| in vitro deletion mapping of the viral strand replication origin of pseudomonas bacteriophage pf3. | the origin of viral strand replication of the filamentous bacteriophage pf3 has been characterized in escherichia coli by in vitro deletion mapping techniques. the origin region was functionally identified by its ability to convey replicative properties to a recombinant plasmid in a pola host in which the replication origin of the vector plasmid is not functional. the origin of pf3 viral strand replication is contained within a dna sequence of 139 bp. this sequence covers almost completely one o ... | 1991 | 1905713 |
| escherichia coli tolq mutants are resistant to filamentous bacteriophages that adsorb to the tips, not the shafts, of conjugative pili. | the tolq (previously fii) mutation in escherichia coli k12 inhibits infection by filamentous bacteriophages f1 and ike but not by rna-containing phage f2. this work extends these observations to other plasmid-specific bacteriophages including various filamentous. rna-containing, and lipid-containing isolates. only tip-adsorbing filamentous phages were affected by tolq and not shaft-adsorbing ones. electron microscopy showed that rp4-specific filamentous phage pf3 was one of the latter kind. seve ... | 1989 | 2575654 |
| the major coat protein gene of the filamentous pseudomonas aeruginosa phage pf3: absence of an n-terminal leader signal sequence. | from in vitro protein synthesis studies and nucleotide sequence analysis it has been deduced that, unlike the major coat proteins of the hitherto studied filamentous bacterial viruses ff (m13, fd and f1), ike and pf1, the major coat protein of the filamentous pseudomonas aeruginosa virus pf3 is not synthesized as a precursor containing a leader signal polypeptide at its n-terminal end. from the elucidated nucleotide sequence of the pf3 major coat protein gene it follows that the coat protein is ... | 1983 | 6316283 |
| conformational transitions in pf3 and their implications for the structure and assembly of filamentous bacterial viruses. | laser raman and circular dichroism spectra of filamentous bacteriophage pf3 show that its coat protein is predominantly alpha-helical, similar to the subunits of bacteriophages pf1 and fd. unlike pf1 and fd, however, the subunits of pf3 are converted to beta-sheet structures by raising the temperature, the transition temperature depending upon phage and nacl concentrations. on cooling, the beta structure reverts to an alpha structure the same as or similar to the native structure. on further hea ... | 1981 | 6789326 |
| solution structure of the single-stranded dna binding protein of the filamentous pseudomonas phage pf3: similarity to other proteins binding to single-stranded nucleic acids. | the three-dimensional structure of the homodimeric single-stranded dna binding protein encoded by the filamentous pseudomonas bacteriophage pf3 has been determined using heteronuclear multidimensional nmr techniques and restrained molecular dynamics. nmr experiments and structure calculations have been performed on a mutant protein (phe36 --> his) that was successfully designed to reduce the tendency of the protein to aggregate. the protein monomer is composed of a five-stranded antiparallel bet ... | 1995 | 7556054 |
| major coat proteins of bacteriophage pf3 and m13 as model systems for sec-independent protein transport. | the membrane insertion of bacteriophage coat proteins occurs independent of the sec-translocase of escherichia coli. detailed study of the pf3 and m13 coat proteins has elucidated two fundamental mechanisms of how proteins invade the membrane, most likely by direct interaction with the lipid bilayer. the sec-independent translocation of amino-terminal regions across the inner membrane is limited to a short length and a small number of charged residues. protein regions that contain several charge ... | 1995 | 7669345 |
| nucleotide sequence of a small plasmid isolated from acetobacter pasteurianus. | a 1440-bp plasmid named pap12875 was isolated from acetobacter pasteurianus and its nucleotide sequence determined. an open reading frame was found capable of coding for a protein that has similarity with the replication protein of pvt736-1 from actinobacillus actinomycetemcomitans and the 32-kda protein of phage pf3 from pseudomonas aeruginosa. | 1995 | 7789800 |
| secondary structure of the single-stranded dna binding protein encoded by filamentous phage pf3 as determined by nmr. | nuclear magnetic resonance spectroscopy was employed to study the single-stranded dna binding protein encoded by the filamentous pseudomonas bacteriophage pf3. the protein is 78 amino acids long and occurs in solution predominantly as a homodimer with a molecular mass of 18 kda. sequence-specific 1h and 15n resonance assignments have been obtained using homo- and heteronuclear two- and three-dimensional experiments. the secondary structure of the protein monomer was determined from a qualitative ... | 1994 | 7925383 |
| sequence analysis of a 1296-nucleotide plasmid from xylella fastidiosa. | a cryptic plasmid from xylella fastidiosa strain atcc 35868 was cloned, sequenced, and the sequence entered into genbank (u71220). the plasmid is 1296 nucleotides in length with 55% gc content and three open reading frames. a plasmid with sequence homology was found in only one other strain of x. fastidiosa, atcc 35878. searches of the genbank reveal nucleotide sequence homology with plasmid pnkh43 from stenotrophomonas maltophilia, and amino acid sequence homology with phage pf3 from pseudomona ... | 1997 | 9351204 |
| functional assembly of the lambda s holin requires periplasmic localization of its n-terminus. | bacteriophage-lambda-induced host-cell lysis requires two phage-encoded proteins, the s holin and the r transglycosylase. at a specific time during infection, the holin forms a lesion in the cytoplasmic membrane that permits access of the r protein to its substrate, the peptidoglycan. the lambda s gene represents the prototype of holin genes with a dual-start motif; they encode two proteins, a lysis effector and a lysis inhibitor. although the two s proteins differ only by two amino acids (met-1 ... | 1999 | 10398749 |
| the pf3 coat protein contacts tm1 and tm3 of yidc during membrane biogenesis. | the coat protein of bacteriophage pf3 is inserted into the plasma membrane of escherichia coli by the insertase yidc. to identify which of the six transmembrane regions of yidc bind the single-spanning pf3 coat protein during membrane protein biogenesis, we used the disulfide cross-linking approach. we generated single cysteines in each of the transmembrane regions of yidc and in the center of the hydrophobic region of pf3 coat protein. we found that the substrate pf3 coat contacts the first and ... | 2008 | 18996118 |
| translocation of n-terminal tails across the plasma membrane. | previously we have shown that the first hydrophobic domain of leader peptidase (lep) can function to translocate a short n-terminal 18 residue antigenic peptide from the phage pf3 coat protein across the plasma membrane of escherichia coli. we have now examined the mechanism of insertion of n-terminal periplasmic tails and have defined the features needed to translocate these regions. we find that short tails of up to 38 residues are efficiently translocated in a seca- and secy-independent manne ... | 1994 | 7925307 |
| role of tyr-22 in the binding of pf3 ssdna binding protein to nucleic acids. | a tyr-22-->phe-22 (y22f) mutant of the single-strand dna binding protein (ssdbp) of the filamentous phage pf3 was obtained by site-directed mutagenesis. an alignment of protein sequences indicates that tyr-22 of the pf3 ssdbp corresponds to tyr-26 of the fd g5p, a tyrosine within the dna-binding loop. the mutant y22f pf3 protein had a cd spectrum very similar to that of native, wild-type pf3 ssdbp and could bind to both dna and rna polymers. in cd titrations of poly[r(a)], poly[r(c)], and pf3 ss ... | 1995 | 7727424 |
| pf3 coat protein forms voltage-gated ion channels in planar lipid bilayers. | the coat protein of bacteriophage pf3 forms discrete and stable ion channels of uniform size in planar bilayers of asolectin. its primary sequence suggests a channel formed by a bundle of transmembrane helices. since the apparent transmembrane region only consists of strongly hydrophobic residues, it represents a new class of channel-forming proteins. the channel activity is strongly voltage-dependent. the single-channel conductance of 60 ps (at 100 mv) in 0.2 m nacl is slightly voltage-dependen ... | 1994 | 7506930 |
| spontaneous deletion mutants of bacteriophage pf3: mapping of signals involved in replication and assembly. | defective deletion mutants (miniphages) arise spontaneously during serial propagation of the filamentous bacteriophage pf3. they contain a circular single-stranded (ss) dna molecule which is up to 80% smaller than the wild-type single-stranded genome. analysis of the genomic structure of three of these miniphages revealed that they consist of sequences that in the wild-type genome are flanked by direct repeats 5-8 nucleotides long; only one copy of these repeats was found again in the miniphage ... | 1987 | 3582091 |
| the function of a leader peptide in translocating charged amino acyl residues across a membrane. | insertion of bacteriophage coat proteins into the membrane of infected bacterial cells can be studied as a model system of protein translocation across membranes. the coat protein of the filamentous bacteriophage pf3--which infects pseudomonas aeruginosa--is 44 amino acids in length and has the same basic structure as the coat protein of bacteriophage m13, which infects escherichia coli. however, unlike the pf3 coat protein, the m13 coat protein is synthesized as a precursor (procoat) with a typ ... | 1990 | 2124001 |
| raman spectroscopic study on the conformation of a peptide fragment representing the dna-binding domain of filamentous virus pf3 coat protein. | raman spectra have been measured of a nonapeptide which has an amino acid sequence identical to that of the c-terminal region of the major coat protein subunit of filamentous bacteriophage pf3. the peptide shows a strong tendency to form a beta-sheet structure in aqueous solution. the beta-sheet formation is significantly promoted by complexation with single-stranded dna but not with double-stranded dna. it is suggested that the c-terminal region of the pf3 coat protein binds to the single-stran ... | 1992 | 1644171 |
| yidc-driven membrane insertion of single fluorescent pf3 coat proteins. | the membrane insertion of single bacteriophage pf3 coat proteins was observed by confocal fluorescence microscopy. within seconds after addition of the purified and fluorescently labeled protein to liposomes or proteoliposomes containing the purified and reconstituted membrane insertase yidc of escherichia coli, the translocation of the labeled residue was detected. the 50-amino-acid-long pf3 coat protein was labeled with atto520 and inserted into the proteoliposomes. translocation of the dye in ... | 2011 | 21798266 |
| specific formation of trypsin-resistant micelles on a hydrophobic peptide observed with triton x-100 but not with octylglucoside. | the manner of interaction of the coat peptide of the pf3 phage (pf3 peptide) with lipid bilayers has been extensively studied. presently, we designed a derivative of the pf3 peptide, referred to as the ddrk peptide, and subjected it to trypsin digestion to understand its physicochemical properties. in the presence of triton x-100 used for solubilization of the peptide, digestion of ddrk with trypsin caused specific cleavage at the lysine (lys) residue in its n-terminal region but not at other ly ... | 2010 | 20646996 |
| augmentation of the antimicrobial efficacy of antibiotics by filamentous phage. | a significant increase in sensitivity to several antibiotics was observed in vitro after infection of the two pseudomonas aeruginosa strains o1 and k with the filamentous phage pf3 and pf1, respectively. moreover, upon infection with phage pf1 a p. aeruginosa k strain harboring a plasmid-borne gentamicin resistance gene could be resensitized to the antibiotic. we further show that balb/c mice were rescued from lethal infections with p. aeruginosa k by concomitant treatment with phage pf1 and low ... | 2006 | 17002542 |
| identification and specificity of pilus adsorption proteins of filamentous bacteriophages infecting pseudomonas aeruginosa. | filamentous bacteriophages pf1 and pf3 infect pseudomonas aeruginosa strains k and o, respectively. we show here that the capsids of these bacteriophages each contain a few copies of a minor coat protein (designated g3p) of high molecular mass, which serves as a pilus adsorption protein, much like the protein g3p of the ff bacteriophages which infect escherichia coli. bacteriophage pf1 was observed to interact with the type iv pak pilus whereas bacteriophage pf3 interacted with the conjugative r ... | 2006 | 16298408 |
| therapy of experimental pseudomonas infections with a nonreplicating genetically modified phage. | bacteriophage therapy of bacterial infections has received renewed attention owing to the increasing prevalence of antibiotic-resistant pathogens. a side effect of many antibiotics as well as of phage therapy with lytic phage is the release of cell wall components, e.g., endotoxins of gram-negative bacteria, which mediate the general pathological aspects of septicemia. here we explored an alternative strategy by using genetically engineered nonreplicating, nonlytic phage to combat an experimenta ... | 2004 | 15388440 |
| orientation and interactions of an essential tryptophan (trp-38) in the capsid subunit of pf3 filamentous virus. | the filamentous bacteriophage pf3 consists of a covalently closed dna single strand of 5833 nucleotides sheathed by approximately 2500 copies of a 44-residue capsid subunit. the capsid subunit contains a single tryptophan residue (trp-38), which is located within the basic c-terminal sequence (-rwikaqff) and is essential for virion assembly in vivo. polarized raman microspectroscopy has been employed to determine the orientation of the trp-38 side chain in the native virus structure. the polariz ... | 2003 | 12609899 |
| the protein capsid of filamentous bacteriophage ph75 from thermus thermophilus. | the ph75 strain of filamentous bacteriophage (inovirus) grows in the thermophilic bacterium thermus thermophilus at 70 degrees c. we have characterized the viral dna and determined the amino acid sequence of the major coat protein, p8. the p8 protein is synthesized without a leader sequence, like that of bacteriophage pf3 but unlike that of bacteriophage pf1, both of which grow in the mesophile pseudomonas aeruginosa. x-ray diffraction patterns from ordered fibres of the ph75 virion are similar ... | 2001 | 11371161 |
| structure and organization of bacteriophage pf3 probed by raman and ultraviolet resonance raman spectroscopy. | the pseudomonas bacteriophage pf3 is a long and narrow filament consisting of a covalently closed dna single strand of 5833 bases sheathed by approximately 2500 copies of a 44-residue subunit. ultraviolet resonance raman spectra excited at 257, 244, 238, and 229 nm and off-resonance raman spectra excited at 514.5 nm are reported for pf3 in both h2o and d2o solutions. the key raman bands are assigned to specific protein and dna groups of the native virion assembly. the results are compared with p ... | 2001 | 11148039 |
| membrane assembly of the bacteriophage pf3 major coat protein. | the pf3 major coat protein of the pf3 bacteriophage is stored in the inner membrane of the infected cell during the reproductive cycle. the protein consists of 44 amino acids, and contains an acidic amphipathic n-terminal domain, a hydrophobic domain, and a short basic c-terminal domain. the mainly alpha-helical membrane-bound protein traverses the membrane once, leaving the c-terminus in the cytoplasm and the n-terminus in the periplasm. a cysteine-scanning approach was followed to measure whic ... | 2000 | 10821689 |
| hydrophobic forces drive spontaneous membrane insertion of the bacteriophage pf3 coat protein without topological control. | bacterial integral inner membrane proteins are either translocated across the lipid bilayer using an energy-driven enzyme, such as the sec translocase, or they might interact directly with the membrane due to hydrophobic forces. we report that the single-spanning pf3 coat protein is spontaneously inserted into the membrane of escherichia coli and requires the electrical component of the membrane potential (deltapsi) to translocate its n-terminal region. this results in a final n(out)c(in) orient ... | 1999 | 10562542 |
| functionally important correlated motions in the single-stranded dna-binding protein encoded by filamentous phage pf3. | to elucidate the interplay between different parts of dimeric single-stranded dna-binding proteins we have studied the correlated motions in the protein encoded by filamentous phage pf3 via the combined use of 15n-nmr relaxation experiments, molecular dynamics simulations and essential dynamics calculations. these studies provide insight into the mechanism underlying the protein-dna binding reaction. the most important motions can be described by a few essential modes. most outstanding is the co ... | 1999 | 10092460 |
| essential spaces defined by nmr structure ensembles and molecular dynamics simulation show significant overlap. | large concerted motions of proteins which span its "essential space," are an important component of protein dynamics. we investigate to what extent structure ensembles generated with standard structure calculation techniques such as simulated annealing can capture these motions by comparing them to long-time molecular dynamics (md) trajectories. the motions are analyzed by principal component analysis and compared using inner products of eigenvectors of the respective covariance matrices. two ve ... | 1998 | 9626697 |
| refined structure, dna binding studies, and dynamics of the bacteriophage pf3 encoded single-stranded dna binding protein. | the solution structure of the 18-kda single-stranded dna binding protein encoded by the filamentous pseudomonas bacteriophage pf3 has been refined using 40 ms 15n- and 13c-edited noesy spectra and many homo- and heteronuclear j-couplings. the structures are highly precise, but some variation was found in the orientation of the beta-hairpin denoted the dna binding wing with respect to the core of the protein. backbone dynamics of the protein was investigated in the presence and absence of dna by ... | 1997 | 9230044 |
| floating stereospecific assignment revisited: application to an 18 kda protein and comparison with j-coupling data. | we report a floating chirality procedure to treat nonstereospecifically assigned methylene or isopropyl groups in the calculation of protein structures from nmr data using restrained molecular dynamics and simulated annealing. the protocol makes use of two strategies to induce the proper conformation of the prochiral centres: explicit atom 'swapping' following an evaluation of the noe energy term, and atom 'floating' by reducing the angle and improper force constants that enforce a defined chira ... | 1997 | 9229503 |
| negatively charged amino acid residues play an active role in orienting the sec-independent pf3 coat protein in the escherichia coli inner membrane. | the coat protein of pseudomonas aeruginosa phage pf3 is transiently inserted into the bacterial inner membrane with a single transmembrane anchor sequence in the n(out)c(in) orientation. the n-terminal sequence immediately flanking the membrane anchor contains one negatively charged residue, whereas the c-terminal hydrophilic segment has two positively charged residues. to investigate how the orientation of this protein is achieved, the three flanking charged amino acid residues were altered. me ... | 1997 | 9171335 |
| characterization of the pf3 single-strand dna binding protein by circular dichroism spectroscopy. | we have used circular dichroism (cd) spectroscopy and gel electrophoresis to characterize the single-strand dna binding protein (ssdbp) of the bacteriophage pf3 and its complexes with pf3 dna and various dna and rna homopolymers. the secondary structure of pf3 ssdbp had < 1% alpha-helix and therefore was probably a beta-sheet structure like the fd gene 5 protein (g5p). from cd titrations, the binding stoichiometry of pf3 ssdbp was two nucleotides per protein monomer (n = 2) for complexes formed ... | 1993 | 8241145 |