Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases

BACKGROUND: The eukaryotic RNA-dependent RNA polymerase (RDRP) is involved in the amplification of regulatory microRNAs during post-transcriptional gene silencing. This enzyme is highly conserved in most eukaryotes but is missing in archaea and bacteria. No evolutionary relationship between RDRP and other polymerases has been reported so far, hence the origin of this eukaryote-specific polymerase remains a mystery. RESULTS: Using extensive sequence profile searches, we identified bacteriophage homologs of the eukaryotic RDRP. The comparison of the eukaryotic RDRP and their homologs from bacteriophages led to the delineation of the conserved portion of these enzymes, which is predicted to harbor the catalytic site. Further, detailed sequence comparison, aided by examination of the crystal structure of the DNA-dependent RNA polymerase (DDRP), showed that the RDRP and the β' subunit of DDRP (and its orthologs in archaea and eukaryotes) contain a conserved double-psi β-barrel (DPBB) domain. This DPBB domain contains the signature motif DbDGD (b is a bulky residue), which is conserved in all RDRPs and DDRPs and contributes to catalysis via a coordinated divalent cation. Apart from the DPBB domain, no similarity was detected between RDRP and DDRP, which leaves open two scenarios for the origin of RDRP: i) RDRP evolved at the onset of the evolution of eukaryotes via a duplication of the DDRP β' subunit followed by dramatic divergence that obliterated the sequence similarity outside the core catalytic domain and ii) the primordial RDRP, which consisted primarily of the DPBB domain, evolved from a common ancestor with the DDRP at a very early stage of evolution, during the RNA world era. The latter hypothesis implies that RDRP had been subsequently eliminated from cellular life forms and might have been reintroduced into the eukaryotic genomes through a bacteriophage. Sequence and structure analysis of the DDRP led to further insights into the evolution of RNA polymerases. In addition to the β' subunit, β subunit of DDRP also contains a DPBB domain, which is, however, distorted by large inserts and does not harbor a counterpart of the DbDGD motif. The DPBB domains of the two DDRP subunits together form the catalytic cleft, with the domain from the β' subunit supplying the metal-coordinating DbDGD motif and the one from the β subunit providing two lysine residues involved in catalysis. Given that the two DPBB domains of DDRP contribute completely different sets of active residues to the catalytic center, it is hypothesized that the ultimate ancestor of RNA polymerases functioned as a homodimer of a generic, RNA-binding DPBB domain. This ancestral protein probably did not have catalytic activity and served as a cofactor for a ribozyme RNA polymerase. Subsequent evolution of DDRP and RDRP involved accretion of distinct sets of additional domains. In the DDRPs, these included a RNA-binding Zn-ribbon, an AT-hook-like module and a sandwich-barrel hybrid motif (SBHM) domain. Further, lineage-specific accretion of SBHM domains and other, DDRP-specific domains is observed in bacterial DDRPs. In contrast, the orthologs of the β' subunit in archaea and eukaryotes contains a four-stranded α + β domain that is shared with the α-subunit of bacterial DDRP, eukaryotic DDRP subunit RBP11, translation factor eIF1 and type II topoisomerases. The additional domains of the RDRPs remain to be characterized. CONCLUSIONS: Eukaryotic RNA-dependent RNA polymerases share the catalytic double-psi β-barrel domain, containing a signature metal-coordinating motif, with the universally conserved β' subunit of DNA-dependent RNA polymerases. Beyond this core catalytic domain, the two classes of RNA polymerases do not have common domains, suggesting early divergence from a common ancestor, with subsequent independent domain accretion. The β-subunit of DDRP contains another, highly diverged DPBB domain. The presence of two distinct DPBB domains in two subunits of DDRP is compatible with the hypothesis that the ultimate ancestor of RNA polymerases was a RNA-binding DPBB domain that had no catalytic activity but rather functioned as a homodimeric cofactor for a ribozyme polymerase

Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members

We report an in-depth computational study of the protein sequences and structures of the superfamily of archaeo-eukaryotic primases (AEPs). This analysis greatly expands the range of diversity of the AEPs and reveals the unique active site shared by all members of this superfamily. In particular, it is shown that eukaryotic nucleo-cytoplasmic large DNA viruses, including poxviruses, asfarviruses, iridoviruses, phycodnaviruses and the mimivirus, encode AEPs of a distinct family, which also includes the herpesvirus primases whose relationship to AEPs has not been recognized previously. Many eukaryotic genomes, including chordates and plants, encode previously uncharacterized homologs of these predicted viral primases, which might be involved in novel DNA repair pathways. At a deeper level of evolutionary connections, structural comparisons indicate that AEPs, the nucleases involved in the initiation of rolling circle replication in plasmids and viruses, and origin-binding domains of papilloma and polyoma viruses evolved from a common ancestral protein that might have been involved in a protein-priming mechanism of initiation of DNA replication. Contextual analysis of multidomain protein architectures and gene neighborhoods in prokaryotes and viruses reveals remarkable parallels between AEPs and the unrelated DnaG-type primases, in particular, tight associations with the same repertoire of helicases. These observations point to a functional equivalence of the two classes of primases, which seem to have repeatedly displaced each other in various extrachromosomal replicons

Phase transition in ultrathin magnetic films with long-range interactions: Monte Carlo simulation of the anisotropic Heisenberg model

Ultrathin magnetic films can be modeled as an anisotropic Heisenberg model with long-range dipolar interactions. It is believed that the phase diagram presents three phases: An ordered ferromagnetic phase I, a phase characterized by a change from out-of-plane to in-plane in the magnetization II, and a high-temperature paramagnetic phase III. It is claimed that the border lines from phase I to III and II to III are of second order and from I to II is first order. In the present work we have performed a very careful Monte Carlo simulation of the model. Our results strongly support that the line separating phases II and III is of the BKT type.Comment: 7 page

Effect of the source charge on charged-beam interferometry

We investigate quantal perturbations of the interferometric correlations of charged bosons by the Coulomb field of an instantaneous, charged source. The source charge increases the apparent source size by weakening the correlation at non-zero relative momenta. The effect is strongest for pairs with a small total momentum and is stronger for kaons than for pions of the same momenta. The experimental data currently available are well described by this effect without invoking Pratt's exploding source model. A simple expression is proposed to account for the effect.Comment: 9 pages TEX, 3 Postscript figures available at http://www.krl.caltech.edu/preprints/MAP.htm

The Statistical Multifragmentation Model with Skyrme Effective Interactions

The Statistical Multifragmentation Model is modified to incorporate the Helmholtz free energies calculated in the finite temperature Thomas-Fermi approximation using Skyrme effective interactions. In this formulation, the density of the fragments at the freeze-out configuration corresponds to the equilibrium value obtained in the Thomas-Fermi approximation at the given temperature. The behavior of the nuclear caloric curve at constant volume is investigated in the micro-canonical ensemble and a plateau is observed for excitation energies between 8 and 10 MeV per nucleon. A kink in the caloric curve is found at the onset of this gas transition, indicating the existence of a small excitation energy region with negative heat capacity. In contrast to previous statistical calculations, this situation takes place even in this case in which the system is constrained to fixed volume. The observed phase transition takes place at approximately constant entropy. The charge distribution and other observables also turn out to be sensitive to the treatment employed in the calculation of the free energies and the fragments' volumes at finite temperature, specially at high excitation energies. The isotopic distribution is also affected by this treatment, which suggests that this prescription may help to obtain information on the nuclear equation of state

Transient response of a quantum wave to an instantaneous potential step switching

The transient response of a stationary state of a quantum particle in a step potential to an instantaneous change in the step height (a simplified model for a sudden bias switch in an electronic semiconductor device) is solved exactly by means of a semianalytical expression. The characteristic times for the transient process up to the new stationary state are identified. A comparison is made between the exact results and an approximate method.Comment: 8 pages, 8 figures, Revtex

Characterization of Landau-Zener Transitions in Systems with Complex Spectra

This paper is concerned with the study of one-body dissipation effects in idealized models resembling a nucleus. In particular, we study the quantum mechanics of a free particle that collides elastically with the slowly moving walls of a Bunimovich stadium billiard. Our results are twofold. First, we develop a method to solve in a simple way the quantum mechanical evolution of planar billiards with moving walls. The formalism is based on the {\it scaling method} \cite{ver} which enables the resolution of the problem in terms of quantities defined over the boundary of the billiard. The second result is related to the quantum aspects of dissipation in systems with complex spectra. We conclude that in a slowly varying evolution the energy is transferred from the boundary to the particle through Landau$-$Zener transitions.Comment: 24 pages (including 7 postcript figures), Revtex. Submitted to PR

Computation in Classical Mechanics

There is a growing consensus that physics majors need to learn computational skills, but many departments are still devoid of computation in their physics curriculum. Some departments may lack the resources or commitment to create a dedicated course or program in computational physics. One way around this difficulty is to include computation in a standard upper-level physics course. An intermediate classical mechanics course is particularly well suited for including computation. We discuss the ways we have used computation in our classical mechanics courses, focusing on how computational work can improve students' understanding of physics as well as their computational skills. We present examples of computational problems that serve these two purposes. In addition, we provide information about resources for instructors who would like to include computation in their courses.Comment: 6 pages, 3 figures, submitted to American Journal of Physic