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PubMed1995

Sites for co-integration of large staphylococcal plasmids.

Site-specific recombination is thought to play an important role in the evolution of multi-resistant plasmids in bacteria, including the human pathogen Staphylococcus aureus (Sa). A mechanism for site- and orientation-specific recombination between large Sa plasmids was identified in Sa strain 1054. A replication-thermosensitive derivative of plasmid pI9789::Tn552 (called pS1) was found to form stable co-integrates with the large plasmid pOX1054 in the Sa strain 1054. Two closely related recombination sites were identified on these plasmids at which recombination occurred to form co-integrates. The sites (rs9789 from plasmid pI9789::Tn552 and rs1054 from pOX1054) were cloned and studies with them showed that the recombination at these sites occurs by a new method. The site rs1054 (27 bp) is deleted and rs9789 (26 bp) is duplicated during recombination. The data show that plasmid pS1 contributes the site for recombination and that the gene(s) encoding the protein(s) involved in recombination are encoded on either pOX1054 or the 1054 chromosome.

Base Sequence↗
PubMed1995

A new plasmid (QpDV) common to Coxiella burnetii isolates associated with acute and chronic Q fever.

Genetic studies of Coxiella burnetii strains suggested the possibility of differentiating new isolates according to their plasmid DNA content. Virulence and/or clinical manifestations ('chronic' and 'acute' Q fever) had been claimed to correlate with this plasmid typing. A new plasmid, named QpDV, was found to be common to C. burnetii isolates obtained from acute and chronic Q fever. According to the results obtained, plasmid usage for detection and differentiation of respective pathovars of C. burnetii and the correlation between gene specificity and pathovar has to be revised. Closer studies suggested a common origin of C. burnetii plasmids, but also showed some differences characteristic for each plasmid, probably reflecting divergent evolution.

Acute Disease↗
PubMed2001

Comparative biology of IncQ and IncQ-like plasmids.

Plasmids belonging to Escherichia coli incompatibility group Q are relatively small (approximately 5 to 15 kb) and able to replicate in a remarkably broad range of bacterial hosts. These include gram-positive bacteria such as Brevibacterium and Mycobacterium and gram-negative bacteria such as Agrobacterium, Desulfovibrio, and cyanobacteria. These plasmids are mobilized by several self-transmissible plasmids into an even more diverse range of organisms including yeasts, plants, and animal cells. IncQ plasmids are thus highly promiscuous. Recently, several IncQ-like plasmids have been isolated from bacteria found in environments as diverse as piggery manure and highly acidic commercial mineral biooxidation plants. These IncQ-like plasmids belong to different incompatibility groups but have similar broad-host-range replicons and mobilization properties to the IncQ plasmids. This review covers the ecology, classification, and evolution of IncQ and IncQ-like plasmids.

Adenosine Triphosphatases↗
PubMed1988

Isolation and characterization of a new plasmid from a Flavobacterium sp. which carries the genes for degradation of 2,4-dichlorophenoxyacetate.

A Flavobacterium sp. (strain 50001), capable of degrading 2,4-dichlorophenoxyacetate (2,4-D), 2-methyl-4-chlorophenoxyacetate, and 2-chlorobenzoate and imparting resistance to mercury, harbored a degradative plasmid, pRC10. Cured strains of the Flavobacterium sp. lost the plasmid as well as the ability to degrade these chlorinated compounds. Comparison of this plasmid with the well-characterized 2,4-D-degradative plasmid pJP4 from Alcaligenes eutrophus showed regions of homology between the two plasmids. Restriction fragments of plasmid pRC10 which shared homology with the regions conferring 2,4-D-degradative genes (tfd) of plasmid pJP4 were cloned into a broad-host-range plasmid and studied in Pseudomonas putida. From the results obtained, the cloned DNA fragment expressed the genes for 2,4-D monooxygenase (tfdA) and 2,4-dichlorophenol hydroxylase (tfdB). In spite of the similarity in function, the size (45 kilobases) and restriction pattern of plasmid pRC10 were considerably different from those of pJP4 (80 kilobases). This may be due to the difference in the microbial background during evolution of the two plasmids.

2,4-Dichlorophenoxyacetic Acid↗
PubMed1994

Codon usage patterns suggest independent evolution of two catabolic operons on toluene-degradative plasmid TOL pWW0 of Pseudomonas putida.

TOL plasmid pWW0 of Pseudomonas putida encodes a set of enzymes responsible for the degradation of toluene. The structural genes for these catobolic enzymes are clustered into two operons--namely, the xy/CMAB and xy/XYZLTEGFJQKIH operons. We examined the codon usage patterns of these catabolic genes by measuring the codon-usage distances between pairs of these catabolic genes. The codon-usage distance, d, between gene 1 and gene 2 was defined as d = [sigma(pj-qj)2]1/2, are the frequencies of the j-th codon in gene 1 and 2, respectively, j being any one of the 64 possible codons. We found that the genes in the same operon exhibit similar codon-usage patterns while genes in the different operons exhibit different codon bias. This observation suggests that genes in the same operon have coevolved, and that the ancestors of the xy/CMAB and xy/XYZLTEGFJQKIH operons evolved in different organisms.

Biodegradation, Environmental↗
PubMed1991

Bacterial resistance.

Pathogenic bacteria remain adaptable to an increasingly hostile environment and a wider variety of more potent antibiotics. Organisms not intrinsically prepared for defense have been able to acquire resistance to newer antimicrobial agents. Chromosomal mutations alone cannot account for the rapid emergence and spread of antibiotic resistance. It has been established that plasmids and transposons are particularly important in the evolution of antibiotic-resistant bacteria. Plasmid- or transposon-mediated resistance provides the bacteria with pre-evolved genes refined to express high-level resistance. In particular, transposons can transfer these resistance determinants in diverse bacterial species, and nature provides in humans and animals large intestinal reservoirs in which such communications are facilitated. Antibiotic therapy exerts selection pressures on bacteria. Eradication or marked reduction in the populations of susceptible organisms promotes the overgrowth of intrinsically resistant strains and favors those resistant as a result of favorable chromosomal mutations or via plasmids or transposons. In our hospitals, where antibiotic consumption continues to increase, the nosocomial flora consists of many resistant bacteria, and infections acquired in the nosocomial setting are now far more severe than their community-acquired counterparts. There is convincing evidence that infection control measures must take into further consideration the contribution of the hospital worker as carrier and mediator of antibiotic resistance.

Anti-Bacterial Agents↗
PubMed2003

Structure of haloacetate-catabolic IncP-1beta plasmid pUO1 and genetic mobility of its residing haloacetate-catabolic transposon.

The self-transmissible plasmid pUO1 from Delftia acidovorans strain B carries two haloacetate-catabolic transposons, TnHad1 and TnHad2, and the mer genes for resistance to mercury. The complete 67,066-bp sequence of pUO1 revealed that the mer genes were also carried by two Tn402/Tn5053-like transposons, Tn4671 and Tn4672, and that the pUO1 backbone regions shared 99% identity to those of the archetype IncP-1beta plasmid R751. Comparison of pUO1 with three other IncP-1beta plasmids illustrated the importance of transposon insertion in the diversity and evolution of this group of plasmids. Mutational analysis of the four outermost residues in the inverted repeats (IRs) of TnHad2, a Tn21-related transposon, revealed a crucial role of the second residue of its IRs in transposition.

Acetates↗
PubMed2005

Chromosomal stasis versus plasmid plasticity in aphid endosymbiont Buchnera aphidicola.

The study of three genomes of the aphid endosymbiont Buchnera aphidicola has revealed an extraordinary stasis: conservation of gene order and genetic composition of the chromosome, while the chromosome size and number of genes has reduced. The reduction in genome size appears to be ongoing since some lineages we now know to have even smaller chromosomes than the first B. aphidicola analysed. The current sequencing by our group of one of these smaller genomes with an estimated size of 450 kb, and its comparison with the other three available genomes provide insights into the nature of processes involved in shrinkage. We discuss whether B. aphidicola might be driven to extinction and be replaced by secondary aphid endosymbionts. In some lineages, genes encoding key enzymes in the pathways leading to tryptophan and leucine biosynthesis (trpEG and leuABCD, respectively) are located on plasmids, rather than the main chromosome. In contrast to the stasis of the main chromosome, plasmid genes have frequently been transferred to the main chromosome and undergone other gene rearrangements. We propose a two-step scenario to explain these contrasting modes of evolution. Essential genes may have escaped regulation by moving to plasmids in a moving B. aphidicola ancestor. B. aphidicola became polyploidy at a given stage of its evolution and plasmid genes have been transferred to the main chromosome through several independent events.

Animals↗
PubMed1980

Plasmids.

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Bacteriocin Plasmids↗
PubMed2004

Evolution of compatible replicons of the related IncQ-like plasmids, pTC-F14 and pTF-FC2.

Two closely related but compatible plasmids of the IncQ-2alpha and IncQ-2beta groups, pTF-FC2 and pTC-F14, were discovered in two acidiphilic chemolithotrophic bacteria. Cross-complementation and cross-regulation experiments by the replication proteins were carried out to discover what changes were necessary when the plasmids evolved to produce two incompatibility groups. The requirement of a pTC-F14 oriV for a RepC DNA-binding protein was plasmid specific, whereas the requirement for the RepA helicase and RepB primase was less specific and could be complemented by the IncQ-2alpha plasmid pTC-FC2, and the IncQ-1beta plasmid pIE1108. None of the IncQ-1alpha plasmid replication proteins could complement the pTC-F14 oriV, and pTC-F14 and RSF1010 were incompatible. This incompatibility was associated with the RepC replication protein and was not due to iteron incompatibility. Replication of pTC-F14 took place from a 5.7 kb transcript that originated upstream of the mobB gene located within the region required for mobilization. A pTC-F14 mobB-lacZ fusion was regulated by the pTC-F14 repB gene product and was plasmid specific, as it was not regulated by the RepB proteins of pTF-FC2 or the IncQ-1alpha and IncQ-1beta plasmids. Plasmid pTC-F14 appears to have evolved independently functioning iterons and a plasmid-specific RepC-binding protein; it also has a major replication transcript that is independently regulated from that of pTF-FC2. However, the RepA and RepB proteins have the ability to function with either replicon.

Bacterial Proteins↗
PubMed1996

Characterization of the drug resistance plasmid R2418: restriction map and role of insertion and deletion in its evolution.

Escherichia coli 2418 strain is resistant to beta-lactam antibiotics (ampicillin, carbenicillin, and cephalothin), streptomycin, tetracycline, kanamycin, and chloramphenicol. This strain contains at least two conjugative plasmids (R2418 and R2418S) encoding resistance to beta lactam antibiotics and resistance to both beta-lactam antibiotics and streptomycin, respectively. Restriction endonuclease mapping of plasmid DNAs indicates that the plasmid R2418S has evolved from R2418 DNA by the insertion of 2.5-kb DNA between BamHI and PvuII sites, and deletion of 0.5-kb DNA within the EcoRI-EcoRV region. The 2.5-kb DNA insert is responsible for streptomycin resistance. This evolution is also associated with a reduction in the efficiency of conjugal transfer for the plasmid R2418S. The conjugal transfer of streptomycin resistance occurs only through the coresidence of the conjugative plasmid R2418 or R2418S in the donor cell. In accordance with the hypothesis that the Smr determinant is due to a putative transposon, plasmid-free transconjugants resistant to streptomycin only were isolated. Southern blot analysis of HindIII chromosomal digests extracted from these transconjugants shows that the Smr determinant is inserted into different sites in chromosomal DNA.

Anti-Bacterial Agents↗
PubMed2001

Pathogen evolution: How good bacteria go bad.

Recent findings suggest that dysentery-causing Shigella strains have arisen several times from Escherichia coli via plasmid acquisition and phenotypic convergence. Similarly, three Bacillus strains with distinct pathogenic properties are derivatives of a single species whose behavior is profoundly altered by acquired plasmids.

Bacillus↗
PubMed1986

Characterization of the ColE9-J plasmid and analysis of its genetic organization.

We have determined the restriction and functional map of the ColE9-J plasmid. By sub-cloning and transposon mutagenesis we have shown that the ColE9imm gene and the ColE5imm gene present on the ColE9-J plasmid are located on separate EcoRI fragments. Using an expression vector we have demonstrated the presence of two lys genes on the ColE9-J plasmid, both of which are dependent upon the colicin E9 structural gene promoter. Promoter mapping studies imply that the colicin E9 structural gene and the ColE5imm gene are transcribed in the same direction, but that the ColE9imm gene is transcribed in the opposite orientation.

Bacteriocin Plasmids↗
PubMed2006

Dissemination and persistence of blaCTX-M-9 are linked to class 1 integrons containing CR1 associated with defective transposon derivatives from Tn402 located in early antibiotic resistance plasmids of IncHI2, IncP1-alpha, and IncFI groups.

This study analyzes the diversity of In60, a class 1 integron bearing CR1 and containing bla(CTX-M-9), and its association with Tn402, Tn21, and classical conjugative plasmids among 45 CTX-M-9-producing clinical strains (41 Escherichia coli strains, 2 Klebsiella pneumoniae strains, 1 Salmonella enterica strain, and 1 Enterobacter cloacae strain). Forty-five patients in a Spanish tertiary care hospital were studied (1996 to 2003). The diversity of In60 and association of In60 with Tn402 or mercury resistance transposons were investigated by overlapping PCR assays and/or hybridization. Plasmid characterization included comparison of restriction fragment length polymorphism patterns and determination of incompatibility group by PCR-based replicon typing, sequencing, and hybridization. CTX-M-9 plasmids belonged to IncHI2 (n = 26), IncP-1alpha (n = 10), IncFI (n = 4), and IncI (n = 1) groups. Genetic platforms containing bla(CTX-M-9) were classified in six types in relation to the In60 backbone and in eight subtypes in relation to Tn402 derivatives. They were associated with Tn21 sequences when located in IncP-1alpha or IncHI2 plasmids. Our study identified bla(CTX-M-9) in a high diversity of CR1-bearing class 1 integrons linked to different Tn402 derivatives, often to Tn21, highlighting the role of recombination events in the evolution of antibiotic resistance plasmids. The presence of bla(CTX-M-9) on broad-host-range IncP-1alpha plasmids might contribute to its dissemination to hosts that were not members of the family Enterobacteriaceae.

DNA Transposable Elements↗
PubMed1995

Evolution of the korA-oriV segment of promiscuous IncP plasmids.

Plasmids belonging to Escherichia coli incompatibility group P are of particular interest because they can transfer between, and be stably maintained in, almost all Gram-negative bacterial species. The segment of the IncP alpha plasmid genome between the key regulatory gene korA and the vegetative replication origin, oriV, encodes a series of operons co-regulated with replication and transfer functions by the KorA protein. To determine which of these genes are likely to have an important role in IncP plasmid survival the equivalent region of the distantly related IncP beta plasmid R751 was sequenced. Sequence comparisons show that the kla operon (formerly the kilA locus, which is also responsible for a cryptic tellurite-resistance determinant) is completely absent from R751. Similarly in the kle region, which encodes genes associated with the KilE+ phenotype of unknown function, kleC and kleD, which we proposed arose by a duplication of kleA and kleB, are also completely absent. The genes that are conserved are klcA (formerly kilC, responsible for the KilC+, and recently proposed to be involved in overcoming restriction barriers during transfer), klcB (an ORF interrupted by Tn1 insertion in RK2), korC (a transcriptional repressor which controls the klcK and kle operons), and kleA, kleB, kleE and kleF. A striking feature of the organization in R751 is the lack of the strong transcriptional termination signals which are present in IncP alpha plasmids. The degree of divergence between the plasmids facilitates the identification of motifs of probable functional importance in the primary protein sequences.

Amino Acid Sequence↗
PubMed1986

Transitory derepression and the maintenance of conjugative plasmids.

It has been proposed that bacterial plasmids cannot be maintained by infectious transfer alone and that their persistence requires positive selection for plasmid-borne genes. To test this hypothesis, the population dynamics of two laboratory and five naturally occurring conjugative plasmids were examined in chemostat cultures of E. coli K-12. Both laboratory plasmids and three of the five wild plasmids failed to increase in frequency when introduced at low frequencies. However, two of the naturally occurring plasmids rapidly increased in frequency, and bacteria carrying them achieved dominance in the absence of selection for known plasmid-borne genes. Three hypotheses for the invasion and persistence of these two plasmids were examined. It is concluded that although these two extrachromosomal genetic elements are repressed for conjugative pili synthesis, as a consequence of high rates of transfer during periods of transitory derepression in newly formed transconjugants, they become established and are maintained by infectious transfer alone. The implications of these observations to the theory of plasmid maintenance and the evolution of repressible conjugative pili synthesis are discussed.

Conjugation, Genetic↗