| altered (copy-up) forms of initiator protein pi suppress the point mutations inactivating the gamma origin of plasmid r6k. | the r6k gamma origin core contains the p2 promoter, whose -10 and -35 hexamers overlap two of the seven binding sites for the r6k-encoded pi protein. two mutations, p2-201 and p2-203, which lie within the -35 region of p2, are shown to confer a promoter-down phenotype. we demonstrate here that these mutations prevent replication of a gamma origin core plasmid. to determine whether or not the reduced promoter activity caused by these mutations is responsible for their effect on replication, we ge ... | 1995 | 7592461 |
| identification of the central regulatory segment of plasmid r6k complexed with the membranes of escherichia coli. | understanding the mechanisms which control replication of chromosomes with multiple origins of replication have been the subject of many investigations. the plasmid, r6k, has three origins of replication, alpha, beta, and gamma. in vivo, alpha and beta are utilized with equal frequencies while the gamma origin is rarely used in the parental plasmid, or remains silent in several miniplasmids. hence, in the present study, the multiple origin plasmid, r6k, was utilized as a model system to investig ... | 1995 | 7731391 |
| cooperative binding of initiator protein to replication origin conferred by single amino acid substitution. | the replication initiator protein pi of plasmid r6k binds seven 22 bp direct repeats (dr) in the gamma origin. the pi protein also binds to an inverted repeat (ir) in the operator of its own gene, pir, which lies outside the gamma origin sequences. a genetic system was devised to select for pi protein mutants which discriminate between ir and dr (york et al., gene (amst.) 116, 7-12, 1992; york and filutowicz, j. biol. chem. 268, 21854-21861, 1993). from this selection the mutant pi s87n protein ... | 1994 | 7937147 |
| binding of dnaa protein to a replication enhancer counteracts the inhibition of plasmid r6k gamma origin replication mediated by elevated levels of r6k pi protein. | replication of the gamma origin of escherichia coli plasmid r6k requires pi protein, encoded by the r6k pir gene, and many host factors, including dnaa protein. pi has dual roles, activating replication at low levels and inhibiting replication at high levels. the inhibitory function of pi is counteracted by integration host factor and a specific sequence of the origin called the enhancer. this 106-bp dna segment contains a binding site for dnaa protein (dnaa box 1). in this study, we mutated thi ... | 1994 | 7961437 |
| in vivo excision and amplification of large segments of the escherichia coli genome. | in vivo excision and amplification of large segments of a genome offer an alternative to heterologous dna cloning. by obtaining predetermined fragments of the chromosome directly from the original organism, the problems of clone stability and clone identification are alleviated. this approach involves the insertion of two recognition sequences for a site-specific recombinase into the genome at predetermined sites, 50-100 kb apart. the integration of these sequences, together with a conditional r ... | 1994 | 8036169 |
| the dimerization domain of r6k plasmid replication initiator protein pi revealed by analysis of a truncated protein. | replication of plasmid r6k is controlled by the homodimeric initiator protein pi, which binds to seven 22-bp direct repeats (iterons) in the gamma-origin. one of the genetically engineered pi variants (delta c164 pi) contains only the 164 n-terminal amino acids (aa) of the 305-aa pi molecule. this truncated pi polypeptide retains the ability to function as a specific inhibitor of r6k replication in vivo, though it neither drives replication, nor binds to iterons [greener et al., mol. gen. genet. ... | 1994 | 8045425 |
| construction of conjugative shuttle and suicide vectors for pasteurella haemolytica and p. multocida. | a shuttle cloning vector, paka16, and suicide derivatives paka19 and paka22 have been developed for gene transfer to pasteurella haemolytica and p. multocida. paka16 was constructed by insertion of the lacz alpha-peptide-encoding region and a multiple cloning site into a plasmid which was originally isolated from p. haemolytica serotype a1. the vector encodes ampicillin resistance, and contains at least 14 unique restriction sites and the property of phenotypic identification of recombinant clon ... | 1994 | 8045428 |
| autoregulation-deficient mutant of the plasmid r6k-encoded pi protein distinguishes between palindromic and nonpalindromic binding sites. | the autogenously regulated gene pir of escherichia coli plasmid r6k encodes the replication protein pi. this protein binds to two sites in the operator region of the pir gene: a 22-base pair nonpalindromic sequence and a pair of palindromic 9-base pair sequences. these pi-binding sites are similar, suggesting that pi uses a single dna-binding domain in recognizing them. we devised a plasmid system permitting isolation of mutants of the pi protein which are altered in autoregulation. a ser87 to a ... | 1993 | 8408040 |
| new suicide vector for gene replacement in yersiniae and other gram-negative bacteria. | a suicide vector named puk4134 was constructed to enlarge the repertoire of vectors available for allelic exchange of mutated sequences in gram-negative bacteria. this plasmid combines the properties of two previously described plasmid vectors, pjm703.1 and prtp1. puk4134 is a suicide vector, carrying the origin of replication of the plasmid r6k and thus requiring the product of the pir gene for its stable maintenance. the rpsl gene encoding escherichia coli ribosomal protein s12 confers strepto ... | 1993 | 8469722 |
| the replication initiator protein pi of the plasmid r6k specifically interacts with the host-encoded helicase dnab. | the replication initiator protein pi of plasmid r6k is known to interact with the seven iterons of the gamma origin/enhancer and activate distant replication origins alpha and beta (ori alpha and ori beta) by pi-mediated dna looping. here we show that pi protein specifically interacts in vitro with the host-encoded helicase dnab. the site of interaction of pi on dnab has been localized to a 37-aa-long region located between amino acids 151 and 189 of dnab. the surface of pi that interacts with d ... | 1996 | 8643608 |
| replication of plasmid r6k gamma origin in vivo and in vitro: dependence on ihf binding to the ihf1 site. | the gamma origin of plasmid r6k requires the specific initiator protein pi for initiation of replication. however, increased pi concentrations inhibit replication. the host-encoded integration host factor (ihf) protein permits gamma origin replication at otherwise inhibitory pi levels. ihf is thought to mediate this positive effect by directly binding to the gamma origin. in this study we demonstrate that ihf binding to one ihf site in the gama origin, ihf1, but not to the other side, ihf2, is n ... | 1996 | 8648623 |
| initiator protein pi can bind independently to two domains of the gamma origin core of plasmid r6k: the direct repeats and the a+t-rich segment. | the pi protein of plasmid r6k functions in both replication and transcription. pi autoregulates its own synthesis and is required for replication of the risk gamma origin. pi performs these functions by binding to specific dna sites arranged as pairs of 6-10 bp inverted repeats (irs) or as a cluster of seven tandem 22 bp direct repeats (drs) which lack symmetry. the sites share the tgagrg nucleotide motif (where r is a or g). the drs and irs flank the central a+t-rich segment of the gamma origin ... | 1996 | 8657577 |
| characterization of bacterial cell membrane attachment sites of plasmid r6k. | in vitro binding studies revealed that plasmid r6k could attach to both inner and outer membrane fractions of its host cell, escherichia coli. derivatives of r6k carrying one or two of its three origins of replication could not bind stably to the same membrane fractions in the presence of salt. however, the derivative, prk35, carrying the intact three origins of replication could bind stably to membrane fractions from its host in the presence or absence of salt. these observations suggest that t ... | 1996 | 8660333 |
| plasmid r6k contains two functional orits which can assemble simultaneously in relaxosomes in vivo. | plasmid r6k contains two functional origins or transfer (orit), in contrast to previously characterized conjugative plasmids. the orits are formed by 98 bp palindromic sequences invertedly orientated with respect to each other and located in the immediate vicinity of the alpha and beta origins of replication. the gene for r6k orit-nickase, taxc, was identified by transposon mutagenesis and sequenced, revealing that taxc belongs to the vird2 nickase family. the protein was overproduced and purifi ... | 1996 | 8757282 |
| preponderance of fis-binding sites in the r6k gamma origin and the curious effect of the penicillin resistance marker on replication of this origin in the absence of fis. | fis protein is shown here to bind to 10 sites in the gamma origin of plasmid r6k. the fis-binding sites overlap all the previously identified binding sites in the gamma origin for the plasmid-encoded pi initiator protein and three host-encoded proteins, dnaa, integration host factor, and rna polymerase. however, the requirement of fis for r6k replication depends on the use of copy-up pi-protein variants and, oddly, the antibiotic resistance marker on the plasmid. in fis-deficient cells, copy-up ... | 1996 | 8759862 |
| three novel plasmid r6k proteins act in concert to distort dna within the alpha and beta origins of dna replication. | three novel r6k genes which are responsible for expression of dna distortion polypeptides (ddp) were identified. the ddps act in vivo in concert to induce similar stepwise dna helix distortions within two long inverted repeats (alpha lir and beta lir), which are essential elements for the two distally located r6k alpha and beta dna replication origins. ddp1 and ddp2 are encoded by two tandem genes located at the 5' end of alpha lir, whereas a gene coding for ddp3 is located at the 3' end of beta ... | 1996 | 8830279 |
| a broad-host-range in vivo pop-out and amplification system for generating large quantities of 50- to 100-kb genomic fragments for direct dna sequencing. | a prerequisite for sequencing large genomes is to obtain 30- to 150-kb genomic dna fragments in adequate quantity. previously, we developed a system which enables one to excise and amplify in vivo such segments directly from the escherichia coli genome. this system, which employed the yeast flp/frt elements for excision and the plasmid r6k-based replication machinery for dna amplification, permits one to bypass conventional cloning [pósfai et al. (1994) nucleic acids res. 22, 2392-2398]. to exte ... | 1996 | 8955645 |
| genes involved in conjugative dna processing of plasmid r6k. | the conjugative transfer region of the incx plasmid r6k (tra(x)) was analysed by transposon mutagenesis and dna sequencing. tn5tac1 insertional mutations localized tra(x) to a 14.8 kb segment containing the alpha origin of transfer (orit alpha), genes involved in conjugative dna-processing (dtr(x)) and genes involved in pilus synthesis and assembly (mpf(x)). a second functional orit, oritbeta, was located at a distance of 5.3 kb from orit alpha and was outside tra(x). mpf(x) occupied a segment o ... | 1997 | 9218765 |
| replication of the r6k gamma origin in vitro: dependence on wt pi and hyperactive pis87n protein variant. | the pi protein of plasmid r6k is involved in control of replication. the aim of this study was to use an in vitro replication system dependent on an r6k-derived gamma origin of replication (gamma ori) to compare replication characteristics of wt pi and a hyperactive variant of pi protein (pis87n; filutowicz et al., 1994b. cooperative binding of initiator protein to replication origin conferred by single amino acid substitution. nucleic acids res. 22, 4211-4215). the characteristics of in vitro r ... | 1997 | 9249072 |
| two forms of replication initiator protein: positive and negative controls. | the pir gene of plasmid r6k encodes the protein, pi, a replication and transcription factor. two translational options for the pir gene give rise to two forms of pi protein: a 35.0-kda form (pi35.0) and a shortened 30.5-kda form (pi30.5). although both proteins bind to a series of 22-bp direct repeats essential for plasmid r6k replication, only pi35.0 can bind to a site in the (a.t)-rich segment of its gamma ori and activate the gamma ori in vivo and in vitro. however, unlike pi35.0, pi30.5can i ... | 1997 | 9391136 |
| cre/loxp-mediated excision and amplification of large segments of the escherichia coli genome. | the isolation and amplification of large, predetermined segments of a genome from its host have been explored. the prototype of our approach was the excisional replication of some viruses such as the lambda-lysogen. similar machinery was used to excise and amplify large genomic segments of escherichia coli in its host. two loxp sequences for a site-specific recombinase cre, together with a conditional replication origin (pi-dependent gamma-ori), were inserted into the genome by homologous recomb ... | 1998 | 9526700 |
| replication of r6k gamma origin in vitro: discrete start sites for dna synthesis dependent on pi and its copy-up variants. | the regulation of the plasmid r6k gamma origin (gamma ori) is accomplished through the ability of the pi protein to act as an initiator and inhibitor of replication. hyperactive variants of this protein, called copy-up pi, allow four to tenfold increases of gamma ori plasmid dna in vivo. the higher activity of copy-up pi variants could be explained by an increase in the initiator function, a decrease in the inhibitor activity, or a derepression of a more efficient mechanism of replication that c ... | 1998 | 9743626 |
| assemblies of replication initiator protein on symmetric and asymmetric dna sequences depend on multiple protein oligomerization surfaces. | the pi35.0 protein of plasmid r6k regulates transcription and replication by binding a dna sequence motif (tgagr) arranged either asymmetrically into 22 bp direct repeats (drs) in the gamma origin, or symmetrically into inverted half-repeats (irs) in the operator of its own gene, pir. the binding patterns of the two natural forms of the pi protein and their heterodimers revealed that the predominant species, pi35.0 (35.0 kda), can bind to a single copy of the dr as either a monomer or a dimer wh ... | 1998 | 9784371 |
| regulatory implications of protein assemblies at the gamma origin of plasmid r6k - a review. | recognition of the replication origin (ori) by initiator protein is a recurring theme for the regulated initiation of dna replication in diverse biological systems. the objective of the work reviewed here is to understand the initiation process focusing specifically on the gamma-ori of the antibiotic-resistance plasmid r6k. the control of gamma-ori copy number is determined by both plasmid-encoded and host-encoded factors. the two central regulatory elements of the plasmid are a multifunctional ... | 1998 | 9858731 |
| hexahistidine (his6)-tag dependent protein dimerization: a cautionary tale. | nickel nitrilotriacetic acid (ni2+-nta) immobilization of hexahistidine (his6) tagged proteins has become one of the most commonly used methods of affinity chromatography. perhaps the greatest utility of this protein purification method stems from the general belief that his-tagged proteins (comprised of his6) are little affected in their activities or efficiencies, while alterations in specificity are unexpected. although this is certainly true in many instances, we present a case in which the ... | 1999 | 10698267 |
| dimers of pi protein bind the a+t-rich region of the r6k gamma origin near the leading-strand synthesis start sites: regulatory implications. | the replication of gamma origin, a minimal replicon derived from plasmid r6k, is controlled by the rep protein pi. at low intracellular concentrations, pi activates the gamma origin, while it inhibits replication at elevated concentrations. additionally, pi acts as a transcription factor (auto)repressing its own synthesis. these varied regulatory functions depend on pi binding to reiterated dna sequences bearing a tgagng motif. however, pi also binds to a "non-iteron" site (i.e., not tgagng) tha ... | 2000 | 10762246 |
| monomer/dimer ratios of replication protein modulate the dna strand-opening in a replication origin. | dna opening is an essential step in the initiation of replication via the cairns mode of replication. the opening reaction was investigated in a gamma ori system by using hyperactive variants of plasmid r6k-encoded initiator protein, pi. reactivity to kmno4 (indicative of opening) within gamma ori dna occurred in both strands of a superhelical template upon the combined addition of wt pi, dnaa and integration host factor (ihf), each protein known to specifically bind gamma ori. ihf, examined sin ... | 2001 | 11237610 |
| simple and efficient vectors for retrofitting bacs and pacs with mammalian neor and egfp marker genes. | bacterial artificial chromosomes (bacs) and p1 artificial chromosomes (pacs) are widely used to investigate the functions of genes and genomes in mammalian cells in vitro and in vivo. we have developed a series of vectors which can simply and efficiently be retrofitted onto bacs or pacs. these vectors carry a neor gene for selection in cells in tissue culture, including es cells, and also an egfp gene driven by the strong cag promoter for quick detection of the dna in cells. all the plasmids are ... | 2001 | 11290429 |
| genetic analysis of pigment biosynthesis in xanthobacter autotrophicus py2 using a new, highly efficient transposon mutagenesis system that is functional in a wide variety of bacteria. | a highly efficient method of transposon mutagenesis was developed for genetic analysis of xanthobacter autotrophicus py2. the method makes use of a transposon delivery vector that encodes a hyperactive tn 5 transposase that is 1,000-fold more active than the wild-type transposase. in this construct, the transposase is expressed from the promoter of the teta gene of plasmid rp4, which is functional in a wide variety of organisms. the transposon itself contains a kanamycin resistance gene as a sel ... | 2002 | 12189420 |
| characterization of his-tagged, r6k-encoded pi protein variants. | the pi protein of plasmid r6k is a multifunctional replication (rep) protein, its different activities attributable, in part, to different oligomeric states: monomers and dimers. we have previously shown that his-tagged variants of the protein can exhibit alterations in dimer stability. herein, we examined the functional properties of selected his-tagged derivatives of pi (his-pi x wt and three hyperactive replication variants) to determine if the functionality of these proteins in replication, ... | 2003 | 12826061 |
| a cryptic plasmid of yersinia enterocolitica encodes a conjugative transfer system related to the regions of clodf13 mob and incx pil. | yersinia enterocolitica 29930 (biotype 1a; o : 7,8), the producing strain of the phage-tail-like bacteriocin enterocoliticin, possesses a plasmid-encoded conjugative type iv transfer system. the genes of the conjugative system were found by screening of a cosmid library constructed from total dna of strain 29930. the cosmid cos100 consists of the vector supercos1 and an insert dna of 40 303 bp derived from a cryptic plasmid of strain 29930. the conjugative transfer system consists of genes encod ... | 2003 | 14523116 |
| pi protein- and atp-dependent transitions from 'closed' to 'open' complexes at the gamma ori of plasmid r6k. | r6k-encoded pi protein can bind to the seven, 22 bp tandem iterons of the gamma origin. in this work, we use a variant of pi, his-pi.f107s, that is hyperactive in replication. in vitro, his-pi.f107s-dependent local dna melting (open complex formation) occurs in the absence of host proteins (ihf/hu or dnaa) and it is positioned in the a + t-rich region adjacent to iterons. experiments described here examine the effects of atp, mg2+ and temperature on the opening reaction. we show that the opening ... | 2003 | 14530447 |
| biochemical investigations of control of replication initiation of plasmid r6k. | the mechanistic basis of control of replication initiation of plasmid r6k was investigated by addressing the following questions. what are the biochemical attributes of mutations in the pi initiator protein that caused loss of negative control of initiation? did the primary control involve only initiator protein-ori dna interaction or did it also involve protein-protein interactions between pi and several host-encoded proteins? mutations at two different regions of the pi-encoding sequence indiv ... | 2004 | 14665626 |
| isomerization and apparent dna bending by pi, the replication protein of plasmid r6k. | plasmid r6k-encoded pi protein has multiple regulatory functions in replication and transcription. these functions rely, in part, on a complex set of interactions between monomers and dimers of the protein and distinct dna targets, the direct and inverted repeats (drs, irs). in the work described here, we examine the isomerization and dna bending properties of pi using electrophoretic mobility shift assays and circular permutation assays. our data suggest that pi dimers can bend irs, and dimer s ... | 2004 | 14706617 |
| binding modes of the initiator and inhibitor forms of the replication protein pi to the gamma ori iteron of plasmid r6k. | discerning the interactions between initiator protein and the origin of replication should provide insights into the mechanism of dna replication initiation. in the gamma origin of plasmid r6k, the rep protein, pi, is distinctive in that it can bind the seven 22-bp iterons in two forms; pi monomers activate replication, whereas pi dimers act as inhibitors. in this work, we used wild type and variants of the pi protein with altered monomer/dimer ratios to study iteron/pi interactions. high resolu ... | 2004 | 15247259 |
| the dnak-dnaj-grpe chaperone system activates inert wild type pi initiator protein of r6k into a form active in replication initiation. | the plasmid r6k is an interesting model system for investigating initiation of dna replication, not only near the primary binding sites of the initiator protein pi but also at a distance, caused by pi -mediated dna looping. an important milestone in the mechanistic analysis of this replicon was the development of a reconstituted replication system consisting of 22 different highly purified proteins (abhyankar, m. a., zzaman, s., and bastia, d. (2003) j. biol. chem. 278, 45476-45484). although th ... | 2004 | 15485812 |
| transformation of escherichia coli mediated by natural phospholipids. | transformation system for escherichia coli based upon introduction of plasmid dna by natural phospholipids has been developed. transformants are easily obtained by treatment with natural phospholipids such as phosphatidylethanolamine, phosphatidylcoline, and phosphatidylserine, where the presence of mgcl2 or cacl2 is essential. this method of transformation is applicable not only for small plasmid phsg399 (2.3 kb) but also for giant plasmid r6k (100 kb). | 2005 | 15665495 |
| characterization of broad host range cryptic plasmid pcr1 from corynebacterium renale. | plasmid pcr1 is a cryptic plasmid harboured by corynebacterium renale. it is the smallest corynebacterial plasmid known to date. although its natural host is animal corynebacteria, it can replicate in several strains of soil corynebacteria. it can also replicate in escherichia coli, in which it is stably maintained. the copy number of pcr1 in this host is higher than that of puc19, with which it shows unidirectional incompatibility. it is also incompatible with pbk2, a plasmid bearing the common ... | 2006 | 16545871 |
| small deletion variants of the replication protein, pi, and their potential for over-replication-based antimicrobial activity. | the emergence of multiply antibiotic-resistant microorganisms in the environment has become a serious public health threat. to address this, our lab has devised a methodology in which antimicrobial agents are transferred into unwanted cells using the process of bacterial conjugation. in the work described here, we pursued proteins that cause plasmid over-replication as potential antimicrobial agents. our focus was on the pir-encoded pi protein of plasmid r6k that possesses both positive and nega ... | 2006 | 16907728 |
| crystal structure of pi initiator protein-iteron complex of plasmid r6k: implications for initiation of plasmid dna replication. | we have determined the crystal structure of a monomeric biologically active form of the pi initiator protein of plasmid r6k as a complex with a single copy of its cognate dna-binding site (iteron) at 3.1-a resolution. the initiator belongs to the family of winged helix type of proteins. the structure reveals that the protein contacts the iteron dna at two primary recognition helices, namely the c-terminal alpha4' and the n-terminal alpha4 helices, that recognize the 5' half and the 3' half of th ... | 2006 | 17124167 |
| mechanism of origin activation by monomers of r6k-encoded pi protein. | one recurring theme in plasmid duplication is the recognition of the origin of replication (ori) by specific rep proteins that bind to dna sequences called iterons. for plasmid r6k, this process involves a complex interplay between monomers and dimers of the rep protein, pi, with seven tandem iterons of gamma ori. remarkably, both pi monomers and pi dimers can bind to iterons, a new paradigm in replication control. dimers, the predominant form in the cell, inhibit replication, while monomers fac ... | 2007 | 17383678 |
| structure-based functional analysis of the replication protein of plasmid r6k: key amino acids at the pi/dna interface. | in previous work, we characterized the bases in an iteron of plasmid r6k that are important for the binding of pi protein monomers and dimers. here we investigate the following six amino acids of pi, encoded by pir, hypothesized to be important for dna contact: ser71, try74, gly131, gly211, arg225, and arg254. | 2007 | 17449630 |
| conjugal transfer of plasmid r6k gamma ori minireplicon derivatives from escherichia coli to various genera of pathogenic bacteria. | three r6k-derived gamma ori minireplicons were successfully transferred by conjugation from escherichia coli to several species of pathogenic bacteria. the pfl129 replicon encodes the wild-type initiation replication protein pi, while plasmids pfl130 and pag101 encode mutant forms of the pi protein conferring the plasmid copy-up phenotype. plasmids could be transferred to all recipient species tested, although high efficiency conjugal transfer was only obtained with genera of the enterobacteriac ... | 2007 | 17909888 |
| nucleotide sequence of pola52: a conjugative incx1 plasmid from escherichia coli which enables biofilm formation and multidrug efflux. | the large conjugative multidrug resistance (mdr) plasmid pola52 was sequenced and annotated. the plasmid encodes two phenotypes normally associated with the chromosomes of opportunistic pathogens, namely mdr via a resistance-nodulation-division (rnd)-type efflux-pump (oqxab), and the formation of type 3 fimbriae (mrkabcdf). the plasmid was found to be 51,602 bp long with 68 putative genes. about half of the plasmid constituted a conserved incx1-type backbone with predicted regions for conjugatio ... | 2008 | 18440636 |
| replication initiation at a distance: determination of the cis- and trans-acting elements of replication origin alpha of plasmid r6k. | plasmid r6k, which contains 3 replication origins called alpha, gamma, and beta, is a favorable system to investigate the molecular mechanism(s) of action at a distance, i.e. replication initiation at a considerable distance from the primary initiator protein binding sites (iterons). the centrally located gamma origin contains 7 iterons that bind to the plasmid-encoded initiator protein, pi. ori alpha, located at a distance of approximately 4 kb from gamma, contains a single iteron that does not ... | 2010 | 20018882 |
| investigations of pi initiator protein-mediated interaction between replication origins alpha and gamma of the plasmid r6k. | a typical plasmid replicon of escherichia coli, such as ori gamma of r6k, contains tandem iterons (iterated initiator protein binding sites), an at-rich region that melts upon initiator-iteron interaction, two binding sites for the bacterial initiator protein dnaa, and a binding site for the dna-bending protein ihf. r6k also contains two structurally atypical origins called alpha and beta that are located on either side of gamma and contain a single and a half-iteron, respectively. individually, ... | 2010 | 20029091 |
| entry exclusion and orit of a conjugative system encoded by the cryptic plasmid p29930 of yersinia enterocolitica. | the conjugative transfer system of yersinia enterocolitica 29930 present on the cryptic plasmid p29930 comprises a mating pore formation system (mpf) related to that of the incx plasmid r6k and a dna transfer and replication system (dtr) with close relationship to the mob region of the mobilizable plasmid clodf13. two regions of the transfer system were selected for more detailed analyses of basic functions of conjugative transfer. the putative open reading frame orf22 located in the mpf region ... | 2010 | 20470820 |
| cooperative binding mode of the inhibitors of r6k replication, pi dimers. | the replication initiator protein, pi, plays an essential role in the initiation of plasmid r6k replication. both monomers and dimers of pi bind to iterons in the gamma origin of plasmid r6k, yet monomers facilitate open complex formation, while dimers, the predominant form in the cell, do not. consequently, pi monomers activate replication, while pi dimers inhibit replication. recently, it was shown that the monomeric form of pi binds multiple tandem iterons in a strongly cooperative fashion, w ... | 2008 | 18295232 |