6 Crystal structure studies of RNA molecules containing 2′–5′-linkages

RNA can play dual roles as a carrier of genetic information and as a catalyst of specific reactions, and it may have been the first biopolymer to have emerged on the early earth. The non-enzymatic replication of RNA was likely a key step in the evolution of simple cellular life from prebiotic chemistry. In the current model of template-directed polymerization of activated monomers, the chemical copying of RNA always generates a mixture of 3′–5′ and 2′–5′ backbone linkages due to the similar nucleophilicity and orientation of the 2′ and 3′ hydroxyl groups on the ribose. This lack of regiospecificity has been regarded as a central problem for the evolution of functional RNAs, since the resulting backbone heterogeneity was expected to disrupt their folding, molecular recognition and catalytic properties of functional RNAs such as ribozymes. However, a recent study from our lab has demonstrated that RNAs with a certain percentage of 2′–5′ linkages can still retain RNA functions, for example, in a FMN-binding aptamer and a hammerhead ribozyme system. More interestingly, it has been known for a long time that 2′–5′ linkages can reduce the melting temperature of RNA duplexes, making it easier to separate the strands. Although the detailed mechanism is still not clear, considering that strand separation is another unsolved big problem for non-enzymatic RNA replication, this feature may actually afford a selective advantage to duplexes exhibiting backbone heterogeneity. In addition, previous studies have revealed that 2′–5′ linkages in a RNA duplex are more easily hydrolyzed compared to normal 3′–5′ linkages. Thus, there is a selective advantage for the evolution of homogeneous RNA systems with more accurate replication. Altogether, the coexistence of 2′–5′ and 3′–5′ linkages may be a central feature that allowed RNA to play a central role in the original stage of life. In this work, we will present several X-ray crystal structures of RNA duplexes and an aptamer that contain 2′–5′ linkages. These structures help us to understand how RNA can adjust its structure to accommodate the backbone heterogeneity.     

7 Imperfect RNA synthesis via model prebiotic reactions and consequences for functional RNAs

Contemporary life synthesizes RNA of homogeneous length and regioisomer composition via sophisticated enzymatic catalysis. Before such catalysts existed, RNA could have been produced only via simpler, non-enzymatic means, which model prebiotic systems have shown produce pools of products that are similar, but varied (e.g. in regioisomer composition). Recently, we have demonstrated that functional RNAs (ribozymes and aptamers) containing mixed-regioisomer backbones (i.e. 2′–5′ vs. 3′–5′ linkages) retain function. This observation, coupled with the well-known fact that mixed-regioisomer RNAs exhibit depressed melting temperatures relative to native RNA, suggests that mixed-regioisomer backbones could actually be adaptive in an RNA (or pre-RNA) world. In this poster, we will show our recent work with functional RNAs representative of those produced in non-enzymatic polymerization reactions and their behaviours as catalysts and receptors.     

Nodavirus RNA Recombination

The genomes of nodaviruses contain two positive-sense RNAs that encode the RNA polymerase and capsid proteins, respectively. In this system, recombination occurs when the polymerase switches templates during negative strand RNA synthesis, usually at a site where the nascent strand can form 4–5 bp with the acceptor template. Two other factors influence the choice of recombination site: (1) template secondary structure, which is predicted to hold the recombination sites in close proximity; and (2) similarity of the cross-over site to an origin of replication, which suggests that the polymerase interacts directly with the acceptor template.     

5 Efficient and high-fidelity copying of an RNA-like model prebiotic system

Nonenzymatic RNA replication would provide an important bridge to the RNA world. However, the demonstration of efficient and high-fidelity copying chemistry remains a great experimental challenge. It requires an efficient mechanism that can lead to both a high rate of polymerization and a high degree of fidelity in the copying chemistry. Previous experiments concerning nonenzymatic template-directed synthesis of RNA with activated monomers have led to the copying of short RNA templates, but these reactions are generally slow (taking days to weeks) and highly error-prone. Therefore, the ability to efficiently and accurately copy arbitrary template sequences remains frustratingly out of reach. N3′-P5′-linked phosphoramidate DNA is a highly reactive model for self-replicating genetic materials and has been used for studies of nonenzymatic RNA self-replication. It is also an excellent RNA mimic, due to its similar overall duplex structure, rigidity, and level of hydration (Tereshko, Gryaznov, & Egli, 1998). Our experiments show that the high reactivity imparted by the presence of an amino nucleophile allows rapid and efficient copying of all four nucleobases on both homopolymeric and mixed templates. On the other hand, G:T wobble pairing leads to a high error rate. We have, therefore, investigated the use of the modified nucleobase, 2-thio T (Ts) (Sintim & Kool, 2006), to suppress formation of the G:T wobble base-pair. Our results illustrate that the 2-thio modification can both increase polymerization rate and enhance fidelity in this self-replicating N3′-P5′-DNA system. These results suggest that this simple nucleobase modification may have played a role in primordial RNA (or proto-RNA) replication. In addition to suppressing the G:T mismatch, an additional benefit gained from its stronger base-pairing with A is that it also reduces A:C mismatch formation. Thus, simple modifications of nucleobases might provide a means of suppressing mismatches to yield better fidelity. Taken together, our results show that a high rate of polymerization and a high degree of fidelity are not mutually exclusive, but can be achieved simultaneously in nonenzymatic copying of N3′-P5′-linked phosphoramidate DNA. The structural similarity of NP-DNA to RNA suggests that these results could be translated to an RNA-only system.     

Qbeta replicase discriminates between legitimate and illegitimate templates by having different mechanisms of initiation

Qbeta replicase (RNA-directed RNA polymerase of bacteriophage Qbeta) exponentially amplifies certain RNAs (RQ RNAs) in vitro. Here we characterize template properties of the 5' and 3' fragments obtained by cleaving one of such RNAs at an internal site. We unexpectedly found that, besides the 3' fragment, Qbeta replicase can copy the 5' fragment and a number of its variants, although they lack the initiator region of RQ RNA. This copying can occur as a 3'-terminal elongation or through de novo initiation. In contradistinction to RQ RNA and its 3' fragment, initiation on these templates occurs without regard to the 3'-terminal or internal oligo(C) clusters, is GTP-independent, and does not result in a stable replicative complex capable of elongation in the presence of aurintricarboxylic acid. The results suggest that, although Qbeta replicase can initiate and elongate on a variety of RNAs, only some of them are recognized as legitimate templates. GTP-dependent initiation on a legitimate template drives the enzyme to a "closed" conformation that may be important for keeping the template and the complementary nascent strand unannealed, without which the exponential replication is impossible. Triggering the GTP-dependent conformational transition at the initiation step could serve as a discriminative feature of legitimate templates providing for the high template specificity of Qbeta replicase.     

E. COLI RNASE HI AND THE PHOSPHONATE-DNA/RNA HYBRID: MOLECULAR DYNAMICS SIMULATIONS

A model for the complex between E. coli RNase HI and the DNA/RNA hybrid (previously refined by molecular dynamics simulations) was used to determine the impact of the internucleotide linkage modifications (either 3′–O–CH₂–P–O–5′ or 3′–O–P–CH₂–O–5′) on the ability of the modified-DNA/RNA hybrid to create a complex with the protein. Modified internucleotide linkages were incorporated systematically at different positions close to the 3′-end of the DNA strand to interfere with the DNA binding site of RNase H. Altogether, six trajectories were produced (length 1.5). Mutual hydrogen bonds connecting both strands of the nucleic acids hybrid, DNA with RNase H, RNA with RNase H, and the scissile bond with the Mg⁺⁺ · 4H₂O chelate complex (bound in the active site) were analyzed in detail. Many residues were involved in binding of the DNA (Arg88, Asn84, Trp85, Trp104, Tyr73, Lys99, Asn100, Thr43, and Asn16) and RNA (Gln76, Gln72, Tyr73, Lys122, Glu48, Asn44, and Cys13) strand to the substrate-binding site of the RNase H enzyme. The most remarkable disturbance of the hydrogen bonding net was observed for structures with modified internucleotide linkages positioned in a way to interact with the Trp104, Tyr73, Lys99, and Asn100 residues (situated in the middle of the DNA binding site, where a cluster of Trp residues forms a rigid core of the protein structure).     

Self-replication of chemical systems based on recognition within a double or a triple helix: a realistic hypothesis.

A scenario is proposed by which non-enzymatic self-replication of short RNA molecules could occur. The hypothesis is illustrated for the self-replication of an oligopyrimidine (Y) strand. The successful replication of Y requires a series of plausible steps. The first, experimentally feasible, step involves the template-directed polynucleotide synthesis, based on Watson-Crick base pairing, of an oligopurine (R) strand using Y as the template, and chemically activated mononucleotides as the building blocks. This step will result in the formation of an oligopyrimidine.oligopurine (YR) double helix. The second step requires the use of the double helix as the template for the synthesis of a second oligopyrimidine (Y') strand from activated pyrimidine monomers. This synthesis could be facilitated by the binding of the monopyrimidines in the major groove of the YR double helix, via Hoogsteen-type base pairing with the R strand, establishing in that sense triple helix recognition. This step, if successful, should result in the formation of a new strand, Y', that runs parallel to the oligopurine strand. Y' differs from Y in that all 3'-5' phosphodiester linkages in Y are replaced by 5'-3' linkages in Y'. The resulting triple helix (YRY') is in dynamic equilibrium with YR and free Y'. In subsequent steps, unassociated Y' directs the synthesis of the complementary oligopurine (R') strand forming a new double helix Y'R' that may direct the synthesis of an oligopyrimidine strand, Y, that is expected to be identical to the first strand that started the whole sequence. An attempt is made to generalize the above hypothesis to mixed oligonucleotides containing all four bases and identify the limitations of this hypothesis.     

Balancing eukaryotic replication asymmetry with replication fidelity

Coordinated replication of eukaryotic nuclear genomes is asymmetric, with copying of a leading strand template preceding discontinuous copying of the lagging strand template. Replication is catalyzed by DNA polymerases α, δ and ?, enzymes that are related yet differ in physical and biochemical properties, including fidelity. Recent studies suggest that Pol ? is normally the primary leading strand replicase, whereas most synthesis by Pol δ occurs during lagging strand replication. New studies show that replication asymmetry can generate strand-specific genome instability resulting from biased deoxynucleotide pools and unrepaired ribonucleotides incorporated into DNA during replication, and that the eukaryotic replication machinery has evolved to most efficiently correct those replication errors that are made at the highest rates.     

Minus-strand initiation by brome mosaic virus replicase within the 3' tRNA-like structure of native and modified RNA templates

An RNA-dependent RNA polymerase (replicase) extract from brome mosaic virus-infected barley leaves has been shown to initiate synthesis of (-) sense RNA from (+) sense virion RNA. Initiation occurred de novo, as demonstrated by the incorporation of [gamma-32P]GTP into the product. Sequencing using cordycepin triphosphate to terminate (-) strands during their synthesis by the replicase generated sequence ladders that confirmed that copying was accurate, and that initiation occurred very close to the 3' end. The precise site of initiation was further defined by testing the replicase template activity after stepwise removal of 3'-terminal nucleotides. Whereas removal of the terminal A did not decrease template activity, removal of the next nucleotide (C-2) did. Thus, initiation almost certainly occurs opposite the penultimate 3'-nucleotide (C-2) in vitro. The structure of the double-stranded replicative form of RNA isolated from brome mosaic virus-infected leaves was consistent with such a mechanism occurring in vivo, in that it lacked the 3'-terminal A found on virion RNAs. The specific site of (-) strand initiation and normal template activity were retained for RNAs with as many as 15 to 30 A residues added to the 3' end. However, only limited oligonucleotide 3' extensions can be present on active templates. In order to assess the 5' extent of sequences required for an active template, a 134-nucleotide-long fragment of brome mosaic virus RNA, corresponding to the tRNA-like structure, was generated. This RNA had high template activity, but a shorter 3' (85-nucleotide) fragment was inactive. RNAs with various heterologous sequences 5' to position 134 also showed high template activity. Thus, the 3'-terminal tRNA-like structure common to all four brome mosaic virus virion RNAs contains all of the signals required for initiation of replication, and sequences 5' to it do not play a role in template selection.     

Defective Interfering Particles of Vesicular Stomatitis Virus: Functions of the Genomic Termini

The functions of thecis-acting sequence elements at the termini of the negative strand RNA virus vesicular stomatitis virus and its defective-interfering particles were evaluated. Either genomic terminus could signal replication but increasing the complementarity of the termini enhanced replication irrespective of whether the termini consisted of the 3′ leader and its complement or the 5′ trailer and its complement. The 5′ trailer region contains an essentialcis-acting requirement for assembly of RNPs into infectious particles. These findings explain why the majority of DI RNAs are of the 5′ copy-back class: RNAs with complementary termini from either end have a replicative advantage, but only 5′ copy-back RNAs contain the signal for assembly into particles.     

Structure of RNAs replicated by the DNA-dependent T7 RNA polymerase.

The DNA-dependent RNA polymerase of bacteriophage T7 efficiently and specifically replicates two structurally related RNAs, termed X and Y RNAs. Replication of both RNAs involves synthesis of complementary strands initiated with pppC and pppG. RNAs transcribed from DNA template containing the established sequences of X and Y RNAs were efficiently replicated by T7 RNA polymerase. Both RNAs possess palindromic sequences with a dual axis of symmetry, permitting formation of hairpin-, dumbbell-, or cloverleaf-type structures. The template must consist of RNA and not DNA sequence, and the terminal unpaired dinucleotides of the RNA are necessary for replication. Nucleotidyl transferase activity of E. coli adenylates the unpaired CCOH dinucleotide at the 3' end of a C strand of X RNA. This feature, as well as the length (64 nucleotides) and compact structure of X and Y RNAs, suggests that they may resemble tRNA molecules and tRNA-like structures at the 3' termini of many plant viral RNA genomes.     

The Origins of Cellular Life

Understanding the origin of cellular life on Earth requires the discovery of plausible pathways for the transition from complex prebiotic chemistry to simple biology, defined as the emergence of chemical assemblies capable of Darwinian evolution. We have proposed that a simple primitive cell, or protocell, would consist of two key components: a protocell membrane that defines a spatially localized compartment, and an informational polymer that allows for the replication and inheritance of functional information. Recent studies of vesicles composed of fatty-acid membranes have shed considerable light on pathways for protocell growth and division, as well as means by which protocells could take up nutrients from their environment. Additional work with genetic polymers has provided insight into the potential for chemical genome replication and compatibility with membrane encapsulation. The integration of a dynamic fatty-acid compartment with robust, generalized genetic polymer replication would yield a laboratory model of a protocell with the potential for classical Darwinian biological evolution, and may help to evaluate potential pathways for the emergence of life on the early Earth. Here we discuss efforts to devise such an integrated protocell model.The emergence of the first cells on the early Earth was the culmination of a long history of prior chemical and geophysical processes. Although recognizing the many gaps in our knowledge of prebiotic chemistry and the early planetary setting in which life emerged, we will assume for the purpose of this review that the requisite chemical building blocks were available, in appropriate environmental settings. This assumption allows us to focus on the various spontaneous and catalyzed assembly processes that could have led to the formation of primitive membranes and early genetic polymers, their coassembly into membrane-encapsulated nucleic acids, and the chemical and physical processes that allowed for their replication. We will discuss recent progress toward the construction of laboratory models of a protocell (Fig. 1), evaluate the remaining steps that must be achieved before a complete protocell model can be constructed, and consider the prospects for the observation of spontaneous Darwinian evolution in laboratory protocells. Although such laboratory studies may not reflect the specific pathways that led to the origin of life on Earth, they are proving to be invaluable in uncovering surprising and unanticipated physical processes that help us to reconstruct plausible pathways and scenarios for the origin of life.Open in a separate windowFigure 1.A simple protocell model based on a replicating vesicle for compartmentalization, and a replicating genome to encode heritable information. A complex environment provides lipids, nucleotides capable of equilibrating across the membrane bilayer, and sources of energy (left), which leads to subsequent replication of the genetic material and growth of the protocell (middle), and finally protocellular division through physical and chemical processes (right). (Reproduced from Mansy et al. 2008 and reprinted with permission from Nature Publishing ©2008.)The term protocell has been used loosely to refer to primitive cells or to the first cells. Here we will use the term protocell to refer specifically to cell-like structures that are spatially delimited by a growing membrane boundary, and that contain replicating genetic information. A protocell differs from a true cell in that the evolution of genomically encoded advantageous functions has not yet occurred. With a genetic material such as RNA (or perhaps one of many other heteropolymers that could provide both heredity and function) and an appropriate environment, the continued replication of a population of protocells will lead inevitably to the spontaneous emergence of new coded functions by the classical mechanism of evolution through variation and natural selection. Once such genomically encoded and therefore heritable functions have evolved, we would consider the system to be a complete, living biological cell, albeit one much simpler than any modern cell (Szostak et al. 2001).     

Residues of the rotavirus RNA-dependent RNA polymerase template entry tunnel that mediate RNA recognition and genome replication

To replicate its segmented, double-stranded RNA (dsRNA) genome, the rotavirus RNA-dependent RNA polymerase, VP1, must recognize viral plus-strand RNAs (+RNAs) and guide them into the catalytic center. VP1 binds to the conserved 3' end of rotavirus +RNAs via both sequence-dependent and sequence-independent contacts. Sequence-dependent contacts permit recognition of viral +RNAs and specify an autoinhibited positioning of the template within the catalytic site. However, the contributions to dsRNA synthesis of sequence-dependent and sequence-independent VP1-RNA interactions remain unclear. To analyze the importance of VP1 residues that interact with +RNA on genome replication, we engineered mutant VP1 proteins and assayed their capacity to synthesize dsRNA in vitro. Our results showed that, individually, mutation of residues that interact specifically with RNA bases did not diminish replication levels. However, simultaneous mutations led to significantly lower levels of dsRNA product, presumably due to impaired recruitment of +RNA templates. In contrast, point mutations of sequence-independent RNA contact residues led to severely diminished replication, likely as a result of improper positioning of templates at the catalytic site. A noteworthy exception was a K419A mutation that enhanced the initiation capacity and product elongation rate of VP1. The specific chemistry of Lys419 and its position at a narrow region of the template entry tunnel appear to contribute to its capacity to moderate replication. Together, our findings suggest that distinct classes of VP1 residues interact with +RNA to mediate template recognition and dsRNA synthesis yet function in concert to promote viral RNA replication at appropriate times and rates.     

RNA-protein interactions directed by the 3' end of human rhinovirus genomic RNA.

The replication of a picornavirus genomic RNA is a template-specific process involving the recognition of viral RNAs as target replication templates for the membrane-bound viral replication initiation complex. The virus-encoded RNA-dependent RNA polymerase, 3Dpol, is a major component of the replication complex; however, when supplied with a primed template, 3Dpol is capable of copying polyadenylated RNAs which are not of viral origin. Therefore, there must be some other molecular mechanism to direct the specific assembly of the replication initiation complex at the 3' end of viral genomic RNAs, presumably involving cis-acting binding determinants within the 3' noncoding region (3' NCR). This report describes the use of an in vitro UV cross-linking assay to identify proteins which interact with the 3' NCR of human rhinovirus 14 RNA. A cellular protein(s) was identified in cytoplasmic extracts from human rhinovirus 14-infected cells which had a marked binding preference for RNAs containing the rhinovirus 3' NCR sequence. This protein(s) showed reduced cross-linking efficiency for a 3' NCR with an engineered deletion. Virus recovered from RNA transfections with in vitro transcribed RNA containing the same 3' NCR deletion demonstrated a defective replication phenotype in vivo. Cross-linking experiments with RNAs containing the poliovirus 3' NCR and cytoplasmic extracts from poliovirus-infected cells produced an RNA-protein complex with indistinguishable electrophoretic properties, suggesting that the appearance of the cellular protein(s) may be a common phenomenon of picornavirus infection. We suggest that the observed cellular protein(s) is sequestered or modified as a result of rhinovirus or poliovirus infection and is utilized in viral RNA replication, perhaps by binding to the 3' NCR as a prerequisite for replication complex assembly at the 3' end of the viral genomic RNA.     

Spatiotemporal Analysis of Hepatitis C Virus Infection

Hepatitis C virus (HCV) entry, translation, replication, and assembly occur with defined kinetics in distinct subcellular compartments. It is unclear how HCV spatially and temporally regulates these events within the host cell to coordinate its infection. We have developed a single molecule RNA detection assay that facilitates the simultaneous visualization of HCV (+) and (−) RNA strands at the single cell level using high-resolution confocal microscopy. We detect (+) strand RNAs as early as 2 hours post-infection and (−) strand RNAs as early as 4 hours post-infection. Single cell levels of (+) and (−) RNA vary considerably with an average (+):(−) RNA ratio of 10 and a range from 1–35. We next developed microscopic assays to identify HCV (+) and (−) RNAs associated with actively translating ribosomes, replication, virion assembly and intracellular virions. (+) RNAs display a defined temporal kinetics, with the majority of (+) RNAs associated with actively translating ribosomes at early times of infection, followed by a shift to replication and then virion assembly. (−) RNAs have a strong colocalization with NS5A, but not NS3, at early time points that correlate with replication compartment formation. At later times, only ~30% of the replication complexes appear to be active at a given time, as defined by (−) strand colocalization with either (+) RNA, NS3, or NS5A. While both (+) and (−) RNAs colocalize with the viral proteins NS3 and NS5A, only the plus strand preferentially colocalizes with the viral envelope E2 protein. These results suggest a defined spatiotemporal regulation of HCV infection with highly varied replication efficiencies at the single cell level. This approach can be applicable to all plus strand RNA viruses and enables unprecedented sensitivity for studying early events in the viral life cycle.