Publications

[selecting the phage displaying tetrodotoxin mimic epitope by phage random peptide library].	to screen the positive phage displaying the mimic epitope of tetrodotoxin (ttx) by using phage random peptide display library technology and to establish immunoassay for the detection of tetrodotoxin.	2010	20568457
crystallization and preliminary x-ray analysis of psu, an inhibitor of the bacterial transcription terminator rho.	psu, a coat protein from bacteriophage p4, inhibits rho-dependent transcription termination both in vivo and in vitro. the psu protein is alpha-helical in nature and appeared to be a dimer in solution. it interacts with rho and affects the atp binding and rna-dependent atpase activity of rho, which in turn reduces the rate of rna release from the elongation complex. crystals of psu were grown in space group i422 in the presence of peg, with unit-cell parameters a = b = 148.76, c = 63.38 a and a ...	2010	20124724
tightly-wound miniknot vectors for gene therapy: a potential improvement over supercoiled minicircle dna.	minimized derivatives of bacterial plasmids with removed bacterial backbones are promising vectors for the efficient delivery and for the long-term expression of therapeutic genes. the absence of the bacterial plasmid backbone, a known inducer of innate immune response and a known silencer of transgene expression, provides a partial explanation for the high efficiency of gene transfer using minimized dna vectors. supercoiled minicircle dna is a type of minimized dna vector obtained via intra-pla ...	2010	19914006
understanding the differences between genome sequences of escherichia coli b strains rel606 and bl21(de3) and comparison of the e. coli b and k-12 genomes.	each difference between the genome sequences of escherichia coli b strains rel606 and bl21(de3) can be interpreted in light of known laboratory manipulations plus a gene conversion between ribosomal rna operons. two treatments with 1-methyl-3-nitro-1-nitrosoguanidine in the rel606 lineage produced at least 93 single-base-pair mutations ( approximately 90% gc-to-at transitions) and 3 single-base-pair gc deletions. two uv treatments in the bl21(de3) lineage produced only 4 single-base-pair mutatio ...	2009	19765592
interaction surface of bacteriophage p4 protein psu required for complex formation with the transcription terminator rho.	rho-dependent transcription termination is an essential function in prokaryotes, and the transcription terminator rho is highly conserved among different species. the bacteriophage p4 capsid-decoration protein, psu, interacts specifically with and inhibits the function of escherichia coli rho. the interaction surface of psu involved in interacting with rho is not known, but knowledge of this is important to understand the mechanism of its action and will be useful to design peptide inhibitor(s) ...	2009	19409394
a comparative analysis of the bifunctional cox proteins of two heteroimmune p2-like phages with different host integration sites.	the cox protein of the coliphage p2 is multifunctional; it acts as a transcriptional repressor of the pc promoter, as a transcriptional activator of the p(ll) promoter of satellite phage p4, and as a directionality factor for site-specific recombination. the cox proteins constitute a unique group of directionality factors since they couple the developmental switch with the integration or excision of the phage genome. in this work, the dna binding characteristics of the cox protein of wphi, a p2- ...	2009	19150106
the role of dna twist in the packaging of viral genomes.	we performed molecular dynamics simulations of the genome packaging of bacteriophage p4 using two coarse-grained models of dna. the first model, 1dna6 (one pseudo-atom per six dna basepairs), represents dna as a string of beads, for which dna torsions are undefined. the second model, 3dna6 (three pseudo-atoms per six dna basepairs), represents dna as a series of base planes with torsions defined by the angles between successive planes. bacteriophage p4 was packaged with 1dna6, 3dna6 in a torsion ...	2008	18192353
production of highly knotted dna by means of cosmid circularization inside phage capsids.	the formation of dna knots is common during biological transactions. yet, functional implications of knotted dna are not fully understood. moreover, potential applications of dna molecules condensed by means of knotting remain to be explored. a convenient method to produce abundant highly knotted dna would be highly valuable for these studies.	2007	18154674
incorporation of scaffolding protein gpo in bacteriophages p2 and p4.	scaffolding proteins act as chaperones for the assembly of numerous viruses, including most double-stranded dna bacteriophages. in bacteriophage p2, an internal scaffolding protein, gpo, is required for the assembly of correctly formed viral capsids. bacteriophage p4 is a satellite phage that has acquired the ability to take control of the p2 genome and use the p2 capsid protein gpn to assemble a capsid that is smaller than the normal p2 capsid. this size determination is dependent on the p4 ext ...	2008	17931675
solution structure of yaeo, a rho-specific inhibitor of transcription termination.	rho-dependent transcription termination is an essential process for the regulation of bacterial gene expression. thus far, only two rho-specific inhibitors of bacterial transcription termination have been described, the psu protein from the satellite bacteriophage p4 and yaeo from escherichia coli. here, we report the solution structure of yaeo, the first of a rho-specific inhibitor of transcription termination. yaeo is an acidic protein composed of an n-terminal helix and a seven-stranded beta ...	2007	17565995
autogenous regulation of escherichia coli polynucleotide phosphorylase during cold acclimation by transcription termination and antitermination.	adaptation of escherichia coli at low temperature implicates a drastic reprogramming of gene expression patterns. mechanisms operating downstream of transcription initiation, such as control of transcription termination, mrna stability and translatability, play a major role in controlling gene expression in the cold acclimation phase. it was previously shown that rho-dependent transcription termination within pnp, the gene encoding polynucleotide phosphorylase (pnpase), was suppressed in pnp non ...	2007	17384964
bacteriophage p4 sut1: a mutation suppressing transcription termination.	in the escherichia coli satellite phage p4, transcription starting from ple is prevalently controlled via premature termination at several termination sites. we identified a spontaneous mutation, p4 sut1 (suppression of termination), in the natural stop codon of p4 orf151 that, by elongating translation, suppresses transcription termination at the downstream t151 site. both the translational and the transcriptional profile of p4 sut1 differed from those of p4 wild-type. first of all, p4 sut1 did ...	2007	17325379
isolation and characterization of the smallest bacteriophage p4 derivatives packaged into p4-size head in bacteriophage p2-p4 system.	bacteriophage p4, a satellite phage of coliphage p2, is a very useful experimental tool for the study of viral capsid assembly and cos-cleavage. for an in vitro cos-cleavage reaction study of the p2-p4 system, new shortened and selectable markers containing p4 derivative plasmids were designed as a substrate molecules. they were constructed by swapping the non-essential segment of p4 dna for either the kanamycin resistance (kmr) gene or the ampicillin resistance (apr) gene. the size of the genom ...	2006	17082747
excision and transfer of the mesorhizobium loti r7a symbiosis island requires an integrase ints, a novel recombination directionality factor rdfs, and a putative relaxase rlxs.	the mesorhizobium loti strain r7a symbiosis island is an integrative conjugative element (ice), herein termed icemlsymr7a, which integrates into a phetrna gene. integration reconstructs the phetrna gene at one junction with the core chromosome, and a direct repeat of the 3-prime 17 bp of the gene is formed at the other junction. we show that the icemlsymr7aints gene, which encodes an integrase of the phage p4 family, is required for integration and excision of the island. excision also depended ...	2006	17076666
dna replication in phage p4: characterization of replicon ii.	the genetic element p4 propagates in its host escherichia coli both as a satellite phage and as a plasmid. two partially overlapping replicons coexist, namely replicon i and replicon ii. the former is composed of two sites, ori1 and crr, and depends on p4 alpha gene product for replication. the p4 alpha protein has primase and helicase activities, and binds specifically to both ori1 and crr. replicon ii is composed of two sites, ori2 and crr, and its replication also depends on p4 alpha primase ...	2006	16908062
expression of phage p4 integrase is regulated negatively by both int and vis.	phage p4 int gene encodes the integrase responsible for phage integration into and excision from the escherichia coli chromosome. here, the data showing that p4 int expression is regulated in a complex manner at different levels are presented. first of all, the pint promoter is regulated negatively by both int and vis, the p4 excisionase. the n-terminal portion of int appears to be sufficient for such a negative autoregulation, suggesting that the int n terminus is implicated in dna binding. sec ...	2006	16847139
mechanism of inhibition of rho-dependent transcription termination by bacteriophage p4 protein psu.	psu, a coat protein from bacteriophage p4, has been shown to inhibit rho-dependent transcription termination in vivo. co-overexpression of psu and rho led to the loss of viability of the cells, which is the consequence of the anti-rho activity of the protein. the antitermination property of psu is abolished either by the deletion of 10 or 20 amino acids from its c terminus or by a mutation, y80c, in rho. all these experiments indicated probable interactions between rho and psu. purified psu prot ...	2006	16829521
dna knots reveal a chiral organization of dna in phage capsids.	icosahedral bacteriophages pack their double-stranded dna genomes to near-crystalline density and achieve one of the highest levels of dna condensation found in nature. despite numerous studies, some essential properties of the packaging geometry of the dna inside the phage capsid are still unknown. we present a different approach to the problems of randomness and chirality of the packed dna. we recently showed that most dna molecules extracted from bacteriophage p4 are highly knotted because of ...	2005	15958528
the yersinia high-pathogenicity island (hpi): evolutionary and functional aspects.	the high-pathogenicity island (hpi) is a genomic island essential for the mouse-virulence phenotype in yersinia and indispensable for pathogenicity of yersinia and certain pathotypes of escherichia coli. in contrast to most genomic islands, the hpi is a functional island widely disseminated among members of the family of enterobacteriaceae. the hpi-encoded phage p4-like integrase together with excisionase and recombination sites make up the genetic mobility module of the island, while the sidero ...	2004	15493818
excision of the high-pathogenicity island of yersinia pseudotuberculosis requires the combined actions of its cognate integrase and hef, a new recombination directionality factor.	the yersinia high-pathogenicity island (hpi) encodes the siderophore yersiniabactin-mediated iron uptake system. the hpi of yersinia pseudotuberculosis i has previously been shown to be able to excise precisely from the bacterial chromosome by recombination between the attb-r and attb-l sites flanking the island. however, the nature of the y. pseudotuberculosis hpi excision machinery remained unknown. we show here that, upon excision, the hpi forms an episomal circular molecule. the island thus ...	2004	15165237
bacteriophage p4 vis protein is needed for prophage excision.	upon infection of its host escherichia coli, satellite bacteriophage p4 can integrate its genome into the bacterial chromosome by int-mediated site-specific recombination between the attp and the attb sites. the opposite event, excision, may either occur spontaneously or be induced by a superinfecting p2 helper phage. in this work, we demonstrate that the product of the p4 vis gene, a regulator of the p4 late promoters p(ll) and p(sid), is needed for prophage excision. this conclusion is support ...	2004	15063119
packaging double-helical dna into viral capsids.	dna packaging in bacteriophage p4 has been examined using a molecular mechanics model with a reduced representation containing one pseudoatom per turn of the double helix. the model is a discretized version of an elastic continuum model. the dna is inserted piecewise into the model capsid, with the structure being reoptimized after each piece is inserted. various optimization protocols were investigated, and it was found that molecular dynamics at a very low temperature (0.3 k) produces the opti ...	2004	14755571
cleavage leads to expansion of bacteriophage p4 procapsids in vitro.	proteolytic cleavage of the structural proteins is an important part of the maturation process for most bacteriophages and other viruses. in the double-stranded dna bacteriophages this cleavage is associated with dna packaging, capsid expansion, and scaffold removal. to understand the role of protein cleavage in the expansion of bacteriophages p2 and p4, we have experimentally cleaved p4 procapsids produced by overexpression of the capsid and scaffolding proteins. the cleavage leads to particle ...	2003	14517054
mechanisms of replication and telomere resolution of the linear plasmid prophage n15.	the prophage of coliphage n15 is not integrated into the bacterial chromosome but exists as a linear plasmid molecule with covalently closed ends. upon infection of an escherichia coli cell, the phage dna circularizes via cohensive ends. a phage-encoded enzyme, protelomerase, then cuts at another site, telrl, and forms hairpin ends (telomeres). purified protelomerase alone processes circular and linear plasmid dna containing the target site telrl to produce linear double-stranded dna with covale ...	2003	12694903
ilg1 : a new integrase-like gene that is a marker of bacterial contamination by the laboratory escherichia coli strain top10f'.	identification of differentially expressed genes between normal and diseased states is an area of intense current medical research that can lead to the discovery of new therapeutic targets. however, isolation of differentially expressed genes by subtraction often suffers from unreported contamination of the resulting subtraction library with clones containing dna sequences not from the original rna samples.	2002	12393938
the structure of p4 procapsids produced by coexpression of capsid and external scaffolding proteins.	the double-stranded dna bacteriophage p4 has a t = 4 icosahedral arrangement of the gpn capsid protein derived from the p2 helper phage. the precursor procapsids in addition contain an external scaffold made up of the p4-encoded sid protein. high yields of pure p4 procapsids have been obtained by coexpressing the gpn and sid proteins from a chimeric plasmid. biochemical measurements show that the ratio of gpn to sid in the procapsids is 2:1, corresponding to 120 copies of sid per procapsid parti ...	2002	12127785
rnase e and polyadenyl polymerase i are involved in maturation of ci rna, the p4 phage immunity factor.	bacteriophage p4 immunity is controlled by a small stable rna (ci rna) that derives from the processing of primary transcripts. in previous works, we observed that the endonuclease rnase p is required for the maturation of ci rna 5'-end; moreover, we found that polynucleotide phosphorylase (pnpase), a 3' to 5' rna-degrading enzyme, is required for efficient 5'-end processing of ci rna, suggesting that 3'-end degradation of the primary transcript might be involved in the production of proper rnas ...	2002	12051840
mobility of a restriction-modification system revealed by its genetic contexts in three hosts.	the flow of genes among prokaryotes plays a fundamental role in shaping bacterial evolution, and restriction-modification systems can modulate this flow. however, relatively little is known about the distribution and movement of restriction-modification systems themselves. we have isolated and characterized the genes for restriction-modification systems from two species of salmonella, s. enterica serovar paratyphi a and s. enterica serovar bareilly. both systems are closely related to the pvuii ...	2002	11948154
phage p4 origin-binding domain structure reveals a mechanism for regulation of dna-binding activity by homo- and heterodimerization of winged helix proteins.	the origin-binding domain of the gpalpha protein of phage p4 (p4-obd) mediates origin recognition and regulation of gpalpha activity by the protein cnr. we have determined the crystal structure of p4-obd at 2.95 a resolution. the structure of p4-obd is that of a dimer with pseudo twofold symmetry. each subunit has a winged helix topology with a unique structure among initiator proteins. the only structural homologue of the p4-obd subunit is the dna-binding domain of the eukaryotic transcriptiona ...	2002	11929537
characterization of the developmental switch region of bacteriophage p2 hy dis.	in this work, the dna sequence of the transcriptional switch that affects the development of the p2 hy dis bacteriophage was determined. the switch contains two face-to-face-located promoters and two repressors, cox and c. the locations of the pc and pe promoters were determined by primer extension analysis. the p2 hy dis homolog of the p2 multifunctional cox protein was shown to be able to substitute for p2 cox in repression of the p2 pc promoter, excision of the p2 prophage, and activation of ...	2001	11883185
characterization of the small antisense ci rna that regulates bacteriophage p4 immunity.	in the immune state bacteriophage p4 prevents expression of the replication functions by premature termination of transcription. a small rna, the ci rna, is the trans acting factor that regulates p4 immunity, by pairing to complementary target sequences and causing premature transcription termination. the ci rna is matured by rnase p and pnpase from the leader region of the same operon it regulates. in this work we better characterize this molecule. ci rna copy number was determined to be around ...	2002	11812128
bacteriophage p2: recombination in the superinfection preprophage state and under replication control by phage p4.	genetic crosses (mixed infection, lytic cycle) with bacteriophage p2 are known to give extremely low recombination frequencies, and these are unaffected by the reca status of the host bacterium. we now show the following: (1) the satellite bacteriophage p4, which interacts with p2 in a number of ways, but is quite different from it in terms of dna replication and its control, is clearly dependent on the host reca+ function for recombination; (2) a chimeric phage (lindqvist's p2/p4 hy19), in whic ...	2001	11713670
nucleotide sequence of coliphage hk620 and the evolution of lambdoid phages.	hk620 is a temperate lambdoid bacteriophage that adsorbs to the o-antigen of its host, escherichia coli h. the genome of a temperature-sensitive clear-plaque mutant consists of 38,297 nucleotides in which we recognize 60 open reading frames (orfs). eighteen of these lie in a region of the genome that we call the virion structure domain. the other 42 orfs lie in what we call the metabolic domain. virions of hk620 resemble those of phage p22. the virion structural orfs encode three kinds of putati ...	2001	11518522
the plasmid status of satellite bacteriophage p4.	p4 is a natural phasmid (phage-plasmid) that exploits different modes of propagation in its host escherichia coli. extracellularly, p4 is a virion, with a tailed icosahedral head, which encapsidates the 11.6-kb-long double-stranded dna genome. after infection of the e. coli host, p4 dna can integrate into the bacterial chromosome and be maintained in a repressed state (lysogeny). alternatively, p4 can replicate as a free dna molecule; this leads to either the lytic cycle or the plasmid state, de ...	2001	11319927
capsid size determination in the p2-p4 bacteriophage system: suppression of sir mutations in p2's capsid gene n by supersid mutations in p4's external scaffold gene sid.	the sid gene of the p2-dependent phage p4 provides an external scaffold so p2 n gene encoded protomers assemble as t = 4 capsids rather than as p2's t = 7 capsids. mutations (sir) in the middle of n interfere with sid's function. we describe a new p4 mutant class, nms ("supersid") mutations, which direct also p2 sir to provide small capsids. three different nms mutations were located near the sid end, commingled with sid(-) mutations. suppression of sir by nms is not allele-specific. our results ...	2001	11312661
genetic organization of the she pathogenicity island in shigella flexneri 2a.	in this study we report the complete nucleotide sequence and genetic organization of the she pathogenicity island (pai) of shigella flexneri 2a strain ysh6000t. the 46 603 bp she pai is situated adjacent to the 3' terminus of the phev trna gene and includes an imperfect direct repeat of the 3'-terminal 22 bp of the phev gene at the right boundary of the pai. the she pai carries a bacteriophage p4-like integrase gene within the phev -proximal boundary of the pai, intact and truncated mobile genet ...	2001	11162180
in vitro assembly of bacteriophage p4 procapsids from purified capsid and scaffolding proteins.	bacteriophage p4 is a satellite virus of bacteriophage p2, which has acquired the ability to utilize the structural gene products of p2 to assemble its own capsid. the normal p2 capsid has a t = 7 icosahedral structure comprised of the gpn-derived capsid protein, whereas the capsid produced under the control of p4 has a smaller, t = 4 structure. the protein responsible for this size determination is the p4-coded gene product sid, which forms an external scaffold on the p4 procapsid. using an in ...	2000	11017795
the yersinia high-pathogenicity island.	a pathogenicity island present only in highly pathogenic strains of yersinia (y. enterocolitica 1b, y. pseudotuberculosis i and y. pestis) has been identified on the chromosome of yersinia spp. and has been designated high-pathogenicity island (hpi). the yersinia hpi carries a cluster of genes involved in the biosynthesis, transport and regulation of the siderophore yersiniabactin. the major function of this island is thus to acquire iron molecules essential for in vivo bacterial growth and diss ...	1999	10943409
antisense rna-dependent transcription termination sites that modulate lysogenic development of satellite phage p4.	in the lysogenic state, bacteriophage p4 prevents the expression of its own replication genes, which are encoded in the left operon, through premature transcription termination. the phage factor responsible for efficient termination is a small, untranslated rna (ci rna), which acts as an antisense rna and controls transcription termination by pairing with two complementary sequences (seqa and seqc) located within the leader region of the left operon. a rho-dependent termination site, timm, was p ...	2000	10844696
the anti-immunity system of phage-plasmid n15: identification of the antirepressor gene and its control by a small processed rna.	n15 is a temperate virus of escherichia coli related to lambdoid phages. however, unlike all other known phages, the n15 prophage is maintained as a low copy number linear dna molecule with covalently closed ends. the primary immunity system at the immb locus is structurally and functionally comparable to that of lambdoid phages, and encodes the immunity repressor cb. we have characterized a second locus, imma, in which clear plaque mutations were mapped, and found that it encodes an anti-immuni ...	1999	10594823
the transcriptional switch of bacteriophage wphi, a p2-related but heteroimmune coliphage.	phage wphi is a member of the nonlambdoid p2 family of temperate phages. the dna sequence of the whole early-control region and the int and attp region of phage wphi has been determined. the phage integration site was located at 88.6 min of the escherichia coli k-12 map, where a 47-nucleotide sequence was found to be identical in the host and phage genomes. the wphi int protein belongs to the int family of site-specific recombinases, and it seems to have the same arm binding recognition sequence ...	1999	10559293
evidence of horizontal transfer of the ecoo109i restriction-modification gene to escherichia coli chromosomal dna.	a dna fragment carrying the genes coding for ecoo109i endonuclease and ecoo109i methylase, which recognize the nucleotide sequence 5'-(a/g)ggncc(c/t)-3', was cloned from the chromosomal dna of escherichia coli h709c. the ecoo109i restriction-modification (r-m) system was found to be inserted between the int and psu genes from satellite bacteriophage p4, which were lysogenized in the chromosome at the p4 phage attachment site of the corresponding leux gene observed in e. coli k-12 chromosomal dna ...	1999	10542186
translation of two nested genes in bacteriophage p4 controls immunity-specific transcription termination.	in phage p4, transcription of the left operon may occur from both the constitutive ple promoter and the regulated pll promoter, about 400 nucleotides upstream of ple. a strong rho-dependent termination site, timm, is located downstream of both promoters. when p4 immunity is expressed, transcription starting at ple is efficiently terminated at timm, whereas transcription from pll is immunity insensitive and reads through timm. we report the identification of two nested genes, kil and eta, located ...	1999	10464191
the e protein of satellite phage p4 acts as an anti-repressor by binding to the c protein of helper phage p2.	temperate phage p2 has the capacity to function as a helper for the defective, unrelated, satellite phage p4. in the absence of a helper, p4 can either lysogenize its host or establish itself as a plasmid. for lytic growth, p4 requires the structural genes, packaging and lysis functions of the helper. p4 can get access to the late genes of prophage p2 by derepression, which is mediated by the p4 e protein. e has been hypothesized to function as an anti-repressor. to locate possible epitopes inte ...	1998	9988480
the high-pathogenicity island of yersinia pseudotuberculosis can be inserted into any of the three chromosomal asn trna genes.	pathogenicity islands (pais) have been identified in several bacterial species. a pai called high-pathogenicity island (hpi) and carrying genes involved in iron acquisition (yersiniabactin system) has been previously identified in yersinia enterocolitica and yersinia pestis. in this study, the hpi of the third species of yersinia pathogenic for humans, y. pseudotuberculosis, has been characterized. we demonstrate that the hpi of strain ip32637 has a physical and genetic map identical to that of ...	1998	9988474
mutational analysis of a satellite phage activator.	the late gene activator, delta, of satellite phage p4 is more efficient than the delta of satellite phage phir73 in utilizing a p2 helper prophage that lacks an activator (ogr) gene. analysis of p4 delta is complicated by the fact that this protein contains two tandem phir73 delta-like domains. we performed a mutational analysis of phir73 delta, in order to select mutations that might not be found using p4 delta. the host rna polymerase alpha subunit mutation rpoa155 (l289f) blocks the growth of ...	1998	9858709
int-b13, an unusual site-specific recombinase of the bacteriophage p4 integrase family, is responsible for chromosomal insertion of the 105-kilobase clc element of pseudomonas sp. strain b13.	pseudomonas sp. strain b13 carries the clcrabde genes encoding chlorocatechol-degradative enzymes on the self-transmissible 105-kb clc element. the element integrates site and orientation specifically into the chromosomes of various bacterial recipients, with a glycine trna structural gene (glyv) as the integration site. we report here the localization and nucleotide sequence of the integrase gene and the activity of the integrase gene product in mediating site-specific integration. the integras ...	1998	9791097
a complex control system for transcriptional activation from the sid promoter of bacteriophage p4.	the sid gene promoter (psid), which controls expression of the late genes from satellite phage p4, is activated by a unique class of small dna-binding proteins. the activators from both satellite and helper phages stimulate transcription from psid. these activators bind to sites centered at position -55 in all the helper and satellite phage late promoters. p4 psid is unique in that it has an additional activator binding site centered at position -18 (site ii). we have constructed a mutant of sit ...	1998	9748449
evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-trna gene.	nodulation and nitrogen fixation genes of mesorhizobium loti are encoded on the chromosome of the bacterium. nevertheless, there is strong evidence that these genes can be transferred from an inoculant strain to nonsymbiotic mesorhizobia in the field environment. here we report that the chromosomal symbiotic element of m. loti strain icmp3153 is transmissible in laboratory matings to at least three genomic species of nonsymbiotic mesorhizobia. the element is 500 kb in size, integrates into a phe ...	1998	9560243
decreased levels of topoisomerase ii alpha in human renal cell carcinoma lines resistant to etoposide.	renal cell carcinoma (rcc) displays strong resistance against many chemotherapeutic drugs. overexpression of p-glycoprotein (pgp) appears to be part of this resistance. the involvement of another resistance mechanism, involving the decreased activity of dna topoisomerase ii (topoii), remains uncertain. by culturing the human rcc lines rc2 and rc21 in the presence of increasing concentrations of etoposide, we derived the variant sublines rc2e, rc21a and rc21e, that had acquired approximately 30-, ...	1997	9393588
enhancement of cole1-type replication promoted by the gp alpha initiator protein of bacteriophage p4.	gp alpha, the phage p4 specific replication protein, increases in vitro replication of pcn51, a pbr322 based replicon, by a factor of two. this effect is dependent on dna polymerase i and requires transcription by host rna polymerase. electron microscopic analysis of replicating intermediates indicates that pcn51 replication occurred from the same origin and with the same directionality in the presence and in the absence of gp alpha. these results reveal that gp alpha can influence the replicati ...	1997	9345759
the helicase domain of phage p4 alpha protein overlaps the specific dna binding domain.	replication initiation depends on origin recognition, helicase, and primase activities. in phage p4, a second dna region, the cis replication region (crr), is also required for replication initiation. the multifunctional alpha protein of phage p4, which is essential for dna replication, combines the three aforementioned activities on a single polypeptide chain. protein domains responsible for the activities were identified by mutagenesis. we show that mutations of residues g506 and k507 are defe ...	1997	9209020
derepression of prophage p2 by satellite phage p4: cloning of the p4 epsilon gene and identification of its product.	escherichia coli phage p4 lacks all of the genetic information necessary for capsid, tail, and lysis functions. p4 is therefore dependent on a helper phage, such as p2, for lytic propagation. during p4 superinfection of a p2 lysogen, the p2 prophage is derepressed by the action of the p4-encoded epsilon gene. we have cloned the epsilon gene and identified the 10-kda e protein. the epsilon gene product is the only p4 protein required to derepress prophage p2, which leads to in situ p2 dna replica ...	1997	9151842
the two p2 ogr-like domains of the delta protein from bacteriophage p4 are required for activity.	the satellite p4 phage delta protein positively regulates the late genes of its helper bacteriophage p2, as well as its own late genes. delta is a member of a class of activators associated with p2-or p4-like phages and is the largest member of this family. it resembles a covalently joined head-to-tail dimer of the other members of this family of activators. we have analyzed the requirement for both standard domains of delta through the isolation of amber mutants and the insertion of amber linke ...	1997	9143285
cnr protein, the negative regulator of bacteriophage p4 replication, stimulates specific dna binding of its initiator protein alpha.	bacteriophage p4 dna replication depends upon the phage-encoded alpha protein, which has dna helicase and dna primase activity and can specifically bind to the replication origin (ori) and to the cis replicating region (crr). the p4 cnr protein functions as a negative regulator of p4 replication, and p4 does not replicate in cells that overexpress cnr. we searched for p4 mutants that suppressed this phenotype (cnr resistant [alpha cr]). eight independent mutants that grew in the presence of high ...	1997	9139894
in vivo and in vitro evidence for an anti-rho activity induced by the phage p4 polarity suppressor protein psu.	the polarity suppression (psu) protein of bacteriophage p4 causes suppression of transcriptional polarity in escherichia coli by overcoming rho termination factor activity. two new psu mutants defective in polarity suppression are described. the psu5 mutation deletes codons 95-98 from about the middle of the gene, and the mutant protein is inactive. the psu6 mutation changes phe169 to val and encodes a temperature-sensitive protein. constitutive overexpression of psu+ from a plasmid prevents col ...	1997	9007066
the n-terminal part of bacteriophage p2 capsid protein is essential for postassembly maturation of p2 and p4 capsids.	during capsid assembly of bacteriophage p2 and its satellite phage p4, gpn undergoes proteolytic cleavage with the removal of the first 31 amino acids. the truncated protein gpn* is unable to support formation of viable phages in complementation tests. a c-myc antigenic epitope (eqkliseedl) exchanged for eleven amino acids in the amino terminal part of gpn results in both proteolytic processing of gpn::c-myc as well as assembly of p2 and p4 procapsid-like structures, but gpn::c-myc failed, like ...	1996	8874520
bacteriophage psp3 and phir73 activator proteins: analysis of promoter specificities.	transcription from the late promoters of bacteriophage p2 and its satellite phage p4 is activated by a unique class of small, zinc-binding proteins. using plasmid expression systems, we compared activators from two p2-like (helper) phages with those encoded by two satellite phages. the helper phage activators have more activity on the p4 phage sid promoter. in contrast, the satellite phage activators function better on the four late p2 promoters and on the p4 late leftward promoter. we purified ...	1996	8824611
polynucleotide phosphorylase of escherichia coli is required for the establishment of bacteriophage p4 immunity.	bacteriophage p4's superinfection immunity mechanism is unique among those of other known bacteriophages in several respects: (i) the p4 immunity factor is not a protein but a short, stable rna (ci rna); (ii) in the prophage the expression of the replication operon is prevented by premature transcription termination rather than by repression of transcription initiation; (iii) transcription termination is controlled via rna-rna interactions between the ci rna and two complementary target sequence ...	1996	8808944
a rho-dependent transcription termination site regulated by bacteriophage p4 rna immunity factor.	the genes required for replication of the temperate bacteriophage p4, which are coded by the phage left operon, are expressed from a constitutive promoter (ple). in the lysogenic state, repression of the p4 replication genes is achieved by premature transcription termination. the leader region of the left operon encodes all the genetic determinants required for prophage immunity, namely: (i) the p4 immunity factor, a short, stable rna (ci rna) that is generated by processing of the leader transc ...	1996	8806540
bacteriophage p4 capsid-size determination and its relationship to p2 helper interference.	the sid (size determination) gene product of phage p4 is known to be involved in capsid-size determination. moreover, the capsid-size determination function interferes with the lytic development of its helper p2, presumably because the helper genome is too large to be packaged into p4-size capsids. in order to study p4-specified helper interference, we cloned the sid gene for expression during phage infection. even though gpsid restores the capsid-size determination function of a sid defective p ...	1996	8638410
mutational analysis of the bacteriophage p4 capsid-size-determining gene.	satellite phage p4 (11,624 bp) depends on the morphopoietic genes (capsid, tail) and lysis genes of its helper phage p2 (33.5 kb) for its lytic development. in the morphopoietic process, p4 redirects the assembly pathway of large, p2 size, capsids (diameter = 60 nm) to yield smaller, p4 size, capsids (diameter = 45 nm), 1/3 in volume of that of its helper. the p4-specified capsid size determination is dependent on the function of the 27-kda gpsid. to study the capsid size-determining function, w ...	1996	8638409
identification of a phage-coded dna-binding protein that regulates transcription from late promoters in bacteriophage p4.	the genetic element p4 can propagate as a temperate phage or as a multicopy plasmid in its host escherichia coli. late in the lytic cycle and in the plasmid condition, transcription of the p4 essential genes depends on the activation of the late promoters p(ll) and p(sid), which control the transcription of the left and right operons, respectively. both p4 late promoters are positively regulated by the product of the p4 delta gene, which is transcribed from p(sid). we have identified a new p4 ge ...	1996	8636979
immunity specificity determinants in the p4-like retronphage phi r73.	retronphage phi r73 exhibits extensive sequence homology to the satellite bacteriophage p4. bacteriophage p4 superinfection immunity is elicited by a small rna (ci rna) that causes premature transcription termination within the operon coding for the p4 replication functions. this control is exerted via interaction of the ci rna with two complementary target sites on the untranslated leader rna of the replication operon. we found that phi r73 is endowed with a similar immunity system but is heter ...	1996	8607268
regulation of the serratia marcescens extracellular nuclease: positive control by a homolog of p2 ogr encoded by a cryptic prophage.	the serratia marcescens extracellular nuclease is a secreted protein that is subject to growth phase and sos control. regulatory mutants affecting nuclease expression have been isolated that define a new locus, nucc, essential for transcription of the nuclease gene nuca. the cloned nucc gene is able to activate efficient expression from the nuca promoter in escherichia coli, where it normally is poorly expressed. nucc is very similar to the bacteriophage p2 ogr protein, a transcriptional activat ...	1996	8594195
probability of dna knotting and the effective diameter of the dna double helix.	during the random cyclization of long polymer chains, knots of different types are formed. we investigated experimentally the distribution of knot types produced by random cyclization of phage p4 dna via its long cohesive ends. the simplest knots (trefoils) predominated, but more complex knots were also detected. the fraction of knots greatly diminished with decreasing solution na+ concentration. by comparing these experimental results with computer simulations of knotting probability, we calcul ...	1993	8506378
capsid localization of the bacteriophage p4 psu protein.	in addition to its polarity-suppressing activity, the psu protein of bacteriophage p4 also serves to stabilize the capsid against heat treatment and binds externally to the phage capsid. however, the heat stability is lost upon purification of the virus, indicating a loss of psu protein from the capsid. by using three-dimensional reconstruction from cryo-electron micrographs of p4 psu1 amber mutants lacking psu, and of p4 virions, which have been saturated with psu protein to regain heat stabili ...	1993	8503181
characterization of the capsid associating activity of bacteriophage p4's psu protein.	the psu (polarity suppression) protein of satellite bacteriophage p4 was first characterized as an anti-terminator of transcription termination in escherichia coli. psu is also a structural component of mature p4 capsids, where it is present as a decoration protein. psu is located externally on the capsid surface, and it appears to protect the capsid from loss of dna through the capsid shell. the ability of psu to specifically bind to the p4 capsid appears not to be dependent on any p4 specific ...	1993	8503180
the cox protein is a modulator of directionality in bacteriophage p2 site-specific recombination.	the p2 cox protein is known to repress the pc promoter, which controls the expression of the p2 immunity repressor c. it has also been shown that cox can activate the late promoter pll of the unrelated phage p4. by this process, a p2 phage infecting a p4 lysogen is capable of inducing replication of the p4 genome, an example of viral transactivation. in this report, we present evidence that cox is also directly involved in both prophage excision and phage integration. while purified cox, in addi ...	1993	8253674
phage p4 alpha protein is multifunctional with origin recognition, helicase and primase activities.	alpha protein of satellite phage p4 of escherichia coli is multifunctional in p4 replication with three activities. first, the protein (subunit m(r) = 84,900) complexes specifically the p4 origin and the cis replication region required for replication. alpha protein interacts with all six type i repeats (tgttcacc) present in the origin. second, associated with the alpha protein is a dna helicase activity that is fueled by hydrolysis of a nucleoside 5' triphosphate. all common ntps except utp and ...	1993	8253092
mechanisms of genome propagation and helper exploitation by satellite phage p4.	temperate coliphage p2 and satellite phage p4 have icosahedral capsids and contractile tails with side tail fibers. because p4 requires all the capsid, tail, and lysis genes (late genes) of p2, the genomes of these phages are in constant communication during p4 development. the p4 genome (11,624 bp) and the p2 genome (33.8 kb) share homologous cos sites of 55 bp which are essential for generating 19-bp cohesive ends but are otherwise dissimilar. p4 turns on the expression of helper phage late ge ...	1993	8246844
bacteriophage p2 and p4 assembly: alternative scaffolding proteins regulate capsid size.	the capsid protein of bacteriophage p2, encoded by the n gene, can assemble into icosahedral capsids of two possible sizes, with diameters of 60 and 45 nm, respectively. only the larger capsid is used by p2 itself, but the smaller one is exploited by the satellite phage p4. we have analyzed the assembly products of gpn expressed in vivo from a plasmid, i.e., in the absence of any other phage proteins, and find that gpn alone forms closed shells of both sizes, although with poor efficiency. coexp ...	1994	8178454
molecular cloning and characterization of bacteriophage p2 genes r and s involved in tail completion.	the sequences of two previously known tail genes, r and s, of the temperate bacteriophage p2 and the sequence of an additional open reading frame (orf-30) located between s and v, were determined. amber mutations mapping within r and s, ram3, ram42, ram23, sam75, and sam89 were sequenced and found to be within their corresponding open reading frames. we constructed overproducing plasmids for r and s and identified these proteins by sds-page of whole-cell lysates and coomassie blue staining. the ...	1994	8178426
active dna topoisomerase ii with minimum molecular mass from regenerating rat liver.	we have purified the type ii dna topoisomerase from regenerating rat liver. the purified topoisomerase ii migrated as two bands with molecular masses of 70 kda and 55 kda on sds-page. immunoblotting analysis using antiserum against rat topoisomerase ii gene product expressed in escherichia coli suggested that the two bands on sds-gel are proteolytic products of the intact 173 kda form. however, these products retained the enzyme activities such as catenation and relaxation of supercoiled circula ...	1994	8038715
phage p4 dna replication in vitro.	phage p4 dna is replicated in cell-free extracts of escherichia coli in the presence of partially purified p4 alpha protein [krevolin and calendar (1985), j. mol. biol. 182, 507-517]. using a modified in vitro replication assay, we have further characterized this process. analysis by agarose gel electrophoresis and autoradiography of in vitro replicated molecules demonstrates that the system yields supercoiled monomeric dna as the main product. electron microscopic analysis of in vitro generated ...	1994	8029013
a new gene of bacteriophage p4 that controls dna replication.	bacteriophage p4 replication may result in either a lytic cycle or plasmid maintenance, depending on the presence or absence, respectively, of helper phase p2 genome. bacteriophage p4 dna replication depends on the product of gene alpha, which has origin recognition, primase, and helicase activities. an open reading frame with the coding capacity for a protein of 106 amino acids (orf106) is located upstream of the alpha gene. genes orf106 and alpha are transcriptionally coregulated. three amber ...	1994	7928967
the gene fimu affects expression of salmonella typhimurium type 1 fimbriae and is related to the escherichia coli trna gene argu.	the gene fimu, located on a recombinant plasmid carrying the salmonella typhimurium type 1 fimbrial gene cluster is closely related to the escherichia coli trna gene argu. the fimu gene complements an e. coli argu mutant that is a p2 lysogen, thereby allowing the phage p4 to grow in this strain but preventing the growth of phage lambda. in addition, fimu was shown to be involved in fimbrial expression since transformants of the e. coli argu mutant could produce fimbriae only in the presence of f ...	1994	7914347
control of transcription termination by an rna factor in bacteriophage p4 immunity: identification of the target sites.	prophage p4 immunity is elicited by a short, 69-nucleotide rna (ci rna) coded for within the untranslated leader region of the same operon it controls. ci rna causes termination of transcription that starts at the promoter ple and prevents the expression of the distal part of the operon that codes for p4 replication functions (alpha operon). in this work, we identify two sequences in the untranslated leader region of the alpha operon, seqa and seqc, that are the targets of the p4 immunity factor ...	1995	7883698
bacteriophage p4 dna replication.	replication of satellite phage p4 of escherichia coli is dependent on three phage-encoded elements: the origin (ori), a cis replication element (crr), and the product of the alpha gene, gp alpha. in p4 replication is origin-specific resulting in monomeric form i dna. dna synthesis requires chromosomally encoded proteins dna polymerase iii holoenzyme, ssb, dna gyrase and probably topoisomerase i; host-encoded initiation and priming functions are dispensable. the alpha protein is multifunctional i ...	1995	7669353
peptide presentation by bacteriophage p4.	this article focuses on bacteriophage p4 as a potential peptide display phage by exploring the possibility of using the p4 capsid decoration component, psu, as a peptide carrier protein. psu is non-essential for p4 growth but it enhances the stability of the p4 capsid by binding to its exterior. we have constructed a unique saci cloning site in the beginning of the psu gene. this site changes the third amino acid of psu from ser to leu. this substitution does not destroy the binding of psu to th ...	1995	7669349
multiple regulatory mechanisms controlling phage-plasmid p4 propagation.	bacteriophage p4 autonomous replication may result in the lytic cycle or in plasmid maintenance, depending, respectively, on the presence or absence of the helper phage p2 genome in the escherichia coli host cell. alternatively, p4 may lysogenize the bacterial host and be maintained in an immune-integrated condition. a key step in the choice between the lytic/plasmid vs. the lysogenic condition is the regulation of p4 alpha operon. this operon may be transcribed from two promoters, ple and pll, ...	1995	7669338
the capsid size-determining protein sid forms an external scaffold on phage p4 procapsids.	although the phages p2 and p4 build their capsids from the same precursor, the product of the p2 n gene, the two capsids differ in size: p2 builds a 60 nm, t = 7 capsid from 420 subunits, whereas p4 makes a 45 nm, t = 4 capsid from 240 subunits. this difference leads to substantial changes in shell geometry and subunit interactions. previous results have demonstrated that the p4 sid gene is responsible for the assembly of p4-sized shells. we have used cryo-electron microscopy and image reconstru ...	1995	7643390
domain structure of phage p4 alpha protein deduced by mutational analysis.	bacteriophage p4 dna replication depends on the product of the alpha gene, which has origin recognition ability, dna helicase activity, and dna primase activity. one temperature-sensitive and four amber mutations that eliminate dna replication in vivo were sequenced and located in the alpha gene. sequence analysis of the entire gene predicted a domain structure for the alpha polypeptide chain (777 amino acid residues, m(r) 84,900), with the n terminus providing the catalytic activity for the pri ...	1995	7635818
analysis of the escherichia coli genome vi: dna sequence of the region from 92.8 through 100 minutes.	the 338.5 kb of the escherichia coli genome described here together with previously described segments bring the total of contiguous finished sequence of this genome to > 1 mb. of 319 open reading frames (orfs) found in this 338.5 kb segment, 147 (46%) are potential new genes. the positions of several genes which had been previously located here by mapping or partial sequencing have been confirmed. several orfs have functions suggested by similarities to other characterised genes but cannot be a ...	1995	7610040
purification and characterization of the bacteriophage p4 delta protein.	the bacteriophage p4 delta protein is a transcriptional activator of the late genes of p4 as well as the late genes of its helpers, such as bacteriophage p2. delta was purified, using a variation of the male fusion system. with this method we purified two forms of delta: a fusion of male and delta and a unfused form. the fusion by itself is not active in vivo or in vitro, but the mixture of the fusion and the unfused delta is active in both. using nitrocellulose filtration and gel mobility shift ...	1995	7601839
excision of a p4-like cryptic prophage leads to alp protease expression in escherichia coli.	the escherichia coli k-12 alpa gene product, when overproduced from a multicopy plasmid, leads to suppression of the capsule overproduction and uv sensitivity phenotypes of cells mutant for the lon atp-dependent protease. this suppression has previously been shown to correlate with increased in vivo activity of a previously unknown energy-dependent proteolytic activity capable of degrading lon substrates, the alp protease. we show in an accompanying paper that alpa, which has homology to a short ...	1994	7511583
division inhibition gene dicf of escherichia coli reveals a widespread group of prophage sequences in bacterial genomes.	the genomes of various eubacteria were analyzed by southern blot hybridization to detect sequences related to the segment of the defective lambdoid prophage kim which encodes dicf rna, an antisense inhibitor of cell division gene ftsz in escherichia coli k-12. among the homologous sequences found, one fragment from e. coli b, similar to a piece of rac prophage, and two fragments from shigella flexneri were cloned and sequenced. dicf-like elements similar to transcriptional terminators were found ...	1994	7508908
bacteriophage p2: genes involved in baseplate assembly.	the sequences of two previously defined tail genes, v and j, of the temperate bacteriophage p2, and those of two new essential tail genes, w and i, were determined. their order is the late gene promoter, vwji, followed by the tail fiber genes h and g, and a transcription terminator. the v gene product is the small spike at the tip of the tail, and the j gene product lies at the edge of the baseplate. the w gene product may be homologous to the product of gene 25 of t4 phage, which is part of the ...	1995	7483254
capsid structure of satellite phage p4 and its p2 helper.		1982	7077742
propagation of satellite phage p4 as a plasmid.	satellite phage p4 has two known options for propagation. in its lytic cycle, its regulatory functions can act in trans to alter the actions of a helper virus (p2), which then provides necessary gene products, including capsid proteins. p4 also can be propagated in the absence of a helper as a prophage, with distinct sites for integration within the escherichia coli chromosome. we determined that a single spontaneous mutation (vir1) of phage p4 allows a third mode of propagation: as a plasmid (a ...	1982	7043461
lysogenization by satellite phage p4.		1981	7023020
mutants of satellite bacteriophage p4 that are defective in the suppression of transcriptional polarity.		1981	7021852
genetic analysis of bacteriophage p4 using p4-plasmid cole1 hybrids.	a set of plasmids that contain fragments of the bacteriophage p4 genome has been constructed by deleting portions of a p4-cole1 hybrid. a p4 genetic map has been established and related to the physical map by examining the ability of these plasmids to rescue various p4 mutations. the p4 virl mutation and p4 genes involved in dna replication (alpha), activation of p2 helper genes (delta and epsilon), polarity suppression (psu) and head size determination (sid) have been mapped, as has the region ...	1980	6929401
the bacteriophage p4 alpha gene is the structural gene for bacteriophage p4-induced rna polymerase.	two temperature-sensitive mutants of satellite phage p4 which do not synthesize p4 dna at the nonpermissive temperature have been isolated. one of these phage is mutated in the p4 alpha gene. it complements a p4 delta mutant, but not a p4 alpha amber mutant; both mutants are phenotypically identical to alpha amber mutants in all properties studied. they synthesize p4 early proteins 1 and 2 as well as two additional p4-induced early proteins, 5 and 6, which are described here. p4 late proteins ar ...	1983	6887349
in vitro activation of bacteriophage p2 late gene expression by extracts from phage p4-infected cells.	we have used a cell-free, dna-dependent protein-synthesizing system to study the stimulation of phage p2 late gene expression by satellite phage p4. an activity is present in extracts prepared from p4-infected cells, which, when added to the in vitro system with p2 dna template, stimulates the synthesis of a number of p2 proteins. these stimulated proteins include the major p2 capsid protein (n gene product) and a major component of the p2 phage tail (fii gene product). extracts prepared from p4 ...	1983	6620459
circular genetic map of satellite bacteriophage p4.	a genetic map of satellite bacteriophage p4 has been constructed by means of standard multifactor crosses. the genetic map appears to be a circular permutation of the mature dna physical map. in addition, a set of markers appear to be linked both to the left and to the right of the same gene alpha. these facts suggest that the p4 genetic map is circular. since terminal redundancy and/or cyclic permutation are not known to be present in p4 mature dna, the circularity of p4 genetic map may reflect ...	1983	6573817
plasmid mode of propagation of the genetic element p4.	the satellite bacteriophage p4, in the presence of a helper phage, can enter either the lytic or the lysogenic cycle. in the absence of the helper, p4 can integrate in the bacterial chromosome. in addition, the partially immunity-insensitive mutant p4 vir1 can be maintained as a plasmid. we have found that in the absence of the helper, p4 wt also can be maintained as a plasmid, and that both p4 wt and p4 vir1 have two options for their intracellular propagation: a repressed-integrated or a derep ...	1984	6492154
an escherichia coli gene required for bacteriophage p2-lambda interference.	the gene old of bacteriophage p2 is known to (i) cause interference with phage lambda growth; (ii) kill recb- mutants of escherichia coli after p2 infection; and (iii) determine increased sensitivity of p2 lysogenic cells to x-ray irradiation. in all of these phenomena, inhibition of protein synthesis occurs. we have isolated bacterial mutants, named pin (p2 interference), able to suppress all of the above-mentioned phenomena caused by the old+ gene product and the concurrent protein synthesis i ...	1983	6355505
bacteriophage p2 late promoters. transcription initiation sites for two late mrnas.	divergent transcription of two of the bacteriophage p2 late mrnas, encoding genes qp and onmlkrs, is initiated from opposite strands of the dna in a region near the left end of the p2 genome. the first gene in each of these transcription units (p and o) has been located in the nucleotide sequence by amino-terminal sequence analysis of the p gene product and by dna sequence determination of the single nucleotide changes in two o amber mutants. the 5' ends of the p and o gene mrnas are separated b ...	1983	6308267
conditionally replicating plasmid vectors that can integrate into the klebsiella pneumoniae chromosome via bacteriophage p4 site-specific recombination.	p4 is a satellite phage of p2 and is dependent on phage p2 gene products for virion assembly and cell lysis. previously, we showed that a virulent mutant of phage p4 (p4 vir1) could be used as a multicopy, autonomously replicating plasmid vector in escherichia coli and klebsiella pneumoniae in the absence of the p2 helper. in addition to establishing lysogeny as a self-replicating plasmid, it has been shown that p4 can also lysogenize e. coli via site-specific integration into the host chromosom ...	1983	6307977