Publications

characterization of eastern oyster (crassostrea virginica gmelin) chromosomes by fluorescence in situ hybridization with bacteriophage p1 clones.	chromosome identification is an essential step in genomic research, which so far has not been possible in oysters. we tested bacteriophage p1 clones for chromosomal identification in the eastern oyster crassostrea virginica, using fluorescence in situ hybridization (fish). p1 clones were labeled with digoxigenin-11-dutp using nick translation. hybridization was detected with fluorescein-isothiocyanate-labeled anti-digoxigenin antibodies and amplified with 2 layers of antibodies. nine of the 21 p ...	2005	15933900
comparative analysis of sequence-specific dna recombination systems in human embryonic stem cells.	the great potential of human embryonic stem cells (hescs) in basic research, regenerative medicine, and gene therapy is widely recognized. controlled manipulation of hesc genomes through sequence-specific dna recombination (ssr) may play a significant role in future hesc applications. however, very little is known about the functionality of ssr systems in hescs. we demonstrate here that mutant phage lambda integrase, phage p1 cre recombinase, and mutant gammadelta resolvase displayed distinct ac ...	2005	15955832
minimal cross-recombination between wild-type and loxp511 sites in vivo facilitates truncating both ends of large dna inserts in pbace3.6 and related vectors.	contrary to several earlier reports, we find that cross-recombination between wild-type and the mutant loxp511 sites is <0.5% of that between two wild-type sites if cre protein is expressed by phage p1 during an infection. the finding enabled us to develop a procedure to truncate dna progressively from both ends of large genomic inserts flanked by these two loxp sites in pbace3.6 and related vectors with transposons carrying either a wild-type or a loxp511 sequence. newly constructed loxp511 tra ...	2005	16061933
the bacteriophage p1 hot gene product can substitute for the escherichia coli dna polymerase iii {theta} subunit.	the theta subunit (hole gene product) of escherichia coli dna polymerase (pol) iii holoenzyme is a tightly bound component of the polymerase core. within the core (alpha-epsilon-theta), the alpha and epsilon subunits carry the dna polymerase and 3' proofreading functions, respectively, while the precise function of theta is unclear. hole homologs are present in genomes of other enterobacteriae, suggestive of a conserved function. putative homologs have also been found in the genomes of bacteriop ...	2005	16077097
high-resolution mapping of the barley leaf rust resistance gene rph5 using barley expressed sequence tags (ests) and synteny with rice.	the rapidly growing expressed sequence tag (est) resources of species representing the poacea family and availability of comprehensive sequence information for the rice (oryza sativa) genome create an excellent opportunity for comparative genome analysis. extensive synteny between rice chromosome 1 and barley (hordeum vulgare l.) chromosome 3 has proven extremely useful for saturation mapping of chromosomal regions containing target genes of large-genome barley with conserved orthologous genes f ...	2005	16195886
nuclear magnetic resonance solution structure of the escherichia coli dna polymerase iii theta subunit.	the catalytic core of escherichia coli dna polymerase iii holoenzyme contains three subunits: alpha, epsilon, and theta. the alpha subunit contains the polymerase, and the epsilon subunit contains the exonucleolytic proofreading function. the small (8-kda) theta subunit binds only to epsilon. its function is not well understood, although it was shown to exert a small stabilizing effect on the epsilon proofreading function. in order to help elucidate its function, we undertook a determination of ...	2005	16199579
agroinfiltration as a tool for transient expression of cre recombinase in vivo.	agroinfiltration was used to express transiently cre recombinase from bacteriophage p1 in planta. activation of gfp expression after cre-mediated excision of a bar intervening sequence served as a marker to monitor site-specific recombination events in lox-target n. benthamiana plants. gfp expressing regenerants from a. tumefaciens infiltrated leaves were obtained with an efficiency of about 34%. in 20% of the regenerants bar gene excision was due to the expression of stably integrated cre gene, ...	2005	16245170
genome engineering in bacillus anthracis using cre recombinase.	genome engineering is a powerful method for the study of bacterial virulence. with the availability of the complete genomic sequence of bacillus anthracis, it is now possible to inactivate or delete selected genes of interest. however, many current methods for disrupting or deleting more than one gene require use of multiple antibiotic resistance determinants. in this report we used an approach that temporarily inserts an antibiotic resistance marker into a selected region of the genome and subs ...	2006	16369025
preferential synapsis of loxp sites drives ordered strand exchange in cre-loxp site-specific recombination.	the bacteriophage p1 cre recombinase catalyzes site-specific recombination between 34-base-pair loxp sequences in a variety of topological contexts. this reaction is widely used to manipulate dna molecules in applications ranging from benchtop cloning to genome modifications in transgenic animals. despite the simple, highly symmetric nature of the cre-loxp system, there is strong evidence that the reaction is asymmetric; the 'bottom' strands in the recombining loxp sites are preferentially excha ...	2005	16408057
cre reporter system to monitor the translocation of type iii secreted proteins into host cells.	central to the study of type iii secretion systems is the availability of reporter systems to monitor bacterial protein translocation into host cells. we report here the development of a bacteriophage p1 cre recombinase-based system to monitor the translocation of bacterial proteins into mammalian cells. bacteriophage p1 cre recombinase fused to the secretion and translocation signals of salmonella enterica serovar typhimurium of the type iii secreted protein sope was secreted in a type iii secr ...	2006	16428755
dna topology and geometry in flp and cre recombination.	the flp recombinase of yeast and the cre recombinase of bacteriophage p1 both belong to the lambda-integrase (int) family of site-specific recombinases. these recombination systems recognize recombination-target sequences that consist of two 13bp inverted repeats flanking a 6 or 8bp spacer sequence. recombination reactions involve particular geometric and topological relationships between dna target sites at synapsis, which we investigate using nicked-circular dna molecules. examination of the t ...	2006	16483600
a chromosomal locus which controls the ability of shigella flexneri to evoke keratoconjunctivitis.	the primary step in the pathogenesis of bacillary dysentery is the penetration of intestinal epithelial cells by shigellae. lacking this capacity, shigella flexneri becomes avirulent. by means of intergeneric conjugation between various escherichia coli k-12 hfr strains and s. flexneri 2a virulent recipients and by reciprocal transduction analysis with phage p1 vir, we established a locus on the genome of s. flexneri 2a which is necessary for the ability of this strain to penetrate epithelial ce ...	1971	16557949
transduction by bacteriophage p1: abnormal phage function of the transducing particles.		1958	16590247
introduction of transposon tn5 into myxococcus for analysis of developmental and other nonselectable mutants.	the transposon tn5, which carries a gene for kanamycin resistance, can be introduced into myxococcus xanthus, an organism that undergoes a primitive cycle of development, from escherichia coli by the specialized transducing phage p1::tn5. tn5 dna sequences, but no p1 sequences, are found in the stable kanamycin-resistant transductants. tn5 transposes from p1 to many different chromosomal sites in myxococcus. in each independent transductant of myxococcus examined, the tn5 element is found in a d ...	1981	16592958
site-specific dna inversion is enhanced by a dna sequence element in cis.	a segment of the bacteriophage p1 genome, called the c segment, can be inverted by site-specific recombination; the two different orientations of the invertible segment confer different host ranges to the phage. inversion is catalyzed by the product of the cin gene which is adjacent to one of the crossover sites flanking the c segment. the cin-catalyzed recombination can be measured in trans by using tester plasmids in which inversion switches on antibiotic-resistance genes. we show here that an ...	1985	16593573
high efficiency site-specific genetic engineering of the mosquito genome.	current techniques for the genetic engineering of insect genomes utilize transposable genetic elements, which are inefficient, have limited carrying capacity and give rise to position effects and insertional mutagenesis. as an alternative, we investigated two site-specific integration mechanisms in the yellow fever mosquito, aedes aegypti. one was a modified cre/lox system from phage p1 and the other a viral integrase system from streptomyces phage phi c31. the modified cre/lox system consistent ...	2006	16640723
structure of the theta subunit of escherichia coli dna polymerase iii in complex with the epsilon subunit.	the catalytic core of escherichia coli dna polymerase iii contains three tightly associated subunits, the alpha, epsilon, and theta subunits. the theta subunit is the smallest and least understood subunit. the three-dimensional structure of theta in a complex with the unlabeled n-terminal domain of the epsilon subunit, epsilon186, was determined by multidimensional nuclear magnetic resonance spectroscopy. the structure was refined using pseudocontact shifts that resulted from inserting a lanthan ...	2006	16740953
dilated cardiomyopathy resulting from high-level myocardial expression of cre-recombinase.	conditional gene inactivation in mice using the bacteriophage p1 cre-loxp recombination system requires transgenic expression of cre-recombinase driven by a tissue-specific or inducible promoter.	2006	16762803
consecutive gene deletions in aspergillus nidulans: application of the cre/loxp system.	the ability to perform multiple gene deletions is an important tool for conducting functional genomics. we report the development of a sequential gene deletion protocol for the filamentous fungus aspergillus nidulans using the cre/loxp recombinase system of bacteriophage p1. a recyclable genetic marker has been constructed by incorporating loxp direct repeats either side of the neurospora crassa pyr-4 gene (encodes orotidine 5'-monophosphate decarboxylase) which is able to complement the a. nidu ...	2006	16783565
[expression of genes of prophage p1 escherichia coli in cells of phytopathogenic erwinia].	it is shown that the temperate coliphage p1cmcts100 can transduce resistance to chloramphenicol in the cells of phytopathogenic bacteria erwinia horticola and e. carotovora subsp. atroseptica. in the latter case the extrachromosomal dna is inherited by recipient cells as the authentic prophage p1. the prophage p1 expresses rectification-modification ecop1, as well as the genes of lysogenic conversion in phytopathogenic erwinia. here the character of superinfection of transductants of e. atrosept ...	2006	16786627
mutator and antimutator effects of the bacteriophage p1 hot gene product.	the hot (homolog of theta) protein of bacteriophage p1 can substitute for the escherichia coli dna polymerase iii theta subunit, as evidenced by its stabilizing effect on certain dnaq mutants that carry an unstable polymerase iii epsilon proofreading subunit (antimutator effect). here, we show that hot can also cause an increase in the mutability of various e. coli strains (mutator effect). the hot mutator effect differs from the one caused by the lack of theta. experiments using chimeric theta/ ...	2006	16885451
comparative polytene chromosome maps of d. montana and d. virilis.	chromosomal inversion polymorphism was characterized in finnish drosophila montana populations. a total of 14 polymorphic inversions were observed in finnish d. montana of which nine had not been described before. the number of polymorphic inversions in each chromosome was not significantly different from that expected, assuming equal chance of occurrence in the euchromatic genome. there was, however, no correlation between the number of polymorphic inversions and that of fixed inversions in eac ...	2007	16906413
structure of the escherichia coli dna polymerase iii epsilon-hot proofreading complex.	the epsilon subunit of escherichia coli dna polymerase iii possesses 3'-exonucleolytic proofreading activity. within the pol iii core, epsilon is tightly bound between the alpha subunit (dna polymerase) and subunit. here, we present the crystal structure of epsilon in complex with hot, the bacteriophage p1-encoded homolog of , at 2.1 a resolution. the epsilon-hot interface is defined by two areas of contact: an interaction of the previously unstructured n terminus of hot with an edge of the epsi ...	2006	16973612
safety assessment of cre recombinase.	cre recombinase, when used as a tool in agricultural biotechnology, can precisely excise dna sequences that may be useful in the introduction of a new trait but are not needed in the commercial product. although the cre genetic material would not be present in the final product, the present studies were performed to assess the safety of cre recombinase to provide confirmatory evidence of the safe use of cre-lox technology in agricultural biotechnology. cre recombinase shares no relevant sequence ...	2006	17061845
[introduction of transpozon tn9 to endogenic plasmids of erwinia carotovora during lysogenization of cells by coliphage p1].	it has been shown that phage p1 of escherichia coli is able not only to lysogenize the cells of erwinia carotovora but also to be a source of transpozon tn9 for mutagenesis of cryptic plasmids of this important phytopathogen. since the amount of the introduction in one of plasmids pca25::tn9 is 3.8 kb, at an average, it is supposed that tn9 is inherited as a double tandem structure. a convenient method is offered for selecting bacterial clones carrying the plasmid pca25::tn9 which is based on co ...	2006	17100326
enterohemorrhagic escherichia coli o157:h7 gal mutants are sensitive to bacteriophage p1 and defective in intestinal colonization.	enterohemorrhagic escherichia coli (ehec), especially e. coli o157:h7, is an emerging cause of food-borne illness. unfortunately, e. coli o157 cannot be genetically manipulated using the generalized transducing phage p1, presumably because its extensive o antigen obscures the p1 receptor, the lipopolysaccharide (lps) core subunit. the gale, galt, galk, and galu proteins are necessary for modifying galactose before it can be assembled into the repeating subunit of the o antigen. here, we construc ...	2007	17158899
conditional mutagenesis reveals immunological functions of widely expressed genes: activation thresholds, homeostatic mechanisms and disease models.	evolutionarily conserved, widely expressed genes provide the functional backbone of most, if not all, cell types. although mouse mutants created by germ line gene inactivation are instrumental in establishing the importance of such genes in vivo, distortion of embryonic development or multiple body systems often preclude detailed functional studies. to overcome this limitation, dna recombination systems such as cre/loxp of bacteriophage p1, have been adapted for use in mammalian cells. the mutag ...	2007	17203660
inorganic polyphosphate essential for lytic growth of phages p1 and fd.	transduction frequency with phage p1 had been observed to be very low in escherichia coli k-12 mutants lacking the operon (ppk1-ppx) responsible for the synthesis of inorganic polyphosphate (poly p). we now find that these mutants, for lack of poly p, are lysogenic for p1 and when infected with phage p1 produce only approximately 1% the number of infective centers compared with the wt host. both phage adsorption and release were unaffected. the host-encoded p1 late-gene transcriptional activator ...	2007	17261797
the bacteriophage p1 hot gene, encoding a homolog of the e. coli dna polymerase iii theta subunit, is expressed during both lysogenic and lytic growth stages.	the bacteriophage p1 hot gene product is a homolog of the theta subunit of e. coli dna polymerase iii. previous studies with hot cloned on a plasmid have shown that hot protein can substitute for theta, as evidenced by its stabilizing effect on certain dnaq mutator mutants carrying an unstable pol iii proofreading subunit (epsilon subunit). these results are consistent with hot, like theta, being a replication protein involved in stabilizing the intrinsically unstable epsilon proofreading functi ...	2007	17482649
[stringent rna polymerase of e. coli and its in vivo transcriptional activity].	several spontaneous e. coli mutants with the similar phenotype as that in the condition of amino acid deficiency were obtained on the selective media. one of the mutants (lch001) showing slow growth phenotype on lb agar plate and pink or white colonies on macconkey agar plate was mapped at rpoc gene encoding the beta' subunit of rna polymerase by phage p1 transduction and transformation assays and found to be a new site mutation from g to t at 3406bp in the rpoc gene, which resulted in the amino ...	2007	17552233
a randomized library approach to identifying functional lox site domains for the cre recombinase.	the bacteriophage p1 cre/loxp site-specific recombination system is a useful tool in a number of genetic engineering processes. the cre recombinase has been shown to act on dna sequences that vary considerably from that of its bacteriophage recognition sequence, loxp. however, little is known about the sequence requirements for functional lox-like sequences. in this study, we have implemented a randomized library approach to identify the sequence characteristics of functional lox site domains. w ...	2007	17702764
auxotrophic complementation as a selectable marker for stable expression of foreign antigens in mycobacterium bovis bcg.	mycobacterium bovis bcg has the potential to be an effective live vector for multivalent vaccines. however, most mycobacterial cloning vectors rely on antibiotic resistance genes as selectable markers, which would be undesirable in any practical vaccine. here we report the use of auxotrophic complementation as a selectable marker that would be suitable for use in a recombinant vaccine. a bcg auxotrophic for the amino acid leucine was constructed by knocking out the leud gene by unmarked homologo ...	2007	17888740
unexpected functional consequences of xenogeneic transgene expression in beta-cells of nod mice.	we describe unexpected alterations in the non-obese diabetic (nod/lt) mouse model of type 1 diabetes (t1d) following forced beta-cell expression of non-mammalian genes ligated to an insulin promoter sequence. these include the jellyfish green fluorescent protein (gfp), useful for beta-cell identification, and the bacteriophage p1 cre recombinase, necessary for beta cell-specific ablation of a gene using a cre-loxp system. homozygous expression of gfp, driven by the mouse insulin 1 gene promoter ...	2007	17919174
sequence characterization and comparative analysis of three plasmids isolated from environmental vibrio spp.	the horizontal transfer of genes by mobile genetic elements such as plasmids and phages can accelerate genome diversification of vibrio spp., affecting their physiology, pathogenicity, and ecological character. in this study, sequence analysis of three plasmids from vibrio spp. previously isolated from salt marsh sediment revealed the remarkable diversity of these elements. plasmids p0908 (81.4 kb), p23023 (52.5 kb), and p09022 (31.0 kb) had a predicted 99, 64, and 32 protein-coding sequences an ...	2007	17921277
s phase-preferential cre-recombination in mammalian cells revealed by hiv-tat-ptd-mediated protein transduction.	the cre recombinase of bacteriophage p1 is a powerful tool for artificial modification of genomic function in mammalian cells. to date, many researchers have studied the enzymatic biochemistry of cre recombinase in loxp site-specific cleavage and rearrangement, as well as its use in gene technology. however, the intricate mechanisms of cre-mediated recombination are still poorly understood. for example, more knowledge is needed in order to understand cre recombinase's dependency on cell cycle, t ...	2008	17965427
pepa and argr do not regulate cre recombination at the bacteriophage p1 loxp site.	in the lysogenic state, bacteriophage p1 is maintained as a low copy-number circular plasmid. site-specific recombination at loxp by the phage-encoded cre protein keeps p1 monomeric, thus helping to ensure stable plasmid inheritance. two escherichia coli dna-binding proteins, pepa and argr, were recently reported to be necessary for maintenance or establishment of p1 lysogeny. pepa and argr bind to regulatory dna sequences upstream of the cole1 cer recombination site to regulate site-specific re ...	2008	18226834
escherichia coli transcription factor yncc (mcbr) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein ybim (mcba).	quorum-sensing signal autoinducer 2 (ai-2) stimulates escherichia coli biofilm formation through the motility regulator mqsr that induces expression of the putative transcription factor encoded by yncc. here, we show that yncc increases biofilm formation by repressing overproduction of the exopolysaccharide identified as colanic acid (corroborated by decreasing mucoidy and increased sensitivity to bacteriophage p1 infection). differential gene expression and gel shift assays demonstrated that yn ...	2008	18309357
minimization of the escherichia coli genome using the tn5-targeted cre/loxp excision system.	efficient genome-engineering tools have been developed for use in whole-genome essentiality studies. in this chapter, we describe a powerful genomic deletion tool, the tn5-targeted cre/loxp excision system, for determining genetic essentiality and minimizing bacterial genomes on a genome-wide scale. this tool is based on the tn5 transposition system, phage p1 transduction, and the cre/loxp excision system. we have generated two large pools of independent transposon insertion mutants in escherich ...	2008	18392973
construction of bacteriophage p1 libraries with large inserts.	the bacteriophage p1 cloning system was originally developed as an alternative to yac and cosmid systems for cloning high-molecular-weight genomic dna. this unit details the preparation of the bacteriophage p1 library. three support protocols provide the raw materials for the basic procedure, including the vector (pad10sacbii), the mammalian dna inserts, and the two packaging extracts that contain the viral proteins necessary to construct a p1 bacteriophage incorporating the vector and insert. a ...	2001	18428291
identification of a peptide sequence that improves transport of macromolecules across the intestinal mucosal barrier targeting goblet cells.	in this study, we demonstrated that the cskssdyqc-peptide ligand which was identified from a random phage-peptide library through an in vivo phage display technique with rats could prominently improve the transport efficiency of macromolecules, such as large filamentous phage particles (m13 bacteriophage), across the intestinal mucosal barrier. synthetic cskssdyqc-peptide ligands significantly inhibited the binding of phage p1 encoding cskssdyqc-peptide ligands to the intestinal mucosal tissue a ...	2008	18440083
a cre::flp fusion protein recombines frt or loxp sites in transgenic maize plants.	summary: the coding sequences of cre (site-specific recombinase from bacteriophage p1) and flp (yeast 2-microm plasmid site-specific recombinase) were fused in frame to produce a novel, dual-function, site-specific recombinase gene. transgenic maize plants containing the cre::flp fusion expression vector were crossed to transgenic plants containing either the loxp or frt excision substrate. complete and precise excisions of chromosomal fragments flanked by the respective target sites were observ ...	2008	18627532
doc of prophage p1 is inhibited by its antitoxin partner phd through fold complementation.	prokaryotic toxin-antitoxin modules are involved in major physiological events set in motion under stress conditions. the toxin doc (death on curing) from the phd/doc module on phage p1 hosts the c-terminal domain of its antitoxin partner phd (prevents host death) through fold complementation. this phd domain is intrinsically disordered in solution and folds into an alpha-helix upon binding to doc. the details of the interactions reveal the molecular basis for the inhibitory action of the antito ...	2008	18757857
crystal structure of mycobacterium tuberculosis yefm antitoxin reveals that it is not an intrinsically unstructured protein.	toxin-antitoxin modules are present on chromosomes of almost all free-living prokaryotes. some are implicated to act as stress-responsive elements, among their many functional roles. the yefm-yoeb toxin-antitoxin system is present in many bacterial species, where yefm belongs to the phd family antidote of phage p1, whereas yoeb is a homolog of the rele toxin of the relbe system, rather than the doc system of phage p1. yoeb, a ribonuclease, is believed to be conformationally stable, whereas yefm ...	2008	18793646
crystallization of doc and the phd-doc toxin-antitoxin complex.	the phd/doc addiction system is responsible for the stable inheritance of lysogenic bacteriophage p1 in its plasmidic form in escherichia coli and is the archetype of a family of bacterial toxin-antitoxin modules. the his66tyr mutant of doc (doc(h66y)) was crystallized in space group p2(1), with unit-cell parameters a = 53.1, b = 198.0, c = 54.1 a, beta = 93.0 degrees . these crystals diffracted to 2.5 a resolution and probably contained four dimers of doc in the asymmetric unit. doc(h66y) in co ...	2008	18997335
generalized transduction.	transduction is the process in which bacterial dna is transferred from one bacterial cell to another by means of a phage particle. there are two types of transduction, generalized transduction and specialized transduction. in this chapter two of the best-studied systems - escherichia coli-phage p1, and salmonella enterica-phage p22 - are discussed from theoretical and practical perspectives.	2009	19066827
recombineering reveals a diverse collection of ribosomal proteins l4 and l22 that confer resistance to macrolide antibiotics.	mutations in ribosomal proteins l4 and l22 confer resistance to erythromycin and other macrolide antibiotics in a variety of bacteria. l4 and l22 have elongated loops whose tips converge in the peptide exit tunnel near the macrolide-binding site, and resistance mutations typically affect residues within these loops. here, we used bacteriophage lambda red-mediated recombination, or "recombineering," to uncover new l4 and l22 alleles that confer macrolide resistance in escherichia coli. we randomi ...	2009	19150357
a simple tae-based method to generate large insert bac libraries from plant species.	large insert libraries are valuable tools for the positional cloning of genes of interest, physical mapping of chromosomes, comparative genomics, and molecular breeding. there are five types of large dna insert libraries: cosmid, yeast artificial chromosomes (yacs), bacteriophage p1, bacterial artificial chromosomes (bacs) and p1-derived artificial chromosomes (pacs) libraries. of these libraries, bac libraries are the most widely used due to their ease of manipulation, large insert size, and st ...	2009	19347648
evaluation of seven promoters to achieve germline directed cre-lox recombination in arabidopsis thaliana.	site-specific recombination systems, such as cre-lox from bacteriophage p1, have become very important tools for plant genome engineering. in many cases a constitutive promoter is used to express the recombinase gene. however, for certain research and commercial applications constitutive cre-mediated recombination may not be desirable. we have evaluated the potential of seven different germline promoter:cre fusions to remove a stably integrated lox cassette through cre-mediated recombination in ...	2009	19652974
multigene expression of protein complexes by iterative modification of genomic bacmid dna.	many cellular multi-protein complexes are naturally present in cells at low abundance. baculovirus expression offers one approach to produce milligram quantities of correctly folded and processed eukaryotic protein complexes. however, current strategies suffer from the need to produce large transfer vectors, and the use of repeated promoter sequences in baculovirus, which itself produces proteins that promote homologous recombination. one possible solution to these problems is to construct bacul ...	2009	19725957
phisite: database of gene regulation in bacteriophages.	we have developed phisite, database of gene regulation in bacteriophages. to date it contains detailed information about more than 700 experimentally confirmed or predicted regulatory elements (promoters, operators, terminators and attachment sites) from 32 bacteriophages belonging to siphoviridae, myoviridae and podoviridae families. the database is manually curated, the data are collected mainly form scientific papers, cross-referenced with other database resources (embl, uniprot, ncbi taxonom ...	2010	19900969
going green in cryptococcus neoformans: the recycling of a selectable drug marker.	cryptococcus neoformans is an opportunistic fungal pathogen that primarily affects immunocompromised individuals. reverse genetics is commonly used to identify and characterize genes involved in a variety of cellular processes. in c. neoformans there is a limited set of positive selectable markers available to make gene deletions or other genetic manipulations. this has hampered the application of reverse genetics in this organism. we have adapted the bacteriophage p1 cre-loxp system for use in ...	2010	19944774
high-frequency phage-mediated gene transfer in freshwater environments determined at single-cell level.	lateral gene transfer by phages has contributed significantly to the genetic diversity of bacteria. to accurately determine the frequency and range of phage-mediated gene transfer, it is important to understand the movement of dna among microbes. using an in situ dna amplification technique (cycling primed in situ amplification-fluorescent in situ hybridization; cprins-fish), we examined the propensity for phage-mediated gene transfer in freshwater environments at the single-cell level. phage p1 ...	2010	20090786
purification and crystallization of phd, the antitoxin of the phd/doc operon.	the antitoxin phd from the phd/doc module of bacteriophage p1 was crystallized in two distinct crystal forms. crystals of his-tagged phd contain a c-terminally truncated version of the protein and diffract to 2.20 a resolution. crystals of untagged phd purified from the phd-doc complex diffract to 2.25 a resolution. these crystals are partially merohedrally twinned and contain the full-length version of the protein.	2010	20124714
replacing the wild type loxp site in bacs from the public domain with lox66 using a lox66 transposon.	abstract:	2010	20170521
[construction of the new escherichia coli k-12 wild-type strain with improved growth characteristics for application in metabolic engineering].	mg1655 of escherichia coli k-12 is frequently used in metabolic engineering as the wild-type strain. however, its two mutations, ilvg and rph-1 provide a negative effect on culture growth. the "polar effect" of rph-1 decreases the level of pyre expression, causing partial auxotrophy for pyrimidines. mutation ilvg leading to the appearance of val(s) phenotype causes retardation of cell growth rate on media containing amino acids. in this work, the substitution of two loci in the genome of mg1655 ...	2010	20391779
characterization of the replication, transfer, and plasmid/lytic phage cycle of the streptomyces plasmid-phage pzl12.	we report here the isolation and recombinational cloning of a large plasmid, pzl12, from endophytic streptomyces sp. 9r-2. pzl12 comprises 90,435 bp, encoding 112 genes, 30 of which are organized in a large operon resembling bacteriophage genes. a replication locus (repa) and a conjugal transfer locus (traa-trac) were identified in pzl12. surprisingly, the supernatant of a 9r-2 liquid culture containing partially purified phage particles infected 9r-2 cured of pzl12 (9r-2x) to form plaques, and ...	2010	20472796
applications of the site-specific recombinase cre to the study of genomic imprinting.	the development of gene targeting approaches has had a tremendous impact on the functional analysis of the mouse genome. a specific application of this technique has been the adaptation of the bacteriophage p1 cre/loxp site-specific recombinase system which allows for the precise recombination between two loxp sites, resulting in deletion or inversion of the intervening sequences. because of the efficiency of this system, it can be applied to conditional deletions of relatively short coding sequ ...	2010	20601421
crystal structures of phd-doc, higa, and yeeu establish multiple evolutionary links between microbial growth-regulating toxin-antitoxin systems.	bacterial toxin-antitoxin (ta) systems serve a variety of physiological functions including regulation of cell growth and maintenance of foreign genetic elements. sequence analyses suggest that ta families are linked by complex evolutionary relationships reflecting likely swapping of functional domains between different ta families. our crystal structures of phd-doc from bacteriophage p1, the higa antitoxin from escherichia coli cft073, and yeeu of the yeeuwv systems from e. coli k12 and shigell ...	2010	20696400
kinetics of methylation by ecop1i dna methyltransferase.	ecop1i dna mtase (m.ecop1i), an n(6)-adenine mtase from bacteriophage p1, is a part of the ecop1i restriction-modification (r-m) system which belongs to the type iii r-m system. it recognizes the sequence 5'-agacc-3' and methylates the internal adenine. m.ecop1i requires mg(2+) for the transfer of methyl groups to dna. m.ecop1i is shown to exist as dimer in solution, and even at high salt concentrations (0.5 m) the dimeric m.ecop1i does not dissociate into monomers suggesting a strong interactio ...	2010	21048863
creating directed double-strand breaks with the ref protein: a novel reca-dependent nuclease from bacteriophage p1.	the bacteriophage p1-encoded ref protein enhances reca-dependent recombination in vivo by an unknown mechanism. we demonstrate that ref is a new type of enzyme; that is, a reca-dependent nuclease. ref binds to ss- and dsdna but does not cleave any dna substrate until reca protein and atp are added to form reca nucleoprotein filaments. ref cleaves only where reca protein is bound. reca functions as a co-nuclease in the ref/reca system. ref nuclease activity can be limited to the targeted strands ...	2010	21193392
conditional mutagenesis of the genome using site-specific dna recombination.	introductionaltering the genome of intact cells and organisms by site-specific dna recombination has become an important gene-transfer methodology. dna modifications produced by gene transfer and homologous recombination are typically static once integrated among target cell chromosomes. in contrast, the inclusion of exogenous recombinase target sequences within transferred dna segments allows subsequent modifications to previously altered genomic structure that increase the utility of gene tran ...	2007	21357131
enhanced error-prone rca mutagenesis by concatemer resolution.	error-prone rolling circle amplification (rca) is a promising alternative to error-prone pcr for random mutagenesis. the main disadvantage of error-prone rca is the low transformation efficiency of the dna concatemer produced in the amplification reaction. we improved the method by introducing loxp recombination site of bacteriophage p1 cre recombinase into the target plasmid and reducing the concatemer by cre recombinase to plasmid-sized units, increasing the number of transformants 50-fold in ...	2011	21453722
visualization of bacteriophage p1 infection by cryo-electron tomography of tiny escherichia coli.	bacteriophage p1 has a contractile tail that targets the conserved lipopolysaccharide on the outer membrane surface of the host for initial adsorption. the mechanism by which p1 dna enters the host cell is not well understood, mainly because the transient molecular interactions between bacteriophage and bacteria have been difficult to study by conventional approaches. here, we engineered tiny e. coli host cells so that the initial stages of p1-host interactions could be captured in unprecedented ...	2011	21745674
assembling new escherichia coli strains by transduction using phage p1.	a protocol is described that allows the transfer of genetic material from one escherichia coli strain to another using bacteriophage p1. p1 transduction can be used to construct new bacterial strains containing multiple alleles, to restore a locus to wild type, to move specific genetic markers from one strain to another, to relocate different mutant genes to a common genetic background, and to evaluate second-site suppression of a mutant allele. because of these abilities, p1 transduction remain ...	2011	21815092
(1)h, (13)c and (15)n nmr assignments of inactive form of p1 endolysin lyz.	lysozyme (lyz) encoded by phage p1 is required for host cell lysis upon infection. lyz has a n-terminal signal anchor release (sar) domain, responsible for its secretion into the periplasm and for its accumulation in a membrane tethered inactive form. here, we report sequence-specific (1)h, (13)c and (15)n resonance assignments for secreted inactive form of lyz at ph 4.5.	2011	21822941
scalable plasmid transfer using engineered p1-based phagemids.	dramatic improvements to computational, robotic, and biological tools have enabled genetic engineers to conduct increasingly sophisticated experiments. further development of biological tools offers a route to bypass complex or expensive mechanical operations, thereby reducing the time and cost of highly parallelized experiments. here, we engineer a system based on bacteriophage p1 to transfer dna from one e. coli cell to another, bypassing the need for intermediate dna isolation (e.g., miniprep ...	2012	23656280