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PubMedDate not supplied

[Effect of R plasmid on cell membrane structure in Salmonella derby].

The structure of membranes of Salmonella derby cells both containing R-plasmid and free of plasmid was studied by small- and large-angle X-ray diffraction. Reflections with interplane distances of 8 and 11 A were detected, which are typical of plasmid-carrying S. derby cells. These reflections are assumed to be due to equidistant well ordered positions of the polar groups of phosphatidylcholine and phosphatidylethanolamine molecules on membrane surface. It is also suggested that the formation of these structures is determined by peculiar hydrophilic-hydrophobic interactions of the phospholipid in membranes.

Cell Membrane↗

PubMed1991

A chloramphenicol-streptomycin-resistance plasmid from a clinical strain of Staphylococcus sciuri and its structural relationships to other staphylococcal resistance plasmids.

A 5.1-kb plasmid, designated pSCS12, isolated from a naturally occurring Staphylococcus sciuri conferred resistance to chloramphenicol (CmR) and streptomycin (SmR). Restriction endonuclease analyses of pSCS12 revealed partial structural homologies to the CmR-plasmids pC221 from S. aureus and pSCS1 from S. intermedius, to the SmR-plasmids pSAI-1 from S. hyicus and pS194 from S. aureus, as well as to the CmR/SmR plasmid pSK68 from S. aureus. Southern-blot hybridization with specific CmR- and SmR-gene probes confirmed these similarities and allowed the mapping of the CmR- and SmR-determinants in the S. sciuri plasmid pSCS12. These observations lead to the suggestion that CmR/SmR-plasmids, such as pSCS12, may have evolved from CmR- and SmR-plasmids by interplasmidic recombination.

Chloramphenicol Resistance↗

PubMed1995

Mechanism of post-segregational killing: secondary structure analysis of the entire Hok mRNA from plasmid R1 suggests a fold-back structure that prevents translation and antisense RNA binding.

The hok/sok system of plasmid R1 mediates plasmid stabilization by killing of plasmid-free cells. The Hok mRNA is very stable and can be translated into Hok killer protein. Translation of the Hok mRNA is inhibited by the small unstable Sok antisense RNA. Translation of hok is coupled to an overlapping reading frame termed mok. Translation of mok is tightly regulated by Sok RNA, and Sok RNA thus regulates hok translation indirectly through mok. The rapid decay of Sok RNA explains the onset of Hok synthesis in newborn plasmid-free segregants. However, a second control level is superimposed on this simple induction scheme, since the full-length Hok mRNA was found to be translationally inactive whereas a 3'-end truncated version of it was active. We have therefore previously suggested, that the 3'-terminal region of the full-length Hok mRNA encodes an element which prevents its translation. This element was termed fbi (fold-back inhibition). Here we describe the in vitro secondary structure of the entire Hok mRNA. Our results suggest a closed structure in which the 3'-end of the full-length Hok mRNA folds back onto the translational initiation region of mok. This structure explains why full-length Hok mRNA is translationally silent. The proposed structure was further supported by results obtained using mutations in the 3'-end fbi element. These "structure closing" mutations affected the structure much further upstream in the mok translational initiation region and concomitantly prevented antisense RNA binding to the same region of the mRNA. These results lend further support to the induction model that explains onset of Hok mRNA translation in plasmid-free segregants. The most important regulatory element in this model is the FBI structure formed between the 3'-end and the mok translational initiation region. This structure renders Hok mRNA translationally inactive and prevents antisense RNA binding, thus allowing the accumulation of a pool of mRNA which, by slow 3'-end processing, is activated in plasmid-free segregants, eventually leading to the elimination of these cells.

Bacterial Proteins↗

PubMed1995

Overproduction of the ATP-dependent nuclease AddAB improves the structural stability of a model plasmid system in Bacillus subtilis.

The effect of the ATP-dependent exonuclease AddAB complex on the structural stability of plasmid pGP1 in Bacillus subtilis was studied. Using deletion mutagenesis and gene amplification techniques, B. subtilis strains were constructed either lacking or overproducing the AddAB complex, a key enzyme in homologous recombination. The deletion mutant possessed no residual ATP-dependent nuclease activity; in contrast, the nuclease activity was up to 30 times higher in lysates of strains carrying multiple copies of the addAB genes in the chromosome. Southern blot analyses of these strains indicated that a linear relationship exists between the number of chromosomal gene copies and the level of AddAB activity. The structural stability of pGP1 was analyzed in the AddAB-deficient and over-producing backgrounds. Frequencies of deletion formation in the plasmid, as monitored by the expression of the pGP1-encoded penP-lacZ fusion on media containing X-gal, were shown to be increased at least 25-fold in the addAB knock-out mutant, whereas the stability of pGP1 was improved up to 15-fold in strains overproducing the AddAB enzyme. A possible explanation for these findings is that interactions between AddAB and plasmid molecules prevent the formation of secondary structures that constitute potential deletion target sites, and thereby enhance the structural stability of plasmids.

Bacillus subtilis↗

PubMed1998

Segregational and structural instability of recombinant plasmid carrying genes for naphthalene degrading pathway.

The stability of recombinant plasmid carrying genes for naphthalene mineralization was determined. A strain of Pseudomonas putida capable of mineralizing naphthalene (Nap+) via salicylate (Sal+) was isolated, and all regulatory and structural genes for the whole pathway were found to be encoded on a 25 kb EcoRI fragment of an approximately 83 kb plasmid present in this strain. The 25 kb EcoRI fragment was cloned into a tetracycline-resistant (TcR) cloning vector pLAFR3 and the recombinant plasmid, pRKJ3 (Nap+, Sal+, TcR), thus obtained was transferred into the plasmid-free strain Pseudomonas putida KT2442 in order to test the stability of the plasmid. Plasmid pRKJ3 was found to be segregationally and/or structurally unstable, depending on the growth conditions. Two types of novel derivative strains having the phenotypes Nap-, Sal+, TcR and Nap-, Sal-, TcR with specific deletions of approximately 2 kb and 18 kb, respectively, were obtained.

Electrophoresis, Agar Gel↗

PubMed1991

Specific structural probing of plasmid-coded ribosomal RNAs from Escherichia coli.

The preferred method for construction and in vivo expression of mutagenised Escherichia coli ribosomal RNAs (rRNAs) is via high copy number plasmids. Transcription of wild-type rRNA from the seven chromosomal rrn operons in strains harbouring plasmid-coded mutant rRNAs leads to a heterogeneous ribosome population, which consequently hinders direct probing of mutant rRNAs. Here, we describe how nonconserved helical regions of plasmid-coded rRNA have been altered in a manner that preserves their secondary structures while creating new sites for primer extension of mutant rRNAs. This facilitates specific biochemical probing of mutagenised rRNA regions despite the background of wild-type molecules. Four priming sites have been made to investigate the structural effects of mutations in the GTPase centre, helix 1200-1250, the peptidyl transferase region and the alpha-sarcin loop of 23S rRNA.

Anti-Bacterial Agents↗

PubMed1995

Structural analysis of invasion plasmid antigen D (IpaD) from Shigella flexneri.

Invaison plasmid antigen D (IpaD) and water-extracted outer-membrane proteins (OMPs) from Shigella flexneri were used to investigate some of the structural relationships of this pathogen's invasions. Extracellular presentation of the three invasion plasmid antigens (Ipa) B, C, and D is required for the S. flexneri invasive phenotype; however, little is known of the structural properties of these essential virulence components. Biochemical data suggest IpaB, C, and D present in S. flexneri OMPs from soluble protein complexes and IpaD may be able to form large homopolymeric complexes.

Antigens, Bacterial↗

PubMed1982

Systematic alteration of the nucleotide sequence preceding the translation initiation codon and the effects on bacterial expression of the cloned SV40 small-t antigen gene.

In the preceding paper (Derom et al., 1981) we described the cloning in bacterial plasmids of the simian virus 40 (SV40) small-t antigen gene under transcriptional control of the bacteriophage lambda pL promoter. Systematic variation of the distance and/or nucleotide sequence between the Shine-Dalgarno ribosome interaction sequence and the small-t translation initiation codon leads to considerable differences in production of small-t by the different plasmids. Secondary structure models derived for the different mRNAs confirm our previous conclusions about the requirement first for an accessible start codon and second for an accessible ribosome interaction site for efficient translation initiation. Secondary structure models for mRNAs from plasmids containing the small-t gene under control of the lac promoter are in agreement with these conclusions.

Antigens, Viral↗

PubMed2026

Gene transfer from NDM-5-producing and OXA-48-producing Enterobacter hormaechei ST79 on contaminated dicloxacillin capsules to other Enterobacterales in Europe, 2020-23: a retrospective, observational, molecular epidemiological study.

BACKGROUND: In February, 2023, an outbreak of Enterobacter hormaechei ST79 carrying blaNDM-5 and blaOXA-48 was linked to contaminated dicloxacillin capsules administered to approximately 79 000 individuals in Denmark. Initial clonal outbreak investigations identified 11 patients with the E hormaechei ST79 outbreak strain, which carried blaNDM-5 on a distinct IncX3 plasmid, and in nine cases, blaOXA-48 was on a distinct IncL plasmid. Interspecies plasmid transfer was observed in one patient, suggesting a potential plasmid-mediated outbreak involving other Enterobacterales. However, no studies have characterised the progression of a clonal outbreak originating from a contaminated medicine into plasmid-mediated dissemination of carbapenemase genes. Hence, we aimed to characterise the clonal and plasmid-mediated spread of carbapenemase genes in this outbreak. METHODS: We conducted a retrospective genomic and epidemiological investigation using existing short-read whole-genome sequencing data from all carbapenemase-producing Enterobacterales (CPE) from the Danish national surveillance, collected between Jan 1, 2014, and Oct 1, 2023. All confirmed CPE isolates were eligible for inclusion. Using in-silico screening for unique fragments of the two outbreak plasmids, we selected 160 isolates for long-read sequencing to obtain complete plasmid sequences for outbreak investigation. Analyses were descriptive and included comparison of sequence identity and coverage to define outbreak-associated plasmids and summary statistics of patient characteristics. FINDINGS: Data from 1829 isolates were obtained. We detected 16 of 53 isolates involved in the outbreak using conventional outbreak detection methods. The remaining 37 isolates were detected using plasmid-specific screening and long-read sequencing. 15 patients carried the outbreak E hormaechei strain, including the 11 patients previously reported. Three of the 15 patients presented with at least one additional bacterial species carrying one or both outbreak plasmids (pDcap_OXA-48 and pDcap_NDM-5). A further 24 patients, sampled between July 1, 2020, and Oct 1, 2023, presented with other Enterobacterales carrying one or both outbreak-associated plasmids but not the original E hormaechei ST79 strain. In four cases, outbreak-associated plasmids differed structurally from the original outbreak plasmid. INTERPRETATION: This study describes how a clonal CPE outbreak caused by a contaminated medicine evolved into a complex plasmid-mediated outbreak involving multiple Enterobacterales species. Most patients related to the outbreak did not present with the original E hormaechei ST79 outbreak strain and were therefore not identified using standard outbreak detection methods. These findings highlight the importance of using plasmid-focused approaches in outbreak investigations. FUNDING: The Danish Ministry of Health, SSI-Seq (cofunded by EU4Health).

Humans↗

PubMed1988

Structural instability of a bifunctional plasmid pZG1 and single-stranded DNA formation in Streptomyces.

Structural instability of a hybrid plasmid pZG1, consisting of Escherichia coli pBR322 and Streptomyces pIJ350 plasmids, has been studied in Streptomyces. After transformation of S. lividans 1326 and S. rimsus R6 protoplasts with pZG1, transformants harbored the intact pZG1 and various deleted plasmid forms. The pattern of deleted plasmids varied with the transformant colony age and changed upon subcultivation. The presence of intact pZG1 in at least a part of the Streptomyces colonies indicated that the plasmid was capable of replicating in the transformants and that deletion events occurred after at least one round of replication. Less instability of pZG1 in S. rimosus R6 was observed when this strain was transformed with the DNA isolated from the same strain. pZG1 and its various derivatives were found in S. lividans 1326 and S. rimosus R6 as double- and single-stranded DNA molecules. Structural instability of pZG1 could therefore be due at least in part to the presence of single-stranded DNA.

Chromosome Deletion↗

PubMed1993

Allele-specific structure probing of plasmid-derived 16S ribosomal RNA from Escherichia coli.

Biochemical analysis of Escherichia coli ribosomes containing mutant 16S or 23S (r)ribosomal RNAs, produced via cloned rDNA genes on multicopy plasmids, has been hindered by the background of wild-type (wt) ribosomes containing host-derived rRNA. Here, we describe a method for the construction of unique priming sites in 16S rRNA that allow allele-specific structure probing of ribosomes containing plasmid-encoded RNA. Phenotypically silent mutations, designed to mimic related eubacterial sequences, have been introduced into four phylogenetically variable regions in the 16S rDNA gene that allow inspection of several 16S rRNA functional sites. When oligodeoxyribonucleotides complementary to these altered sequences are used to prime cDNA synthesis in primer extension reactions using reverse transcriptase, only plasmid-derived 16S rRNA is used as a template, thus rendering the wt background invisible. Unexpectedly, we were unable to introduce silent mutations into one nonconserved helix in 16S rRNA, suggesting that constraints in addition to Watson-Crick pairing are important in this region.

Alleles↗

PubMed1998

Structure and function of plasmid pColD157 of enterohemorrhagic Escherichia coli O157 and its distribution among strains from patients with diarrhea and hemolytic-uremic syndrome.

In this study, pColD157, a 6.7-kb colicinogenic plasmid of enterohemorrhagic Escherichia coli (EHEC) O157:H7 strain CL40cu, was characterized by restriction mapping and determination of its complete nucleotide sequence. The sequence consists of 6,675 bp and shows a high degree of similarity to the nucleotide sequence of colicinogenic plasmids pColD-CA23 and pColK. Seven potential genes were located on pColD157, three of which were closely related (>97.9%) to the colicin D structural gene and the corresponding immunity and lysis genes of plasmid pColD-CA23, and these were therefore designated cda, cdi, and cdl, respectively, using the reference extension -CL40 for differentiation. The adjacent 3' region is related to the origin of replication of pColD-CA23. In contrast, the remaining part of the plasmid harbors a cluster of genes, closely related to the mobilization genes of pColK, which is followed by a 0.3-kb stretch homologous to the pColK resolution function. These determinants were designated mbdA, mbdB, mbdC, and mbdD and cdr, respectively. Southern blot analysis was performed with a probe specific for the cda gene of pColD157 and two groups of EHEC O157:H7 isolates from patients with diarrhea or hemolytic-uremic syndrome resident in Germany. Whereas 16 of 46 E. coli O157 strains isolated between 1987 and 1991 harbored plasmid pColD157, only 1 of 50 strains isolated during 1996 carried this plasmid. In addition, all strains harboring plasmid pColD157 were shown to have colicinogenic activity.

Base Sequence↗

PubMed1989

Analysis of structural and biological parameters affecting plasmid deletion formation in Bacillus subtilis.

Deletions generated following stimulation by the deletion hot spot of plasmid pHV15-1 were studied in Bacillus subtilis. Nucleotide sequencing showed that deletions extend between short direct repeat sequences. Such direct repeat sequences may have homology to the sequence of the hot spot. Deletion formation is recE-independent, but requires an active exonuclease V (AddAB) enzyme. Other structural parameters like plasmid size and structure influence deletion formation.

Bacillus subtilis↗

PubMed2000

[Ecological effect of CdCl2 on plasmid and role of plasmid in Cd-tolerance of its host].

After treating the plasmid of Escherichia coli HB101 by CdCl2 in vitro or in vivo, the effect of Cd on the structure of plasmid pWH58 DNA was studied through argarose gel electrophesis and restriction fragment length polymorphism analysis. By comparing the growth of E. coli with and without plasmid cultured in the medium with Amp LB and non-anti LB under different concentrations of CdCl2, the effect of Cd on plasmid E. coli of in vivo and the role of plasmid in Cd-tolerance of its host were studied. Cd treatments of E. coli in vitro or in vivo didn't cause an obvious change of the structure of plasmid pWH58 DNA. Plasmid pWh58 could replicate for regeneration and gene express under Cd stress. Plasmid pWH58 of E. coli in vivo lowered Cd-tolerance of its host form 75 mg.L-1 to 50 mg.L-1. Cd-tolerance of E. coli ascended markedly after Cd taming, but had a trend of reversing to original level after restoration, indicating that Cd-tolerance of E. coli could be tamed, but the tamed Cd-tolerance still had no genetic basis.

Cadmium Chloride↗

PubMedDate not supplied

Structural alteration of linear plasmids encoding the genes for polychlorinated biphenyl degradation in Rhodococcus strain RHA1.

Polychlorinated biphenyl (PCB) tolerant derivatives of a strong PCB degrader, Rhodococcus strain RHA1, were selected after growth in the presence of 100 micrograms/ml PCBs. Some of the derivatives did not grow on biphenyl but accumulated a yellow coloured metabolite suggesting a defect in the meta-ring-cleavage compound hydrolase step encoded by the bphD gene. Other derivatives failed to grow on biphenyl and exhibited little PCB transformation activity suggesting a defect in the initial ring-hydroxylation dioxygenase step encoded by the bphA gene. These organisms had a structural alteration in the linear plasmids coding for the bph genes in RHA1, which included the bph gene deletion. When a bphD containing plasmid was introduced into a tolerant derivative, RCD1, which was shown to have bphD deletion, the defect in the growth on biphenyl of RCD1 was overcome. The bph gene deletion seems to play a key role in these tolerant derivatives thereby suggesting that the toxic metabolic intermediate would be a main cause of the growth inhibition of RHA1 in the presence of high concentration PCBs.

Benzene Derivatives↗

PubMedDate not supplied

An in vitro method generating base substitutions in preselected regions of plasmid DNA: application to structural analysis of the replication origin of the Escherichia coli K-12 chromosome.

A method for introducing base substitutions in defined regions of plasmid DNA has been developed. In principle, a circular heteroduplex DNA containing a gap is constructed by annealing of two kinds of linear molecules derived from the same plasmid: One is the molecule shortened either by exonucleolytic digestion from the termini generated at a restriction site or by removal of a region flanked by two restriction sites, and the other the full-length molecule linearized at a different site. The deleted region in the shorter linear molecule becomes a single-stranded gap in the circular heteroduplex DNA. The heteroduplex is then treated with sodium bisulfite that converts specifically cytosine residues to uracil residues in single-stranded regions. After filling in the gap by repair synthesis, transformation is carried out to isolate mutant plasmids. Since two kinds of circular heteroduplexes are formed by annealing in which the sequences in the gaps are complementary to each other, mutagenesis of both strands can be accomplished in one experiment. This method was applied to construction of mutants with base substitutions in the replication origin region (oriC) of the Escherichia coli K-12 chromosome which had previously been cloned in colicin E1 plasmid vectors, and various mutants in defined regions of oriC were successfully isolated at high efficiencies. Analysis of these mutants provided evidence that oriC contains special regions, designated spacers, which separate neighboring important sequences specifying interactions with initiation factors for DNA replication at precise distances.

Base Sequence↗

PubMed2001

Integrated structures of the linear plasmid SCP1 in two bidirectional donor strains of Streptomyces coelicolor A3(2).

The linear plasmid SCP1 is integrated into the central region of the chromosome of Streptomyces coelicolor A3(2). The integrated structures of SCP1 in two bidirectional donor strains, 2612 and A634, were analyzed by cloning and sequencing of the junctions between the SCP1 DNA and the chromosomal DNA. In the NF (normal fertility) strain 2612, SCP1 is integrated in a right-handed direction into ORF-X at the left end of the IS cluster in AseI fragment E. An almost intact left end of SCP1 is retained, while the right terminal inverted repeat (TIR-R) of SCP1 and a 33-kb chromosomal DNA segment including the IS cluster are deleted. In the NF-like strain A634, SCPI is also integrated into AseI fragment E in a left-handed direction. The left junction is composed of IS466 with complete deletion of TIR-R of SCP1, and the right junction is located at the left end of IS468A* with half of TIR-L being deleted. During the integration event, a 5.4-kb chromosomal DNA segment including IS468A, IS468B, IS469 and IS466A was duplicated so that this sequence is now present on both sides of SCP1. Since 2612 and A634 exhibit a similar bidirectional gradient of gene transfer, it is surprising that their chromosomal structures are so different.

Base Sequence↗

PubMed2002

Construction of pGFP-FL plasmid and its application in preparing FL-secreting tumor vaccine.

OBJECTIVE: To construct a plasmid containing a green fluorescent protein (GFP) reporter gene as the effective vector for preparing fms-like tyrosine kinase receptor-3 ligand (FL)-secreting tumor vaccines. METHODS: A pGFP-FL plasmid, harboring a FL gene and a GFP gene, was designed and constructed by routine molecular cloning techniques. In this plasmid, FL gene was under the control of cytomegalovirus promoter, while EF-1a promoter acted to drive GFP gene. A prokaryotic/eukaryotic selective gene Kan(R)/neo was also introduced into the plasmid. After structure identification by restriction analysis, pGFP-FL plasmid was further transferred into Hepa1-6 cells, and the expression of GFP and FL genes was examined by way of fluorescent microscopy and reverse transcriptase-PCR respectively. RESULTS: Restriction analysis showed that the structure of pGFP-FL plasmid was exactly the same as anticipated. Further results indicated that both GFP and FL genes were simultaneously expressed in Hepa1-6 cells. CONCLUSION: A new plasmid has been established as the vector for studying the FL-secreting tumor vaccines, in which GFP gene can serve as a reporter gene reflecting the expression of FL gene.

Animals↗