Detailed analysis of base preferences at the cleavage site of a trans-acting HDV ribozyme: a mutation that changes cleavage site specificity
Detailed analysis of base preferences at the cleavage site of a trans -acting HDV ribozyme: a mutation that changes cleavage site specificityFumiko Nishikawa1, Hamid Fauzi1,2 and Satoshi Nishikawa1,*
1National Institute of Bioscience and Human Technology, AIST, MITI, 1-1 Higashi, Tsukuba Science City, Ibaraki 305, Japan and 2Institute of Applied Biochemistry, University of Tsukuba, Tsukuba Science City, Ibaraki 305, Japan
Received November 13, 1996; Revised and Accepted March 3, 1997
ABSTRACT
In our previous attempt at in vitro selectionof a trans- acting human hepatitis delta virus (HDV) ribozyme, we found that one of the variants, G10-68-725G, cleaved a 13 nt substrate, HDVS1, at two sites [Nishikawa,F., Kawakami,J., Chiba,A., Shirai,M., Kumar,P.K.R. and Nishikawa,S. (1996)Eur. J. Biochem., 237, 712-718]. One site was the normal cleavage site and the other site was shifted 1 nt toward the 3'-end. To clarify the interactions between nucleotides around the cleavage site of the trans-acting HDV ribozyme, we analyzed the efficiency of the reaction for every possible base pair between the substrate and the ribozyme at positions -1 (-1N:726N) and +1 (+1N:725N) relative to the cleavage site using the genomic HDV ribozyme, TdS4(Xho), and derivatives of the most active variant, G10-68. These mutagenesis analyses revealed that the +1 base of the substrate affects the structure of the catalytic core in the complex with G10-68-725G, substrate and divalent metal ions, and it shifts the cleavage site. In a comparison with other variants of the trans-acting HDV ribozyme, we found that this cleavage site shift occurred only with G10-68-725G.
INTRODUCTION
The genome of the human hepatitis delta virus (HDV) is a single-stranded circular RNA of ~1700 nt, which appears to replicate through a rolling circle RNA-to-RNA pathway, as do some plant pathogenic RNA viruses (1 -3 ). Both genomic and antigenomic HDV RNAs have self-cleavage activity (ribozyme) in the presence of divalent metal ions, producing a 2',3'-cyclic phosphate and 5'-OH group (1 -2 ) as do other known ribozymes, such as hammerhead and hairpin ribozymes. However, the primary sequence does not resemble those of the ribozymes of the latter two types and details of the reaction mechanism are unknown.
Several models of the secondary structure have been proposed for genomic and antigenomic HDV ribozymes (4 -7 ). Many attempts have been made to understand the roles of different bases and to define the structure of the catalytic core of the HDV ribozyme (reviewed in 8 ,9 ). We also constructed several variants with point and random mutations in single-stranded and stem regions (10 -14 ). Results of further chemical probing studies (15 ) and an analysis of the interference by phosphorothioate substitutions (16 ) have elucidated important bases and phosphates. A model of the tertiary structure of the HDV ribozyme has been proposed based on the pseudoknot structure (17 ,18 ). It was recently suggested that this pseudoknot structure probably exists and functions in vivo (19 ). In attempts to design a trans-acting ribozyme capable of the site-specific cleavage of a substrate, the cis-acting HDV ribozyme has been truncated and divided into substrate and ribozyme portions (7 ,20 -22 ).
In our previous in vitro selection study of trans-acting HDV ribozymes (23 ), we obtained a dominant clone, designated G10-68, from the random RNA pool based on the truncated trans-acting HDV ribozyme, TdS4(Xho). TdS4(Xho) is constructed from the original sequence by shortening stem IV, which is not important for activity (Fig. 1 a). Further investigations indicated that the G10-68-725G variant, with a change at 725C to 725G in G10-68 (Fig. 1 ), cleaved the substrate at two sites and yielded two types of products. The new product was generated because the cleavage site was shifted to the +1 position relative to the original site due to the mutation. Several analyses involving the mutagenesis of the cis-acting HDV ribozyme around the cleavage site have been previously reported, but cleavage site shifting has not been studied thoroughly (8 ,24 ,25 ).
MATERIALS AND METHODS
Synthesis of substrates and ribozymes
All oligonucleotides were synthesized on an automated DNA/RNA synthesizer (model 392 or 394; Applied Biosystems). DNA and RNA phosphoramidites were purchased from Glen Research. Products were purified as described in the user bulletin from ABI (no. 53; 1989) with minor modifications.
Substrates sequences (-1N HDVS1, +1N HDVS1) were as follows. -1N HDVS1, 5'-GA-1(A,U,C,G)GGCCGGCAUG-3'; +1N HDVS1, 5'-GAU+1(A,U,C,G)GCCGGCAUG-3'. All ribozymes were prepared by run-off transcription (AmpliScribe T7 transcription kit; Epicentre Technologies) of the appropriate plasmids after digestion with XbaI, and purified on 8% polyacrylamide denaturing gel that contained 7 M urea.
Mutants of trans-acting ribozymes [TdS4(Xho) and G10-68]
The trans-acting ribozymes TdS4(Xho) and G10-68 (Fig. 1 ) were constructed as described previously (23 ). Mutant variants were prepared using a system for oligonucleotide-directed in vitro mutagenesis (Amersham) after isolation of the single-stranded DNA. Primer sequences were as follows (mutated bases are underlined):
G10-68-725N, d[GAATGTTACC(A,C,T)GCCGGCACCA];
G10-68-726N, d[AGAATGTTAC(A,G,T)GGCCGGCACC];
a-1, d(AATGTTGCCCCGCCGGCGCCA);
b-1, d(CCGAAGAATGCCCGGCCGGCA);
b-2, d(CCGAAGAATGCCCCGCCGGCACCA);
b-3, d(GAATGTTACCGCCGGCACCA).
Cloning and vectors
Vector pUCT7 was a modified version of pUC118; it included the promoter for T7 RNA polymerase and a XhoI site at the EcoRI-BamHI site (14 ). All experiments were conducted with Escherichia coli MV1184 as the host. Plasmid DNA was prepared from an overnight culture and purified with QIAGEN-tip 20 (QIAGEN).
Cleavage activity of ribozymes
The 5'-end of each substrate was labeled with [[gamma]-32P]ATP by T4 polynucleotide kinase (Takara). The cleavage reaction was conducted under ribozyme saturating (single-turnover) conditions as follows: 5 or 10 [mu]M ribozyme, 0.01 [mu]M substrate, 10 mM Mg2+ in 50 mM Tris-HCl (pH 7.4) at 37oC. The reaction solution containing the ribozyme and substrate in Tris-HCl solution without MgCl2 was denatured at 90oC for 2 min and then the solution was cooled on ice. The solution was then incubated at 37oC for 10 min and the reaction was initiated by addition of MgCl2 solution. At appropriate times, aliquots of the reaction mixture were removed and the reaction was stopped by addition of an equal volume of stop solution (9 M urea, 50 mM EDTA, 0.1% bromophenol blue and 0.1% xylene cyanol) on ice. After electrophoretic fractionation on a gel that contained 20% polyacrylamide and 7 M urea, the radioactivity of the bands (substrate, 13 nt; product, 3 or 4 nt) on the gel was determined with a Bioimaging Analyzer (BAS2000; Fuji Film).
Cleavage activity was indicated by the rate of cleaved product formation. For kinetic analysis, we used a simple pseudo-first order equation: cleaved yield (%) = [EP][middot](1 - e-kt) (Table 1 ) and experimental data were fitted to a curve (23 ). This is based on the assumption that under the excess ribozyme condition, substrates are saturated for the ribozyme at time zero. The reverse rate constants for the formation of active and inactive complexes are very much smaller than the rate constant for cleavage. Thus, substrate cleavage would proceed as a first order reaction. The cleavage reaction consists of two steps, namely conformational change and chemical reaction. From our kinetic analysis, we cannot conclude that kobs reflects either the conformational change or chemical step.
Alkaline hydrolysis ladders of HDVS1 were generated by incubating the 5' labeled HDVS1 in 50 mM NaHCO3/Na2CO3 (pH 9.2) containing 1 mM EDTA and 5 [mu]g carrier tRNA for 9 min at 90oC. The partially digested HDVS1 was loaded as a size marker.
Cleavage efficiency for base pair combinations that involve the -1 position
Ribozyme, G10-68-726N or TdS4(Xho)-726N; substrate, -1N HDVS1. [Ribozyme], 10 [mu]M; [substrate], 0.01 [mu]M; [Mg2+], 10 mM and 50 mM Tris-HCl (pH 7.4) at 37oC. Values in brackets are end points (EP) of reactions calculated from the pseudo-first order equation: fraction cleaved (%) = [EP][middot](1 - e-kt). nd, no cleavage reaction was detected in 60 min. In cases of low cleavage activity, percentage cleavage after 60 min is shown.
The pseudoknot secondary structures of genomic and antigenomic HDV ribozymes consist of two stems (I, II), two stem-loops (III, IV) and three single-stranded regions in the cis-acting structure (5 ,13 ,17 ,26 ). Based on this pseudoknot secondary structure, the trans-acting HDV ribozyme TdS4(Xho) was designed (Fig. 1 a) by separation of the structure into two molecules at the junction between stem I and II, and truncation of stem IV (23 ). A variant G10-68 (23 ) which was obtained by in vitro selection has several base changes compared with TdS4(Xho) (open letters, Fig. 1 b). When we examined the effect of mutation on G10-68, we found that one of the variants (G10-68-725G), in which 725C was changed to 725G, produced two cleavage products from a 13mer substrate, HDVS1. Cleavage patterns on a 20% polyacrylamide gel containing 7M urea are shown in Figure 2 a. Cleavages by this ribozyme were observed at two sites, the original one and a site one base closer to the 3'-end, as was confirmed by partial alkaline hydrolysis of the substrate. This two site cleavage seemed specific to some sequences around the cleavage site. In the present study, to obtain more details about the base specificity around the cleavage site of the trans-acting HDV ribozyme, we modified TdS4(Xho), G10-68 and the substrate HDVS1 (Fig. 1 ; Materials and Methods) and examined their effect on cleavage reactions. Schematic representations of sites of cleavage of substrates by ribozymes are shown in Figure 1 c and d.
CONCLUSIONS
Figure 4. Schematic representation of cleavage routes that produced 3 and 4 nt products. Ribozyme, G10-68-725G-726N; substrate, +1N HDVS1. Reaction conditions were the same as those described in legends of Tables 1 and 2.In studying the base specificity of the trans-acting HDV ribozyme cleavage site, we introduced base substitutions at the +1 position (+1N:725N), the -1 position (-1N:726N) and SSrA region (the junction region between stems I and IV) of TdS4(Xho) and G10-68. In the characteristic cleavage patterns by the G10-68-725G ribozyme (Fig. 4 ), the pathway that produces each product is shown (absolute rates of cleavage not shown). Clearly, (i) 726G, the counterpart of the base at the cleavage site is essential; (ii) as the next 3' base, 727G is favoured for cleavage; and (iii) the G10-68-725G ribozyme shifts the cleavage site of the substrate because of a change in the +1 base. This phenomenon appears to be unique to the G10-68 variant that was obtained by selection in vitro.
ACKNOWLEDGEMENTS
We thank Penmetcha Kumar, Daesety Vishuvardhan and Junji Kawakami for comments on the manuscript.
REFERENCES
1 Kuo,M.Y.P., Sharmeen,L., Sharmeen,L., Dinter-Gottlieb,G. and Taylor,J. (1988) J. Virol. 62, 4439-4444.
2 Sharmeen,L., Kuo,M.Y.P., Dinter-Gottlieb,G. and Taylor,J. (1988) J. Virol. 62, 2674-2679.MEDLINE Abstract
3 Wu,H.-N., Lin,Y.-J., Lin,F.-P., Makino,S., Chang,M.-F. and Lai,M.M.C. (1989) Proc. Natl. Acad. Sci. USA. 86, 1831-1835.MEDLINE Abstract
4 Smith,J.B., Gottlieb,P.A. and Dinter-Gottlieb,G. (1992) Biochemistry 31, 9629-9635.
5 Perrotta,A.T., and Been,M.D. (1991) Nature 350, 434-436.
6 Rosenstein,S.P. and Been,M.D. (1991) Nucleic Acids Res. 19, 5409-5416.
7 Branch,A.D. and Robertson,H.D. (1991) Proc. Natl. Acad. Sci. USA. 88, 10163-10167.