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Protein-Switched Ribozymes

* and .

* Corresponding Author: Tan Inoue—Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan. Email: tan@kuchem.kyoto-u.ac.jp

Specific RNA-binding proteins regulate RNA conformations in protein-switched ribozymes. Ribozyme activity can be regulated with RNA-binding proteins, as in the case of natural RNP ribozymes like RNase P that consist of an RNA subunit and an RNA-binding protein. Recent studies have shown that both natural and artificial catalytic RNAs are convertible to allosterically regulated ribozymes by molecular design at the secondary structure or three-dimensional levels and also by performing selections from combinatorial libraries. In protein-switched ribozymes, the specific binding of a protein stabilizes a particular conformation of RNA in active or inactive form such that ribozyme activity is regulated by the presence or absence of the RNA-binding protein. In applications, a protein-regulated ribozyme can be utilized as a biosensor that detects the concentration of the binding proteins in vitro and in vivo. Further advances in the design and construction of protein-regulated ribozymes are expected because of rapid progress in structural biology. Future studies will also shed new light on the molecular evolution pathways of ribozymes.

Introduction

Most functional RNAs in cells are physically associated with protein molecules to form a ribonucleoprotein (RNP) complex. The structure of RNA in an RNP is stabilized via RNA-protein interactions that promote catalysis and other tasks required for gene expression. RNA itself folds hierarchically starting with double-helix formation based on Watson-Crick base pairs and the G-U wobble base pair.1 Because a number of base-pairing combinations are available, the same RNA molecule can form many alternative structures. Because these alternative conformations are often equally stable, the stabilization of a particular conformation is needed to give an RNA molecule its characteristic structure and allow it to perform its functional role. A high concentration of cations is particularly effective for stabilizing a unique RNA conformation.2,3 However, high cation concentrations can also promote unwanted conformations, and therefore this approach is impractical in vivo. To overcome this dilemma, a protein that can specifically bind to a particular RNA conformation can be employed to enable a unique RNA function. In many cases, cationic residues such as arginine and lysine in proteins are involved in intermolecular interactions with negatively charged RNA surfaces.

Nature has produced catalytic RNAs that are regulated by RNA-binding proteins. As a prelude to discussing artificial protein-switched ribozymes, here we describe two well-studied natural RNPs with enzymatic function, RNase P and the ribosome. RNase P catalyzes specific phosphodiester bond hydrolysis in pre-tRNAs to produce mature tRNA 5'-ends.4-6 The examples of RNase P identified so far are holoenzymes comprising one RNA molecule and at least one protein molecule. A bacterial RNase P typically consists of a large RNA subunit (350-400 nucleotides; 100-130 kDa) and one small protein subunit (˜120 amino acids; 12-13 kDa).7 The active site of the enzyme is contained in RNA components that function in vitro without protein in the presence of a high concentration of cations.8 However, a protein component is required for catalysis under physiological conditions. It is believed that the protein component stabilizes the holoenzyme against electrostatic distortion and increases the turnover rate by specifically binding the substrate over the product.2,7,9

The RNA component of bacterial RNase P consists of two major domains, catalytic (C) and specificity (S).10-12 RNase P variants can be categorized into two types, A and B, on the basis of sequence characteristics of peripheral elements located outside the core domains of conserved C and S.12-14 The most rigorously investigated RNase Ps are those from E. coli and B. subtilis that belong to types A and B, respectively. The X-ray crystal structures of the S domains of types A and B RNase P RNAs from T. thermophilus and B. subtilis, respectively, have been solved. These structures offer insights into the evolution of the architecture of RNase P RNA as an assemblage of modular structural components.15,16

Among RNase P proteins consisting of ˜120 amino acids, ˜40 amino acids are conserved or nearly so.17 Consistent with phylogenic data, both the A-type and B-type protein can activate the other type of RNA in vitro. Furthermore, the A-type protein can complement B-type RNA in vivo.2 Thus the two types of RNA and protein are expected to share structural elements that participate in RNA-protein interactions for the activation of RNA. Structural data on the protein subunits of A and B types are available.7,17,18 Both A-type and B-type proteins share high structural similarity in that they are a mixed α-β protein with an unusual left-handed β-α-β turn, which is similar to ribosomal protein S9, domain II of ribosomal protein S5, and also domain IV of elongation factor EF-G. In the case of S5 and EF-G, the left-handed β-α-β turn contains an RNP box motif responsible for RNA binding. Since the RNP box motif is the most conserved region among RNase P proteins, these proteins primarily recognize RNase P RNAs via direct interactions with RNA's phylogenically conserved core. In addition, the protein is also known to interact with the pre-tRNA leader region, indicating that this interaction increases the turnover rate.19-21 Recently the crystal structure of the C-domain of type B RNase P from B. stearothermophilus was determined (N. R. Pace, personal communication). This achievement enables us to view not only the whole structure of RNase P ribozyme but also its ternary complex with its protein cofactor and the substrate tRNA.

In bacterial ribosomes, approximately two-thirds and one-third of the mass consist of RNA and protein, respectively.22 The proteins are named according to the subunit of the ribosome in which they are found, such that they belong to the small (S1 to S31) and large (L1 to L44) subunits. Most of the proteins are located at the core of ribosomal RNA (rRNA). Ribosomal proteins, particularly those of the large subunit, are composed of a globular, surface-exposed domain with long finger-like projections that extend into the rRNA core to stabilize its conformation.23-25 Generally, the proteins interact with multiple RNA elements in different domains. In the large subunit, approximately one-third of the 23S rRNA nucleotides are in van der Waals' contact with protein, and the L22 protein associates with all six domains of the 23S RNA. Proteins termed S4 and S7 promote the assembly of 16S rRNA by interacting with two helices in the RNA.25 Thus proteins are responsible for the organization and stabilization of the higher-order rRNA structure, thereby finely tuning the structure for optimal function. It has been shown that 16S and 23S rRNA are responsible for decoding and peptide synthesis, respectively,24,26,27 indicating that proteins play an active role to conduct the entire translation process smoothly.

A comparison of the ribosome from mammalian mitochondria and E. coli revealed an interesting evolutionary relationship between rRNA and ribosomal protein. The two ribosomes have approximately the same molecular weight, but the RNA:protein ratios of the mitochondrial and E. coli ribosome are 1:2 and 2:1, respectively (Fig. 1). This suggests that during evolution, certain RNA components were replaced by protein components in mitochondria. The structural analyses of these ribosomes clarified that proteins compensated for shortened or lost portions of rRNAs.28,29

Figure 1. 3D model for a mitochondrial large ribosomal RNA based on the crystal structure of the 50S subunit.

Figure 1

3D model for a mitochondrial large ribosomal RNA based on the crystal structure of the 50S subunit. All atomic coordinates of the H. marismortui 50S subunit were obtained from the Protein Data Bank (pdb id 1FFK). A) A model structure for the mitochondrial (more...)

In this chapter, we will describe artificial protein-switched ribozymes for which the enzymatic function of RNA is under the allosteric control of RNA-binding proteins. Rational molecular design at the atomic level and combinatorial techniques were employed for ribozyme construction. Three classes of protein-switched ribozymes will be presented here: the group I intron ribozyme, the hammerhead ribozyme, and the artificial L1 RNA ligase. The group I intron ribozyme was engineered to mimic the evolution of a ribozyme into an RNP, whereas the hammerhead ribozyme and L1 ligase were engineered for biotechnology applications.

At present, the regulation of protein function is less sophisticated in artificially developed protein-switched ribozymes when compared with their natural counterparts. In the natural systems, highly evolved proteins control the entire catalysis or translation process. However, it has become clear that simple molecular design and/or selection for incorporating naturally occurring RNA-protein interactions into a natural or artificial ribozyme is highly effective for regulating ribozyme function. We expect that the rather primitive artificial proteins of the present will continue to be refined with advanced molecular design and selection techniques that mimic evolutionary pathways.

From a Self-Splicing Group I Intron RNA to a Self-Splicing RNP

Self-splicing group I intron RNAs possess a catalytic core that is responsible for catalyzing RNA splicing reactions. In vivo, most group I introns are thought to be associated with specific proteins that stabilize the active RNA conformation.30 For example, CYT-18, a tRNA synthetase of Neurospora crassa, functions as a group I intron specific splicing factor by binding to the conserved P4-P6-P6a region of various group I introns.31,32 In the Tetrahymena group I intron RNA, its large peripheral domain termed P5abc interacts with the P4-P6-P6a region. This peripheral domain is important for performing efficient splicing reactions under physiological conditions;33,34 its deletion drastically reduces activity. However, the addition of CYT-18 to a reaction mixture containing a Tetrahymena RNA derivative lacking P5abc results in considerable RNA activation due to formation of specific RNA-protein interactions. This indicates that group I intron RNAs share conserved and interchangeable modular units.32

On the basis of this observation, the Tetrahymena group I intron RNA was converted to a self-splicing RNP by employing a molecular modeling technique.35 The RNP was designed to fix two newly introduced structural elements in a derivative of the intron RNA that interacts with an artificial protein (Fig. 2A). The conserved P4-P6 domain, which has a hairpin-shaped structure, serves as a scaffold for correct folding of the active form of the intron RNA. In P4-P6, specific interactions between the terminal P5b tetraloop and a tetraloop receptor within P6 act as a clamp to enforce the overall structure (Fig. 2A, left).36-40 Disruption of the tetraloop-receptor interaction causes a significant loss of splicing activity.35 Fixation of these interacting elements with the designed protein is expected if the protein can appropriately bind to the RNA. An RNA derivative was devised by replacing the terminal P5b tetraloop and the internal receptor loop in P6, which directly interact in the original RNA, with two peptide-binding motifs, boxB and RRE from bacteriophage λ and HIV-1, respectively (Fig. 2A, right).41,42 The structure of the RNA-binding peptide was superimposed on the corresponding peptide-binding motif in a computationally designed model RNA derivative. In the modeled structure, two terminal regions consisting of RNA-binding peptides, λN1-19 and HIV-1 Rev34-50 that respectively bind to boxB and RRE were joined via a linker peptide consisting of four consecutive alanines (Fig. 2A, right). High-resolution structures of RNA-peptide interactions employed in the design have been characterized by NMR spectroscopy.43,44

Figure 2. Molecular design of an RNA-protein complex based on the Tetrahymena ribozyme.

Figure 2

Molecular design of an RNA-protein complex based on the Tetrahymena ribozyme. A) Left, RNA-RNA interaction (red) between the P5b GAAA tetraloop and the 11-nt receptor within P6 in the crystal structure of the P4-P6 domain of the Tetrahymena ribozyme. (more...)

The binding of the designed protein facilitates RNA splicing reactions both in vitro and in vivo. The final yield of the splicing reaction increased up to eight-fold in the presence of the corresponding protein.35 However, the protein is not involved in the reaction steps, because Km for the guanosine cofactor and kcat were barely influenced by the presence of the protein.35 Two natural group I intron splicing factors, CBP2 and CYT-18, are also known to bind to intron RNAs to stabilize their active forms by facilitating RNA folding.45 Interestingly, these two proteins can increase kcat up to several hundred times compared with RNA alone, as determined with the bi5 intron RNA.46,47

In our modeled structure, the two terminal regions of the designed proteins were joined via four consecutive alanine residues, Ala-Ala-Ala-Ala (which form part of a stable α-helix). The protein with Ala-Ala-Ala-Ala linker functions twice as effectively as the structurally flexible Gly-Gly-Gly-Gly linker (eight-fold versus four-fold activation), although both facilitate folding. The optimized linker sequence was Gly-Val-Gly-Arg, which was determined using in vivo selection because modeling is impractical for such optimization.35 The protein with the selected sequence that binds to RNA with high affinity facilitated RNA folding much better than the original Ala-Ala-Ala-Ala linker in vitro. A different selection was performed to obtain alternative forms of the Rev-RRE interaction.48 Newly established RNA-protein interactions efficiently regulate and enhance splicing reactions in vivo and in vitro. The affinity between RNA and the selected protein was comparable to the Rev-RRE interaction, demonstrating that it is possible to develop a variety of artificial RNA-protein interactions in an allosterically regulated catalytic RNP.

Another molecular design for converting the Tetrahymena intron to a self-splicing RNP was attempted on the basis of high-resolution three-dimensional RNA and protein structures. In this study, molecules were designed to mimic a molecular evolution pathway from a ribozyme to a catalytic RNP.49 One model molecule that mimicked a putative intermediary stage where RNA-RNA and RNA-protein interactions coexisted was more active than the parental Tetrahymena intron RNA,49 suggesting that the association of a ribozyme with a protein might be advantageous for improving ribozyme activity (Fig. 2B). As expected, a newly designed protein that binds to a newly designed RNA facilitates reactivity in the absence of the original RNA-RNA interaction between the P5b tetraloop and the P6 receptor as described above. This demonstrates that molecular modeling serves as a versatile method for designing an RNP.49

Design of Protein-Dependent Allosteric Hammerhead Ribozymes

Rational molecular design is also applicable to the hammerhead ribozyme, which is a naturally occurring small ribozyme.50-54 A protein-dependent hammerhead ribozyme was designed and constructed using the HIV-1 Rev protein (Fig. 3A).55 Domain II of the hammerhead ribozyme was modified by fusing an RRE domain via a very short connection consisting of two base pairs. Presumably due to conformational alteration, the modified ribozyme is allosterically inactivated when HIV-1 Rev protein binds to the RRE. Ribozyme activity can be restored by the addition of an antibiotic that dissociates the protein from the RNA. Thus the concentration of the Rev protein and the corresponding antibiotic can be detected by monitoring ribozyme activity.

Figure 3. Allosteric control of the hammerhead ribozyme via an RNA-protein interaction.

Figure 3

Allosteric control of the hammerhead ribozyme via an RNA-protein interaction. Cleavage sites are indicated with arrows, and sequences to be cleaved are shown with lowercase letters. A) The catalytically active ribozyme is inactivated by binding of Rev (more...)

Alternatively, an inactive hammerhead ribozyme was constructed to use as a protein-dependent ribozyme by employing the Rev-RRE interaction (Fig. 3B).55 The modified ribozyme possesses an additional oligonucleotide region that serves not only as an inhibitor that disrupts the binding of substrate RNA but also as a part of the binding site for the Rev protein. This design allows the substrate to bind to the ribozyme due to the displacement of the inhibitor region by the protein. In this design, the ribozyme is allosterically activated via a specific interaction between protein and RNA.

Analogously, a protein-binding domain for the protein kinase ERK2 was incorporated into the hammerhead ribozyme (Fig. 3C).56,57 Fifty-fold activation of the modified ribozyme was achieved by adding the ERK2 kinase. As in the case of Rev-RRE, the inhibitor RNA strand is released from the ribozyme so that the specific binding of ERK2 establishes the active form. In another rational design, a newly incorporated protein-binding domain specific to the phosphorylated form of ERK2 allowed the construction of a hammerhead ribozyme activated specifically by phosphorylated ERK2. These ERK2-dependent ribozymes are competent both in vitro and in cell lysates, indicating that they can function as biosensors for detecting modified and unmodified proteins in signal transduction cascades.

Molecular design was also found to be applicable for allosteric regulation of the hammerhead ribozyme by employing the HIV-1 Tat-TAR interaction.58 Ribozymes that can be modestly up-regulated or down-regulated by a Tat protein were constructed by installing a TAR motif into the ribozyme. An analogous design was successfully applied to construct a hammerhead ribozyme that is allosterically down-regulated by HIV-1 reverse transcriptase.59

Selection of Protein-Activated Artificial Ribozymes

An allosterically activated artificial ribozyme derived from the L1 ligase (Fig. 4A)60 was attempted to be designed by employing a natural RNA-binding protein.61 However, the L1 ligase ribozyme could not be converted to a protein-dependent ribozyme by installation of the corresponding protein-binding module, indicating that in this case protein binding was ineffective for converting the RNA structure into an alternative form. Because of this unsuccessful molecular design, new protein-binding domains responsible for activating the ribozyme were selected in vitro from a combinatorial library consisting of 50 random nucleotides, placed near the catalytic core of the RNA (Fig. 4B).61 This enabled the construction of L1 derivatives for which activity is up-regulated by either CYT-18 or hen egg white lysozyme (Fig. 4C). Analogously, another peptide-dependent L1 ribozyme was selected in vitro from the same library (Fig. 4D).62 This ribozyme was activated via a specific interaction with the HIV-1 Rev arginine-rich motif; the motif was recognized in the context of full-length HIV-1 Rev protein. These ribozymes have the potential to function as biosensors that specifically detect RNA-binding proteins. The simultaneous detection of many analytes has been achieved in an array format by immobilizing a variety of L1 ligase derivatives that can be regulated by specific RNA-binding proteins or other factors.63

Figure 4. The protein-dependent L1 ligase ribozyme.

Figure 4

The protein-dependent L1 ligase ribozyme. A) Secondary structure of the L1 ligase ribozyme. B) Location of the N50 pool consisting of 50 random nucleotides that overlaps with a portion of the catalytic core of the L1 ligase. C,D) CYT-18-dependent and (more...)

Applications of Protein-Switched Ribozymes

In conjunction with this expanding repertoire of protein-switched ribozymes, their use in biotechnology applications such as biosensing and gene therapy seems particularly attractive. Allosteric ribozymes regulated by small molecules have been demonstrated to function as biosensors.53 Accordingly, the concentration of a target protein was successfully monitored with fluorescently labeled ribozymes.55,63 A designed trans-splicing intron RNA can serve as a useful tool for repairing aberrant mRNA.64 If these RNAs can be regulated by specific protein factors expressed in particular cells or tissues, the resulting protein-switched ribozymes could be employed for specific therapeutic purposes.

Perspective

In protein-switched ribozymes, specific RNA-binding proteins regulate RNA conformations to turn on or off ribozyme activity. Both in vitro and in vivo, this activity can be regulated with RNA-binding proteins in the case of natural ribozymes such as RNase P. Many experiments have demonstrated that natural and artificial catalytic RNAs are convertible to allosterically regulated ribozymes by practicing molecular design at the secondary or 3D structural levels or by performing selections from combinatorial libraries. The repertoire of RNA-protein combinations in these examples is currently restricted by the limited number of RNA motifs that are known to bind to protein. However, we expect that the number of such protein-binding motifs will soon increase because of rapid progress in the structural analyses of RNA-protein interactions in the ribosome and spliceosome, as well as those involving small noncoding RNAs. Moreover, in vitro selection techniques have been successfully applied for developing new artificial RNA-protein interactions.57 Further advancements in the design and construction of protein-regulated ribozymes are expected by incorporating such newly identified interactions. Future studies along these lines are anticipated to delineate the rules governing the molecular evolution of functional RNPs in cells.

Acknowledgements

The work in our laboratories is supported by Grants-in-Aid for Scientific Research on Priority Areas (T. I. and Y. I.) as well as the Takeda Science Foundation (T.I.), the Inamori and Iketani Foundations (Y.I.) and the Kyushu University Foundation (Y.I.).

References

1.
Brion P, Westhof E. Hierarchy and dynamics of RNA folding. Annu Rev Biophys Biomol Struct. 1997;26:113–137. [PubMed: 9241415]
2.
Day-Storms JJ, Niranjanakumari S, Fierke CA. Ionic interactions between PRNA and P protein in Bacillus subtilis RNase P characterized using a magnetocapturebased assay. RNA. 2004;10:1595–608. [PMC free article: PMC1370646] [PubMed: 15337847]
3.
Herschlag D. RNA chaperones and the RNA folding problem. J Biol Chem. 1995;270:20871–20874. [PubMed: 7545662]
4.
Altman S, Kirsebom L, Talbot S. Recent studies of ribonuclease P. FASEB J. 1993;7:7–14. [PubMed: 7916700]
5.
Pace NR, Brown JW. Evolutionary perspective on the structure and function of ribonuclease P, a ribozyme. J Bacteriol. 1995;177:1919–1928. [PMC free article: PMC176831] [PubMed: 7536728]
6.
Harris ME, Christian EL. Recent insights into the structure and function of the ribonucleoprotein enzyme ribonuclease P. Curr Opin Struct Biol. 2003;13:325–333. [PubMed: 12831883]
7.
Kazantsev AV, Krivenko AA, Harrington DJ. et al. High-resolution structure of RNase P protein from Thermotoga maritima. Proc Natl Acad Sci USA. 2003;100:7497–7502. [PMC free article: PMC164615] [PubMed: 12799461]
8.
Guerrier-Takada C, Gardiner K, Marsh T. et al. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell. 1983;35:849–857. [PubMed: 6197186]
9.
Reich C, Olsen GJ, Pace B. et al. Role of the protein moiety of ribonuclease P, a ribonucleoprotein enzyme. Science. 1988;239:178–181. [PubMed: 3122322]
10.
Pan T. Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry. 1995;34:902–909. [PubMed: 7827048]
11.
Loria A, Pan T. Domain structure of the ribozyme from eubacterial ribonuclease P. RNA. 1996;2:551–563. [PMC free article: PMC1369394] [PubMed: 8718684]
12.
Massire C, Jaeger L, Westhof E. Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis. J Mol Biol. 1998;279:773–793. [PubMed: 9642060]
13.
Waugh DS, Green CJ, Pace NR. The design and catalytic properties of a simplified ribonuclease P RNA. Science. 1989;244:1569–1571. [PubMed: 2472671]
14.
Haas ES, Banta AB, Harris JK. et al. Structure and evolution of ribonuclease P RNA in Gram-positive bacteria. Nucleic Acids Res. 1996;24:4775–4782. [PMC free article: PMC146312] [PubMed: 8972865]
15.
Krasilnikov AS, Yang X, Pan T. et al. Crystal structure of the specificity domain of ribonuclease P. Nature. 2003;421:760–764. [PubMed: 12610630]
16.
Krasilnikov AS, Xiao Y, Pan T. et al. Basis for structural diversity in homologous RNAs. Science. 2004;306:104–107. [PubMed: 15459389]
17.
Spitzfaden C, Nicholson N, Jones JJ. et al. The structure of ribonuclease P protein from Staphylococcus aureus reveals a unique binding site for single-stranded RNA. J Mol Biol. 2000;295:105–115. [PubMed: 10623511]
18.
Stams T, Niranjanakumari S, Fierke CA. et al. Ribonuclease P protein structure: Evolutionary origins in the translational apparatus. Science. 1998;280:752–755. [PubMed: 9563955]
19.
Crary SM, Niranjanakumari S, Fierke CA. The protein component of Bacillus subtilis ribonuclease P increases catalytic efficiency by enhancing interactions with the 5' leader sequence of pretRNAAsp. Biochemistry. 1998;37:9409–9416. [PubMed: 9649323]
20.
Kurz JC, Niranjanakumari S, Fierke CA. Protein component of Bacillus subtilis RNase P specifically enhances the affinity for precursor-tRNAAsp. Biochemistry. 1998;37:2393–2400. [PubMed: 9485387]
21.
Niranjanakumari S, Stams T, Crary SM. et al. Protein component of the ribozyme ribonuclease P alters substrate recognition by directly contacting precursor tRNA. Proc Natl Acad Sci USA. 1998;95:15212–15217. [PMC free article: PMC28022] [PubMed: 9860948]
22.
Green R, Noller HF. Ribosomes and translation. Annu Rev Biochem. 1997;66:679–716. [PubMed: 9242921]
23.
Ban N, Nissen P, Hansen J. et al. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science. 2000;289:905–920. [PubMed: 10937989]
24.
Nissen P, Hansen J, Ban N. et al. The structural basis of ribosome activity in peptide bond synthesis. Science. 2000;289:920–930. [PubMed: 10937990]
25.
Moore PB, Steitz TA. The involvement of RNA in ribosome function. Nature. 2002;418:229–235. [PubMed: 12110899]
26.
Ogle JM, Carter AP, Ogle JM. et al. Insights into the decoding mechanism from recent ribosome structures. Trends Biochem Sci. 2003;28:259–266. [PubMed: 12765838]
27.
Youngman EM, Brunelle JL, Kochaniak AB. et al. The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release. Cell. 2004;117:589–599. [PubMed: 15163407]
28.
Suzuki T, Terasaki M, Takemoto-Hori C. et al. Structural compensation for the deficit of rRNA with proteins in the mammalian mitochondrial ribosome. Systematic analysis of protein components of the large ribosomal subunit from mammalian mitochondria. J Biol Chem. 2001;276:21724–21736. [PubMed: 11279069]
29.
O'Brien TW. Evolution of a protein-rich mitochondrial ribosome: Implications for human genetic disease. Gene. 2002;286:73–79. [PubMed: 11943462]
30.
Caprara MG, Lehnert V, Lambowitz AM. et al. A tyrosyl-tRNA synthetase recognizes a conserved tRNA-like structural motif in the group I intron catalytic core. Cell. 1996;87:1135–1145. [PubMed: 8978617]
31.
Wallweber GJ, Mohr S, Rennard R. et al. Characterization of Neurospora mitochondrial group I introns reveals different CYT-18 dependent and independent splicing strategies and an alternative 3' splice site for an intron ORF. RNA. 1997;3:114–131. [PMC free article: PMC1369467] [PubMed: 9042940]
32.
Mohr G, Caprara MG, Guo Q. et al. A tyrosyl-tRNA synthetase can function similarly to an RNA structure in the Tetrahymena ribozyme. Nature. 1994;370:147–150. [PubMed: 8022484]
33.
Joyce GF, van der Horst G, Inoue T. Catalytic activity is retained in the Tetrahymena group I intron despite removal of the large extension of element P5. Nucleic Acids Res. 1989;17:7879–7889. [PMC free article: PMC334894] [PubMed: 2477801]
34.
van der Horst G, Christian A, Inoue T. Reconstitution of a group I intron self-splicing reaction with an activator RNA. Proc Natl Acad Sci USA. 1991;88:184–188. [PMC free article: PMC50774] [PubMed: 1986364]
35.
Atsumi S, Ikawa Y, Shiraishi H. et al. Design and development of a catalytic ribonucleoprotein. EMBO J. 2001;20:5453–5460. [PMC free article: PMC125660] [PubMed: 11574477]
36.
Murphy FL, Cech TR. GAAA tetraloop and conserved bulge stabilize tertiary structure of a group I intron domain. J Mol Biol. 1994;236:49–63. [PubMed: 8107125]
37.
Cate JH, Gooding AR, Podell E. et al. Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science. 1996;273:1678–1685. [PubMed: 8781224]
38.
Zarrinkar PP, Williamson JR. Kinetic intermediates in RNA folding. Science. 1994;265:918–924. [PubMed: 8052848]
39.
Sclavi B, Sullivan M, Chance MR. et al. RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science. 1998;279:1940–1943. [PubMed: 9506944]
40.
Young BT, Silverman SK. The GAAA tetraloop-receptor interaction contributes differentially to folding thermodynamics and kinetics for the P4-P6 RNA domain. Biochemistry. 2002;41:12271–12276. [PubMed: 12369814]
41.
Weiss MA, Narayana N. RNA recognition by arginine-rich peptide motifs. Biopolymers. 1998;48:167–180. [PubMed: 10333744]
42.
Patel DJ. Adaptive recognition in RNA complexes with peptides and protein modules. Curr Opin Struct Biol. 1999;9:74–87. [PubMed: 10047585]
43.
Battiste JL, Mao H, Rao NS. et al. Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complex. Science. 1996;273:1547–1551. [PubMed: 8703216]
44.
Legault P, Li J, Mogridge J. et al. NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: Recognition of a GNRA fold by an arginine-rich motif. Cell. 1998;93:289–299. [PubMed: 9568720]
45.
Weeks KM. Protein-facilitated RNA folding. Curr Opin Struct Biol. 1997;7:336–342. [PubMed: 9204274]
46.
Weeks KM, Cech TR. Efficient protein-facilitated splicing of the yeast mitochondrial bI5 intron. Biochemistry. 1995;34:7728–7738. [PubMed: 7540041]
47.
Webb AE, Rose MA, Westhof E. et al. Protein-dependent transition states for ribonucleoprotein assembly. J Mol Biol. 2001;309:1087–1100. [PubMed: 11399081]
48.
Atsumi S, Ikawa Y, Shiraishi H. et al. Selections for constituting new RNA-protein interactions in catalytic RNP. Nucleic Acids Res. 2003;31:661–669. [PMC free article: PMC140506] [PubMed: 12527775]
49.
Ikawa Y, Tsuda K, Matsumura S. et al. Putative intermediary stages for the molecular evolution from a ribozyme to a catalytic RNP. Nucleic Acids Res. 2003;31:1488–1496. [PMC free article: PMC149818] [PubMed: 12595557]
50.
Hammann C, Lilley DM. Folding and activity of the hammerhead ribozyme. Chembiochem. 2002;3:690–700. [PubMed: 12203967]
51.
Vaish NK, Kore AR, Eckstein F. Recent developments in the hammerhead ribozyme field. Nucleic Acids Res. 1998;26:5237–5242. [PMC free article: PMC148018] [PubMed: 9826743]
52.
Soukup GA, Breaker RR. Nucleic acid molecular switches. Trends Biotechnol. 1999;17:469–476. [PubMed: 10557159]
53.
Breaker RR. Engineered allosteric ribozymes as biosensor components. Curr Opin Biotechnol. 2002;13:31–39. [PubMed: 11849955]
54.
Silverman SK. Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA. RNA. 2003;9:377–383. [PMC free article: PMC1370404] [PubMed: 12649489]
55.
Hartig JS, Najafi-Shoushtari SH, Grune I. et al. Protein-dependent ribozymes report molecular interactions in real time. Nat Biotechnol. 2002;20:717–722. [PubMed: 12089558]
56.
Vaish NK, Dong F, Andrews L. et al. Monitoring post-translational modification of proteins with allosteric ribozymes. Nat Biotechnol. 2002;20:810–815. [PubMed: 12118241]
57.
Vaish NK, Kossen K, Andrews LE. et al. Monitoring protein modification with allosteric ribozymes. Methods. 2004;32:428–436. [PubMed: 15003605]
58.
Wang DY, Sen D. Rationally designed allosteric variants of hammerhead ribozymes responsive to the HIV-1 Tat protein. Comb Chem High Throughput Screen. 2002;5:301–312. [PubMed: 12052181]
59.
Hartig JS, Famulok M. Reporter ribozymes for real-time analysis of domain-specific interactions in biomolecules: HIV-1 reverse transcriptase and the primer-template complex. Angew Chem Int Ed. 2002;41:4263–4266. [PubMed: 12434357]
60.
Robertson MP, Ellington AD. In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nat Biotechnol. 1999;17:62–66. [PubMed: 9920271]
61.
Robertson MP, Ellington AD. In vitro selection of nucleoprotein enzymes. Nat Biotechnol. 2001;19:650–655. [PubMed: 11433277]
62.
Robertson MP, Knudsen SM, Ellington AD. In vitro selection of ribozymes dependent on peptides for activity. RNA. 2004;10:114–127. [PMC free article: PMC1370523] [PubMed: 14681590]
63.
Hesselberth JR, Robertson MP, Knudsen SM. et al. Simultaneous detection of diverse analytes with an aptazyme ligase array. Anal Biochem. 2003;312:106–112. [PubMed: 12531194]
64.
Long MB, Jones III JP, Sullenger BA. et al. Ribozyme-mediated revision of RNA and DNA. J Clin Invest. 2003;112:312–318. [PMC free article: PMC166303] [PubMed: 12897196]
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