Tetrahymena dynamin-related protein 6 self-assembles independent of membrane association

Self-assembly on target membranes is one of the important properties of all dynamin family proteins. Drp6, a dynaminrelated protein in Tetrahymena, controls nuclear remodelling and undergoes cycles of assembly/disassembly on the nuclear envelope. To elucidate the mechanism of Drp6 function, we have characterized its biochemical and biophysical properties using size exclusion chromatography, chemical cross-linking and electron microscopy. The results demonstrate that Drp6 readily forms high-molecular-weight self-assembled structures as determined by size exclusion chromatography and chemical cross-linking. Negative stain electron microscopy revealed that Drp6 assembles into rings and spirals at physiological ionic strength. We have also shown that the recombinant Drp6 expressed in bacteria is catalytically active and its GTPase activity is not enhanced by low salt. These results suggest that, in contrast to dynamins but similar to MxA, Drp6 self-assembles in the absence of membrane templates, and its GTPase activity is not affected by ionic strength of the buffer. We discuss the self-assembly structure of Drp6 and explain the basis for lack of membrane-stimulated GTPase activity.

Tetrahymena Cilia Cap is Built in a Multi-step Process: A Study by Atomic Force Microscopy

Cilia are complex and dynamic organelles that have motility and sensory functions. Defects in cilia biogenesis and function are at the origin of human ciliopathies. In motile cilia, a basal body organizes the axoneme composed of nine microtubule doublets surrounding a central pair of singlet microtubules. The distal ends of axonemal microtubules are attached to the membrane by microtubule-capping structures. Little is known about the early steps of cilium assembly. Although cilia grow and resorb from their distal tips, it remains poorly understood where and when the components of the caps are first assembled. By using Atomic Force Microscopy in tapping mode, with resolution at the nanometer range and with minimum sample manipulation, we show that Tetrahymena cilia assembly requires transient assembly of structures, composed of three components that are placed asymmetrically on an early elongating axoneme. In small uncapped axonemes the microtubule central pair was never observed. Additionally, we show that cilia cap assembly is a multi-step process in which structures of different sizes and shapes are put together in close proximity before the axoneme appears capped. We propose that the cap modifies the axoneme microtubule rate of polymerization and present a model for Tetrahymena cilia cap assembly.

Lectins and Tetrahymena - A review

The unicellular ciliate Tetrahymena is a complete organism, one of the most highly developed protozoans, which has specialized organelles performing each of the functions characteristic to the cells of higher ranked animals. It is also able to produce, store, and secrete hormones of higher ranked animals and also react to them. It produces lectins that can bind them and has functions, which are influenced by exogenous lectins. The review lists the observations on the relationship between lectins and Tetrahymena and try to construe them on the basis of the data, which are at our disposal. Considering the data, lectins can be used by Tetrahymena as materials for influencing conjugation, for stimulating hormone receptors, and by this, mimic the hormonal functions. Lectins can influence phagocytosis and movement of the cells as well as the cell division. As Tetrahymena can recognize both related and hostile cells by the help of lectins and surface sugars, it could be surmised a complex predator-prey system. This could determine the survival of the population as well as the nourishment conditions. When Tetrahymena is pathogenic, it can use lectins as virulence factors.

Folding pathways of the Tetrahymena ribozyme

Like many structured RNAs, the Tetrahymena group I intron ribozyme folds through multiple pathways and intermediates. Under standard conditions in vitro, a small fraction reaches the native state (N) with kobs ≈ 0.6 min(-1), while the remainder forms a long-lived misfolded conformation (M) thought to differ in topology. These alternative outcomes reflect a pathway that branches late in folding, after disruption of a trapped intermediate (Itrap). Here we use catalytic activity to probe the folding transitions from Itrap to the native and misfolded states. We show that mutations predicted to weaken the core helix P3 do not increase the rate of folding from Itrap but they increase the fraction that reaches the native state rather than forming the misfolded state. Thus, P3 is disrupted during folding to the native state but not to the misfolded state, and P3 disruption occurs after the rate-limiting step. Interestingly, P3-strengthening mutants also increase native folding. Additional experiments show that these mutants are rapidly committed to folding to the native state, although they reach the native state with approximately the same rate constant as the wild-type ribozyme (~1 min(-1)). Thus, the P3-strengthening mutants populate a distinct pathway that includes at least one intermediate but avoids the M state, most likely because P3 and the correct topology are formed early. Our results highlight multiple pathways in RNA folding and illustrate how kinetic competitions between rapid events can have long-lasting effects because the "choice" is enforced by energy barriers that grow larger as folding progresses.

RNA catalytic activity as a probe of chaperone-mediated RNA folding

For structured RNAs that possess catalytic activity, this activity provides a powerful probe for measuring the progress of folding and the effects of RNA chaperone proteins on the folding rate. The crux of this approach is that only the natively folded RNA is able to perform the catalytic reaction. This method can provide a quantitative measure of the fraction of native RNA over time, and it can readily distinguish the native state from all misfolded conformations. Here we describe an activity-based method measuring native folding of ribozymes derived from self-splicing group I introns, and we show how the assay can be used to monitor acceleration of native folding by DEAD-box RNA helicase proteins that function as general RNA chaperones. By measuring the amount of substrate that is converted to product in a rapid first turnover, we describe how to determine the fraction of the ribozyme population that is present in the native state. Further, we describe how to perform a two-stage or discontinuous assay in which folding proceeds in stage one and then solution conditions are changed in stage two to permit catalytic activity and block further folding. This protocol allows folding to be followed under a broad range of solution conditions, including those that do not support catalytic activity, and facilitates studies of chaperone proteins.

G-quadruplexes form ultrastable parallel structures in deep eutectic solvent

G-quadruplex DNA is highly polymorphic. Its conformation transition is involved in a series of important life events. These controllable diverse structures also make G-quadruplex DNA a promising candidate as catalyst, biosensor, and DNA-based architecture. So far, G-quadruplex DNA-based applications are restricted done in aqueous media. Since many chemical reactions and devices are required to be performed under strictly anhydrous conditions, even at high temperature, it is challenging and meaningful to conduct G-quadruplex DNA in water-free medium. In this report, we systemically studied 10 representative G-quadruplexes in anhydrous room-temperature deep eutectic solvents (DESs). The results indicate that intramolecular, intermolecular, and even higher-order G-quadruplex structures can be formed in DES. Intriguingly, in DES, parallel structure becomes the G-quadruplex DNA preferred conformation. More importantly, compared to aqueous media, G-quadruplex has ultrastability in DES and, surprisingly, some G-quadruplex DNA can survive even beyond 110 °C. Our work would shed light on the applications of G-quadruplex DNA to chemical reactions and DNA-based devices performed in an anhydrous environment, even at high temperature.

Tetrahymena in the laboratory: strain resources, methods for culture, maintenance, and storage

The ciliated protozoan Tetrahymena thermophila has been an important model system for biological research for many years. During that time, a variety of useful strains, including highly inbred stocks, a collection of diverse mutant strains, and wild cultivars from a variety of geographical locations have been identified. In addition, thanks to the efforts of many different laboratories, optimal conditions for growth, maintenance, and storage of Tetrahymena have been worked out. To facilitate the efficient use of Tetrahymena, especially by those new to the system, this chapter presents a brief description of many available Tetrahymena strains and lists possible resources for obtaining viable cultures of T. thermophila and other Tetrahymena species. Descriptions of commonly used media, methods for cell culture and maintenance, and protocols for short- and long-term storage are also presented.

Structure-function analysis from the outside in: long-range tertiary contacts in RNA exhibit distinct catalytic roles

The conserved catalytic core of the Tetrahymena group I ribozyme is encircled by peripheral elements. We have conducted a detailed structure-function study of the five long-range tertiary contacts that fasten these distal elements together. Mutational ablation of each of the tertiary contacts destabilizes the folded ribozyme, indicating a role of the peripheral elements in overall stability. Once folded, three of the five tertiary contact mutants exhibit defects in overall catalysis that range from 20- to 100-fold. These and the subsequent results indicate that the structural ring of peripheral elements does not act as a unitary element; rather, individual connections have distinct roles as further revealed by kinetic and thermodynamic dissection of the individual reaction steps. Ablation of P14 or the metal ion core/metal ion core receptor (MC/MCR) destabilizes docking of the substrate-containing P1 helix into tertiary interactions with the ribozyme's conserved core. In contrast, ablation of the L9/P5 contact weakens binding of the guanosine nucleophile by slowing its association, without affecting P1 docking. The P13 and tetraloop/tetraloop receptor (TL/TLR) mutations had little functional effect and small, local structural changes, as revealed by hydroxyl radical footprinting, whereas the P14, MC/MCR, and L9/P5 mutants show structural changes distal from the mutation site. These changes extended into regions of the catalytic core involved in docking or guanosine binding. Thus, distinct allosteric pathways couple the long-range tertiary contacts to functional sites within the conserved core. This modular functional specialization may represent a fundamental strategy in RNA structure-function interrelationships.

Turning limited experimental information into 3D models of RNA

Our understanding of RNA functions in the cell is evolving rapidly. As for proteins, the detailed three-dimensional (3D) structure of RNA is often key to understanding its function. Although crystallography and nuclear magnetic resonance (NMR) can determine the atomic coordinates of some RNA structures, many 3D structures present technical challenges that make these methods difficult to apply. The great flexibility of RNA, its charged backbone, dearth of specific surface features, and propensity for kinetic traps all conspire with its long folding time, to challenge in silico methods for physics-based folding. On the other hand, base-pairing interactions (either in runs to form helices or isolated tertiary contacts) and motifs are often available from relatively low-cost experiments or informatics analyses. We present RNABuilder, a novel code that uses internal coordinate mechanics to satisfy user-specified base pairing and steric forces under chemical constraints. The code recapitulates the topology and characteristic L-shape of tRNA and obtains an accurate noncrystallographic structure of the Tetrahymena ribozyme P4/P6 domain. The algorithm scales nearly linearly with molecule size, opening the door to the modeling of significantly larger structures.

Metal ion dependence of cooperative collapse transitions in RNA

Positively charged counterions drive RNA molecules into compact configurations that lead to their biologically active structures. To understand how the valence and size of the cations influences the collapse transition in RNA, small-angle X-ray scattering was used to follow the decrease in the radius of gyration (R(g)) of the Azoarcus and Tetrahymena ribozymes in different cations. Small, multivalent cations induced the collapse of both ribozymes more efficiently than did monovalent ions. Thus, the cooperativity of the collapse transition depends on the counterion charge density. Singular value decomposition of the scattering curves showed that folding of the smaller and more thermostable Azoarcus ribozyme is well described by two components, whereas collapse of the larger Tetrahymena ribozyme involves at least one intermediate. The ion-dependent persistence length, extracted from the distance distribution of the scattering vectors, shows that the Azoarcus ribozyme is less flexible at the midpoint of transition in low-charge-density ions than in high-charge-density ions. We conclude that the formation of sequence-specific tertiary interactions in the Azoarcus ribozyme overlaps with neutralization of the phosphate charge, while tertiary folding of the Tetrahymena ribozyme requires additional counterions. Thus, the stability of the RNA structure determines its sensitivity to the valence and size of the counterions.

The Beamline X28C of the Center for Synchrotron Biosciences: a national resource for biomolecular structure and dynamics experiments using synchrotron footprinting

Structural mapping of proteins and nucleic acids with high resolution in solution is of critical importance for understanding their biological function. A wide range of footprinting technologies have been developed over the last ten years to address this need. Beamline X28C, a white-beam X-ray source at the National Synchrotron Light Source of Brookhaven National Laboratory, functions as a platform for synchrotron footprinting research and further technology development in this growing field. An expanding set of user groups utilize this national resource funded by the National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health. The facility is operated by the Center for Synchrotron Biosciences and the Center for Proteomics of Case Western Reserve University. The facility includes instrumentation suitable for conducting both steady-state and millisecond time-resolved footprinting experiments based on the production of hydroxyl radicals by X-rays. Footprinting studies of nucleic acids are routinely conducted with X-ray exposures of tens of milliseconds, which include studies of nucleic acid folding and their interactions with proteins. This technology can also be used to study protein structure and dynamics in solution as well as protein-protein interactions in large macromolecular complexes. This article provides an overview of the X28C beamline technology and defines protocols for its adoption at other synchrotron facilities. Lastly, several examples of published results provide illustrations of the kinds of experiments likely to be successful using these approaches.

Group II intron folding under near-physiological conditions: collapsing to the near-native state

The folding of group II intron ribozymes has been studied extensively under optimal conditions for self-splicing in vitro (42 degrees C and high magnesium ion concentrations). In these cases, the ribozymes fold directly to the native state by an apparent two-state mechanism involving the formation of an obligate intermediate within intron domain 1. We have now characterized the folding pathway under near-physiological conditions. We observe that compaction of the RNA proceeds slowly to completion, even at low magnesium concentration (3 mM). Kinetic analysis shows that this compact species is a "near-native" intermediate state that is readily chased into the native state by the addition of high salt. Structural probing reveals that the near-native state represents a compact domain 1 scaffold that is not yet docked with the catalytic domains (D3 and D5). Interestingly, native ribozyme reverts to the near-native state upon reduction in magnesium concentration. Therefore, while the intron can sustain the intermediate state under physiological conditions, the native structure is not maintained and is likely to require stabilization by protein cofactors in vivo.

Microtubule acetylation promotes kinesin-1 binding and transport

Long-distance intracellular delivery is driven by kinesin and dynein motor proteins that ferry cargoes along microtubule tracks . Current models postulate that directional trafficking is governed by known biophysical properties of these motors-kinesins generally move to the plus ends of microtubules in the cell periphery, whereas cytoplasmic dynein moves to the minus ends in the cell center. However, these models are insufficient to explain how polarized protein trafficking to subcellular domains is accomplished. We show that the kinesin-1 cargo protein JNK-interacting protein 1 (JIP1) is localized to only a subset of neurites in cultured neuronal cells. The mechanism of polarized trafficking appears to involve the preferential recognition of microtubules containing specific posttranslational modifications (PTMs) by the kinesin-1 motor domain. Using a genetic approach to eliminate specific PTMs, we show that the loss of a single modification, alpha-tubulin acetylation at Lys-40, influences the binding and motility of kinesin-1 in vitro. In addition, pharmacological treatments that increase microtubule acetylation cause a redirection of kinesin-1 transport of JIP1 to nearly all neurite tips in vivo. These results suggest that microtubule PTMs are important markers of distinct microtubule populations and that they act to control motor-protein trafficking.

Identification of histone H3 lysine 36 acetylation as a highly conserved histone modification

Histone lysine acetylation is a major mechanism by which cells regulate the structure and function of chromatin, and new sites of acetylation continue to be discovered. Here we identify and characterize histone H3K36 acetylation (H3K36ac). By mass spectrometric analyses of H3 purified from Tetrahymena thermophila and Saccharomyces cerevisiae (yeast), we find that H3K36 can be acetylated or methylated. Using an antibody specific to H3K36ac, we show that this modification is conserved in mammals. In yeast, genome-wide ChIP-chip experiments show that H3K36ac is localized predominantly to the promoters of RNA polymerase II-transcribed genes, a pattern inversely related to that of H3K36 methylation. The pattern of H3K36ac localization is similar to that of other sites of H3 acetylation, including H3K9ac and H3K14ac. Using histone acetyltransferase complexes purified from yeast, we show that the Gcn5-containing SAGA complex that regulates transcription specifically acetylates H3K36 in vitro. Deletion of GCN5 completely abolishes H3K36ac in vivo. These data expand our knowledge of the genomic targets of Gcn5, show H3K36ac is highly conserved, and raise the intriguing possibility that the transition between H3K36ac and H3K36me acts as an "acetyl/methyl switch" governing chromatin function along transcription units.

Multiple tubulin forms in ciliated protozoan Tetrahymena and Paramecium species

Tetrahymena and Paramecium species are widely used representatives of the phylum Ciliata. Ciliates are particularly suitable model organisms for studying the functional heterogeneity of tubulins, since they provide a wide range of different microtubular structures in a single cell. Sequencing projects of the genomes of members of these two genera are in progress. Nearly all members of the tubulin superfamily (alpha-, beta-, gamma-, delta-, epsilon-, eta-, theta-, iota-, and kappa-tubulins) have been identified in Paramecium tetraurelia. In Tetrahymena spp., the functional consequences of different posttranslational tubulin modifications (acetylation, tyrosination and detyrosination, phosphorylation, glutamylation, and glycylation) have been studied by different approaches. These model organisms provide the opportunity to determine the function of tubulins found in ciliates, as well as in humans, but absent in some other model organisms. They also give us an opportunity to explore the mechanisms underlying microtubule diversity. Here we review current knowledge concerning the diversity of microtubular structures, tubulin genes, and posttranslational modifications in Tetrahymena and Paramecium species.

Phospholipids of the Differentiating Species of Tetrahymena

The whole-cell phospholipid composition of the six known polymorphic species of Tetrahymena has been examined by [(3)H]acetate and [(3)H]myristic acid radiolabeling, and by gas-liquid chromatography of total phospholipid-bound fatty acids. Five of the polymorphic species contained similar phospholipid profiles following radiolabeling in that phosphatidylethanolamine (PE) was the predominant phospholipid; however, in cells of Tetrahymena patula LFF, aminoethylphosphonolipid was present in amounts nearly equal to PE. Tetrahymena patula LFF contained an unusually large percentage of sphingolipid (16.2% by [(3)H]acetate radiolabeling). Substantial differences were found in the fatty acid profiles of the polymorphic species, which included the degree of fatty acid unsaturation and relative weight percentages of odd-chain fatty acids. Tetrahymena vorax contained a low ratio of unsaturated C(18) fatty acids to saturated C(18) fatty acids as compared with all other species examined. The differentiating species generally contained a lesser percentage of monoenoic fatty acids and a lower ratio of unsaturated C(16) fatty acids to saturated C(16) fatty acids as compared with the two monomorphic species examined.

Force production by disassembling microtubules

Microtubules (MTs) are important components of the eukaryotic cytoskeleton: they contribute to cell shape and movement, as well as to the motions of organelles including mitotic chromosomes. MTs bind motor enzymes that drive many such movements, but MT dynamics can also contribute to organelle motility. Each MT polymer is a store of chemical energy that can be used to do mechanical work, but how this energy is converted to motility remains unknown. Here we show, by conjugating glass microbeads to tubulin polymers through strong inert linkages, such as biotin-avidin, that depolymerizing MTs exert a brief tug on the beads, as measured with laser tweezers. Analysis of these interactions with a molecular-mechanical model of MT structure and force production shows that a single depolymerizing MT can generate about ten times the force that is developed by a motor enzyme; thus, this mechanism might be the primary driving force for chromosome motion. Because even the simple coupler used here slows MT disassembly, physiological couplers may modulate MT dynamics in vivo.

D-3 phosphoinositides of the ciliate Tetrahymena: Characterization and study of their regulatory role in lysosomal enzyme secretion

Phosphatidylinositol 3-phosphate, PtdIns3P, is a phosphoinositide which is implicated in regulating membrane trafficking in both mammalian and yeast cells. It also serves as a precursor for the synthesis of phosphatidylinositol 3,5-bisphosphate, PtdIns3,5P2, a phosphoinositide, the exact functions of which remain unknown. In this report, we show that these two phosphoinositides are constitutive lipid components of the ciliate Tetrahymena. Using HPLC analysis, PtdIns3P and PtdIns3,5P2 were found to comprise 16% and 30-40% of their relevant phosphoinositide pools, respectively. Treatment of Tetrahymena cells with wortmannin (0.1-10 microM) resulted in the depletion of PtdIns3P and PtdIns3,5P2 without any effect on D-4 phosphoinositides. Wortmannin was further used for the investigation of D-3 phosphoinositide involvement in the regulation of lysosomal vesicular trafficking. Incubation of Tetrahymena cells with wortmannin resulted in enhanced secretion of two different lysosomal enzymes without any change in their total activities. Experiments performed with a T. thermophila secretion mutant strain verified that the wortmannin-induced secretion is specific and it is not due to a diversion of lysosomal enzymes to other secretory pathways. Moreover, experiments performed with a phagocytosis-deficient T. thermophila strain showed that a substantial fraction of wortmannin-induced secretion was dependent on the presence of functional phagosomes/phagolysosomes.

RNA and protein folding: common themes and variations

Visualizing the navigation of an ensemble of unfolded molecules through the bumpy energy landscape in search of the native state gives a pictorial view of biomolecular folding. This picture, when combined with concepts in polymer theory, provides a unified theory of RNA and protein folding. Just as for proteins, the major folding free energy barrier for RNA scales sublinearly with the number of nucleotides, which allows us to extract the elusive prefactor for RNA folding. Several folding scenarios can be anticipated by considering variations in the energy landscape that depend on sequence, native topology, and external conditions. RNA and protein folding mechanism can be described by the kinetic partitioning mechanism (KPM) according to which a fraction (Phi) of molecules reaches the native state directly, whereas the remaining fraction gets kinetically trapped in metastable conformations. For two-state folders Phi approximately 1. Molecular chaperones are recruited to assist protein folding whenever Phi is small. We show that the iterative annealing mechanism, introduced to describe chaperonin-mediated folding, can be generalized to understand protein-assisted RNA folding. The major differences between the folding of proteins and RNA arise in the early stages of folding. For RNA, folding can only begin after the polyelectrolyte problem is solved, whereas protein collapse requires burial of hydrophobic residues. Cross-fertilization of ideas between the two fields should lead to an understanding of how RNA and proteins solve their folding problems.

A Dicer-like protein in Tetrahymena has distinct functions in genome rearrangement, chromosome segregation, and meiotic prophase

Previous studies indicated that genome rearrangement involving DNA sequence elimination that occurs at late stages of conjugation in Tetrahymena is epigenetically controlled by siRNA-like scan (scn) RNAs produced from nongenic, heterogeneous, bidirectional, micronuclear transcripts synthesized at early stages of conjugation. Here, we show that Dcl1p, one of three Tetrahymena Dicer-like enzymes, is required for processing the micronuclear transcripts to scnRNAs. DCL1 is also required for methylation of histone H3 at Lys 9, which, in wild-type cells, specifically occurs on the sequences (IESs) being eliminated. These results argue that Dcl1p processes nongenic micronuclear transcripts to scnRNAs and is required for IES elimination. This is the first evidence linking nongenic micronuclear transcripts, scnRNAs, and genome rearrangement. Dcl1p also is required for proper mitotic and meiotic segregation of micronuclear chromosomes and for normal chromosome alignment in meiotic prophase, suggesting that DCL1 has multiple functions in regulating chromosome dynamics.

The dynein heavy chain family

Dynein is the large molecular motor that translocates to the (-) ends of microtubules. Dynein was first isolated from Tetrahymena cilia four decades ago. The analysis of the primary structure of the dynein heavy chain and the discovery that many organisms express multiple dynein heavy chains have led to two insights. One, dynein, whose motor domain comprises six AAA modules and two potential mechanical levers, generates movement by a mechanism that is fundamentally different than that which underlies the motion of myosin and kinesin. And two, organisms with cilia or flagella express approximately 14 different dynein heavy chain genes, each gene encodes a distinct dynein protein isoform, and each isoform appears to be functionally specialized. Sequence comparisons demonstrate that functionally equivalent isoforms of dynein heavy chains are well conserved across species. Alignments of portions of the motor domain result in seven clusters: (i) cytoplasmic dynein Dyhl; (ii) cytoplasmic dynein Dyh2; (iii) axonemal outer arm dynein alpha; (iv) outer arm dyneins beta and gamma; (v) inner arm dynein 1alpha; (vi) inner arm dynein 1beta; and (vii) a group of apparently single-headed inner arm dyneins. Some of the dynein groups contained more than one representative from a single organism, suggesting that these may be tissue-specific variants.

Modulation of telomere length dynamics by the subtelomeric region of tetrahymena telomeres

Tetrahymena telomeres usually consist of approximately 250 base pairs of T(2)G(4) repeats, but they can grow to reach a new length set point of up to 900 base pairs when kept in log culture at 30 degrees C. We have examined the growth profile of individual macronuclear telomeres and have found that the rate and extent of telomere growth are affected by the subtelomeric region. When the sequence of the rDNA subtelomeric region was altered, we observed a decrease in telomere growth regardless of whether the GC content was increased or decreased. In both cases, the ordered structure of the subtelomeric chromatin was disrupted, but the effect on the telomeric complex was relatively minor. Examination of the telomeres from non-rDNA chromosomes showed that each telomere exhibited a unique and characteristic growth profile. The subtelomeric regions from individual chromosome ends did not share common sequence elements, and they each had a different chromatin structure. Thus, telomere growth is likely to be regulated by the organization of the subtelomeric chromatin rather than by a specific DNA element. Our findings suggest that at each telomere the telomeric complex and subtelomeric chromatin cooperate to form a unique higher order chromatin structure that controls telomere length.

Localization by indirect immunofluorescence of tetrin, actin, and centrin to the oral apparatus and buccal cavity of the macrostomal form of Tetrahymena vorax

We have taken advantage of the size of the macrostomal oral apparatus of Tetrahymena vorax to investigate the immunofluorescent localization of three cytoskeletal proteins--tetrin, actin, and centrin. Tetrin and actin antibodies co-localize to cross-connectives that anchor the membranelles. These antibodies also recognize the coarse filamentous reticulum, a filament associated with the undulating membrane. Actin-specific localization extends beyond the coarse filamentous reticulum-undulating membrane complex into a region called the specialized cytoplasm. A centrin antibody localizes to the fine filamentous reticulum which, along with microtubules of the oral ribs, circumscribes the cytostomal opening. Models of phagocytic contraction based on these data are presented.

Two-repeat Tetrahymena telomeric d(TGGGGTTGGGGT) Sequence interconverts between asymmetric dimeric G-quadruplexes in solution

Recently, the two-repeat human telomeric d(TAGGGTTAGGGT) sequence has been shown to form interconverting parallel and antiparallel G-quadruplex structures in solution. Here, we examine the structures formed by the two-repeat Tetrahymena telomeric d(TGGGGTTGGGGT) sequence, which differs from the human sequence only by one G-for-A replacement in each repeat. We show by NMR that this sequence forms two novel G-quadruplex structures in Na+-containing solution. Both structures are asymmetric, dimeric G-quadruplexes involving a core of four stacked G-tetrads and two edgewise loops. The adjacent strands of the G-tetrad core are alternately parallel and antiparallel. All G-tetrads adopt syn.syn.anti.anti alignments, which occur with 5'-syn-anti-syn-anti-3' alternations along G-tracks. In the first structure (head-to-head), two loops are at one end of the G-tetrad core; in the second structure (head-to-tail), two loops are located on opposite ends of the G-tetrad core. In contrast to the human telomere counterpart, the proportions of the two forms here are similar for a wide range of temperatures; their unfolding rates are also similar, with an activation enthalpy of 153 kJ/mol.

Identification and molecular cloning of Tetrahymena 138-kDa protein, a transcription elongation factor homologue that interacts with microtubules in vitro

Macronucleus of Tetrahymena divides amitotically, although in a microtubule-dependent fashion. Besides the localization study and pharmacological study of macronuclear microtubules, mechanism of the macronuclear division is poorly understood. A biochemical search for microtubule-associated protein was attempted from the isolated macronucleus. Improvement on macronucleus isolation method and microtubule coprecipitation assay led to the cloning of p138, a new homologue of transcription elongation factor FACT (facilitates chromatin transcription) 140kDa subunit. DNase treatment test of macronuclear extract and the sequence of p138 suggested that p138 is associated with chromosome in the macronucleus. The release tests of p138 from microtubules indicated that p138 is released from microtubules in the presence of ATP but not in the presence of AMP-PNP. Together, the results suggest a novel function of FACT homologue, that p138 interacts with both microtubules and chromosome.

NMR solution structure of the L 9.1a region of Tetrahymena group I intron

The solution structure of 20 mer RNA contained of the loop 9.1a region of Tetrahymena group I intron was studied by NMR. This RNA oligomer has hairpin and duplex structures at high concentration (1 mM) of the sample even at low NaCl concentration (5 mM). In the hairpin structure, GC base pairs by the loop-loop interaction are formed. As study of NOESY measurements, and by the compared with the sequence, this loop region is presumed to interact with the loop 5c.

Small structural costs for evolution from RNA to RNP-based catalysis

Typical RNA-based cellular catalysts achieve their active structures only as complexes with protein cofactors, implying that protein binding compensates for some structural deficiencies in the RNA. An unresolved question was the extent to which protein-facilitation imposes additional structural costs, by requiring that an RNA maintain structures required for protein binding, beyond those required for catalysis. We used nucleotide analog interference to identify initially 71 functional group substitutions at phosphate, 2'-ribose, and adenosine base positions that compromise RNA self-splicing in the bI5 group I intron. Protein-facilitated splicing by CBP2 suppresses 11 of 30 interfering substitutions at the RNA backbone and a greater fraction, 27 of 41, at the adenosine base, including at structures conserved among group I introns. Only one substitution directly interferes with protein binding but not with self-splicing. This substitution, plus three adenosine base modifications that interfere more strongly in CBP2-dependent splicing than in self-splicing, yield a cost for protein facilitation of only four functional groups, as approximated by this set of analogs. The small observed structural cost provides a strong physical rationale for the evolutionary drive from RNA to RNP-based function in biology. Remarkably, the four extra requirements do not appear to report disruption of direct protein-RNA contacts and instead likely reflect design against misfolding rather than for maintenance of a protein-binding site.

Identification of the inositol isomers present in Tetrahymena

The inositol isomer composition of phosphoinositides, polyphosphoinositols, phosphatidylinositol-linked glycans, and glycosyl phosphatidylinositol-anchored proteins of logarithmic phase Tetrahymena vorax was determined by GC-MS analysis of trimethylsilylimadazole derivatives. The most abundant inositol found was the myo-isomer; however, appreciable percentages of scylloinositol were present in the free inositol pool, phosphatidylinositol-linked glycan fraction, and glycosyl phosphatidylinositol-anchored protein fraction. Trace quantities of chiro- and neo-inositols also were present.

Omnipotent decoding potential resides in eukaryotic translation termination factor eRF1 of variant-code organisms and is modulated by the interactions of amino acid sequences within domain 1

In eukaryotes, a single translational release factor, eRF1, deciphers three stop codons, although its decoding mechanism remains puzzling. In the ciliate Tetrahymena thermophila, UAA and UAG codons are reassigned to Gln codons. A yeast eRF1-domain swap containing Tetrahymena domain 1 responded only to UGA in vitro and failed to complement a defect in yeast eRF1 in vivo at 37 degrees C. This finding demonstrates that decoding specificity of eRF1 from variant code organisms resides at domain 1. However, the wild-type eRF1 hybrid fully restored the growth of eRF1-deficient yeast at 30 degrees C. Tetrahymena eRF1 contains a variant sequence, KATNIKD, at the tip of domain 1. The TASNIKD variant of hybrid eRF1 rendered the eRF1-nullified yeast viable, although in an in vitro assay, the same hybrid eRF1 responded only to UGA. Nevertheless, the yeast eRF1 bearing the KATNIKD motif instead of the TASNIKS heptapeptide present in higher eukaryotes remains omnipotent in vivo. Collectively, these data suggest that variant genetic code organisms like Tetrahymena have an intrinsic potential to decode three stop codons in vivo, and that interaction within domain 1 between the KAT tripeptide and other sequences modulates the decoding specificity of Tetrahymena eRF1.

Exploring the folding landscape of a structured RNA

Structured RNAs achieve their active states by traversing complex, multidimensional energetic landscapes. Here we probe the folding landscape of the Tetrahymena ribozyme by using a powerful approach: the folding of single ribozyme molecules is followed beginning from distinct regions of the folding landscape. The experiments, combined with small-angle x-ray scattering results, show that the landscape contains discrete folding pathways. These pathways are separated by large free-energy barriers that prevent interconversion between them, indicating that the pathways lie in deep channels in the folding landscape. Chemical protection and mutagenesis experiments are then used to elucidate the structural features that determine which folding pathway is followed. Strikingly, a specific long-range tertiary contact can either help folding or hinder folding, depending on when it is formed during the process. Together these results provide an unprecedented view of the topology of an RNA folding landscape and the RNA structural features that underlie this multidimensional landscape.

Specific metal-ion binding sites in a model of the P4-P6 triple-helical domain of a group I intron

Divalent metal ions play a crucial role in RNA structure and catalysis. Phosphorothioate substitution and manganese rescue experiments can reveal phosphate oxygens interacting specifically with magnesium ions essential for structure and/or activity. In this study, phosphorothioate interference experiments in combination with structural sensitive circular dichroism spectroscopy have been used to probe molecular interactions underlying an important RNA structural motif. We have studied a synthetic model of the P4-P6 triple-helical domain in the bacteriophage T4 nrdB group I intron, which has a core sequence analogous to the Tetrahymena ribozyme. Rp and Sp sulfur substitutions were introduced into two adjacent nucleotides positioned at the 3' end of helix P6 (U452) and in the joining region J6/7 (U453). The effects of sulfur substitution on triple helix formation in the presence of different ratios of magnesium and manganese were studied by the use of difference circular dichroism spectroscopy. The results show that the pro-Sp oxygen of U452 acts as a ligand for a structurally important magnesium ion, whereas no such effect is seen for the pro-Rp oxygen of U452. The importance of the pro-Rp and pro-Sp oxygens of U453 is less clear, because addition of manganese could not significantly restore the triple-helical interactions within the isolated substituted model systems. The interpretation is that U453 is so sensitive to structural disturbance that any change at this position hinders the proper formation of the triple helix.

Formation of a GNRA tetraloop in P5abc can disrupt an interdomain interaction in the Tetrahymena group I ribozyme

The secondary structure of a truncated P5abc subdomain (tP5abc, a 56-nucleotide RNA) of the Tetrahymena thermophila group I intron ribozyme changes when its tertiary structure forms. We have now used heteronuclear NMR spectroscopy to determine its conformation in solution. The tP5abc RNA that contains only secondary structure is extended compared with the tertiary folded form; both forms coexist in slow chemical exchange (the interconversion rate constant is slower than 1 s(-1)) in the presence of magnesium. Kinetic experiments have shown that tertiary folding of the P5abc subdomain is one of the earliest folding transitions in the group I intron ribozyme, and that it leads to a metastable misfolded intermediate. Previous mutagenesis studies suggest that formation of the extended P5abc structure described here destabilize a misfolded intermediate. This study shows that the P5abc RNA subdomain containing a GNRA tetraloop in P5c (in contrast to the five-nucleotide loop P5c in the tertiary folded ribozyme) can disrupt the base-paired interdomain (P14) interaction between P5c and P2.

Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA--solvent interactions

BACKGROUND

The structure of P4-P6, a 160 nucleotide domain of the self-splicing Tetrahymena thermophila intron, was solved previously. Mutants of the P4-P6 RNA that form a more stable tertiary structure in solution were recently isolated by successive rounds of in vitro selection and amplification.

RESULTS

We show that a single-site mutant (Delta C209) possessing greater tertiary stability than wild-type P4-P6 also crystallizes much more rapidly and under a wider variety of conditions. The crystal structure provides a satisfying explanation for the increased stability of the mutant; the deletion of C209 allows the adjacent bulged adenine to enter the P4 helix and form an A-G base pair, presumably attenuating the conformational flexibility of the helix. The structure of another mutant (Delta A210) was also solved and supports this interpretation. The crystals of Delta C209 diffract to a higher resolution limit than those of wild-type RNA (2.25 A versus 2.8 A), allowing assignment of innersphere and outersphere coordination contacts for 27 magnesium ions. Structural analysis reveals an intricate solvent scaffold with a preponderance of ordered water molecules on the inside rather than the surface of the folded RNA domain.

CONCLUSIONS

In vitro evolution facilitated the identification of a highly stable, structurally homogeneous mutant RNA that was readily crystallizable. Analysis of the structure suggests that improving RNA secondary structure can stabilize tertiary structure and perhaps promote crystallization. In addition, the higher resolution model provides new details of metal ion-RNA interactions and identifies a core of ordered water molecules that may be integral to RNA tertiary structure formation.

Determination of macromolecular folding and structure by synchrotron x-ray radiolysis techniques

Radiolysis of water by synchrotron X-rays generates oxygen-containing radicals that undergo reactions with solvent accessible sites of macromolecules inducing stable covalent modifications or cleavage on millisecond time scales. The extent and site of these reactions are determined by gel electrophoresis and mass spectrometry analysis. These data are used to construct a high-resolution map of solvent accessibility at individual reactive sites. The experiments can be performed in a time-resolved manner to provide kinetic rate constants for dynamic events occurring at individual sites within macromolecules or can provide equilibrium parameters of binding and thermodynamics of folding processes. The application of this synchrotron radiolysis technique to the study of lysozyme protein structure and the equilibrium urea induced unfolding of apomyoglobin are described. The Mg2+-induced folding of Tetrahymena thermophila group I ribozyme shows the capability of the method to study kinetics of folding.

A collapsed state functions to self-chaperone RNA folding into a native ribonucleoprotein complex

Most large RNAs achieve their active, native structures only as complexes with one or more cofactor proteins. By varying the Mg(2+) concentration, the catalytic core of the bI5 group I intron RNA can be manipulated into one of three states, expanded, collapsed or native, or into balanced equilibria between these states. Under near-physiological conditions, the bI5 RNA folds rapidly to a collapsed but non-native state. Hydroxyl radical footprinting demonstrates that assembly with the CBP2 protein cofactor chases the RNA from the collapsed state to the native state. In contrast, CBP2 also binds to the RNA in the expanded state to form many non-native interactions. This structural picture is reinforced by functional splicing experiments showing that RNA in an expanded state forms a non-productive, kinetically trapped complex with CBP2. Thus, rapid folding to the collapsed state functions to self-chaperone bI5 RNA folding by preventing premature interaction with its protein cofactor. This productive, self-chaperoning role for RNA collapsed states may be especially important to avert misassembly of large multi-component RNA-protein machines in the cell.

Refolding of rRNA exons enhances dissociation of the Tetrahymena intron

Self-splicing of the Tetrahymena pre-rRNA is inhibited by a conserved rRNA hairpin P(-1) upstream of the 5' splice site. P(-1) inhibits self-splicing by competing with formation of the P1 splice site helix. Here we show that the P(-1) hairpin also enhances dissociation of the spliced products, which was monitored by native gel electrophoresis. Mutations that stabilize the rRNA hairpin increase the rate of dissociation approximately 10-fold, from 0.5 min(-1) for the wild-type RNA to approximately 4 min(-1) at 30 degrees C. Conversely, mutations or oligonucleotides that inhibit refolding of the exons and that stabilize the P1 helix decrease the rate of product release. The results suggest that refolding of products can be used to stimulate the turnover of ribozyme-catalyzed reactions. In the pre-rRNA, this conformational change helps shift the equilibrium of self-splicing toward the mature rRNA.

Characterization of inositol phospholipids and identification of a mastoparan-induced polyphosphoinositide response in Tetrahymena pyriformis

The unicellular eukaryote Tetrahymena is a popular model for the study of lipid metabolism. Less attention, however, has been given to the inositol phospholipids of the cell, although it is known that this class of lipids plays an important role in eukaryotic cell signaling. Tetrahymena pyriformis phosphatidylinositol was isolated, purified, and characterized by proton nuclear magnetic resonance analysis and [2-(3)H]myoinositol labeling. Labeling was also used for polyphosphoinositide (phosphatidylinositol phosphate and phosphatidylinositol bisphosphate) identification. Tetrahymena inositol phospholipids were found to belong to the diacylglycerol group, although major Tetrahymena phospholipids, phosphatidylcholine and aminoethylphosphonoglycerides, have been found to be mainly alkylacylglyceroderivatives. Further characterization of Tetrahymena phosphatidylinositol by gas chromatographic analysis indicated that 80% of fatty acids were myristic acid and palmitic acid. This is also in contrast to the fatty acid profile of Tetrahymena phosphatidylcholine and phosphatidylethanolamine, with respect both to the fatty acid length and degree of unsaturation, and may indicate that specific diacylglycerol species are connected with the phosphatidylinositol metabolism in this cell. Treatment of [3H]inositol-labeled Tetrahymena cells with mastoparan, a G-protein-activating peptide, induced changes in the polyphosphoinositide levels, suggesting that inositol phospholipids may form in Tetrahymena a functional signaling system similar to that of higher eukaryotes. Addition of 10 microM mastoparan resulted in a rapid and transient increase in [3H]phosphatidylinositol phosphate followed by a decrease in [3H]phosphatidylinositol bisphosphate. Similar changes in lipids have been reported when phosphoinositide-phospholipase C pathway is activated in both animal and plant cells.

Recent insights on RNA folding mechanisms from catalytic RNA

Methods for probing RNA structure in real time have revealed that initial folding steps are complete in less than a second. Refolding of large catalytic RNAs in vitro often results in long-lived intermediates that reach the native structure very slowly. These kinetically trapped intermediates arise from alternative secondary structures that form early in the folding process. In cells, proteins modulate the outcome of RNA folding reactions by stabilizing specific conformations or by accelerating refolding of misfolded intermediates. At the same time, competition between metastable conformations provides a means for regulating the biological activity of transcripts.

Structural polymorphism of telomeres studied by photon correlation spectroscopy

Photon Correlation Spectroscopy (PCS) was used to study the dynamics and structure of Tetrahymena telomeric sequence d(5'-TGGGGT-3')4. Two different modes were observed, corresponding to the following structures: intermolecular (tetramolecular) G-quadruplex and intramolecular (monomeric) G-quartet. Experimental values of translational diffusion coefficients DT were obtained for each structural form. The value of DT for the monomer equals to 1.4 x 10(6) (cm2/s), while for the tetramolecular structure, to 0.8 x 10(6) (cm2/s). The relative weight concentrations of these two forms were analyzed versus the concentration of NaCl varied from 10 mM to 500 mM. The values of experimentally determined diffusion coefficients were compared with those calculated assuming the "bead model" and with the atomic coordinates from the NMR and X-ray crystallographic data. For both structures the experimental and calculated values of DT were in reasonable agreement. In the entire NaCl concentration range studied, the contribution of the relative weight concentration of the monomeric telomere form changed from 85% for 10 mM NaCl to 60% for 500 mM NaCl.

The effect of long-range loop-loop interactions on folding of the Tetrahymena self-splicing RNA

Bas?e-pairing between the terminal loops of helices P2.1 and P9.1a (P13) and P2 and P5c (P14) stabilize the folded structure of the Tetrahymena group I intron. Using native gel electrophoresis to analyze the folding kinetics of a natural pre-RNA containing the Tetrahymena intron, we show that P13 and P14 are the only native loop-loop interactions among six possible combinations. Other base-pairing interactions of the loop sequences stabilize misfolded and inactive pre-RNAs. Mismatches in P13 or P14 raised the midpoints and decreased the cooperativity of the Mg(2+)-dependent eqXuilibrium folding transitions. Although some mutations in P13 resulted in slightly higher folding rates, others led to slower folding compared to the wild-type, suggesting that P13 promotes formation of P3 and P7. In contrast, mismatches in P14 increased the rate of folding, suggesting that base-pairing between P5c and P2 stabilizes intermediates in which the catalytic core is misfolded. Although the peripheral helices stabilize the native structure of the catalytic core, our results show that formation of long-range interactions, and competition between correct and incorrect loop-loop base-pairs, decrease the rate at which the active pre-RNA structure is assembled.

Efficient side-chain and backbone assignment in large proteins: application to tGCN5

In determining the structure of large proteins by NMR, it would be desirable to obtain complete backbone, side-chain, and NOE assignments efficiently, with a minimum number of experiments and samples. Although new strategies have made backbone assignment highly efficient, side-chain assignment has remained more difficult. Faced with the task of assigning side-chains in a protein with poor relaxation properties, the Tetrahymena histone acetyltransferase tGCN5, we have developed an assignment strategy that would provide complete side-chain assignments in cases where fast 13C transverse relaxation causes HCCH-TOCSY experiments to fail. Using the strategy presented here, the majority of aliphatic side-chain proton and carbon resonances can be efficiently obtained using optimized H(CC-CO)NH-TOCSY and (H)C(C-CO)NH-TOCSY experiments on a partially deuterated protein sample. Assignments can be completed readily using additional information from a 13C-dispersed NOESY-HSQC spectrum. Combination of these experiments with H(CC)NH-TOCSY and (H)C(C)NH-TOSCY may provide complete backbone and side-chain assignments for large proteins using only one or two samples.

A nuclear protein involved in apoptotic-like DNA degradation in Stylonychia: implications for similar mechanisms in differentiating and starved cells

Ciliates are unicellular eukaryotic organisms containing two types of nuclei: macronuclei and micronuclei. After the sexual pathway takes place, a new macronucleus is formed from a zygote nucleus, whereas the old macronucleus is degraded and resorbed. In the course of macronuclear differentiation, polytene chromosomes are synthesized that become degraded again after some hours. Most of the DNA is eliminated, and the remaining DNA is fragmented into small DNA molecules that are amplified to a high copy number in the new macronucleus. The protein Pdd1p (programmed DNA degradation protein 1) from Tetrahymena has been shown to be present in macronuclear anlagen in the DNA degradation stage and also in the old macronuclei, which are resorbed during the formation of the new macronucleus. In this study the identification and localization of a Pdd1p homologous protein in Stylonychia (Spdd1p) is described. Spdd1p is localized in the precursor nuclei in the DNA elimination stage and in the old macronuclei during their degradation, but also in macronuclei and micronuclei of starved cells. In all of these nuclei, apoptotic-like DNA breakdown was detected. These data suggest that Spdd1p is a general factor involved in programmed DNA degradation in Stylonychia.

Energetics and cooperativity of tertiary hydrogen bonds in RNA structure

Tertiary interactions that allow RNA to fold into intricate three-dimensional structures are being identified, but little is known about the thermodynamics of individual interactions. Here we quantify the tertiary structure contributions of individual hydrogen bonds in a "ribose zipper" motif of the recently crystallized Tetrahymena group I intron P4-P6 domain. The 2'-hydroxyls of P4-P6 nucleotides C109/A184 and A183/G110 participate in forming the "teeth" of the zipper. These four nucleotides were substituted in all combinations with their 2'-deoxy and (separately) 2'-methoxy analogues, and thermodynamic effects on the tertiary folding DeltaG degrees ' were assayed by the Mg2+ dependence of electrophoretic mobility in nondenaturing gels. The 2'-deoxy series showed a consistent trend with an average contribution to the tertiary folding DeltaG degrees' of -0.4 to -0.5 kcal/mol per hydrogen bond. Contributions were approximately additive, reflecting no cooperativity among the hydrogen bonds. Each "tooth" of the ribose zipper (comprising two hydrogen bonds) thus contributes about -1.0 kcal/mol to the tertiary folding DeltaG degrees'. Single 2'-methoxy substitutions destabilized folding by approximately 1 kcal/mol, but the trend reversed with multiple 2'-methoxy substitutions; the folding DeltaG degrees' for the quadruple 2'-methoxy derivative was approximately unchanged relative to wild-type. On the basis of these data and on temperature-gradient gel results, we conclude that entropically favorable hydrophobic interactions balance enthalpically unfavorable hydrogen bond deletions and steric clashes for multiple 2'-methoxy substitutions. Because many of the 2'-deoxy derivatives no longer have the characteristic hydrogen-bond patterns of the ribose zipper motif but simply have individual long-range ribose-base or ribose-ribose hydrogen bonds, we speculate that the energetic value of -0.4 to -0.5 kcal/mol per tertiary hydrogen bond may be more generally applicable to RNA folding.

A chemogenetic approach to RNA function/structure analysis

Almost two dozen nucleotide analogs have been synthesized with alpha-phosphorothioate-tagged triphosphates and utilized in an interference modification approach termed Nucleotide Analog Interference Mapping. This method has made it possible to determine the chemical basis of RNA function and structure, including the identification of new rules for RNA helix packing, the functional analysis of a binding site for monovalent metal ions within RNA and the characterization of the catalytic mechanism of RNA enzymes.

Intercalated cytosine motif and novel adenine clusters in the crystal structure of the Tetrahymena telomere

The cytosine-rich strand of the Tetrahymena telomere consists of multiple repeats of sequence d(AACCCC). We have solved the crystal structure of the crystalline repeat sequence at 2.5 A resolution. The adenines form two different and previously unknown clusters (A clusters) in orthogonal directions with their counterparts from other strands, each containing a total of eight adenines. The clusters appear to be stable aggregates held together by base stacking and three different base-pairing modes. Two different types of cytosine tetraplexes are found in the crystal. Each four-stranded complex is composed of two intercalated parallel-stranded duplexes pointing in opposite directions, with hemiprotonated cytosine-cytosine (C.C+) base pairs. The outermost C.C+base pairs are from the 5'-end of each strand in one cytosine tetraplex and from the 3'-end of each strand in the other. The A clusters and the cytosine tetraplexes form two alternating stacking patterns, creating continuous base stacking in two perpendicular directions along the x - and z -axes. The adenine clusters could be organizational motifs for macromolecular RNA.

Thermodynamic stability of the P4-P6 domain RNA tertiary structure measured by temperature gradient gel electrophoresis

The P4-P6 domain RNA from the Tetrahymena self-splicing group I intron is an independent unit of tertiary structure that, in the kinetic folding pathway, folds before the rest of the intron and then stabilizes the remainder of the intron's tertiary structure. We have employed temperature gradient gel electrophoresis (TGGE) to examine the unfolding of the tertiary structure of P4-P6. In 0.9 mM Mg2+, the global tertiary fold of the molecule has a melting temperature of approximately 40 degreesC and is completely unfolded by 60 degreesC. Calculated thermodynamic parameters for folding of P4-P6 are DeltaH degrees' = -28 +/- 3 kcal/mol and DeltaS degrees' = -91 +/- 8 eu under these conditions. Chemical probing of the P4-P6 tertiary structure using dimethyl sulfate and CMCT confirms that these TGGE experiments monitor the unfolding of the global tertiary fold of the domain and that the secondary structure is largely unaffected over this temperature range. Thus, unlike the entropically driven P1 docking and guanosine binding steps of Tetrahymenagroup I intron self-splicing, which have positive or zero DeltaH terms, P4-P6 tertiary structure formation is stabilized by a negative DeltaH term. This implies that enthalpically favorable hydrogen bond formation, nucleotide base stacking, and/or binding of Mg2+ within the folded structure are responsible for stabilizing the P4-P6 domain.

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.