Publications

a plasmid rk2-based broad-host-range cloning vector useful for transfer of metagenomic libraries to a variety of bacterial species.	the majority of microorganisms in natural environments are difficult to cultivate, but their genes can be studied via metagenome libraries. to enhance the chances that these genes become expressed we here report the construction of a broad-host-range plasmid vector (prs44) for fosmid and bacterial artificial chromosome (bac) cloning. prs44 can be efficiently transferred to numerous hosts by conjugation. it replicates in such hosts via the plasmid rk2 origin of replication, while in escherichia c ...	2009	19459950
dual role of dna in regulating atp hydrolysis by the sopa partition protein.	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 walker-box partition atpases the molecular mechanism is unknown. atpase activity appears to be essential for this process. dna and centromere-binding proteins are known to stimulate the atpase activity but mol ...	2009	19740757
pard toxin-antitoxin system of plasmid r1--basic contributions, biotechnological applications and relationships with closely-related toxin-antitoxin systems.	toxin-antitoxin systems, as found in bacterial plasmids and their host chromosomes, play a role in the maintenance of genetic information, as well as in the response to stress. we describe the basic biology of the pard/kiskid toxin-antitoxin system of escherichia coli plasmid r1, with an emphasis on regulation, toxin activity, potential applications in biotechnology and its relationships with related toxin-antitoxin systems. special reference is given to the ccd toxin-antitoxin system of plasmid ...	2010	20569269
characterization and global gene expression of f- phenocopies during escherichia coli biofilm formation.	the ecological role of horizontal gene transfer within biofilms has been recently investigated, and it has been reported that conjugation directly induces bacteria to form biofilms via expression of conjugative pili. in this report, we described the contribution of bacterial conjugation during biofilm formation by escherichia coli harboring a natural incf conjugative f plasmid (f(+)). we showed that cell-to-cell pili interactions through the homosexual mating-pair formation among f(+) × f(+) cel ...	2010	20809290
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
effect of extremely low frequency magnetic field exposure on dna transposition in relation to frequency, wave shape and exposure time.	purpose: to examine the effect of extremely low frequency magnetic field (elf-mf) exposure on transposon (tn) mobility in relation to the exposure time, the frequency and the wave shape of the field applied. materials and methods: two escherichia coli model systems were used: (1) cells unable to express β-galactosidase (lacz(-)), containing a mini-transposon tn10 element able to give ability to express β-galactosidase (lacz(+)) upon its transposition; therefore in these cells transposition activ ...	2011	21504343
centromere binding specificity in assembly of the f plasmid partition complex.	the segregation of plasmid f of escherichia coli is highly reliable. the sop partition locus, responsible for this stable maintenance, is composed of two genes, sopa and sopb and a centromere, sopc, consisting of 12 direct repeats of 43 bp. each repeat carries a 16-bp inverted repeat motif to which sopb binds to form a nucleoprotein assembly called the partition complex. a database search for sequences closely related to sopc revealed unexpected features that appeared highly conserved. we have i ...	2011	21653553
trbb from conjugative plasmid f is a structurally distinct disulfide isomerase that requires dsbd for redox state maintenance.	trbb, a periplasmic protein encoded by the conjugative plasmid f, has a predicted thioredoxin-like fold and possesses a c-x-x-c redox active site motif. trbb may function in the conjugative process by serving as a disulfide bond isomerase, facilitating proper folding of a subset of f-plasmid-encoded proteins in the periplasm. previous studies have demonstrated that a +ötrbb f plasmid in escherichia coli lacking dsbc(e.coli), its native disulfide bond isomerase, experiences a 10-fold decrease in ...	2011	21742866
An activation domain of plasmid R1 TraI protein delineates stages of gene transfer initiation.	Bacterial conjugation is a form of type IV secretion that transports protein and DNA to recipient cells. Specific bacteriophage exploit the conjugative pili and cell envelope spanning protein machinery of these systems to invade bacterial cells. Infection by phage R17 requires F-like pili and coupling protein TraD, which gates the cytoplasmic entrance of the secretion channel. Here we investigate the role of TraD in R17 nucleoprotein uptake and find parallels to secretion mechanisms. The relaxos ...	2011	22066957
differences in unfolding energetics of ccdb toxins from v. fischeri and e. coli.	ccd system is a toxin-antitoxin module (operon) located on plasmids and chromosomes of bacteria. ccdbf encoded by ccd operon located on escherichia coli plasmid f and ccdbvfi encoded by ccd operon located on vibrio fischeri chromosome are members of the ccdb family of toxins. native ccdbs are dimers that bind to gyrase-dna complexes and inhibit dna transcription and replication. while thermodynamic stability and unfolding characteristics of the plasmidic ccdbf in denaturant solutions are reporte ...	2012	24061309
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
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
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
insight into centromere-binding properties of parb proteins: a secondary binding motif is essential for bacterial genome maintenance.	parb proteins are one of the three essential components of partition systems that actively segregate bacterial chromosomes and plasmids. in binding to centromere sequences, parb assembles as nucleoprotein structures called partition complexes. these assemblies are the substrates for the partitioning process that ensures dna molecules are segregated to both sides of the cell. we recently identified the sopc centromere nucleotides required for binding to the parb homologue of plasmid f, sopb. this ...	2013	23345617
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
thioredoxin-like proteins in f and other plasmid systems.	bacterial conjugation is the process by which a conjugative plasmid transfers from donor to recipient bacterium. during this process, single-stranded plasmid dna is actively and specifically transported from the cytoplasm of the donor, through a large membrane-spanning assembly known as the pore complex, and into the cytoplasm of the recipient. in gram negative bacteria, construction of the pore requires localization of a subset of structural and catalytically active proteins to the bacterial pe ...	2013	23721857
crispr-cas systems preferentially target the leading regions of mobf conjugative plasmids.	most prokaryotes contain crispr-cas immune systems that provide protection against mobile genetic elements. we have focused on the ability of crispr-cas to block plasmid conjugation, and analyzed the position of target sequences (protospacers) on conjugative plasmids. the analysis reveals that protospacers are non-uniformly distributed over plasmid regions in a pattern that is determined by the plasmid's mobilization type (mob). while mobp plasmids are most frequently targeted in the region ente ...	2013	23535265
metagenomic chromosome conformation capture (meta3c) unveils the diversity of chromosome organization in microorganisms.	genomic analyses of microbial populations in their natural environment remain limited by the difficulty to assemble full genomes of individual species. consequently, the chromosome organization of microorganisms has been investigated in a few model species, but the extent to which the features described can be generalized to other taxa remains unknown. using controlled mixes of bacterial and yeast species, we developed meta3c, a metagenomic chromosome conformation capture approach that allows ch ...	2014	25517076
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
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