Isolation and sequencing of the replication region of plasmid pBFp1 isolated from a marine biofilm

A 24 kb plasmid, pBFp1, encoding mercury resistance was previously isolated from a marine biofilm. Isolation and sequencing of a 4280 bp DNA fragment containing the plasmid replicon (rep-pBFp1) revealed a putative open reading frame encoding a RepA protein and an oriV-like region containing an A+T rich sub-region, iterons, and DnaA boxes. Sequence comparisons showed significant similarities to the incW plasmid pSa both for the RepA amino acid sequence and in the iteron DNA sequence. Plasmid pBFp1 was also shown to be incompatible with pSa in standard incompatibility testing. A probe from the repA gene of pBFp1 was further made and tested on a collection of plasmids exogenously isolated from marine habitats in a previous study.     

Analysis of replication region of the cryptic plasmid pAG20 from Acetobacter aceti 3620

The DNA sequence of small cryptic plasmid pAG20 in Acetobacter aceti was determined at 3064 bp with 51.6% GC pairs. The plasmid encoded a 186 amino acid protein which is important for plasmid replication in Gram-negative bacteria except Escherichia coli. Two 21 bp large direct repeat sequence 1 and two 13 bp direct repeat sequence 2 were determined in the regulation region upstream from gene encoded Rep protein. Vector pAG24 with kanamycin gene and two deletion derivatives pAG25 and pAG26 without rep gene from plasmid pAG20 were constructed. Plasmid pAG24 was replicated in a broad host range like E. coli, Acetobacter pasteurianus, A. aceti, Comanomonas spp., Serratia marcescens, and Shigella spp.     

Elimination of R plasmids from the photosynthetic bacterium Rhodobacter capsulatus

Rhodobacter capsulatus (formerly Rhodopseudomonas capsulata) could be cured of R plasmids of the P1 incompatibility group, including derivatives used as cloning vectors, by repeated subculturing in a growth medium containing only yeast extract and peptone (YP medium). Loss of R plasmid material from the cells was complete, as shown by agarose gel electrophoresis, and by the absence of hybridization between total DNA and radioactively labelled R plasmid DNA. Prolonged subculturing in YP medium often resulted in the accumulation of auxotrophs, and led to the appearance of strains containing chromosomal insertions of plasmid DNA.     

Isolation of plasmids present in thermophilic strains from hot springs in Jordan

The plasmid profile of two thermophilic bacterial strains isolated from recreation thermal springs in Jordan has been investigated. These strains are Streptococcus thermophilus and Bacillus sp1, which have been isolated from Zerka – Maeen and Himma hot springs respectively. Supercoiled and circular plasmid forms were detected, explaining the effect of DNA conformation on the mobility of the plasmid in the agarose gel electrophoresis. Two plasmids have been isolated and characterized by restriction endonucleases to facilitate their use as cloning vectors in thermophilic strains. The sizes of the plasmids were approximately 3 kb (from Streptococcus thermophilus) and 7 kb (from Bacillus spl). These plasmids were then digested with three different restriction enzymes (EcoRI, Bam HI, and HindIII), one of which was found to possess a single site for both plasmids, this enzyme is EcoRI.     

Conjugal transfer of antibiotic resistances and plasmids from Campylobacter jejuni clinical isolates

Six Campylobacter jejuni clinical isolates were examined for the occurrence of plasmids in association with antibiotic resistances as well as conjugal transfer. All the isolates were found to carry three similar plasmids of 78 kb, 12.6 kb and 3.3 kb in size. Multiple resistance to at least three of the antibiotics tested was observed with resistance to tetracycline most common. En bloc transfer of donor resistances at frequencies ranging from 10(-8) to 10(-4) were seen in all but one of the isolates during conjugation. The conjugal transfer of erythromycin, neomycin and streptomycin were observed to occur at frequencies similar to that of chloramphenicol, kanamycin and tetracycline. In isolate ABA94, three different antibiotic resistance phenotypes of the transconjugants were seen. In addition to en bloc transfer of the donor resistances, in approximately 10% of the transconjugants the streptomycin resistance was lost although these transconjugants carried the donor complement of three plasmids. In a further 1% of the transconjugants, resistance to kanamycin only was detected and these transconjugants did not carry any plasmids.     

Approaches to investigating the ecology of plasmids in marine bacterial communities

To better understand prokaryotic gene flux in marine ecosystems and to determine whether or not environmental parameters can effect the composition and structure of plasmid populations in marine bacterial communities, information on the distribution, diversity, and ecological traits of marine plasmids is necessary. This mini-review highlights recent insights gained into the molecular diversity and ecology of plasmids occurring in marine microbial communities.     

The plasmids found in isolates of the acidothermophilic archaebacterium Thermoplasma acidophilum

Abstract Plasmids were detected in isolates of an acidothermophilic archaebacterium Thermoplasma acidophilum . One of the plasmids, pTA1, was characterized. The plasmid was a circular DNA of 15.2 kbp. A physical map was constructed using three restriction endonucleases. A copy number of this plasmid was estimated to be 7–13 per cell. The homologous sequence was not found in the chromosomal DNA of the host cell.     

Detection and characterization of naturally occurring plasmids in Bacillus licheniformis

Twenty-two Bacillus licheniformis strains, freshly isolated from pasture-land, were studied for the presence of plasmid DNA. Among these strains, 14 were shown to harbor one or more plasmids of different size. Southern-hybridization experiments showed a high homology between all plasmids investigated and a 2.2-kb PvuII/HindIII fragment of pBL1, a B. licheniformis plasmid previously isolated. Three fragments of pBL1, including the 2.2-kb PvuII/HindIII region, were cloned into pJH101 vector. The resulting chimeras were able to transform Bacillus subtilis. The fragment with high homology probably contains the region with the replicative functions of plasmids from B. licheniformis species.     

Stability and transmissibility of the cryptic plasmids of Rhizobium meliloti GR4

Rhizobium meliloti strain GR4 harbours two cryptic plasmids sharing extensive regions of homology between them and with other non-symbiotic plasmids of different strains of R. meliloti. They both are very stable showing a segregation rate of less than 0.1% loss per generation. pRmeGR4a (115 MDa) is a self-transmissible plasmid at a variable frequency to other species, and it is also responsible for promoting, at low frequency, the contransfer of pRmeGR4b (140 MDa), the other cryptic plasmid of the strain. A 4.8 kb PstI fragment of pRmeGR4a, responsible for the high stability in cis of this plasmid, has been isolated and several recombinant plasmids have been constructed showing different segregation rates in the strains used in this study. Their stabilities can be considerably improved by insertion of the stabilization mrs/par region of RK2.     

Detection of the etx gene (ε-toxin inducer) in plasmids of high molecular weight in Clostridium perfringens type D

The purpose of this work is to correlate the production of epsilon-toxin in a set of strains of Clostridium perfringens type D with the presence of the etx gene, either genomic or in plasmids. Total DNA obtained from strains with a different level of toxin production was explored by PCR and all the strains showed the amplification signal. Different methods were used to obtain plasmid profiles and all of the bands were assayed by PCR. The detection of the etx gene was only shown in several high molecular plasmids. These results were confirmed by a Southern blot. We suggest that the localization of the etx gene in different plasmids could be associated with the epsilon-toxin production level.     

光遗传学工具的开发及其应用研究

细胞所处微环境的动态变化对细胞分化、细胞信号通路、个体生长以及疾病等有很大影响。光遗传学技术利用基因编码蛋白质表达并结合光控的手段为动态调控细胞信号通路、细胞定位和基因表达等方面提供了一种全新、无损、可逆、非侵入、时空特异性的研究手段。文中总结了光遗传学元件的类型以及涉及的细胞信号通路,并探讨了光控细胞信号通路的应用与未来发展前景。     

Analysis of the sequence of a new cryptic plasmid, pRJF2, from a rumen bacterium of the genus Butyrivibrio: Comparison with other Butyrivibrio plasmids and application in the development of a cloning vector

Abstract A small cryptic plasmid, pRJF2, from Butyrivibrio fibrisolvens strain OB157 was isolated and sequenced. The plasmid is similar in organisation to the previously sequenced Butyrivibrio plasmid, pRJF1, with two open reading frames, ORF1 and ORF2, flanking a region tentatively identified as the replication origin, and a region of unknown function defined by terminal 79 bp invert repeats. The sequences of ORF1, ORF2, and the presumptive replication origin are highly conserved. The sequence between the 79 bp invert repeats is not, and is therefore presumed to be of lesser functional significance, although the 5' and 3' termini are still highly conserved. The functional importance for plasmid replication of these regions was tested by constructing potential shuttle vectors, each lacking one or more of the regions of interest. When the region between the invert repeats was deleted and replaced by the erythromycin resistance gene from pAM β1 together with pUC18, to produce the 7.9 kb chimaeric plasmid pYK4, the construct was successfully transformed into E. coli and B. fibrisolvens by electroporation, and was stably maintained in both hosts. Both ORF1 and ORF2 were required for successful transformation of B. fibrisolvens .     

Specificity of the interactions between the Rep proteins and the origins of replication of Staphylococcus aureus plasmids pT181 and pC221

Summary pT181 and pC221 are closely relatedStaphylococcus aureus plasmids with the same genome organization, which is characterized by the overlapping of the origin of replication with the sequence encoding a protein, Rep, essential for plasmid replication. Former results have shown the lack of in vivo cross-complementation between these two plasmids, while in vitro studies have revealed the ability of both Rep proteins to act on either origin. One possible explanation for this difference was based on a previous analysis of the incompatibility expressed by the origin of replication of these plasmids, showing that the origin embedded in therep gene competes for Rep utilization with the origin of a test plasmid and that changes in the sequence of the origin reduce its ability to compete. To avoid this problem, in the present work special hybrids were constructed in which the origin of replication overlapping therep gene was mutationally inactivated, without changing the amino acid sequence of the encoded protein. The level of Rep expression by these hybrids could be varied by taking advantage of what is presently known about the control of Rep synthesis in plasmid pT181. The results of complenentation studies conducted using these hybrids have shown that: (i) at the usual level of expression for a wild-type plasmid each Rep protein can initiate replication strictly from its corresponding origin; (ii) when overproduced, the pT181 RepC protein could also act efficiently on the pC221 origin; a functional pT181 origin present in the same host completely prevented this complementation; (iii) in excess, the RepD protein encoded by pC221 could replicate a plasmid carrying the pT181 origin but could not ensure the hereditary stability of such a plasmid in the absence of another active replication system; (iv) when overproduced both RepC and RepD could act on the origin of replication of three other related plasmids pS194, pC223 and pUB112.     

Development and use of molecular diagnostic tools to determine trophic links and interspecific interactions in aphid-parasitoid communities in Hawaii

There has been much debate regarding the impact of parasitoid competition and hyperparasitism on the successful biological control of aphid pests. Difficulty in the evaluation of interspecific interactions and trophic links using conventional rearing and dissection methods has prevented a deeper understanding of such relationships. The analysis of trophic links in the parasitoid community associated with the melon aphid (Aphis gossypii) in Hawaii provides a unique opportunity to assess complex interactions that occur in a system where all of the aphids and parasitoids have been introduced. Here, we developed and applied multiplex PCR assays to investigate the occurrence of in-host competition between parasitoids and/or hyperparasitoids on melon aphids collected from fields of Colocasia esculenta. To fully document the parasitoid-hyperparasitoid community within A. gossypii, both live and mummified aphids were examined. A total of 818 live and 245 mummified aphids were analyzed using the multiplex assays, with congruent rearing of over 600 mummified aphids serving as a basis for qualitative comparisons in terms of species composition and trophic linkages. The rearing and the DNA methods showed similar trends, with sharp declines in one parasitoid species followed by sharp increases in another during the course of the season. Molecular analyses revealed that hyperparasitism and multiparasitism of live aphids is remarkably low, whereas hyperparasitism of mummified aphids was extraordinarily high in both rearing and molecular analyses. In comparison to reared samples, molecular analysis of the parasitoid community was more complete and permitted the identification of previously unknown or unconfirmed trophic linkages. The potential of this approach in future studies on the biological control of aphids in Hawaii, particularly in light of new parasitoid introductions, is discussed.     

大熊猫轮状病毒PCR检测方法的建立及应用

轮状病毒是威胁大熊猫健康的主要病原微生物之一。为了对大熊猫轮状病毒进行快速、方便且准确地检测,研发适合于基层饲养单位和保护区的检测方法是非常有必要的。本研究通过合成大熊猫轮状病毒Vp7基因序列,构建了PUC-VP7的重组质粒,并将其作为阳性对照对大熊猫轮状病毒样本进行PCR检测和分析。结果表明,在进行PCR扩增分析时,该质粒和病毒cDNA二者均在340 bp处出现了特异性条带。此外,对收集到的45份大熊猫粪便样本进行轮状病毒抗原检测时,其中2份样品在340 bp处出现条带,该基因片段与大熊猫轮状病毒CH-1株的相似性为99.89%。本研究构建的PUC-VP7质粒不但可以作为大熊猫轮状病毒PCR检测中的阳性质控品,而且还能有效地促进该PCR病毒检测技术在基层饲养单位和保护区的推广和应用。     

Diversity of mercury resistance plasmids obtained by exogenous isolation from the bacteria of sugar beet in three successive years

Abstract: Self-transmissible plasmids conferring mercury resistance were exogenously isolated from the bacterial populations of sugar beet roots (rhizoplane) and leaves (phyllosphere) into a Pseudomonas putida recipient. Fifty rhizoplane plasmids and 29 phyllosphere plasmids (60–383 kb) were purified. Numerical analysis of plasmid DNA restriction enzyme digest patterns identified five distinct groups. Three of these plasmid groups were isolated from sugar beet crops grown at the same site over three consecutive years, demonstrating their established presence. Each group of plasmids comprised individual isolates with structural additions or deletions. The frequency of exogenous isolation correlated with factors likely to influence plant growth, bacterial activity and the physiological state of donors prior to sampling. All plasmids investigated conferred narrow spectrum mercury resistance with a reductase detoxification mechanism. None of the plasmids conferred resistance to a range of antibiotics, other heavy metals, or to UV, and following transfer to recipient bacteria the range of carbon source utilisation was not altered. This is the first report of the persistence of Pseudomonas spp. plasmid structural types isolated over several years from a terrestrial habitat.