| characterization of phi 12, a bacteriophage related to phi 6: nucleotide sequence of the small and middle double-stranded rna. | the isolation of additional bacteriophages containing segmented double-stranded rna genomes has expanded the cystoviridae family to nine members. comparing the genomic sequences of these viruses has allowed evaluation of important genetic as well as structural motifs. these comparative studies are resulting in greater understanding of viral evolution and the role played by genetic and structural variation in the assembly mechanisms of the cystoviruses. in this regard, the small and middle double ... | 2002 | 11853405 |
| characterization of phi12, a bacteriophage related to phi6: nucleotide sequence of the large double-stranded rna. | the isolation of additional bacteriophages besides phi6 containing segmented double-stranded rna genomes (dsrna) has expanded the cystoviridae family to nine members. comparing the genomic sequences of these viruses has allowed evaluation of important genetic as well as structural motifs. these comparative studies are resulting in greater understanding of viral evolution and the role played by genetic and structural variation in the assembly mechanisms of the cystoviruses. in this regard, the la ... | 2002 | 12033785 |
| cloning of complete genome sets of six dsrna viruses using an improved cloning method for large dsrna genes. | cloning full-length large (>3 kb) dsrna genome segments from small amounts of dsrna has thus far remained problematic. here, a single-primer amplification sequence-independent dsrna cloning procedure was perfected for large genes and tailored for routine use to clone complete genome sets or individual genes. nine complete viral genome sets were amplified by pcr, namely those of two human rotaviruses, two african horsesickness viruses (ahsv), two equine encephalosis viruses (eev), one bluetongue ... | 2002 | 12185276 |
| temperature requirements for initiation of rna-dependent rna polymerization. | to continue the molecular characterization of rna-dependent rna polymerases of dsrna bacteriophages (cystoviridae), we purified and biochemically characterized the wild-type (wt) and a temperature-sensitive (ts) point mutant of the polymerase subunit (pol) from bacteriophage phi12. interestingly, initiation by both wt and the ts phi12 pol was notably more sensitive to increased temperatures than the elongation step, the absolute value of the nonpermissive temperature being lower for the ts enzym ... | 2003 | 14554097 |
| production, crystallization and preliminary x-ray crystallographic studies of the bacteriophage phi 12 packaging motor. | the hexameric atpase p4 from bacteriophage phi 12 is responsible for packaging single-stranded genomic precursors into the viral procapsid. p4 was overexpressed in escherichia coli and purified. crystals of native and selenomethionine-derivatized p4 have been obtained that belong to space group i222, with half a hexamer in the asymmetric unit and unit-cell parameters a = 105.0, b = 130.5, c = 158.9 a. a second crystal form of different morphology can occur in the same crystallization drop. the s ... | 2004 | 14993703 |
| packaging motor from double-stranded rna bacteriophage phi12 acts as an obligatory passive conduit during transcription. | double-stranded rna viruses sequester their genomes within a protein shell, called the polymerase complex. translocation of ssrna into (packaging) and out (transcription) of the polymerase complex are essential steps in the life cycle of the dsrna bacteriophages of the cystoviridae family (phi6-phi14). both processes require a viral molecular motor p4, an ntpase, which bears structural and functional similarities to hexameric helicases. in effect, switching between the packaging and the transcri ... | 2004 | 15247341 |
| atomic snapshots of an rna packaging motor reveal conformational changes linking atp hydrolysis to rna translocation. | many viruses package their genome into preformed capsids using packaging motors powered by the hydrolysis of atp. the hexameric atpase p4 of dsrna bacteriophage phi12, located at the vertices of the icosahedral capsid, is such a packaging motor. we have captured crystallographic structures of p4 for all the key points along the catalytic pathway, including apo, substrate analog bound, and product bound. substrate and product binding have been observed as both binary complexes and ternary complex ... | 2004 | 15369673 |
| cooperative mechanism of rna packaging motor. | p4 is a hexameric atpase that serves as the rna packaging motor in double-stranded rna bacteriophages from the cystoviridae family. p4 shares sequence and structural similarities with hexameric helicases. a structure-based mechanism for mechano-chemical coupling has recently been proposed for p4 from bacteriophage phi12. however, coordination of atp hydrolysis among the subunits and coupling with rna translocation remains elusive. here we present detailed kinetic study of nucleotide binding, hyd ... | 2005 | 15840563 |
| interaction of packaging motor with the polymerase complex of dsrna bacteriophage. | many viruses employ molecular motors to package their genomes into preformed empty capsids (procapsids). in dsrna bacteriophages the packaging motor is a hexameric atpase p4, which is an integral part of the multisubunit procapsid. structural and biochemical studies revealed a plausible rna-translocation mechanism for the isolated hexamer. however, little is known about the structure and regulation of the hexamer within the procapsid. here we use hydrogen-deuterium exchange and mass spectrometry ... | 2006 | 16643976 |
| electron cryo-tomographic structure of cystovirus phi 12. | bacteriophage phi 12 is a member of the cystoviridae virus family and contains a genome consisting of three segments of double-stranded rna (dsrna). this virus family contains eight identified members, of which four have been classified in regard to their complete genomic sequence and encoded viral proteins. a phospholipid envelope that contains the integral proteins p6, p9, p10, and p13 surrounds the viral particles. in species phi 6, host infection requires binding of a multimeric p3 complex t ... | 2008 | 18022662 |
| structural basis of mechanochemical coupling in a hexameric molecular motor. | the p4 protein of bacteriophage phi12 is a hexameric molecular motor closely related to superfamily 4 helicases. p4 converts chemical energy from atp hydrolysis into mechanical work, to translocate single-stranded rna into a viral capsid. the molecular basis of mechanochemical coupling, i.e. how small approximately 1 a changes in the atp-binding site are amplified into nanometer scale motion along the nucleic acid, is not understood at the atomic level. here we study in atomic detail the mechano ... | 2008 | 18057007 |
| structure and dynamics of the p7 protein from the bacteriophage phi 12. | cystoviruses are a class of enveloped double-stranded rna viruses that use a multiprotein polymerase complex (px) to replicate and transcribe the viral genome. although the structures of the polymerase and atpase components of the cystoviral px are known and their functional behavior is understood to a large extent, no atomic-resolution structural information is available for the major capsid protein p1 that defines the overall structure and symmetry of the viral capsid and the essential protein ... | 2008 | 18647606 |
| three-dimensional structure of the enveloped bacteriophage phi12: an incomplete t = 13 lattice is superposed on an enclosed t = 1 shell. | bacteriophage phi12 is a member of the cystoviridae, a unique group of lipid containing membrane enveloped bacteriophages that infect the bacterial plant pathogen pseudomonas syringae pv. phaseolicola. the genomes of the virus species contain three double-stranded (dsrna) segments, and the virus capsid itself is organized in multiple protein shells. the segmented dsrna genome, the multi-layered arrangement of the capsid and the overall viral replication scheme make the cystoviridae similar to th ... | 2009 | 19727406 |
| characterization of phi2954, a newly isolated bacteriophage containing three dsrna genomic segments. | bacteriophage phi12 is a member of the cystoviridae and is distinct from phi6, the first member of that family. we have recently isolated a number of related phages and five showed high similarity to phi12 in the amino acid sequences of several proteins. bacteriophage phi2954 is a member of this group. | 2010 | 20170499 |
| mechanochemistry of a viral dna packaging motor. | the pentameric atpase motor gp16 packages double-stranded dna into the bacteriophage phi29 virus capsid. on the basis of the results of single-molecule experimental studies, we propose a push and roll mechanism to explain how the packaging motor translocates the dna in bursts of four 2.5 bp power strokes, while rotating the dna. in this mechanism, each power stroke accompanies p(i) release after atp hydrolysis. since the high-resolution structure of the gp16 motor is not available, we borrowed c ... | 2010 | 20452360 |