| the f plasmid ccdb protein induces efficient atp-dependent dna cleavage by gyrase. | dna topoisomerases perform essential roles in dna replication, gene transcription, and chromosome segregation. recently, we identified a new type of topoisomerase ii poison: the ccdb protein of plasmid f. when its action is not prevented by ccda protein, the ccdb protein is a potent cytotoxin. in this paper, using purified ccdb, ccda and gyrase, we show that ccdb protein efficiently traps gyrase in a cleavable complex. the ccda protein not only prevents the gyrase poisoning activity of ccdb but ... | 1993 | 8254658 |
| indirect sos induction is promoted by ultraviolet light-damaged minif and requires the minif lyna locus. | indirect prophage induction is produced by transfer to recipients of u.v.-damaged f plasmid (95 kb). we tested whether the sos signal can be produced by minif, a 9.3 kb restriction fragment, coding for the replication and segregation functions of plasmid f. we used lambda minif, a hybrid phage-plasmid. u.v.-irradiated lambda minif induced prophages phi 80 or lambda and sfia, a chromosomal sos gene, in more than 50% of the infected cells. the maximal inducing dose produced about 0.5 pyrimidine di ... | 1984 | 6096551 |
| promoters in the transfer region of plasmid f. | | 1985 | 3893413 |
| mini-f e protein: the carboxy-terminal end is essential for e gene repression and mini-f copy number control. | mini-f is a segment of the conjugative plasmid f consisting of two origins of replication flanked by regulatory regions, which ensure a normal control of replication and partitioning. adjacent to the ori-2 origin is a complex coding region that consists of the e gene overlapped by three open reading frames with the coding potential for 9000 mr polypeptides here designated 9 kd-1, 9 kd-2 and 9 kd-3. in this paper, we show that open reading frame 9 kd-3 is preceded by active promoter and shine-dal ... | 1986 | 3018261 |
| two functions of the e protein are key elements in the plasmid f replication control system. | by using a plasmid carrying a translational fusion between the e gene of the incfi plasmid f and the lacz gene, we located the operator of the autogenously regulated e gene to an inverted repeat overlapping the e-gene promoter and showing perfect homology to part of the sequence found in all the direct repeats of two regions exerting an inhibitory effect on f replication, incb and incc. excess e protein provided in trans to an f plasmid increased the replication frequency of the f plasmid. this ... | 1985 | 2999077 |
| a common origin for the bacterial toxin-antitoxin systems pard and ccd, suggested by analyses of toxin/target and toxin/antitoxin interactions. | bacterial toxin-antitoxin (ta) systems encode two proteins, a potent inhibitor of cell proliferation (toxin) and its specific antidote (antitoxin). structural data has revealed striking similarities between the two model ta toxins ccdb, a dna gyrase inhibitor encoded by the ccd system of plasmid f, and kid, a site-specific endoribonuclease encoded by the pard system of plasmid r1. while a common structural fold seemed at odds with the two clearly different modes of action of these toxins, the po ... | 2012 | 23029540 |
| diversity of pili-specific bacteriophages: genome sequence of incm plasmid-dependent rna phage m. | bacteriophages of the leviviridae family are small rna viruses with linear, positive-sense, single-stranded rna genomes that encode only four proteins. all phages of this family require bacterial pili to attach to and infect cells. leviviridae phages utilizing f-pili for this purpose have been extensively studied. rna phages specific for conjugative plasmid-encoded pili other than that of plasmid f have been isolated, but are much less understood and their relation to the f-pili-specific phages ... | 2012 | 23176223 |
| structural insights into the chaperone activity of the 40-kda heat shock protein dnaj: binding and remodeling of a native substrate. | hsp40 chaperones bind and transfer substrate proteins to hsp70s and regulate their atpase activity. the interaction of hsp40s with native proteins modifies their structure and function. a good model for this function is dnaj, the bacterial hsp40 that interacts with repe, the repressor/activator of plasmid f replication, and together with dnak regulates its function. we characterize here the structure of the dnaj-repe complex by electron microscopy, the first described structure of a complex betw ... | 2013 | 23580641 |
| chemical shift assignments of a reduced n-terminal truncation mutant of the disulfide bond isomerase trbb from plasmid f, trbbδ29. | trbb from the conjugative plasmid f is a 181-residue disulfide bond isomerase that plays a role in the correct folding and maintenance of disulfide bonds within f plasmid encoded proteins in the bacterial periplasm. as a member of the thioredoxin-like superfamily, trbb has a predicted thioredoxin-like fold that contains a c-x-x-c active site required for performing specific redox chemistries on protein substrates. here we report the sequence-specific assignments of the reduced form of the n-term ... | 2014 | 24771093 |
| a high security double lock and key mechanism in huh relaxases controls orit-processing for plasmid conjugation. | relaxases act as dna selection sieves in conjugative plasmid transfer. most plasmid relaxases belong to the huh endonuclease family. trwc, the relaxase of plasmid r388, is the prototype of the huh relaxase family, which also includes trai of plasmid f. in this article we demonstrate that trwc processes its target nic-site by means of a highly secure double lock and key mechanism. it is controlled both by trwc-dna intermolecular interactions and by intramolecular dna interactions between several ... | 2014 | 25123661 |
| characterization of the phd-doc and ccd toxin-antitoxin cassettes from vibrio superintegrons. | toxin-antitoxin (ta) systems have been reported in the genomes of most bacterial species, and their role when located on the chromosome is still debated. ta systems are particularly abundant in the massive cassette arrays associated with chromosomal superintegrons (si). here, we describe the characterization of two superintegron cassettes encoding putative ta systems. the first is the phd-doc(si) system identified in vibrio cholerae n16961. we determined its distribution in 36 v. cholerae strain ... | 2013 | 23475970 |
| the transfer operon of plasmid r1 extends beyond fino into the downstream replication genes. | fino is the final gene in the 35.4 kb transfer operon of incfi plasmid f that is known to be involved in self-conjugative transfer. the genetic region distal to fino separates the conjugation and replication control modules of incfii plasmid r100 and carries uncharacterized genes not found in plasmid f. however, comparison of the r100 gene organization with database entries of f-like plasmids suggests its broad conservation. we determined the dna sequence of this region of incfii plasmid r1 and ... | 2010 | 21145348 |
| molecular basis of the supercoil deficit induced by the mini-f plasmid partition complex. | formation of a partition complex on plasmid f by binding of sopb protein to the sopc centromere is the first step in the partition process that ensures stability of f in dividing cells. establishment of the complex enables nonspecific binding of sopb to neighboring dna, which extends the partition complex and provokes reduction of negative supercoiling of the plasmid. this reduction is believed to reflect winding of dna into positive supercoils about sopb to create a nucleoprotein structure of p ... | 2009 | 19001378 |
| polymerization of sopa partition atpase: regulation by dna binding and sopb. | in bacteria, mitotic stability of plasmids and many chromosomes depends on replicon-specific systems which comprise a centromere, a centromere-binding protein and an atpase. dynamic self-assembly of the atpase appears to enable active partition of replicon copies into cell-halves, but for most atpases (the walker-box type) the mechanism is unknown. also unknown is how the host cell contributes to partition. we have examined the effects of non-sequence-specific dna on in vitro self-assembly of th ... | 2007 | 17166176 |
| hydrodynamic plasmid dna gene therapy model in liver transplantation. | there is great interest in the field of transplantation to genetically modify grafts to decrease preservation injury or allograft rejection. although adenoviral gene transfer has been effective in experimental liver transplantation, viral toxicity and safety concerns limit potential use in clinical trials. therefore, the purpose of this study was to develop a model of nonviral gene transfer in the liver transplant setting, allowing for efficient transgene expression. | 2006 | 16926028 |
| inter- and intramolecular determinants of the specificity of single-stranded dna binding and cleavage by the f factor relaxase. | the trai protein of conjugative plasmid f factor binds and cleaves a single-stranded region of the plasmid prior to transfer to a recipient. trai36, an n-terminal trai fragment, binds ssdna with a subnanomolar k(d) and remarkable sequence specificity. the structure of the trai36 y16f variant bound to ssdna reveals specificity determinants, including a ssdna intramolecular 3 base interaction and two pockets within the protein's binding cleft that accommodate bases in a knob-into-hole fashion. mut ... | 2005 | 16216584 |
| energetics of the sequence-specific binding of single-stranded dna by the f factor relaxase domain. | transfer of conjugative plasmids between bacteria requires the activity of relaxases or mobilization proteins. these proteins nick the plasmid in a site- and strand-specific manner prior to transfer of the cut strand from donor to recipient. trai36, the relaxase domain of trai from plasmid f factor, binds a single-stranded dna (ssdna) oligonucleotide containing an f factor sequence with high affinity and sequence specificity. to better understand the energetics of this interaction, we examined t ... | 2004 | 15123728 |
| dna recognition by f factor trai36: highly sequence-specific binding of single-stranded dna. | the trai protein has two essential roles in transfer of conjugative plasmid f factor. as part of a complex of dna-binding proteins, trai introduces a site- and strand-specific nick at the plasmid origin of transfer (orit), cutting the dna strand that is transferred to the recipient cell. trai also acts as a helicase, presumably unwinding the plasmid strands prior to transfer. as an essential feature of its nicking activity, trai is capable of binding and cleaving single-stranded dna oligonucleot ... | 2001 | 11560509 |
| [the study of heterogeneity of plasmid-bearing and plasmid-f ree populations of bacillus subtilis under different environmental conditions]. | the population heterogeneity of recombinant and plasmid-free bacillus subtilis strains introduced into aquatic microcosms was studied. after introduction, the population of the plasmid-free strain b. subtilis 2335 in microcosms has long been represented by both vegetative cells and spores, whereas, already ten days after introduction, the population of the recombinant strain b. subtilis 2335/105 (km[symbol: see text]nf+) was represented only by spores. the number of plasmid copies in the spore i ... | 2000 | 10776630 |
| plasmids isolated from marine sediment microbial communities contain replication and incompatibility regions unrelated to those of known plasmid groups. | two hundred ninety-seven bacteria carrying plasmids that range in size from 5 to 250 kb were identified from more than 1,000 aerobic heterotrophic bacteria isolated from coastal california marine sediments. while some isolates contained numerous (three to five) small (5- to 10-kb) plasmids, the majority of the natural isolates typically contained one large (40- to 100-kb) plasmid. by the method of plasmid isolation used in this study, the frequency of plasmid incidence ranged from 24 to 28% depe ... | 1997 | 9055407 |