Key Points
-
RNA structure comprises secondary and tertiary motifs, which fold in a hierarchical sequence of events. The difficulty that RNA molecules have in defining a single native structure is known as 'the RNA-folding problem'.
-
In vitro, some RNAs are able to self-fold under precise conditions of salt and temperature. In vivo, proteins with a wide variety of activities help RNAs to fold and to assemble into ribonucleoprotein (RNP) particles.
-
Some proteins recognize specific sequences or structures, and by binding they stabilize these structures. RNA helicases, which are specifically recruited to their target RNA, unfold RNA structures by ATP hydrolysis.
-
A growing number of proteins have been assigned RNA-chaperone activity, which is defined as a structural destabilizing activity that non-specifically resolves misfolded conformations without ATP consumption. The influence that proteins with RNA-chaperone activity have on the global folding state of RNA molecules within cells remains a mystery.
-
The ribosome is a highly dynamic RNP complex. The assembly of three large RNAs and more than 50 proteins requires a precise coordinated sequence of events. The interplay between ribosomal proteins and RNA is still unclear; however, a large number of ribosomal proteins have RNA-chaperone activity — an unfolding activity, which could be of advantage not only during assembly but also during translation to prevent the RNA from misfolding.
-
The spliceosome consists of five small nuclear RNP particles (snRNPs) and many other proteins, which assemble anew on each intron. In the course of intron excision and exon ligation, many interactions between the snRNAs and pre-mRNA are formed and then rearranged to allow the reactions to proceed. These dynamic RNA interactions need protein assistance. This review discusses spliceosomal proteins that have the potential to assist RNA folding and refolding within this large RNP complex.
Abstract
RNA is structurally very flexible, which provides the basis for its functional diversity. An RNA molecule can often adopt different conformations, which enables the regulation of its function through folding. Proteins help RNAs reach their functionally active conformation by increasing their structural stability or by chaperoning the folding process. Large, dynamic RNA–protein complexes, such as the ribosome or the spliceosome, require numerous proteins that coordinate conformational switches of the RNA components during assembly and during their respective activities.
Similar content being viewed by others
References
Herschlag, D. RNA chaperones and the RNA folding problem. J. Biol. Chem. 270, 20871–20874 (1995).
Michel, F. & Westhof, E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216, 585–610 (1990).
Schultes, E. A. & Bartel, D. P. One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science 289, 448–452 (2000).
Mandal, M. & Breaker, R. R. Gene regulation by riboswitches. Nature Rev. Mol. Cell Biol. 5, 451–463 (2004).
Naberhaus, F. mRNA mediated detection of environmental conditions. Arch. Microbiol. 178, 404–410 (2002).
Yusupov, M. M. et al. Crystal structure of the ribosome at 5.5 Å resolution. Science 292, 883–896 (2001).
Ban, N., Nissen, P., Hansen, J., Moore, P. B. & Steitz, T. A. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289, 905–920 (2000).
Moore, P. B. & Steitz, T. A. The structural basis of large ribosomal subunit function. Annu. Rev. Biochem. 72, 813–850 (2003).
Ramakrishnan, V. Ribosome structure and the mechanism of translation. Cell 108, 557–572 (2002). The elucidation of how the ribosome discriminates between correct and incorrect interactions between codons and anticodons: two conserved adenines of the 16S ribosomal RNA contact the minor groove of the first and second base pairs in the coding triplet via the A-minor motif and sense the correctness of base pairing between codons and anticodons through shape complementarity.
Brion, P. & Westhof, E. Hierarchy and dynamics of RNA folding. Annu. Rev. Biophys. Biomol. Struct. 26, 113–137 (1997).
Batey, R. T., Rambo, R. P. & Doudna, J. A. Tertiary motifs in RNA structure and folding. Angew. Chem. Int. Ed. Engl. 38, 2326–2343 (1999).
Leontis, N. B. & Westhof, E. Geometric nomenclature and classification of RNA base pairs. RNA 7, 499–512 (2001). All possible combinations of base pairs in RNA structure are explained and systematically annotated, and a comprehensive nomenclature is given.
Battiste, J. L. et al. α-helix-RNA major groove recognition in an HIV-1 rev peptide–RRE RNA complex. Science 273, 1547–1551 (1996).
Murphy, F. L. & Cech, T. R. An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry 32, 5291–5300 (1993).
Schroeder, R. Translation. Dissecting RNA function. Nature 370, 597–598 (1994).
Draper, D. E. A guide to ions and RNA structure. RNA 10, 335–343 (2004).
Hanna, R. & Doudna, J. A. Metal ions in ribozyme folding and catalysis. Curr. Opin. Chem. Biol. 4, 166–170 (2000).
Pyle, A. M. Metal ions in the structure and function of RNA. J. Biol. Inorg. Chem. 7, 679–690 (2002).
Lilley, D. M. Structure, folding and catalysis of the small nucleolytic ribozymes. Curr. Opin. Struct. Biol. 9, 330–338 (1999).
Hohng, S. et al. Conformational flexibility of four-way junctions in RNA. J. Mol. Biol. 336, 69–79 (2004).
Khvorova, A., Lescoute, A., Westhof, E. & Jayasena, S. D. Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nature Struct. Biol. 10, 708–712 (2003). Most of the folding studies carried out on the minimal version of the hammerhead ribozyme have to be re-evaluated, as this study showed that the lack of essential peripheral parts, which strongly stabilize the ribozyme core and reduce the Mg2+ requirement, are essential for in vivo activity.
Treiber, D. K., Rook, M. S., Zarrinkar, P. P. & Williamson, J. R. Kinetic intermediates trapped by native interactions in RNA folding. Science 279, 1943–1946 (1998).
Treiber, D. K. & Williamson, J. R. Beyond kinetic traps in RNA folding. Curr. Opin. Struct. Biol. 11, 309–314 (2001).
Woodson, S. A. Recent insights on RNA folding mechanisms from catalytic RNA. Cell. Mol. Life Sci. 57, 796–808 (2000).
Su, L. J., Brenowitz, M. & Pyle, A. M. An alternative route for the folding of large RNAs: apparent two-state folding by a group II intron ribozyme. J. Mol. Biol. 334, 639–652 (2003).
Pan, J., Thirumalai, D. & Woodson, S. A. Folding of RNA involves parallel pathways. J. Mol. Biol. 273, 7–13 (1997).
Russell, R. & Herschlag, D. New pathways in folding of the Tetrahymena group I RNA enzyme. J. Mol. Biol. 291, 1155–1167 (1999).
Pan, J., Deras, M. L. & Woodson, S. A. Fast folding of a ribozyme by stabilizing core interactions: evidence for multiple folding pathways in RNA. J. Mol. Biol. 296, 133–144 (2000).
Russell, R. et al. Rapid compaction during RNA folding. Proc. Natl Acad. Sci. USA 99, 4266–4271 (2002).
Crothers, D. M., Cole, P. E., Hilbers, C. W. & Shulman, R. G. The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J. Mol. Biol. 87, 63–88 (1974).
Sclavi, B., Sullivan, M., Chance, M. R., Brenowitz, M. & Woodson, S. A. RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science 279, 1940–1943 (1998).
Russell, R., Millett, I. S., Doniach, S. & Herschlag, D. Small angle X-ray scattering reveals a compact intermediate in RNA folding. Nature Struct. Biol. 7, 367–370 (2000).
Russell, R. et al. Rapid compaction during RNA folding. Proc. Natl Acad. Sci. USA 99, 4266–4271 (2002).
Das, R. et al. The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. J. Mol. Biol. 332, 311–319 (2003).
Kim, H. D. et al. Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules. Proc. Natl Acad. Sci. USA 99, 4284–4289 (2002).
Zhuang, X. et al. A single-molecule study of RNA catalysis and folding. Science 288, 2048–2051 (2000).
Liphardt, J., Onoa, B., Smith, S. B., Tinoco, I. Jr & Bustamante, C. Reversible unfolding of single RNA molecules by mechanical force. Science 292, 733–737 (2001).
Tinoco, I. Jr. Force as a useful variable in reactions: unfolding RNA. Annu. Rev. Biophys. Biomol. Struct. 33, 363–385 (2004).
Onoa, B. et al. Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme. Science 299, 1892–1895 (2003).
Schroeder, R., Grossberger, R., Pichler, A. & Waldsich, C. RNA folding in vivo. Curr. Opin. Struct. Biol. 12, 296–300 (2002).
Caprara, M. G., Lehnert, V., Lambowitz, A. M. & Westhof, E. A tyrosyl-tRNA synthetase recognizes a conserved tRNA-like structural motif in the group I intron catalytic core. Cell 87, 1135–1145 (1996).
Mohr, S., Stryker, J. M. & Lambowitz, A. M. A DEAD-box protein functions as an ATP-dependent RNA chaperone in group I intron splicing. Cell 109, 769–779 (2002).
Lorsch, J. R. RNA chaperones exist and DEAD box proteins get a life. Cell 109, 797–800 (2002).
Solem, A., Chatterjee, P. & Caprara, M. G. A novel mechanism for protein-assisted group I intron splicing. RNA 8, 412–425 (2002).
Buchmueller, K. L., Webb, A. E., Richardson, D. A. & Weeks, K. M. A collapsed non-native RNA folding state. Nature Struct. Biol. 7, 362–366 (2000).
Buchmueller, K. L. & Weeks, K. M. Near native structure in an RNA collapsed state. Biochemistry 42, 13869–13878 (2003). Twelve structural constraints for the collapsed state of the bI5 group-I intron were determined before monitoring structural changes that were due to binding of the CBP2 protein, which chases the RNA into the native state.
Webb, A. E. & Weeks, K. M. A collapsed state functions to self-chaperone RNA folding into a native ribonucleoprotein complex. Nature Struct. Biol. 8, 135–140 (2001). The rapid collapse of the bI5 RNA into a compact state indicates that this is a strategy for the RNA to avoid the fact that the CBP2 protein stabilizes misfolded conformers. The role of Mg2+ in establishing a balance between different folding states shows that physiological concentrations are best suited to avoid misfolding.
Williamson, J. R. Induced fit in RNA–protein recognition. Nature Struct. Biol. 7, 834–837 (2000).
Uhlenbeck, O. C. Keeping RNA happy. RNA 1, 4–6 (1995).
Pan, T., Fang, X. & Sosnick, T. Pathway modulation, circular permutation and rapid RNA folding under kinetic control. J. Mol. Biol. 286, 721–731 (1999).
Lewicki, B. T., Margus, T., Remme, J. & Nierhaus, K. H. Coupling of rRNA transcription and ribosomal assembly in vivo. Formation of active ribosomal subunits in Escherichia coli requires transcription of rRNA genes by host RNA polymerase which cannot be replaced by bacteriophage T7 RNA polymerase. J. Mol. Biol. 231, 581–593 (1993).
Semrad, K. & Schroeder, R. A ribosomal function is necessary for efficient splicing of the T4 phage thymidylate synthase intron in vivo. Genes Dev. 12, 1327–1337 (1998).
Waldsich, C., Semrad, K. & Schroeder, R. Neomycin B inhibits splicing of the td intron indirectly by interfering with translation and enhances missplicing in vivo. RNA 4, 1653–1663 (1998).
Pichler, A. & Schroeder, R. Folding problems of the 5′ splice-site containing P1 stem of the group I td intron: substrate binding inhibition in vitro and mis-splicing in vivo. J. Biol. Chem. 277, 17987–17993 (2002).
Clodi, E., Semrad, K. & Schroeder, R. Assaying RNA chaperone activity in vivo using a novel RNA folding trap. EMBO J. 18, 3776–3782 (1999).
Zhang, A., Derbyshire, V., Salvo, J. L. & Belfort, M. Escherichia coli protein StpA stimulates self-splicing by promoting RNA assembly in vitro. RNA 1, 783–793 (1995).
Zhang, A., Rimsky, S., Reaban, M. E., Buc, H. & Belfort, M. Escherichia coli protein analogs StpA and H-NS: regulatory loops, similar and disparate effects on nucleic acid dynamics. EMBO J. 15, 1340–1349 (1996).
Waldsich, C., Masquida, B., Westhof, E. & Schroeder, R. Monitoring intermediate folding states of the td group I intron in vivo. EMBO J. 19, 5281–5291 (2002).
Waldsich, C., Grossberger, R. & Schroeder, R. RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo. Genes Dev. 16, 2300–2312 (2002).
Feng, Y. X. et al. The human immunodeficiency virus type 1 Gag polyprotein has nucleic acid chaperone activity: possible role in dimerization of genomic RNA and placement of tRNA on the primer binding site. J. Virol. 73, 4251–4256 (1999).
Rein, A., Henderson, L. E. & Levin, J. G. Nucleic-acid-chaperone activity of retroviral nucleocapsid proteins: significance for viral replication. Trends Biochem. Sci. 23, 297–301 (1998).
Tsuchihashi, Z., Khosla, M. & Herschlag, D. Protein enhancement of hammerhead ribozyme catalysis. Science 262, 99–102 (1993).
Martin, S. L. & Bushman, F. D. Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon. Mol. Cell. Biol. 21, 467–475 (2001).
Cristofari, G., Ficheux, D. & Darlix, J. L. The GAG-like protein of the yeast Ty1 retrotransposon contains a nucleic acid chaperone domain analogous to retroviral nucleocapsid proteins. J. Biol. Chem. 275, 19210–19217 (2000).
Wolin, S. L. & Cedervall, T. The La protein. Annu. Rev. Biochem. 71, 375–403 (2002).
Chakshusmathi, G., Kim, S. D., Rubinson, D. A. & Wolin, S. L. A La protein requirement for efficient pre-tRNA folding. EMBO J. 22, 6562–6572 (2003).
Pannone, B. K., Xue, D. & Wolin, S. L. A role for the yeast La protein in U6 snRNP assembly: evidence that the La protein is a molecular chaperone for RNA polymerase III transcripts. EMBO J. 15, 7442–7453 (1998).
Franze de Fernandez, M. T., Eoyang, L. & August, J. T. Factor fraction required for the synthesis of bacteriophage Qβ-RNA. Nature 219, 588–590 (1968).
Zhang, A. et al. Global analysis of small RNA and mRNA targets of Hfq. Mol. Microbiol. 50, 1111–1124 (2003).
Storz, G. An expanding universe of noncoding RNAs. Science 296, 1260–1263 (2002).
Geissmann, T. A. & Touati, D. Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator. EMBO J. 23, 396–405 (2004). Hfq binds to the 5′ UTR of the sodB mRNA and, as a consequence, opens a stem–loop structure, rendering it accessible to the small RNA RyhB . Base-paring interaction between sodB mRNA and RyhB blocks translation of sodB mRNA.
Lenz, D. H. et al. The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell 118, 69–82 (2004).
Sonnleitner, E. et al. Reduced virulence of a hfq mutant of Pseudomonas aeruginosa O1. Microb. Pathog. 35, 217–228 (2003).
Schumacher, M. A., Pearson, R. F., Moller, T., Valentin-Hansen, P. & Brennan, R. G. Structures of the pleiotropic translational regulator Hfq and an Hfq–RNA complex: a bacterial Sm-like protein. EMBO J. 21, 3546–3556 (2002).
Karpel, R. L., Miller, N. S. & Fresco, J. R. Mechanistic studies of ribonucleic acid renaturation by a helix-destabilizing protein. Biochemistry 21, 2102–2108 (1982).
Pontius, B. W. & Berg, P. Rapid assembly and disassembly of complementary DNA strands through an equilibrium intermediate state mediated by A1 hnRNP protein. J. Biol. Chem. 267, 13815–13818 (1992).
Coetzee, T., Herschlag, D. & Belfort, M. Escherichia coli proteins, including ribosomal protein S12, facilitate in vitro splicing of phage T4 introns by acting as RNA chaperones. Genes Dev. 8, 1575–1588 (1994).
Arthur, D. C. et al. FinO is an RNA chaperone that facilitates sense–antisense RNA interactions. EMBO J. 22, 6346–6355 (2003). The protein FinO represses F-plasmid conjugative transfer by facilitating interactions between the TraJ mRNA and the antisense RNA, FinP . FinO promotes strand exchange by destabilizing internal secondary structures of both RNAs.
Wang, C. C. et al. Nucleic acid binding properties of the nucleic acid chaperone domain of hepatitis delta antigen. Nucleic Acids Res. 31, 6481–6492 (2003).
Gabus, C., Mazroui, R., Tremblay, S., Khandjian, E. W. & Darlix, J. L. The fragile X mental retardation protein has nucleic acid chaperone properties. Nucleic Acids Res. 32, 2129–2137 (2004).
Gabus, C. et al. The prion protein has RNA binding and chaperoning properties characteristic of nucleocapsid protein NCP7 of HIV-1. J. Biol. Chem. 276, 19301–19309 (2001).
Derrington, E. et al. PrPC has nucleic acid chaperoning properties similar to the nucleocapsid protein of HIV-1. C. R. Acad. Sci. III 325, 17–23 (2002).
Deleault, N. R., Lucassen, R. W. & Supattapone, S. RNA molecules stimulate prion protein conversion. Nature 425, 717–720 (2003).
Jiang, W., Hou, Y. & Inouye, M. CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone. J. Biol. Chem. 272, 196–202 (1997).
Ladomery, M. Multifunctional proteins suggest connections between transcriptional and post-transcriptional processes. Bioessays 19, 903–909 (1997).
Brow, D. A. Allosteric cascade of spliceosome activation. Annu. Rev. Genet. 36, 333–360 (2002).
Held, W. A., Ballou, B., Mizushima, S. & Nomura, M. Assembly mapping of 30 S ribosomal proteins from Escherichia coli. Further studies. J. Biol. Chem. 249, 3103–3111 (1974).
Nierhaus, K. H. & Dohme, F. Total reconstitution of functionally active 50S ribosomal subunits from Escherichia coli. Proc. Natl Acad. Sci. USA 71, 4713–4717 (1974).
Agalarov, S. C. & Williamson, J. R. A hierarchy of RNA subdomains in assembly of the central domain of the 30 S ribosomal subunit. RNA 6, 402–408 (2000).
Stern, S., Powers, T., Changchien, L. M. & Noller, H. F. RNA–protein interactions in 30S ribosomal subunits: folding and function of 16S rRNA. Science 244, 783–790 (1989).
Agalarov, S. C. et al. In vitro assembly of a ribonucleoprotein particle corresponding to the platform domain of the 30S ribosomal subunit. Proc. Natl Acad. Sci. USA 95, 999–1003 (1998).
Samaha, R. R., O'Brien, B., O'Brien, T. W. & Noller, H. F. Independent in vitro assembly of a ribonucleoprotein particle containing the 3′ domain of 16S rRNA. Proc. Natl Acad. Sci. USA 91, 7884–7888 (1994).
Held, W. A., Mizushima, S. & Nomura, M. Reconstitution of Escherichia coli 30 S ribosomal subunits from purified molecular components. J. Biol. Chem. 248, 5720–5730 (1973).
Fromont-Racine, M., Senger, B., Saveanu, C. & Fasiolo, F. Ribosome assembly in eukaryotes. Gene 313, 17–42 (2003).
Maki, J. A., Schnobrich, D. J. & Culver, G. M. The DnaK chaperone system facilitates 30S ribosomal subunit assembly. Mol. Cell 10, 129–138 (2002).
Charollais, J., Pflieger, D., Vinh, J., Dreyfus, M. & Iost, I. The DEAD-box RNA helicase SrmB is involved in the assembly of 50S ribosomal subunits in Escherichia coli. Mol. Microbiol. 48, 1253–1265 (2003).
Diges, C. M. & Uhlenbeck, O. C. Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA. EMBO J. 20, 5503–5512 (2001).
Limbach, P. A., Crain, P. F. & McCloskey, J. A. Summary: the modified nucleosides of RNA. Nucleic Acids Res. 22, 2183–2196 (1994).
Green, R. & Noller, H. F. In vitro complementation analysis localizes 23S rRNA posttranscriptional modifications that are required for Escherichia coli 50S ribosomal subunit assembly and function. RNA 2, 1011–1021 (1996).
Semrad, K. & Green, R. Osmolytes stimulate the reconstitution of functional 50S ribosomes from in vitro transcripts of Escherichia coli 23S rRNA. RNA 8, 401–411 (2002).
Noon, K. R., Bruenger, E. & McCloskey, J. A. Posttranscriptional modifications in 16S and 23S rRNAs of the archaeal hyperthermophile Sulfolobus solfataricus. J. Bacteriol. 180, 2883–2888 (1998).
Kawai, G. et al. Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2′-hydroxyl group. Biochemistry 31, 1040–1046 (1992).
Dalluge, J. J. et al. Posttranscriptional modification of tRNA in psychrophilic bacteria. J. Bacteriol. 179, 1918–1923 (1997).
Dalluge, J. J., Hashizume, T., Sopchik, A. E., McCloskey, J. A. & Davis, D. R. Conformational flexibility in RNA: the role of dihydrouridine. Nucleic Acids Res. 24, 1073–1079 (1996). NMR studies on uridine- and dihydrouridine-containing RNAs show that compounds with dihydrouridine are stabilized within the C2′-endo sugar conformation, which allows greater conformational flexibility. By contrast, uridine-containing molecules are stabilized in the more rigid C3′-endo sugar conformation.
Gabashvili, I. S. et al. Major rearrangements in the 70S ribosomal 3D structure caused by a conformational switch in 16S ribosomal RNA. EMBO J. 18, 6501–6507 (1999).
Valle, M. et al. Locking and unlocking of ribosomal motions. Cell 114, 123–134 (2003). Using cryo-electron microscopy, it was shown that during translocation significant rearrangements occur within the ribosome. These motions are unlocked or locked depending on whether the P-site tRNA is deacetylated or not.
Cukras, A. R., Southworth, D. R., Brunelle, J. L., Culver, G. M. & Green, R. Ribosomal proteins S12 and S13 function as control elements for translocation of the mRNA:tRNA complex. Mol. Cell 12, 321–328 (2003).
Jurica, M. S. & Moore, M. J. Pre-mRNA splicing: awash in a sea of proteins. Mol. Cell 12, 5–14 (2003).
Malca, H., Shomron, N. & Ast, G. The U1 snRNP base pairs with the 5′ splice site within a penta-snRNP complex. Mol. Cell. Biol. 23, 3442–3455 (2003).
Rocak, S. & Linder, P. DEAD-box proteins: the driving forces behind RNA metabolism. Nature Rev. Mol. Cell Biol. 5, 232–241 (2004).
Bartels, C., Urlaub, H., Luhrmann, R. & Fabrizio, P. Mutagenesis suggests several roles of Snu114p in pre-mRNA splicing. J. Biol. Chem. 278, 28324–28334 (2003).
Biamonti, G. & Riva, S. New insights into the auxiliary domains of eukaryotic RNA binding proteins. FEBS Lett. 340, 1–8 (1994).
Dreyfuss, G., Matunis, M. J., Pinol-Roma, S. & Burd, C. G. hnRNP proteins and the biogenesis of mRNA. Annu. Rev. Biochem. 62, 289–321 (1993).
Krecic, A. M. & Swanson, M. S. hnRNP complexes: composition, structure, and function. Curr. Opin. Cell Biol. 11, 363–371 (1999).
Pontius, B. W. & Berg, P. Renaturation of complementary DNA strands mediated by purified mammalian heterogeneous nuclear ribonucleoprotein A1 protein: implications for a mechanism for rapid molecular assembly. Proc. Natl Acad. Sci. USA 87, 8403–8407 (1990).
Munroe, S. H. & Dong, X. F. Heterogeneous nuclear ribonucleoprotein A1 catalyzes RNA. RNA annealing. Proc. Natl Acad. Sci. USA 89, 895–899 (1992).
Shamoo, Y., Krueger, U., Rice, L. M., Williams, K. R. & Steitz, T. A. Crystal structure of the two RNA binding domains of human hnRNP A1 at 1.75 Å resolution. Nature Struct. Biol. 4, 215–222 (1997).
Ding, J. et al. Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA. Genes Dev. 13, 1102–1115 (1999).
Varani, G. & Nagai, K. RNA recognition by RNP proteins during RNA processing. Annu. Rev. Biophys. Biomol. Struct. 27, 407–445 (1998).
Krainer, A. R., Conway, G. C. & Kozak, D. Purification and characterization of pre-mRNA splicing factor SF2 from HeLa cells. Genes Dev. 4, 1158–1171 (1990).
Lee, C. G., Zamore, P. D., Green, M. R. & Hurwitz, J. RNA annealing activity is intrinsically associated with U2AF. J. Biol. Chem. 268, 13472–13478 (1993).
Valcarcel, J., Gaur, R. K., Singh, R. & Green, M. R. Interaction of U2AF65 RS region with pre-mRNA branch point and promotion of base pairing with U2 snRNA. Science 273, 1706–1709 (1996).
Graveley, B. R. Sorting out the complexity of SR protein functions. RNA 6, 1197–1211 (2000).
Will, C. L. & Luhrmann, R. Spliceosomal UsnRNP biogenesis, structure and function. Curr. Opin. Cell Biol. 13, 290–301 (2001).
Zhang, A., Wassarman, K. M., Ortega, J., Steven, A. C. & Storz, G. The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol. Cell 9, 11–22 (2002).
Moller, T. et al. Hfq. A bacterial Sm-like protein that mediates RNA–RNA interaction. Mol. Cell 9, 23–30 (2002).
Zhang, D., Abovich, N. & Rosbash, M. A biochemical function for the Sm complex. Mol. Cell 7, 319–329 (2001).
Mayes, A. E., Verdone, L., Legrain, P. & Beggs, J. D. Characterization of Sm-like proteins in yeast and their association with U6 snRNA. EMBO J. 18, 4321–4331 (1999).
Achsel, T. et al. A doughnut-shaped heteromer of human Sm-like proteins binds to the 3′-end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro. EMBO J. 18, 5789–5802 (1999).
McConnell, T. S., Lokken, R. P. & Steitz, J. A. Assembly of the U1 snRNP involves interactions with the backbone of the terminal stem of U1 snRNA. RNA 9, 193–201 (2003).
Will, C. L. & Luhrmann, R. Molecular biology. RNP remodeling with DExH/D boxes. Science 291, 1916–1917 (2001).
Staley, J. P. & Guthrie, C. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 92, 315–326 (1998).
Lorsch, J. R. & Herschlag, D. The DEAD box protein eIF4A. 2. A cycle of nucleotide and RNA-dependent conformational changes. Biochemistry 37, 2194–2206 (1998).
Fuller-Pace, F. V. RNA helicases: modulators of RNA structure. Trends Cell Biol. 4, 271–274 (1994).
Staley, J. P. & Guthrie, C. An RNA switch at the 5′ splice site requires ATP and the DEAD box protein Prp28p. Mol. Cell 3, 55–64 (1999).
Chen, J. Y. et al. Specific alterations of U1-C protein or U1 small nuclear RNA can eliminate the requirement of Prp28p, an essential DEAD box splicing factor. Mol. Cell 7, 227–232 (2001). A mutation in the U1C protein, which disrupts its interaction with the pre-mRNA, was shown to circumvent the lethality of a Prp28 deletion, which argues that the U1C mutation alone leads to the displacement of the U1 snRNP, and that the main action of Prp28 is in disrupting the U1C-protein–pre-mRNA interaction.
Kistler, A. L. & Guthrie, C. Deletion of MUD2, the yeast homolog of U2AF65, can bypass the requirement for sub2, an essential spliceosomal ATPase. Genes Dev. 15, 42–49 (2001).
Jankowsky, E., Gross, C. H., Shuman, S. & Pyle, A. M. Active disruption of an RNA–protein interaction by a DExH/D RNA helicase. Science 291, 121–125 (2001). A model study of the vaccinia virus DEXH/D protein NPH-II with an RNA duplex that contained two binding sites for U1A protein indicated that NPH-II uses energy from ATP hydrolysis to displace U1A from RNA.
Donahue, C. P., Yadava, R. S., Nesbitt, S. M. & Fedor, M. J. The kinetic mechanism of the hairpin ribozyme in vivo: influence of RNA helix stability on intracellular cleavage kinetics. J. Mol. Biol. 295, 693–707 (2000).
Yadava, R. S., Mahen, E. M. & Fedor, M. J. Kinetic analysis of ribozyme–substrate complex formation in yeast. RNA 10, 863–879 (2004).
Winkler, W. C., Nahvi, A., Roth, A., Collins, J. A. & Breaker, R. R. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428, 281–286 (2004). Translation of the B. subtilis glmS mRNA is regulated via an allosteric ribozyme that is located in its 5′ UTR. The substrate glucosamine-6-phosphate, when present in excess, binds to the ribozyme, thereby activating its cleavage.
Portman, D. S. & Dreyfuss, G. RNA annealing activities in HeLa nuclei. EMBO J. 13, 213–221 (1994).
Huang, Z. S., Su, W. H., Wang, J. L. & Wu, H. N. Selective strand annealing and selective strand exchange promoted by the N-terminal domain of hepatitis delta antigen. J. Biol. Chem. 278, 5685–5693 (2003).
Patel, D. A., Steitz J. A. Splicing double: insights from the second spliceosome. Nature Rev. Mol. Cell Biol. 4, 960–970 (2003).
Lehnert, V., Jaeger, L., Michel, F. & Westhof, E. New loop–loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem. Biol. 3, 993–1009 (1996).
Cech, T. R., Damberger, S. H. & Gutell, R. R. Representation of the secondary and tertiary structure of group I introns. Nature Struct. Biol. 1, 273–280 (1994).
Golden, B. L., Gooding, A. R., Podell, E. R. & Cech, T. R. A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science 282, 259–264 (1998).
Kambach, C. et al. Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs. Cell 96, 375–387 (1999).
Semrad, K., Green, R. & Schroeder R. RNA chaperone activity of large ribosomal subunit proteins from Escherichia coli. RNA (in the press).
Acknowledgements
The preparation of this review was supported by the Austrian Science Fund FWF grants to A.B. as part of the Special Research Program on RNA.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Related links
Related links
DATABASES
Entrez
Interpro
Saccharomyces genome database
Swiss-Prot
FURTHER INFORMATION
Glossary
- RNA-FOLDING PROBLEM
-
The RNA-folding problem was first described by D. Herschlag and corresponds to the multitude of possible structures that RNA can adopt. Only a single or a few possible structures usually lead to function, therefore the RNA must avoid the problem of folding into alternative, non-functional structures.
- GROUP-I INTRONS
-
A group of autocatalytic intervening sequences with a common core structure and a common splicing mechanism, which is initiated by the nucleophilic attack of the 3′ hydroxyl group of the cofactor guanosine.
- RIBOSWITCH
-
A conformational switch in an RNA molecule that is induced by a small metabolite, and which leads to a switch in gene-regulatory function.
- RIBOZYME
-
An enzyme whose catalytic component is an RNA.
- A-FORM DOUBLE HELIX
-
A right-handed double helix that is formed by the base pairing of complementary RNA strands. Every 2.3 nm, the helix turns, which results in 11 base pairs per turn. The B-form helix, which is also right-handed and is usually present in double-stranded DNA, turns every 3.4 nm, which results in 10 base pairs per turn.
- SMALL NUCLEOLYTIC RIBOZYMES
-
A group of self-cleaving ribozymes, which includes the hammerhead, hairpin and hepatitis delta virus ribozymes. Their core structures range in size from 40 to 155 nucleotides and they produce 2′–3′ cyclic phosphate and 5′ hydroxyl ends after cleavage.
- LARGE RIBOZYMES
-
A class of ribozymes that includes RNase P, self-splicing group-I and group-II introns. They are several hundred nucleotides in size and they produce 3′ hydroxyl ends and 5′ phosphates (RNase P) or new phosphodiester linkages (introns).
- GROUP-II INTRONS
-
A rare class of autocatalytic introns, the excision of which is assisted by, but does not require, trans-acting proteins. The splicing mechanism is identical to that of the spliceosome. Splicing is initiated by a nucleophilic attack of the 2′ hydroxyl group of an endogenous adenosine at the 5′ splice site, forming a lariat structure.
- RNA HELICASE
-
An enzyme that resolves RNA base pairing through ATP hydrolysis, which leads to unfolding.
- DEAD-BOX PROTEINS AND DEXD/H ATPases
-
RNA helicases that contain the DEAD (Asp-Glu-Ala-Asp) or DEXD/H (Asp-Glu-X-Asp/His, where X represents any amino acid) motif. These proteins unwind RNA through ATP hydrolysis.
- RNA-BINDING DOMAINS IN PROTEINS
-
The RRM (RNA-recognition motif) contains two short consensus sequences embedded in a structurally conserved region of approximately 80 amino acids. The KH (K-homology) domain is ∼ 60 amino acids long with a characteristic pattern of hydrophobic amino acids and is structurally similar to the RRM domain. RGG (Arg-Gly-Gly) is a hallmark amino-acid motif present in many RNA-binding proteins. Zn-knuckle is a conserved CX2CX4HX4C (where X represents any amino acid) motif that coordinates zinc binding.
- CHAPERONE
-
A protein or RNA molecule that facilitates the folding of a protein or RNA by preventing misfolding and aggregation, or by resolving misfolded structures.
- NUCLEOID
-
The bacterial genome that contains compacted DNA, but which is not separated by a membrane (as it is in eukaryotes).
- SMALL NUCLEAR RIBONUCLEOPROTEIN PARTICLE
-
(snRNP). A nuclear particle that consists of a short RNA (<300 nucleotides) and one or more tightly bound proteins. They are involved in pre-mRNA processing and tRNA biogenesis.
- SM AND SM-LIKE PROTEINS
-
A group of seven core proteins that form heteroheptameric complexes, which bind to U-rich sequences in snRNPs that are involved in splicing. The exception is U6 snRNP, which contains Sm-like (Lsm) proteins.
- HETEROGENOUS NUCLEAR RIBONUCLEOPROTEIN
-
(hnRNP). A group of more than 20 different nuclear proteins that were found associated as a complex with heterogenous nuclear RNA. This diverse group of RNA-binding proteins have various nuclear and cytoplasmic functions.
- F-PLASMID CONJUGATIVE TRANSFER
-
DNA transfer from a donor cell to a recipient cell by direct physical contact that is mediated by genes that are encoded on the fertility (F) plasmid.
- KINETIC FOLDING TRAP
-
An aberrant and metastable RNA structure that slows down folding.
- OSMOLYTE
-
A small organic compound that accumulates in water-stressed organisms.
- THERMOPHILIC, MESOPHILIC, PSYCHROPHILIC
-
Tolerating high, intermediate and low temperatures, respectively.
- C2′-ENDO SUGAR CONFORMATION
-
A ribose conformation in which the C2′ carbon is orientated towards the C5′ carbon, which is typical of B-form helices. A-form RNA helices adopt the C3′-endo sugar conformation.
- INTRON BRANCH SITE
-
An adenosine within the branch-site sequence, the 2′-OH of which is ligated to the 5′ end of the intron in the first step of splicing, which results in a branched RNA molecule (lariat)
- SPLICEOSOME
-
A large dynamic nuclear complex, which consists of five snRNPs as well as numerous proteins. It mediates the excision of pre-mRNA introns and the ligation of exons, thereby generating the mature mRNA.
- SR PROTEINS
-
A protein family of highly conserved RNA-splicing factors, with at least one RRM motif and patches of serine (S) and arginine (R) di-peptides.
Rights and permissions
About this article
Cite this article
Schroeder, R., Barta, A. & Semrad, K. Strategies for RNA folding and assembly. Nat Rev Mol Cell Biol 5, 908–919 (2004). https://doi.org/10.1038/nrm1497
Issue Date:
DOI: https://doi.org/10.1038/nrm1497
- Springer Nature Limited
This article is cited by
-
Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development
Signal Transduction and Targeted Therapy (2020)
-
Prediction and differential analysis of RNA secondary structure
Quantitative Biology (2020)
-
Epitranscriptomic technologies and analyses
Science China Life Sciences (2020)
-
A Modified In Vitro Transcription Approach to Improve RNA Synthesis and Ribozyme Cleavage Efficiency
Molecular Biotechnology (2019)
-
Bioinformatics comparisons of RNA-binding proteins of pathogenic and non-pathogenic Escherichia coli strains reveal novel virulence factors
BMC Genomics (2017)