of Molecular Biology 250: 37–51.

Gultyaev AP, van Batenburg FHD and Pleij CWA (1999) An approximation of loop free energy values of RNA H‐pseudoknots. RNA 5: 609–617.

Gultyaev AP, Heus HA and Olsthoorn RCL (2007) An RNA conformational shift in recent H5N1 influenza A viruses. Bioinformatics 23: 272–276.

Gultyaev AP and Olsthoorn RCL (2010) A family of non‐classical pseudoknots in influenza A and B viruses. RNA Biology 7: 125–129.

Hansen TM, Reihani NS, Oddershede LB and Sorensen MA (2007) Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting. Proceedings of the National Academy of Sciences of the USA 104: 5830–5835.

Isambert H (2009) The jerky and knotty dynamics of RNA. Methods 49: 189–196.

Isambert H and Siggia ED (2000) Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme. Proceedings of the National Academy of Sciences of the USA 97: 6515–6520.

Klein DJ, Edwards TE and Ferre‐D'Amare AR (2009) Cocrystal structure of a class I riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase. Nature Structural & Molecular Biology 16: 343–344.

Kolk MH, van der Graaf M, Wijmenga SS et al. (1998) NMR structure of a classical pseudoknot: interplay of single‐ and double‐stranded RNA. Science 280: 434–438.

Leontis NB and Westhof E (2001) Geometric nomenclature and classification of RNA base pairs. RNA 7: 499–512.

Liu B, Shankar N and Turner DH (2010) Fluorescence competition assay measurements of free energy changes for RNA pseudoknots. Biochemistry 49: 623–634.

Liu L and Chen SJ (2010) Computing the conformational entropy for RNA folds. Journal of Chemical Physics 132: 235104.

Livieratos IC, Eliasco E, Müller G et al. (2004) Analysis of the RNA of Potato yellow vein virus: evidence for a tripartite genome and conserved 3′‐terminal structures among members of the genus Crinivirus. Journal of General Virology 85: 2065–2075.

Marzi S, Myasnikov AG, Serganov A et al. (2007) Structured mRNAs regulate translation initiation by binding to the platform of the ribosome. Cell 130: 1019–1031.

McPheeters DS, Stormo GD and Gold L (1988) Autogenous regulatory site on the bacteriophage T4 gene 32 messenger RNA. Journal of Molecular Biology 201: 517–535.

Michel F and Westhof E (1990) Modelling of the three‐dimensional architecture of group I catalytic introns based on comparative sequence analysis. Journal of Molecular Biology 216: 585–610.

Michiels PJ, Versleijen AA, Verlaan PW et al. (2001) Solution structure of the pseudoknot of SRV‐1 RNA, involved in ribosomal frameshifting. Journal of Molecular Biology 310: 1109–1123.

Mironov AA and Lebedev VF (1993) A kinetic model of RNA folding. Biosystems 30: 49–56.

Narayanan R, Velmurugu Y, Kuznetsov SV and Ansari A (2011) Fast folding of RNA pseudoknots initiated by laser temperature‐jump. Journal of the American Chemical Society 133: 18767–18774.

Nixon PL, Cornish PV, Suram SV and Giedroc DP (2002) Thermodynamic analysis of conserved loop‐stem interactions in P1–P2 framshifting RNA pseudoknots from plant Luteoviridae. Biochemistry 41: 10665–10674.

Olsthoorn RC, Reumerman R, Hilbers CW, Pleij CWA and Heus HA (2010) Functional analysis of the SRV‐1 RNA frameshifting pseudoknot. Nucleic Acids Research 38: 7665–7672.

Olsthoorn RCL and Bol JF (2001) Sequence comparison and secondary structure analysis of the 3′ noncoding region of flavivirus genomes reveals multiple pseudoknots. RNA 7: 1370–1377.

Perreault J, Weinberg Z, Roth A et al. (2011) Identification of hammerhead ribozymes in all domains of life reveals novel structural variations. PLoS Computational Biology 7: e1002031.

Pleij CWA, Rietveld K and Bosch L (1985) A new principle of RNA folding based on pseudoknotting. Nucleic Acids Research 13: 1717–1731.

Puglisi JD, Wyatt JR and Tinoco I (1991) RNA pseudoknots. Accounts of Chemical Research 24: 152–158.

Qiu H, Kaluarachchi K, Du Z, Hoffman DW and Giedroc DP (1996) Thermodynamics of folding of the RNA pseudoknot of the T4 gene 32 autoregulatory messenger RNA. Biochemistry 35: 4176–4186.

Reeder J and Giegerich R (2004) Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics 5: 104.

Rietveld K, Van Poelgeest R, Pleij CWA et al. (1982) The tRNA‐like structure at the 3′ terminus of turnip yellow mosaic virus RNA. Differences and similarities with canonical tRNA. Nucleic Acids Research 10: 1929–1946.

Rivas E and Eddy SR (1999) A dynamic programming algorithm for RNA structure prediction including pseudoknots. Journal of Molecular Biology 285: 2053–2068.

Schlax PJ, Xavier KA, Gluick TC and Draper DE (2001) Translational repression of the E. coli alpha operon mRNA: importance of an mRNA conformational switch and a ternary entrapment complex. Journal of Biological Chemistry 276: 38494–38501.

Shapiro BA and Wu JC (1997) Predicting RNA H‐type pseudoknots with the massively parallel genetic algorithm. Computer Applications in the Biosciences 13: 459–471.

Shapiro BA, Yingling YG, Kasprzak W and Bindewald E (2007) Bridging the gap in RNA structure prediction. Current Opinion in Structural Biology 17: 157–165.

Shefer K, Brown Y, Gorkovoy V et al. (2007) A triple helix within a pseudoknot is a conserved and essential element of telomerase RNA. Molecular and Cellular Biology 27: 2130–2143.

Silva PAGC, Pereira CF, Dalebout TJ et al. (2010) An RNA pseudoknot is required for production of yellow fever virus subgenomic RNA by the host nuclease XRN1. Journal of Virology 84: 11395–11406.

Soto AM, Misra V and Draper DE (2007) Tertiary structure of an RNA pseudoknot is stabilized by ‘diffuse’ Mg2+ ions. Biochemistry 46: 2973–2983.

Su L, Chen L, Egli M et al. (1999) Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot. Nature Structural Biology 6: 285–292.

Westhof E and Jaeger L (1992) RNA pseudoknots. Current Opinion in Structural Biology 2: 327–333.

Yu CH, Noteborn MH, Pleij CWA and Olsthoorn RCL (2011) Stem‐loop structures can effectively substitute for an RNA pseudoknot in ‐1 ribosomal frameshifting. Nucleic Acids Research 39: 8952–8959.

Further Reading

Barends S, Bink HH, van den Worm SH, Pleij CWA and Kraal B (2003) Entrapping ribosomes for viral translation: tRNA mimicry as a molecular Trojan horse. Cell 112: 123–129.

Blackburn EH and Collins K (2011) Telomerase: an RNP enzyme synthesizes DNA. Cold Spring Harbor Perspectives in Biology 3: a003558.

Filbin ME and Kieft JS (2009) Towards a structural understanding of IRES RNA function. Current Opinion in Structural Biology 19: 267–276.

Gan HH, Pasquali S and Schlick T (2003) Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. Nucleic Acids Research 31: 2926–2943.

Gaspin C and Westhof E (1995) An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints. Journal of Molecular Biology 254: 163–174.

Giedroc DP and Cornish PV (2009) Frameshifting RNA pseudoknots: structure and mechanism. Virus Research 139: 193–208.

Hajdin CE, Ding F, Dokholyan NV and Weeks KM (2010) On the significance of an RNA tertiary structure prediction. RNA 16: 1340–1349.

Mans RMW and Pleij CWA (1993) RNA pseudoknots. Nucleic Acids and Molecular Biology 7: 250–270.

Moore SD and Sauer RT (2007) The tmRNA system for translational surveillance and ribosome rescue. Annual Reviews of Biochemistry 76: 101–124.

Taufer M, Licon A, Araiza R et al. (2009) PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots. Nucleic Acids Research 37: D127–D135.

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Gultyaev, Alexander P, Olsthoorn, René CL, Pleij, Cornelis WA, and Westhof, Eric(Sep 2012) RNA Structure: Pseudoknots. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0003134.pub2]