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- Characterization of the Campylobacter jejuni cryptic plasmid pTIW94 recovered from wild birds in the southeastern United States. [JOURNAL ARTICLE]
- Plasmid 2013 Apr 30.
The complete nucleotide sequence was determined for a cryptic plasmid, pTIW94, recovered from several Campylobacter jejuni isolates from wild birds in the southeastern United States. pTIW94 is a circular molecule of 3860 nucleotides, with a G+C content (31.0%) similar to that of many Campylobacter spp. genomes. A typical origin of replication, with iteron sequences, was identified upstream of DNA sequences that demonstrated similarity to replication initiation proteins. A total of five open reading frames (ORFs) were identified; two of the five ORFs demonstrated significant similarity to plasmid pCC2228-2 found within Campylobacter coli. These two ORFs were similar to essential replication proteins RepA (100%; 26/26 aa identity) and RepB (95%; 327/346 aa identity). A third identified ORF demonstrated significant similarity (99%; 421/424 aa identity) to the MOB protein from C. coli 67-8, originally recovered from swine. The other two identified ORFs were either similar to hypothetical proteins from other Campylobacter spp., or exhibited no significant similarity to any DNA or protein sequence in the GenBank database. Promoter regions (-35 and -10 signal sites), ribosomal binding sites upstream of ORFs, and stem-loop structures were also identified within the plasmid. These results demonstrate that pTIW94 represents a previously un-reported small cryptic plasmid with unique sequences as well as highly similar sequences to other small plasmids found within Campylobacter spp., and that this cryptic plasmid is present among Campylobacter spp. recovered from different genera of wild birds.
- Characterisation of the stbD/E toxin-antitoxin system of pEP36, a plasmid of the plant pathogen Erwinia pyrifoliae. [JOURNAL ARTICLE]
- Plasmid 2013 Apr 28.
pEP36 is a plasmid ubiquitously present in Erwinia pyrifoliae, a pathogen which causes black stem blight of Asian pear. pEP36 is highly stable in its host, even in the absence of selective pressure. The plasmid is closely related to pEA29, which is widespread in E. amylovora, the causative agent of fire blight of apple and pear trees. Here we report that pEP36 possesses a functional hybrid toxin-antitoxin module, stbD/EpEP36, with the toxin showing homology to the RelE/ParE proteins and the antidote belonging to the Phd/YefM antitoxin family. Bacteria expressing the StbEpEP36 toxin arrest cell growth and enter a viable but non-culturable stage. However, they maintain their typical cell length and do not show filamentation. Pulse-chase experiments revealed that StbEpEP36 acts as a global inhibitor of protein synthesis while it does not interfere with DNA and RNA synthesis. The StbDpEP36 antitoxin is capable of neutralising StbEpEP36 toxicity. Additional experiments show that the stbD/EpEP36 module can stabilise plasmids at least 20-fold. Thus the toxin-antitoxin system may contribute to the remarkable stability of pEP36.
- F conjugation: Back to the beginning. [JOURNAL ARTICLE]
- Plasmid 2013 Apr 28.
Bacterial conjugation as mediated by the F plasmid has been a topic of study for the past 65years. Early research focused on events that occur on the cell surface including the pilus and its phages, recipient cell receptors, mating pair formation and its prevention via surface or entry exclusion. This short review is a reminder of the progress made in those days that will hopefully kindle renewed interest in these subjects as we approach a complete understanding of the mechanism of conjugation.
- Phylogeny and organization of recombinase in trio (RIT) elements. [JOURNAL ARTICLE]
- Plasmid 2013 Apr 28.
Recombinase in trio (RIT) elements are composed of three adjacent tyrosine based site-specific recombinases that commonly occur in bacterial genomes. In this study, we examine RIT elements found in the genomes of strains from 63 different genera across 7 phyla of Eubacteria and examine the specific organization of these elements, their phylogenetic and environmental distribution, and their potential for mobility. We have found that each recombinase in this RIT arrangement is associated with a distinct sub-family of the tyrosine recombinases, and that the order and orientation of these sub-families is consistently maintained. We have determined that the distribution of these elements suggests that they are an ancient feature of bacterial genomes, but identical copies found within individual strains indicates that they are capable of intragenomic mobility. The occurrence of identical elements on both the main chromosome and one or more plasmids within individual strains, coupled with the finding that in some cases related genera are carrying highly similar RIT elements indicates that horizontal transfer has in some cases proceeded through a plasmid intermediate.
- Interactions of the excision proteins of CTnDOT in the attR intasome. [JOURNAL ARTICLE]
- Plasmid 2013 Apr 17.
Excision of the conjugative transposon CTnDOT from the chromosome of Bacteroides spp. involves four CTnDOT-encoded proteins: IntDOT, Xis2c, Xis2d, and Exc along with a host factor. These proteins form excisive intasomes on the attR and attL sites which undergo synapsis and recombination to form the attDOT and attB sites. We recently developed an in vitro intramolecular excision reaction where the attL and attR sites are on the same plasmid. This reaction requires IntDOT, Xis2c, Xis2d, and is stimulated by Exc. We used this reaction to identify the binding sites of the IntDOT, Xis2c, and Xis2d. In this paper, we show that three of the six arm-type sites are absolutely required for excision. Furthermore, we also identified two binding sites for Xis2d and two possible binding sites for Xis2c on the attR site. We also showed that IntDOT interacts cooperatively with the Xis2c and Xis2d proteins on the attR site.
- Improvement of pBBR1MCS plasmids, a very useful series of broad-host-range cloning vectors. [JOURNAL ARTICLE]
- Plasmid 2013 Apr 10.
pBBR1MCS vectors are small in size, contain unique cloning sites within the lacZα gene, and are mobilizable and compatible with various plasmid incompatibility groups. We cloned four genes for aminoglycoside resistance methyltransferases from the Arm and Kam families into pBBR1MCS-3 and expressed them in Escherichia coli. The activity of two of these enzymes was impaired because of the fusion with the first 20 amino acids of the β-galactosidase α-peptide derived from the pBBR1MCS-3 vector. In order to overcome this problem, we introduced by site-directed mutagenesis a new NdeI restriction site into pBBR1MCS-3 to generate a start codon directly at the beginning of lacZα gene. We modified the pBBR1MCS-2, 4 and 5 plasmids in the same manner and obtained the enhanced pBBR1MCS_START vector series that retains all the useful features of the previous vectors, but eliminates the unknown effect of the fusion with the β-galactosidase α-peptide.
- Structural independence of conjugative coupling protein TrwB from its Type IV secretion machinery. [JOURNAL ARTICLE]
- Plasmid 2013 Apr 10.
The stability of components of multiprotein complexes often relies on the presence of the functional complex. To assess structural dependence among the components of the R388 Type IV secretion system (T4SS), the steady-state level of several Trw proteins was determined in the absence of other Trw components. While several Trw proteins were affected by the lack of others, we found that the coupling protein TrwB is not affected by the absence of other T4SS components, nor did its absence alter significantly the levels of integral components of the complex, underscoring the independent role of the coupling protein on the T4SS architecture. The cytoplasmic ATPases TrwK (VirB4) and TrwD (VirB11) were affected by the absence of several core complex components, while the pilus component TrwJ (VirB5) required the presence of all other Trw proteins (except for TrwB) to be detectable. Overall, the results delineate a possible assembly pathway for the T4SS of R388. We have also tested structural complementation of TrwD (VirB11) and TrwJ (VirB5) by their homologues in the highly related Trw system of Bartonella tribocorum (Bt). The results reveal a correlation with the functional complementation data previously reported.
- Bacillus subtilis EdmS (formerly PgsE) participates in the maintenance of episomes. [JOURNAL ARTICLE]
- Plasmid 2013 Apr 10.
Extrachromosomal DNA maintenance (EDM) is an important process in molecular breeding and for various applications in the construction of genetically engineered microbes. Here we describe a novel Bacillus subtilis gene involved in EDM function called edmS (formerly pgsE). Functional gene regions were identified using molecular genetics techniques. We found that EdmS is a membrane-associated protein that is crucial for EDM. We also determined that EdmS can change a plasmid vector with an unstable replicon and worse-than-random segregation into one with better-than-random segregation, suggesting that the protein functions in the declustering and/or partitioning of episomes. EdmS has two distinct domains: an N-terminal membrane-anchoring domain and a C-terminal assembly accelerator-like structure, and mutational analysis of edmS revealed that both domains are essential for EDM. Further studies using cells of Bacillus megaterium and its edmS (formerly capE) gene implied that EdmS has potential as a molecular probe for exploring novel EDM systems.
- Global transcriptional regulator KorC coordinates expression of three backbone modules of the broad-host-range RA3 plasmid from IncU incompatibility group. [JOURNAL ARTICLE]
- Plasmid 2013 Apr 11.
The broad-host-range conjugative RA3 plasmid from IncU incompatibility group has been isolated from the fish pathogen Aeromonas hydrophila. DNA sequencing has revealed a mosaic modular structure of RA3 with the stabilization module showing some similarity to IncP-1 genes and the conjugative transfer module highly similar to that from PromA plasmids. The integrity of the mosaic plasmid genome seems to be specified by its regulatory network. In this paper the transcriptional regulator KorC was analyzed. KorCRA3 (98 amino acids) is encoded in the stabilization region and represses four strong promoters by binding to a conserved palindrome sequence, designated OC on the basis of homology to the KorC operator sequences in IncP-1 plasmids. Two of the KorCRA3-regulated promoters precede the first two cistrons in the stabilization module, one fires towards replication module, remaining one controls a tricistronic operon, whose products are involved in the conjugative transfer process. Despite the similarity between the binding sites in IncU and IncP-1 plasmids, no cross-reactivity between their KorC proteins has been detected. KorC emerges as a global regulator of RA3, coordinating all its backbone functions: replication, stable maintenance and conjugative transfer.
- Evolution of IncHI1 plasmids: Two distinct lineages. [JOURNAL ARTICLE]
- Plasmid 2013 Apr 6.
The IncHI1 plasmid pSRC27-H from Salmonella enterica serovar Typhimurium carries a region containing several genes that confer resistance to different antibiotics, and this resistance region is in the same position as related resistance regions in a group of sequenced IncHI1 plasmids from various sources that includes pHCM1. Four further additional segments are found in pHCM1 relative to another IncHI1 plasmid, R27. Using PCR or DNA sequencing to detect the presence or absence of each of these additional segments in the same position in the IncHI1 backbone, plasmid pSRC27-H was found to include them. However, in one case the additional segment was smaller in pSRC27-H, lacking a transposon carrying a second resistance region in pHCM1. The sequences of IncHI1 plasmids, pO111_1 and pMAK1, were also examined and found to share the same or closely related additional segments. The structure of the additional material in pHCM1, pO111_1 and pMAK1 was examined, and potential novel transposons were identified. These additional segments define an IncHI1 lineage (pHCM1, pO111_1, pMAK1, pSRC27-H) which we designated type 2 to distinguish it from type 1 (R27, pAKU_1, pP-stx-12). A segment from the Escherichia coli genome and an adjacent copy of IS1 in pHCM1 was defined by comparison to pO111_1 and pMAK1, which lack it. pSRC27-H also lacks it. This structure is present in the same position in R27 and type 1 plasmids, but in the opposite orientation, and appears to have been incorporated via IS1-mediated transposition. The PCRs developed provide a simple means of distinguishing type 1 and type 2 IncHI1 plasmids based on the presence or absence of variable regions.