Representation of the secondary and tertiary structure of group I introns

A conserved motif in group IC3 introns is a new class of GNRA receptor

Terminal tetraloops consisting of GNRA sequences are often found in biologically active large RNAs. The loops appear to contribute towards the organization of higher order RNA structures by forming specific tertiary interactions with their receptors. Group IC3 introns which possess a GAAA loop in the L2 region often have a phylogenetically conserved motif in their P8 domains. In this report, we show that this conserved motif stands as a new class of receptor that distinguishes the sequences of GNRA loops less stringently than previously known receptors. The motif can functionally substitute an 11 nt motif receptor in the Tetrahymena ribozyme. Its structural and functional similarity to one class of synthetic receptors obtained from in vitro selection is observed.

Sporadic distribution of tRNA(Arg)CCU introns among alpha-purple bacteria: evidence for horizontal transmission and transposition of a group I intron

A group I intron interrupts the tRNA(Arg)CCU gene of the alpha-purple bacterium Agrobacterium tumefaciens (B. Reinhold-Hurek and D. A. Shub, Nature [London] 357:173-176, 1992). In this study, we assess the distribution of the corresponding intron among 12 additional species of alpha-purple bacteria. Of 10 newly identified tRNA(Arg)CCU genes, we found only two that contained an intron homologous to that of the Agrobacterium intron. This restricted and scattered distribution of the tRNA(Arg)CCUg intron among alpha-purple bacteria is consistent with a recent origin and horizontal transmission. Primary and secondary structural similarities between tRNA(Leu)UAA introns found in strains of the cyanobacterium Microcystis aeruginosa (K. Rudi and K. S. Jacobsen, FEMS Microbiol. Lett. 156:293-298, 1997) and alpha-purple tRNA(Arg)CCU introns suggest that these introns share a more recent common ancestor than either does with other known cyanobacterial tRNA(Leu)UAA introns.

Ribosomal genes of Histoplasma capsulatum var. duboisii and var. farciminosum

A total of 1704 basepairs of the 18S rDNA of Histoplasma capsulatum var. duboisii (HCD, strain CBS175.57) and H. capsulatum var. farciminosum (HCF, strain CBS478.64) were sequenced (EMBL accession no. Z75306 and no. Z75307). The 18S rDNA of HCD was 100% identical to a published sequence of H. capsulatum var. capsulatum (HCC). The 18S rDNA of HCF showed one transversional point mutation at the nucleotide position 114 (ref. Saccharomyces cerevisiae). Hybridization confirmed that, in the 18S rDNA of two out of five strains of HCF, guanine was substituted for cytosine at the nucleotide position 114. Furthermore, identical group 1C1 introns (403 bp) were found to be inserted after position 1165 in four out of five strains of HCF, including the two strains with point mutations in the 18S rDNA, and a slightly different group 1C1 intron (408 bp) was detected in one strain of HCC without this point mutation. Intraspecific sequence variability in the highly conserved 18S rDNA because of occurrence of introns and mutations as a possible source of error in molecular diagnostics is discussed. In addition, internal transcribed spacer regions between the 18S rDNA and the 5.8S rDNA (ITS1) of three strains of HCF, and one strain each of HCC and HCD showed significant sequence variability between varieties and strains of H. capsulatum.

A preorganized active site in the crystal structure of the Tetrahymena ribozyme

Group I introns possess a single active site that catalyzes the two sequential reactions of self-splicing. An RNA comprising the two domains of the Tetrahymena thermophila group I intron catalytic core retains activity, and the 5.0 angstrom crystal structure of this 247-nucleotide ribozyme is now described. Close packing of the two domains forms a shallow cleft capable of binding the short helix that contains the 5' splice site. The helix that provides the binding site for the guanosine substrate deviates significantly from A-form geometry, providing a tight binding pocket. The binding pockets for both the 5' splice site helix and guanosine are formed and oriented in the absence of these substrates. Thus, this large ribozyme is largely preorganized for catalysis, much like a globular protein enzyme.

Antibiotic inhibition of RNA catalysis: neomycin B binds to the catalytic core of the td group I intron displacing essential metal ions

The aminoglycoside antibiotic neomycin B induces misreading of the genetic code during translation and inhibits several ribozymes. The self-splicing group I intron derived from the T4 phage thymidylate synthase (td) gene is one of these. Here we report how neomycin B binds to the intron RNA inhibiting splicing in vitro. Footprinting experiments identified two major regions of protection by neomycin B: one in the internal loop between the stems P4 and P5 and the other in the catalytic core close to the G-binding site. Mutational analyses defined the latter as the inhibitory site. Splicing inhibition is strongly dependent on pH and Mg2+ concentration, suggesting electrostatic interactions and competition with divalent metal ions. Fe2+-induced hydroxyl radical (Fe-OH.) cleavage of the RNA backbone was used to monitor neomycin-mediated changes in the proximity of the metal ions. Neomycin B protected several positions in the catalytic core from Fe-OH. cleavage, suggesting that metal ions are displaced in the presence of the antibiotic. Mutation of the bulged nucleotide in the P7 stem, a position which is strongly protected by neomycin B from Fe-OH. cleavage and which has been proposed to be involved in binding an essential metal ion, renders splicing resistant to neomycin. These results allowed the docking of neomycin to the core of the group I intron in the 3D model.

Group I twintrons: genetic elements in myxomycete and schizopyrenid amoeboflagellate ribosomal DNAs

Protists are unicellular eukaryotes which represent a significant fraction of the global biodiversity. The myxomycete Didymium and the schizopyrenid amoeboflagellate Naegleria are distantly related protists. However, we have noted several striking similarities in life cycle, cell morphology, and ribosomal DNA organization between these organisms. Both have multicopy nuclear extrachromosomal ribosomal DNAs. Here the small subunit ribosomal RNA genes are interrupted by an optional group I twintron, a novel category among the group I introns. Group I twintrons are mobile self-splicing introns of 1.3-1.4 kb in size, with a complex organization at the RNA level. A group I twintron consists of two distinct ribozymes (catalytic RNAs) with different functions in RNA processing, and an open reading frame encoding a functional homing endonuclease--all with prospects of application as molecular tools in biotechnology. Updated RNA secondary structure models of group I twintrons, as well as an example of in vitro ribozyme activity, are presented. We suggest that the group I twintrons have been independently established in myxomycetes and schizopyrenid amoeboflagellates by horizontal gene transfer due to a combination of the phagocytotic behavior in natural environments and the extrachromosomal multicopy nature of ribosomal DNA.

Structure of the large subunit rDNA from a diatom, and comparison between small and large subunit ribosomal RNA for studying stramenopile evolution

The aim of this study was to compare the usefulness of complete small and large subunit rRNA, and a combination of both molecules, for reconstructing stramenopile evolution. To this end, phylogenies from species of which both sequences are known were constructed with the neighbor-joining, maximum parsimony, and maximum likelihood methods. Also the use of structural features of the rRNAs was evaluated. The large subunit rRNA from the diatom Skeletonema pseudocostatum was sequenced in order to have a more complete taxon sampling, and a group I intron was identified. Our results indicated that heterokont algae are monophyletic, with diatoms diverging first. However, as the analysis was restricted to a particular data set containing merely six taxa, the outcome has limited value for elucidating stramenopile relationships. On the other hand, this approach permits comparison of the performance of both rRNA molecules without interference from other factors, such as a different species selection for each molecule. For the taxa used, the large subunit rRNA clearly contained more phylogenetic information than the small subunit rRNA. Although this result can definitely not be generalized and depends on the phylogeny to be studied, in some cases determining complete large subunit rRNA sequences certainly seems worthwhile.

Folding intermediates of a self-splicing RNA: mispairing of the catalytic core

The Tetrahymena thermophila self-splicing RNA is trapped in an inactive conformation during folding reactions at physiological temperatures. The structure of this metastable intermediate was probed by chemical modification interference and site-directed mutagenesis. In the inactive structure, an incorrect base-pairing, which we call Alt P3, displaces the P3 helix in the catalytic core of the intron. Mutations that stabilize Alt P3 increase the fraction of pre-rRNA that becomes trapped in the inactive structure, whereas mutations that destabilize Alt P3 reduce accumulation of this conformer. At high concentrations of Mg2+, the yield of correctly folded mutant pre-rRNAs is similar to wild-type RNA. Under these conditions, the rate of folding for mutant RNAs is slower than for the wild-type, but is increased by addition of urea. The results show that slow folding of the Tetrahymena pre-rRNA is a consequence of non-native secondary structure in the catalytic core of the intron, which is linked to an alternative hairpin in the 5' exon. This illustrates how kinetically stable, long-range interactions shape RNA folding pathways.

A ribosomal function is necessary for efficient splicing of the T4 phage thymidylate synthase intron in vivo

Splicing of the group I intron of the T4 thymidylate synthase (td) gene was uncoupled from translation by introducing stop codons in the upstream exon. This resulted in severe splicing deficiency in vivo. Overexpression of a UGA suppressor tRNA partially rescued splicing, suggesting that this in vitro self-splicing intron requires translation for splicing in vivo. Inhibition of translation by the antibiotics chloramphenicol and spectinomycin also resulted in splicing deficiency. Ribosomal protein S12, a protein with RNA chaperone activity, and CYT-18, a protein that stabilizes the three-dimensional structure of group I introns, efficiently rescued the stop codon mutants. We identified a region in the upstream exon that interferes with splicing. Point mutations in this region efficiently alleviate the effect of a nonsense codon. We infer from these results that the ribosome acts as an RNA chaperone to facilitate proper folding of the intron.

RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting

Radiolysis of water with a synchrotron x-ray beam permits the hydroxyl radical-accessible surface of an RNA to be mapped with nucleotide resolution in 10 milliseconds. Application of this method to folding of the Tetrahymena ribozyme revealed that the most stable domain of the tertiary structure, P4-P6, formed cooperatively within 3 seconds. Exterior helices became protected from hydroxyl radicals in 10 seconds, whereas the catalytic center required minutes to be completely folded. The results show that rapid collapse to a partially disordered state is followed by a slow search for the active structure.

Visualizing metal-ion-binding sites in group I introns by iron(II)-mediated Fenton reactions

BACKGROUND

Most catalytic RNAs depend on divalent metal ions for folding and catalysis. A thorough structure-function analysis of catalytic RNA therefore requires the identification of the metal-ion-binding sites. Here, we probed the binding sites using Fenton chemistry, which makes use of the ability of Fe2+ to functionally or structurally replace Mg2+ at ion-binding sites and to generate short-lived and highly reactive hydroxyl radicals that can cleave nucleic acid and protein backbones in spatial proximity of these ion-binding sites.

RESULTS

Incubation of group I intron RNA with Fe2+, sodium ascorbate and hydrogen peroxide yields distinctly cleaved regions that occur only in the correctly folded RNA in the presence of Mg2+ and can be competed by additional Mg2+, suggesting that Fe2+ and Mg2+ interact with the same sites. Cleaved regions in the catalytic core are conserved for three different group I introns, and there is good correlation between metal-ion-binding sites determined using our method and those determined using other techniques. In a model of the T4 phage-derived td intron, cleaved regions separated in the secondary structure come together in three-dimensional space to form several metal-ion-binding pockets.

CONCLUSIONS

In contrast to structural probing with Fe2+/EDTA, cleavage with Fe2+ detects metal-ion-binding sites located primarily in the inside of the RNA. Essentially all metal-ion-binding pockets detected are formed by tertiary structure elements. Using this method, we confirmed proposed metal-ion-binding sites and identified new ones in group I intron RNAs. This approach should allow the localization of metal-ion-binding sites in RNAs of interest.

Sequence variation of the tRNA(Leu) intron as a marker for genetic diversity and specificity of symbiotic cyanobacteria in some lichens

We examined the genetic diversity of Nostoc symbionts in some lichens by using the tRNA(Leu) (UAA) intron as a genetic marker. The nucleotide sequence was analyzed in the context of the secondary structure of the transcribed intron. Cyanobacterial tRNA(Leu) (UAA) introns were specifically amplified from freshly collected lichen samples without previous DNA extraction. The lichen species used in the present study were Nephroma arcticum, Peltigera aphthosa, P. membranacea, and P. canina. Introns with different sizes around 300 bp were consistently obtained. Multiple clones from single PCRs were screened by using their single-stranded conformational polymorphism pattern, and the nucleotide sequence was determined. No evidence for sample heterogenity was found. This implies that the symbiont in situ is not a diverse community of cyanobionts but, rather, one Nostoc strain. Furthermore, each lichen thallus contained only one intron type, indicating that each thallus is colonized only once or that there is a high degree of specificity. The same cyanobacterial intron sequence was also found in samples of one lichen species from different localities. In a phylogenetic analysis, the cyanobacterial lichen sequences grouped together with the sequences from two free-living Nostoc strains. The size differences in the intron were due to insertions and deletions in highly variable regions. The sequence data were used in discussions concerning specificity and biology of the lichen symbiosis. It is concluded that the tRNA(Leu) (UAA) intron can be of great value when examining cyanobacterial diversity.

Origin and evolution of group I introns in cyanobacterial tRNA genes

Many tRNA(Leu)UAA genes from plastids contain a group I intron. An intron is also inserted in the same gene at the same position in cyanobacteria, the bacterial progenitors of plastids, suggesting an ancient bacterial origin for this intron. A group I intron has also been found in the tRNA(fMet) gene of some cyanobacteria but not in plastids, suggesting a more recent origin for this intron. In this study, we investigate the phylogenetic distributions of the two introns among cyanobacteria, from the earliest branching to the more derived species. The phylogenetic distribution of the tRNA(Leu)UAA intron follows the clustering of rRNA sequences, being either absent or present in clades of closely related species, with only one exception in the Pseudanabaena group. Our data support the notion that the tRNA(Leu)UAA intron was inherited by cyanobacteria and plastids through a common ancestor. Conversely, the tRNA(fMet) intron has a sporadic distribution, implying that many gains and losses occurred during cyanobacterial evolution. Interestingly, a phylogenetic tree inferred from intronic sequences clearly separates the different tRNA introns, suggesting that each family has its own evolutionary history.

A phylogenetic analysis of three group I introns found in the nuclear small subunit ribosomal RNA gene of the ballistoconidiogenous anamorphic yeast-like fungus Tilletiopsis flava

There are three group I introns in the nuclear small subunit ribosomal RNA gene (SSU rDNA) of the ballistoconidiogenous anamorphic yeast-like fungus Tilletiopsis flava JCM 5186. The size of these sequences were 325 nt (position 516), 335 nt (position 1199) and 437 nt (position 1506), respectively. The introns at position 516 (T.flav516) and position 1199 (T.flav1199) belonged to subgroup IB3, and that of position 1506 (T.flav1506) belonged to subgroup IC1. The results of comparison with other group I introns found in SSU rDNA of eucaryotes showed that the positions 516 and 1199 were common positions to IB3 group I introns of fungi and green algae, and that positions 943, 1506 and 1512 were those to IC1 group I introns of fungi, and green and red algae. It is indicated that the insertion position of introns have close relationship with the nature of the subgroup to which they belonged. For phylogenetic analysis, we employed 9 IB3 introns, in which 7 were at position 516 and 2 were at position 1199, and 25 IC1 introns. The maximum likelihood tree based on the conserved region alignment showed that group I introns of subgroup IB3 were phylogenetically distant from those of subgroup IC1. T.flav516 (basidiomycete) constituted a subcluster with R.dacr516 (basidiomycete) and M.albo516 (ascomycete). T. flav1199 was located at the closer position of C.chlo1199 (green alga) than other IB3 introns at position 516. T.flav1506 was located at the subcluster, which was constituted by the 1506 introns found in SSU rDNA of fungi (B.yama1506, P.cari1506, and P.inou1506) and those of green algae (C.elli1506, C.mira1506, G.spir1506, and M.sacl1506) with IC1 introns at the position 1512 (D.parv1512 and C.sacc1512). The analysis of flanking regions showed that both 5' and 3' flanking sequences were well conserved in each insertion site, and indicated that the ancestors of the intron at different site had been inherited from the different origin. Therefore, the two IB3 introns found positions 516 and 1199, T.flav516 and T.flav1199, were supposed to have the independent ancestors. Our results supported the theory of the diversity of group I introns that group I introns had been transferred horizontally to the distinct insertion site, and were inherited and diverged vertically.

RNA structure: crystal clear?

Structured RNAs play an essential role in chromosome maintenance, RNA processing, protein biosynthesis, and protein transport. To understand RNA function in these diverse biological systems, the rules for RNA folding and recognition must be learned. Recent crystal structures of hammerhead ribozymes, a group I intron domain, and RNA duplexes provide new insights into the principles of RNA folding and function.

The Cbp2 protein stimulates the splicing of the omega intron of yeast mitochondria

The Cbp2 protein is encoded in the nucleus and is required for the splicing of the terminal intron of the mitochondrial COB gene in Saccharomyces cerevisiae . Using a yeast strain that lacks this intron but contains a related group I intron in the precursor of the large ribosomal RNA, we have determined that Cbp2 protein is also required for the normal accumulation of 21S ribosomal RNA in vivo . Such strains bearing a deletion of the CBP2 gene adapt slowly to growth in glycerol/ethanol media implying a defect in derepression. At physiologic concentrations of magnesium, Cbp2 stimulates the splicing of the ribosomal RNA intron in vitro . Nevertheless, Cbp2 is not essential for splicing of this intron in mitochondria nor is it required in vitro at magnesium concentrations >5 mM. A similar intron exists in the large ribosomal RNA (LSU) gene of Saccharomyces douglasii . This intron does need Cbp2 for catalytic activity in physiologic magnesium. Similarities between the LSU introns and COB intron 5 suggest that Cbp2 may recognize conserved elements of the these two introns, and protein-induced UV crosslinks occur in similar sites in the substrate and catalytic domains of the RNA precursors.

Time-resolved synchrotron X-ray "footprinting", a new approach to the study of nucleic acid structure and function: application to protein-DNA interactions and RNA folding

Hydroxyl radicals (.OH) can cleave the phosphodiester backbone of nucleic acids and are valuable reagents in the study of nucleic acid structure and protein-nucleic acid interactions. Irradiation of solutions by high flux "white light" X-ray beams based on bending magnet beamlines at the National Synchrotron Light Source (NSLS) yields sufficient concentrations of .OH so that quantitative nuclease protection ("footprinting") studies of DNA and RNA can be conducted with a duration of exposure in the range of 50 to 100 ms. The sensitivity of DNA and RNA to X-ray mediated .OH cleavage is equivalent. Both nucleic acids are completely protected from synchrotron X-ray induced cleavage by the presence of thiourea in the sample solution, demonstrating that cleavage is suppressed by a free radical scavenger. The utility of this time-dependent approach to footprinting is demonstrated with a synchrotron X-ray footprint of a protein-DNA complex and by a time-resolved footprinting analysis of the Mg(2+)-dependent folding of the Tetrahymena thermophilia L-21 ScaI ribozyme RNA. Equilibrium titrations reveal differences among the ribozyme domains in the cooperativity of Mg(2+)-dependent .OH protection. RNA .OH protection progress curves were obtained for several regions of the ribozyme over timescales of 30 seconds to several minutes. Progress curves ranging from > or = 3.5 to 0.4 min-1 were obtained for the P4-P6 and P5 sub-domains and the P3-P7 domain, respectively. The .OH protection progress curves have been correlated with the available biochemical, structural and modeling data to generate a model of the ribozyme folding pathway. Rate differences observed for specific regions within domains provide evidence for steps in the folding pathway not previously observed. Synchrotron X-ray footprinting is a new approach of general applicability for the study of time-resolved structural changes of nucleic acid conformation and protein-nucleic acid complexes.

Joining the two domains of a group I ribozyme to form the catalytic core

Self-splicing group I introns, like other large catalytic RNAs, contain structural domains. Although the crystal structure of one of these domains has been determined by x-ray analysis, its connection to the other major domain that contains the guanosine-binding site has not been known. Site-directed mutagenesis and kinetic analysis of RNA splicing were used to identify a base triple in the conserved core of both a cyanobacterial (Anabaena) and a eukaryotic (Tetrahymena) group I intron. This long-range interaction connects a sequence adjacent to the guanosine-binding site with the domain implicated in coordinating the 5' splice site helix, and it thereby contributes to formation of the active site. The resulting five-strand junction, in which a short helix forms base triples with three separate strands in the Tetrahymena intron, reveals exceptionally dense packing of RNA.

New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme

BACKGROUND

Group I introns self-splice via two consecutive trans-esterification reactions in the presence of guanosine cofactor and magnesium ions. Comparative sequence analysis has established that a catalytic core of about 120 nucleotides is conserved in all known group I introns. This core is generally not sufficient for activity, however, and most self-splicing group I introns require non-conserved peripheral elements to stabilize the complete three-dimensional (3D) structure. The physico-chemical properties of group I introns make them excellent systems for unraveling the structural basis of the RNA-RNA interactions responsible for promoting the self-assembly of complex RNAs.

RESULTS

We present phylogenetic and experimental evidence for the existence of three additional tertiary base pairings between hairpin loops within peripheral components of subgroup IC1 and ID introns. Each of these new long range interactions, called P13, P14 and P16, involves a terminal loop located in domain 2. Although domains 2 of IC and ID introns share very strong sequence similarity, their terminal loops interact with domains 5 and 9 (subgroup IC1) and domain 6 (subgroup ID). Based on these tertiary contacts, comparative sequence analysis, and published experimental results such as Fe(II)-EDTA protection patterns, we propose 3D models for two entire group I introns, the subgroup IC1 intron in the large ribosomal precursor RNA of Tetrahymena thermophila and the SdCob.1 subgroup ID intron found in the cytochrome b gene of Saccharomyces douglasii.

CONCLUSIONS

Three-dimensional models of group I introns belonging to four different subgroups are now available. They all emphasize the modular and hierarchical organization of the architecture of group I introns and the widespread use of base-pairings between terminal hairpin loops for stabilizing the folded and active structures of large and complex RNA molecules.

Secrets of RNA folding revealed

The structure of a domain of the group I intron, the largest structure of an RNA to date, reveals structural details of tertiary interactions required for the folding of a large RNA.

Crystal structure of a group I ribozyme domain: principles of RNA packing

Group I self-splicing introns catalyze their own excision from precursor RNAs by way of a two-step transesterification reaction. The catalytic core of these ribozymes is formed by two structural domains. The 2.8-angstrom crystal structure of one of these, the P4-P6 domain of the Tetrahymena thermophila intron, is described. In the 160-nucleotide domain, a sharp bend allows stacked helices of the conserved core to pack alongside helices of an adjacent region. Two specific long-range interactions clamp the two halves of the domain together: a two-Mg2+-coordinated adenosine-rich corkscrew plugs into the minor groove of a helix, and a GAAA hairpin loop binds to a conserved 11-nucleotide internal loop. Metal- and ribose-mediated backbone contacts further stabilize the close side-by-side helical packing. The structure indicates the extent of RNA packing required for the function of large ribozymes, the spliceosome, and the ribosome.

The Cbp2 protein suppresses splice site mutations in a group I intron

The Cbp2 protein facilitates the folding of a group I intron in the COB pre-mRNA of yeast mitochondria. Based on its ability to suppress mutations affecting the auto-catalytic reaction, the protein appears to play a role in the selection of splice sites. Adding Cbp2 did not overcome the effects of mutations in P1 whose primary effect was on the first step of splicing. In contrast, most mutations affecting the ligation of exons were suppressed in vitro by Cbp2. These included mutations in P1, P9.0 and P10. In fact, a mutant transcript lacking both P9.0 and P10 ligated efficiently in the presence of Cbp2. P9.0 and P10 mutations also reduced the rate of cleavage at the 5' splice junction, and this effect was only partially mitigated by adding Cbp2. A competitive secondary structure near the 3' splice junction blocked Cbp2-stimulated splicing, but this mutation could be suppressed by co-transcriptional splicing in the presence of Cbp2. Our data underscore the importance of the interaction between the 5' and 3' splice junctions in group I introns and suggest that nucleotide-nucleotide interactions that stabilize the structure of group I introns can be superceded by protein-RNA interactions.

The structure of an RNA dodecamer shows how tandem U-U base pairs increase the range of stable RNA structures and the diversity of recognition sites

BACKGROUND

Non-canonical base pairs are fundamental building blocks of RNA structures. They can adopt geometries quite different from those of canonical base pairs and are common in RNA molecules that do not transfer sequence information. Tandem U-U base pairs occur frequently, and can stabilize duplex formation despite the fact that a single U-U base pair is destabilizing.

RESULTS

We determined the crystal structure of the RNA dodecamer GGCGCUUGCGUC at 2.4 A resolution. The molecule forms a duplex containing tandem U-U base pairs, which introduce an overall bend of 11-12 degrees in the duplex resulting from conformational changes at each interface between the tandem U-U base pairs and a flanking duplex sequence. The formation of the U-U base pairs cause small changes in several backbone torsion angles; base stacking is preserved and two hydrogen bonds are formed per base pair, explaining the stability of the structure.

CONCLUSIONS

Tandem U-U base pairs can produce stable structures not accessible to normal A-form RNA, which may allow the formation of specific interfaces for RNA-RNA or RNA-protein recognition. These base-pairs show an unusual pattern of hydrogen-bond donors and acceptors in the major and minor grooves, which could also act as a recognition site.

A strategy of exon shuffling for making large peptide repertoires displayed on filamentous bacteriophage

It has been suggested that recombination and shuffling between exons has been a key feature in the evolution of proteins. We propose that this strategy could also be used for the artificial evolution of proteins in bacteria. As a first step, we illustrate the use of a self-splicing group I intron with inserted lox-Cre recombination site to assemble a very large combinatorial repertoire (> 10(11) members) of peptides from two different exons. Each exon comprised a repertoire of 10 random amino acids residues; after splicing, the repertoires were joined together through a central five-residue spacer to give a combinatorial repertoire of 25-residue peptides. The repertoire was displayed on filamentous bacteriophage by fusion to the pIII phage coat protein and selected by binding to several proteins, including beta-glucuronidase. One of the peptides selected against beta-glucuronidase was chemically synthesized and shown to inhibit the enzymatic activity (inhibition constant: 17 nM); by further exon shuffling, an improved inhibitor was isolated (inhibition constant: 7 nM). Not only does this approach provide the means for making very large peptide repertoires, but we anticipate that by introducing constraints in the sequences of the peptides and of the linker, it may be possible to evolve small folded peptides and proteins.

The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding

We have probed the nature of the individual kinetic steps in the folding of the Tetrahymena ribozyme by studying the folding kinetics of mutant ribozymes. After rapid formation of the first structural subdomain, a slow step precedes stable formation of the second subdomain. The two central helices of the second subdomain form in an interdependent manner, and this structural subunit therefore also constitutes a kinetic folding unit. The slow folding step includes formation of tertiary interactions in a triple-helical scaffold that orients the two subdomains of the RNA. The rapid and early formation of short range secondary structure, the hierarchical formation of kinetic folding units corresponding to structural subdomains, and the formation of tertiary interactions between subdomains late during the folding process appear to be common features of the folding mechanism for both RNA and proteins.

A small insertion in the SSU rDNA of the lichen fungus Arthonia lapidicola is a degenerate group-I intron

Insertions of less than 100 nt occurring in highly conserved regions of the small subunit ribosomal DNA (SSU rDNA) may represent degenerate forms of the group-I introns observed at the same positions in other organisms. A 63-nt insertion at SSU rDNA position 1512 (relative to the Escherichia coli SSU rDNA) of the lichen-forming fungus Arthonia lapidicola can be folded into a secondary structure with two stem loops and a pairing of the insertion and flanking sequences. The two stem loops may correspond to the P1 and P2, and the insertion-flanking pairing to the P10, of a group-I intron. Considering these small insertions as degenerate introns provides important clues to the evolution and catalytic function of group-I introns. Keywords Ribosomal DNA middle dot Small subunit middle dot 18s middle dot Degenerate introns middle dot Ascomycetes

An RNA fragment consisting of the P7 and P9.0 stems and the 3'-terminal guanosine of the Tetrahymena group I intron

On the basis of the nucleotide sequence of Tetrahymena group I intron, we constructed a 31 residue RNA that has the P7 stem and the 3'-terminal guanosine residue (3'-G) with a putative stem-loop structure (P9.0) intervening between them. For this model RNA (P7/P9.0/G), four residues around the guanosine binding site (GBS) in the P7 stem were found to exhibit much lower sensitivities to ribonuclease V1 than those of a variant RNA having adenosine in place of the 3'-G, suggesting that the 3'-G contacts around the GBS. NMR analyses of the imino proton resonances of the P7/P9.0/G RNA indicated that the base pairing in the GBS is retained on the interaction with the 3'-G, and that the two base pairs of the putative P9.0 stem-loop are definitely formed. Comparison of the RNA with its variants with either A (3'-A) or a deletion in place of the 3'-G suggested that the stability of the P9.0 stem-loop is affected by the GBS-3'-G interaction. The melting temperatures of the P9.0 stem-loop were determined from the UV absorbances of these RNAs, which quantitatively indicated that the P9.0 stem-loop is significantly stabilized by the interaction of the GBS with the 3'-G, rather than the 3'-A, and also by direct interaction with divalent cations (Mg2+, Ca2+ or Mn2+). Upon replacement of the G-C base pair by C-G in the GBS of the P7/P9.0/G RNA, the specificity was switched from 3'-G to 3'-A, as in the case of the intact intron.

The P9.1-P9.2 peripheral extension helps guide folding of the Tetrahymena ribozyme

We have previously proposed a hierarchical model for the folding mechanism of the Tetrahymena ribozyme that may illustrate general features of the folding pathways of large RNAs. While the role of elements in the conserved catalytic core of this ribozyme during the folding process is beginning to emerge, the participation of non-conserved peripheral extensions in the kinetic folding mechanism has not yet been addressed. We now show that the 3'-terminal P9.1-P9.2 extension of the Tetrahymena ribozyme plays an important role during the folding process and appears to guide formation of the catalytic core.

Primary and secondary structure analyses of the rDNA group-I introns of the Zygnematales (Charophyta)

The Zygnematales (Charophyta) contain a group-I intron (subgroupIC1) within their nuclear-encoded small subunit ribosomal DNA (SSU rDNA) coding region. This intron, which is inserted after position 1506 (relative to the SSU rDNA of Escherichia coli), is proposed to have been vertically inherited since the origin of the Zygnematales approximately 350-400 million years ago. Primary and secondary structure analyses were carried out to model group-I intron evolution in the Zygnematales. Secondary structure analyses support genetic data regarding sequence conservation within regions known to be functionally important for in vitro self-splicing of group-I introns. Comparisons of zygnematalean group-I intron secondary structures also provided some new insights into sequences that may have important roles in in vivo RNA splicing. Sequence analyses showed that sequence divergence rates and the nucleotide compositions of introns and coding regions within any one taxon varied widely, suggesting that the "1506" group-I introns and rDNA coding regions in the Zygnematales evolve independently.

RNA tectonics: towards RNA design

Our understanding of the structural, folding and catalytic properties of RNA molecules has increased enormously in recent years. The discovery of catalytic RNA molecules by Sidney Altman and Tom Cech, the development of in vitro selection procedures, and the recent crystallizations of hammerhead ribozymes and of a large domain of an autocatalytic group 1 intron are some of the milestones that have contributed to the explosion of the RNA field. The availability of a three-dimensional model for the catalytic core of group 1 introns contributed also a heuristic drive toward the development of new techniques and approaches for unravelling RNA architecture, folding and stability. Here, we emphasize the mosaic structure of RNA and review some of the recent literature pertinent to this working framework. In the long run, RNA tectonics aims at constructing combinatorial libraries, using RNA mosaic units for creating molecules with dedicated shapes and properties.

Function of a pseudoknot in the suppression of an alternative splicing event in a group I intron

Like most mitochondrial group I introns with a free-standing open reading frame (ORF) located downstream of their catalytic core, the Sd.cob, 1 intron in the gene coding for the cytochrome b of Saccharomyces douglasii mitochondria possesses a putative proximal 3' splice site. However, incubation of Sd.cob, 1 preRNA transcripts under optimal in vitro splicing conditions essentially results in splicing at the authentic, distal 3' splice junction. The mechanism by which the proximal splicing event is suppressed in vitro involves formation of a tertiary interaction which is only found in the Sd.cob, 1 intron. Core nucleotides located in loop L5 block proximal splicing by forming Watson-Crick base pairs with the nucleotide sequence of the proximal 3' splice site. This tertiary base pairing, also important for the folding of the intron into an active conformation, may be regarded as equivalent to the L9/P5, GNRA-loop/helix interaction found in more than one-third of known group I introns.

Protein facilitation of group I intron splicing by assembly of the catalytic core and the 5' splice site domain

The yeast mitochondrial group I intron b15 undergoes self-splicing at high Mg2+ concentrations, but requires the splicing factor CBP2 for reaction under physiological conditions. Chemical accessibility and UV cross-linking experiments now reveal that self-processing is slow because functional elements are not properly positioned in an active tertiary structure. Folding energy provided by CBP2 drives assembly of two RNA domains that comprise the catalytic core and meditates association of an approximately 100 nt 5' domain that contains the 5' splice site. Thus, the protein assembles RNA secondary structure elements into a specific three-dimensional array while the RNA provides the catalytic center. The division of labor between RNA and protein illustrated by this simple system reveals principles applicable to complex ribonucleoprotein assemblies such as the spliceosome and ribosome.

RNA folding

The number of known motifs for RNA folding and RNA tertiary organization is expanding rapidly as we learn more about the diverse biological functions of RNA. Problems in protein and RNA folding have melded in recent investigations of ribonucleoprotein folding. Theoretical and experimental models are rapidly being developed for the pathways and stabilizing forces involved in RNA folding.

Minor groove recognition of the conserved G.U pair at the Tetrahymena ribozyme reaction site

The guanine-uracil (G.U) base pair that helps to define the 5'-splice site of group I introns is phylogenetically highly conserved. In such a wobble base pair, G makes two hydrogen bonds with U in a geometry shifted from that of a canonical Watson-Crick pair. The contribution made by individual functional groups of the G.U pair in the context of the Tetrahymena ribozyme was examined by replacement of the G.U pair with synthetic base pairs that maintain a wobble configuration, but that systematically alter functional groups in the major and minor grooves of the duplex. The substitutions demonstrate that the exocyclic amine of G, when presented on the minor groove surface by the wobble base pair conformation, contributes substantially (2 kilocalories.mole-1) to binding by making a tertiary interaction with the ribozyme active site. It contributes additionally to transition state stabilization. The ribozyme active site also makes tertiary contacts with a tripod of 2'-hydroxyls on the minor groove surface of the splice site helix. This suggests that the ribozyme binds the duplex primarily in the minor groove. The alanyl aminoacyl transfer RNA (tRNA) synthetase recognizes the exocyclic amine of an invariant G.U pair and contacts a similar array of 2'-hydroxyls when binding the tRNA(Ala) acceptor stem, providing an unanticipated parallel between protein-RNA and RNA-RNA interactions.

Coaxially stacked RNA helices in the catalytic center of the Tetrahymena ribozyme

Coaxial stacking of helical elements is a determinant of three-dimensional structure in RNA. In the catalytic center of the Tetrahymena group I intron, helices P4 and P6 are part of a tertiary structural domain that folds independently of the remainder of the intron. When P4 and P6 were fused with a phosphodiester linkage, the resulting RNA retained the detailed tertiary interactions characteristic of the native P4-P6 domain and even required lower magnesium ion concentrations for folding. These results indicate that P4 and P6 are coaxial in the P4-P6 domain and, therefore, in the native ribozyme. Helix fusion could provide a general method for identifying pairs of coaxially stacked helices in biological RNA molecules.

A comparative database of group I intron structures

We have created a database of comparatively derived group I intron secondary structure diagrams. This collection currently contains a broad sampling of phylogenetically and structurally similar and diverse structures from over 200 publicly available intron sequences. As more group I introns are sequenced and added to the database, we anticipate minor refinements in these secondary structure diagrams. These diagrams are directly accessible by computer as well as from the authors.