Both open reading frames of the linear plasmid pMC3-2 from the ascomycete Morchella conica are transcribed in vivo

Mitochondrial RNA was isolated from the morel strain Morchella conica 3 harbouring the linear plasmid pMC3-2 and subjected to gel electrophoresis followed by a Northern analysis using cloned fragments of the plasmid pMC3-2 as probes. Hybridization was obtained only with central parts of pMC3-2 and specific bands of mtRNA. The hybridization bands (2.8 kb and 1.0 kb) correspond in size to the length of the two ORFs of pMC3-2 which were deduced from nucleotide-sequence data. Thus, both ORFs, one encoding a DNA polymerase and the other a yet unknown protein, are transcribed in the mitochondria of the plasmid-bearing Morchella conica strain.     

Cloning of maltase regulatory genes in Saccharomyces cerevisiae

Summary By hybridization with a putative MAL2p regulatory sequence we have identified a 19 kb long BamH1 DNA fragment to contain the MALp sequence in a MAL4 strain. A mixture of recombinant plasmids was prepared by ligation of purified 19 kb BamH1 fragments partially digested with Sau3A into the multicopy vector YEp1357. The source of DNA was a strain carrying the MAL4 locus. Yeast maltose non-fermenting strains were transformed with the plasmid mixture. A recombinant plasmid, pRM-4, containing the MAL4p regulatory gene was isolated that complements the maltose-negative phenotype. The plasmid was shown to confer the ability to synthesize maltase to recipient strains grown under inducing as well as under repressing conditions.The MAL4p regulatory sequence cloned was used as a probe in hybridization experiments to study the degrees of homology between the different MAL regulatory genes. The results showed that the sequence from MAL4 strains is strongly homologous to that of MAL3 strains whereas it shows significant differences to the ones of MAL1 and MAL2 strains.Southern analysis of the segregants of crosses between maltose-positive strains and ma10 strains allowed us to localize the maltase regulatory sequence of each MAL locus within a characteristic BamH1 fragment of genomic DNA hybridizing to the isolated sequence.     

Characterization of non-virulence plasmids with homology to the virulence plasmid of Salmonella dublin

Six wild-type (wt) strains of Salmonella typhimurium, one wt strain of S. heidelberg and 12 wt strains of Escherichia coli were isolated based on both hybridization to a 6-kb HindIII fragment of the non-virulence coding part of the S. dublin serovar-specific virulence plasmid and the absence of hybridization to the virulence genes (spv genes) of the same plasmid. Such hybridization was shown to be caused by resident plasmids in all strains and to involve the same region of 30 to 37 kb of consecutive HindIII fragments on the S. dublin virulence plasmid, suggesting a common origin of this plasmid DNA. Nine of the plasmids were selected for detailed characterization and were shown not to be of the same plasmid species. They varied in size between 44 and 88 kb, they showed incompatibility with the plasmid K-MP10, or belonged to incompatibility group X, and with the exception of five plasmids from E. coli, they showed different HindIII restriction profile patterns.     

Cloning and expression on a multicopy vector of five invertase genes of Saccharomyces cerevisiae

Summary Six unlinked loci for invertase structural genes are known in the yeast Saccharomyces cerevisiae: SUC1-SUC5 and SUC7. These genes are similar in structure and expression but not identical. Different yeast strains possess none, one or several of these genes.We have isolated the genes SUC1-SUC5, subcloned them into the multicopy vector YEp24 and compared the expression of the five SUC genes in one recipient strain. SUC2 was isolated by transformation of a suc0 strain with a gene pool and complementation to sucrose fermentation. SUC4 was cloned from a minipool of chromosomal fragments which were shown to contain SUC4 by Southern hybridization. SUC1, SUC3 and SUC5 were isolated using the method of plasmid eviction. A plasmid containing regions flanking SUC4 was integrated next to these SUC genes. The plasmid together with the SUC genes were then cut out of the chromosome using an appropriate restriction endonuclease.The length of chromosomal DNA fragments containing the different SUC genes were 4.8 kb for SUC1, 5.2 kb for SUC2, 4.8 kb for SUC3, 12.8 kb for SUC4 and 17.2 kb for SUC5.Fragments containing the complete SUC genes and the sequences controlling their expression were subcloned into YEp24 and transformed into a strain without any active invertase gene. Invertase activity of transformants was measured after growth repressing (8% glucose) and derepressing (2% raffinose) conditions. As expected from results with strains carrying the individual SUC genes in a chromosomal location, the SUC genes were expressed to a different extent.Dedicated to Prof. Dr. Fritz Kaudewitz on the occasion of his 65th birthdayThis work was supported by Deutsche Forschungsgemeinschaft     

Identification of autonomous replication sequences in genomic and mitochondrial DNA of Crithidia fasciculata

High frequency transformation of Saccharomyces cerevisiae was used as a functional assay to isolate autonomous replication sequences (ars) from the genomic and kinetoplast DNA of the insect trypanosomatid Crithidia fasciculata. Three independent cloned genomic sequences and one kinetoplast DNA sequence promoted high frequency transformation and extrachromosomal maintenance of the YIp5 plasmid DNA in yeast. The kinetoplast DNA clone was sub-cloned to further localize the DNA sequence essential for ars activity. This element was shown to be contained in a 2 kb HindIII-EcoRI fragment derived from a 8 kb HindIII fragment of the maxicircle component of the kinetoplast DNA. This 2 kb fragment is within a DNA sequence that has been shown to strongly hybridize to Trypanosoma brucei maxicircle DNA.     

Demonstration of extrachromosmal DNA fromBabesia equi merozoites

An extrachromosomal nucleic acid element was detected in high-molecular-weight DNA preparations formBabesia equi merozoites. This extrachromosomal element was shown to be DNA rather than RNA and had an apparent fragment size of about 9 kilobasepairs (kb). Hybridization experiments using purified 9-kb DNA as a probe revealed sequence homologies with extrachromosomal DNA from two otherBabesia species.     

Construction of an R-prime plasmid carrying the hup genes of Azorhizobium caulinodans ORS571 and its transfer to and stability in Rhizobium meliloti

An R-prime plasmid (pJB3JI-18) carrying a 10 kb region of Azorhizobium caulinodans ORS571 DNA which codes for uptake hydrogenase activity was isolated from a Km⁸ derivative of R68.45. R-prime plasmids were obtained by transferring R68.45 to ORS571, retransferring it to E. coli, and selecting transconjugants for hydrogenase activity by means of a colour test based on methylene blue. The R-prime plasmid DNA was hybridized with a DNA region which contained the hup genes of Bradyrhiobium japonicum, indicating homology between the heterologous hup genes. Transfer of the R-prime plasmid to different Hup^? mutants restored the Hup⁺ phenotype. When it was introduced to R. meliloti strains, it maintained its molecular weight and did not affect indigenous plasmids in two of three recipients. In the third recipient cointegrate formation and incompatibility with indigenous plasmids were found.     

Characterization of a linear DNA plasmid from the filamentous fungal plant pathogen Glomerella musae [Anamorph: Colletotrichum musae (Berk. & Curt.) Arx.]

A 7.4-kilobase (kb) DNA plasmid was isolated from Glomerella musae isolate 927 and designated pGML1. Exonuclease treatments indicated that pGML1 was a linear plasmid with blocked 5′ termini. Cell-fractionation experiments combined with sequence-specific PCR amplification revealed that pGML1 resided in mitochondria. The pGML1 plasmid hybridized to cesium chloride-fractionated nuclear DNA but not to A + T-rich mitochondrial DNA. An internal 7.0-kb section of pGML1 was cloned and did not hybridize with either nuclear or mitochondrial DNA from G. musae. Sequence analysis revealed identical terminal inverted repeats (TIR) of 520 bp at the ends of the cloned 7.0-kb section of pGML1. The occurrence of pGML1 did not correspond with the pathogenicity of G. musae on banana fruit. Four additional isolates of G. musae possessed extrachromosomal DNA fragments similar in size and sequence to pGML1. Received: 27 June 1996 / 2 April 1997     

Cloning of the orotidine 5′-phosphate decarboxylase (ODC) gene of Schwanniomyces occidentalis by complementation of the ura3 mutation in S. cerevisiae

Summary A DNA fragment containing the gene encoding orotidine 5-phosphate decarboxylase (ODC) from the yeast, Schwanniomyces occidentalis (formerly castellii) has been isolated from a genomic library constructed in the S. cerevisiae expression vector, pYcDE8. A recombinant plasmid, p2-lA, containing a 2.47 kb insert was shown to complement the ura3-52 mutation of several strains of S. cerevisiae. This DNA insert was shown to be from Schwanniomyces occidentalis by Southern hybridization analysis. A restriction enzyme cleavage map of the insert has been derived and the ODC gene localized to a 1.1 kb region by deletion analysis. In addition, we have demonstrated that expression of ODC is not dependent on the ADHI promoter carried on pYcDE8. This is the first report of the cloning of a gene from a member of the genus Schwanniomyces.     

Analysis of the prevaccine population of noncapsulateHaemophilus influenzae and identification of a putative epidemic clone

For six months prior to the introduction ofHaemophilus influenzae serotype b vaccines, all noncapsulateHaemophilus influenzae received by our laboratory were characterised by biotyping, antibiogram, outer-membrane protein profiling, and ribotyping. Simpson's index of diversity (SID) showed the population was heterogeneous with multiple clones. The study identified a clone within noncapsulateHaemophilus influenzae biotype II that caused more disease than other strains. This clone was shown to have previously caused two outbreaks of respiratory disease and to possess a small extrachromosomal plasmid encoding ampicillin resistance. The study shows that describing the diversity within a bacterial population with SID may negate the need for retrospective subtyping comparisons.     

Trehalose and maltose metabolism in yeast transformed by a MAL4 regulatory gene cloned from a constitutive donor strain

Summary A 6.8 kb fragment of DNA containing the regulatory sequence MAL4p has been cloned from a genomic library prepared from Saccharomyces cerevisiae strain 1403-7A which ferments maltose constitutively. The library was prepared by ligation of 5–20 kb Sau3AI restriction fragments of total yeast DNA into the BamH1 restriction site of shuttle vector YEp13. A restriction map of the cloned fragment indicates that it encompasses a 2.6 kb segment which closely resembles the regulatory MAL6 gene previously identified (Needleman et al. 1984). The hybrid plasmid, p(MAL4p)4, could transform maltose-nonfermenting strains which contain cryptic -glucosidase and maltose permease genes (malp MALg), but could not transform strains containing a functional regulatory sequence and a defective maltase-permease region (MAlp malg). A correlated absence of maltase and permease DNA from the cloned fragment was indicated by the restriction map. Although the cloned DNA fragment was derived from a constitutive strain, maltose fermentation and -glucosidase formation by yeast transformed with p(MAL4p)4 was largely inducible by maltose and sensitive to catabolite repression. Moreover, the active trehalose accumulation pattern (TAC(+) phenotype) linked to the complete MAL4 locus in strain 1403-7A and other constitutive MAL strains (Oliveira et al. 1981b) was not found in p(MAL4p)4 transformants. It may be concluded that constitutivity of maltose fermentation and the associated active trehalose accumulation are not merely consequences of a cis-dominant mutation causing constitutive formation of the MALp regulatory product. Moreover, constitutivity may not be caused solely by a mutation within the structural region of the MALp gene.     

Molecular Characterization and Transfer Among Staphylococcus Strains of a Plasmid Conferring High-Level Resistance to Mupirocin

 In this work, mupirocin resistance was correlated with the presence of plasmids in methicillin-resistant Staphylococcus aureus (MRSA) strains isolated in the Rio de Janeiro Federal University Hospital in Brazil, where topical mupirocin has been used extensively since 1990. Of 19 strains studied, those exhibiting high-level resistance carried a large and relaxable plasmid of about 35 kb. Mupirocin-sensitive derivatives, obtained by growth at 42  °C of a strain exhibiting high-level resistance, were devoid of the large plasmid, which was designated pMG1. Mupirocin resistance was transferred to strain RN8411 during overnight filter-matings at low frequencies (7.0×10^–9/donor). The pMG1 plasmid was shown to be responsible for high-level mupirocin resistance in our isolates and to be incompatible with pGO1. Hybridization experiments suggested that mupirocin resistance in pMG1 is due to the presence of the ileS-2 gene. The pMG1 plasmid was successfully and bidirectionally transferred from Staphylococcus aureus to Staphylococcus epidermidis, suggesting that the latter may be a reservoir of this resistance plasmid. No transfer was detected to Staphylococcus haemolyticus. The development of self-transferable high-level mupirocin resistance should be considered when using mupirocin to control the spread of MRSA in hospitals.     

Integrative and replicative genetic transformation of Aureobasidium pullulans

A hybrid selectable marker for transformation was constructed by placing the promoter (TEF1p) from the gene encoding the Aureobasidium pullulans translation elongation factor 1- (TEF1) adjacent to the 5 end of the Escherichia coli hygromycin B phosphotransferase gene (HPT). Plasmids containing this hybrid gene (TEF1p/HPT) transformed A. pullulans strain R106 to a hygromycin B-resistant (HmB^R) phenotype. A PCR-generated DNA fragment consisting of the TEF1p/HPT resistance marker flanked by 41 bp of homologous DNA has also been shown to transform A. pullulans to HmB^R. Linearized plasmid DNA consistently produced more transformants than circular plasmid DNA. Analyses of 23 HmB^R transformants revealed integration of the plasmid in only eight of these transformants. In two transformants, integration into the largest chromosome (VIII) resulted in an alteration of the molecular karyotype. In four other transformants, integration occurred in chromosome VI (the chromosome containing TEF1) but only one was the result of homologous recombination with the genomic copy of the TEF1 promoter. The remainder of the transformants contained replicative plasmids that could be visualized on an agarose gel by ethidium bromide staining. These plasmids were generally 7–8 kb in size. One transformant appeared to contain four plasmids ranging in size from 4 to 8 kb, suggesting rearrangement of the transforming DNA. One plasmid obtained from a HmB^R A. pullulans transformant was able to transform E. coli to ampicillin resistance. However, after recovery from E. coli, this plasmid (approximately 4 kb) was unable to transform A. pullulans to HmB^R.     

Isolation of new plasmids from hyperthermophilic Archaea of the order Thermococcales

A collection of 57 strains of hyperthermophilic Archaea from the order Thermococcales was screened for the presence of plasmids; 9 plasmids present in six of these strains were isolated and characterized in terms of size and cross-hybridization. The Notl macrorestriction patterns of genomic DNA of strains harbouring these plasmids were obtained. Pyrococcus abyssi strains GE27 and GE23 as well as Thermococcus sp. GE31 contained a single plasmid of 3.5 kb (pGN27), 16.8 kb (pGN23) and 5.3 kb (pGN31), respectively, whilst the three strains 1559, 1560 and 1690 all contained two plasmids of 3.5 kb (pSN559, PSIM560, pSN690) and 24 kb (pLN559, pLN560, pLIM690), respectively. Plasmid pGN27 strongly cross-hybridized with the previously described plasmid pGT5 from P. abyssi strain GE5, whilst plasmids pGN23 and pGN31 did not cross-hybridize with each other, nor with any other plasmid. The three small plasmids of strains I559,1560 and I690 crosshybridized, as well as their three large plasmids. Macrorestriction pattern analysis and the results of plasmid cross-hybridization experiments indicated that these three strains were different but closely related, and likely belonged to the genus Thermococcus. This study shows that plasmids are widespread in hyperthermophilic archaea, and significantly increases the number and diversity of plasmids available for laboratory work.Une collection de 57 souches d'Archaea hyperthermophiles de l'ordre des Thermococcales a été criblée pour la présence de plasmides. Neuf plasmides, présents dans six de ces souches, ont été isolés et caractérisés. Les profils de macrorestriction NotI de l'ADN génomique des souches possédant ces plasmides sont présentés. Les souches de Pyrococcus abyssi GE27 et GE23, de même que la souche Thermococcus sp. GE31, possèdent un seul plasmide dont les tailles respectives sont de 3,5 kb (pGN27), 16,8 kb (pGN23) et 5,3 kb (pGN31). Le plasmide pGN27 hybride fortement avec le plasmide pGT5 de la souche GE5 de P. abyssi, tandis que les plasmides pGN23 et pGN31 ne donnent aucun signal en hybridation croisée, ni entre eux ni avec aucun des autres plasmides analysés. Les trois petits plasmides présents dans les souches 1559, 1560 et 1690 faybrident entre eux, ainsi que les trois grands plasmides présents dans ces mêmes souches. Le profil de macrorestriction et les résultats des expériences d'hybridation croisées montrent que ces trois souches sont différentes mais proches, et appartiennent probablement au genre Thermococcus. Ce travail montre que les plasmides sont répandus chez les Archaea hyperthermophiles et augmente de façon significative le nombre et la diversité des plasmides disponibles pour l'étude de ces microorganismes.     

Comparative genomics of extrachromosomal elements in Bacillus thuringiensis subsp. israelensis

Bacillus thuringiensis subsp. israelensis is one of the most important microorganisms used against mosquitoes. It was intensively studied following its discovery and became a model bacterium of the B. thuringiensis species. Those studies focused on toxin genes, aggregation-associated conjugation, linear genome phages, etc. Recent announcements of genomic sequences of different strains have not been explicitly related to the biological properties studied. We report data on plasmid content analysis of four strains using ultra-high-throughput sequencing. The strains were commercial product isolates, with their putative ancestor and type B. thuringiensis subsp. israelensis strain sequenced earlier. The assembled contigs corresponding to published and novel data were assigned to plasmids described earlier in B. thuringiensis subsp. israelensis and other B. thuringiensis strains. A new 360 kb plasmid was identified, encoding multiple transporters, also found in most of the earlier sequenced strains. Our genomic data show the presence of two toxin-coding plasmids of 128 and 100 kb instead of the reported 225 kb plasmid, a co-integrate of the former two. In two of the sequenced strains, only a 100 kb plasmid was present. Some heterogeneity exists in the small plasmid content and structure between strains. These data support the perception of active plasmid exchange among B. thuringiensis subsp. israelensis strains in nature.     

Detection of the cryptic prophage-like molecule pBtic235 in Bacillus thuringiensis subsp. israelensis

Bacillus thuringiensis has long been recognized to carry numerous extrachromosomal molecules. Of particular interest are the strains belonging to the B. thuringiensis subsp. israelensis lineage, as they can harbor at least seven extrachromosomal molecules. One of these elements seems to be a cryptic molecule that may have been disregarded in strains considered plasmid-less. Therefore, this work focused on this cryptic molecule, named pBtic235. Using different approaches that included transposition-tagging, large plasmid gel electrophoresis and Southern blotting, conjugation and phage-induction experiments, in combination with bioinformatics analyses, it was found that pBtic235 is a hybrid molecule of 235,425 bp whose genome displays potential plasmid- and phage-like modules. The sequence of pBtic235 has been identified in all sequenced genomes of B. thuringiensis subsp. israelensis strains. Here, the pBtic235 sequence was considered identical to that of plasmid pBTHD789-2 from strain HD-789. Despite the fact that the pBtic235 genome possesses 240 putative CDSs, many of them have no homologs in the databases. However, CDSs coding for potential proteins involved in replication, genome packaging and virion structure, cell lysis, regulation of lytic-lysogenic cycles, metabolite transporters, stress and metal resistance, were identified. The candidate plasmidial prophage pBtic235 exemplifies the notable diversity of the extrachromosomal realm found in B. thuringiensis.     

Adherence of multiresistant strains of Klebsiella pneumoniae to cerebrospinal fluid shunts: correlation with plasmid content

A nosocomial multiresistant Klebsiella pneumoniae strain (KMD01) isolated from a patient with an infected ventriculoperitoneal (V-P) shunt was found to contain three plasmids of mol. wts (10(6)) c. 85, 50 and 2.4. A derivative isogenic strain (KMD11) carrying only the plasmids of mol. wts (10(6)) 50 and 2.4 was obtained spontaneously by plating the parent strain. The absence of the plasmid of mol. wt 85 X 10(6) in strain KMD11 correlated with an increased adherence to V-P catheters and glass surfaces, as well as autoagglutination in minimal medium. Bacterial cells containing the whole set of plasmids (strain KMD01) also showed the incorporation into the outer membrane of a new polypeptide (mol. wt, c. 41 X 10(3)), when grown in minimal medium. The presence of this polypeptide correlated with absence of autoagglutination, as shown by strain KMD01 under these cultural conditions. These data suggest that the cell-surface characteristics in K. pneumoniae may be affected by the plasmid content of the strain. Since nosocomial strains of K. pneumoniae usually contain one or more plasmids, and strains easily exchange these extrachromosomal elements, it seems reasonable to speculate that new variants with higher V-P shunt colonisation effectiveness, like the one described in this work, may also evolve in nature.     

Tn5 mutagenesis of the Salmonella typhimurium 100 kb plasmid: definition of new virulence regions

In this study, the 100 kb plasmid of Salmonella typhimurium, which is known to contribute to the pathogenicity of the organism, was tagged with the transposon Tn5 to define regions of the plasmid contributing to overall virulence. Eleven randomly selected vir::Tn5 plasmids carried by the plasmid-free S. typhimurium strain WS1321 were physically mapped and then examined in mice for subcutaneous LD₅₀ value, ability to induce splenomegaly, and ability to grow to high numbers in the spleens of infected mice. Nine strains were found to be virulence-attenuated and showed varied levels of growth in the spleens of subcutaneously infected BALB/c mice. Eight of these nine strains carried Tn5 insertions which lie outside the previously defined virulence region. These studies corroborate the findings of other investigators as well as defining novel regions of the 100 kb virulence plasmid involved in the pathogenicity of this organism.     

Proteins are attached to the ends of a linear plasmid in the filamentous fungus Ascobolus immersus

Summary In seven out of eleven wild strains of the Ascomycete Ascobolus immersus plasmid DNA was found. There was great variability with respect to size and number of the plasmids in the strains concerned. For a further analysis two plasmids originating from one wild strain were submitted to restriction analysis and electron microscopy. Both turned out to be linear having different molecular weights (pAIl = 7.9 kb, pAI2 = 5.6 kb). Denaturation of pAI2 and subsequent renaturation revealed the presence of inverted repeats (0.7 kb) at both ends. After treatment with proteinase K and 5 and 3 specific exonucleases it became evident that the 5 ends of pAI2 are linked with proteins. In this respect it is similar in structure to other linear genetic elements such as the linear plasmids found in Zea mays and the genomes of adenoviruses.Dedicated to Prof. Dr. Fritz Kaudewitz on the occasion of his 65th birthday     

Maintenance of the recombinant plasmid pIJ2 in chemostat cultures of Streptomyces lividans 66 (pIJ2)

The maintenance of the recombinant plasmid pIJ2 in chemostat cultures of Streptomyces lividans 66 (pIJ2) was investigated. The presence of the plasmid coding for a neomycin phosphotransferase was detected by plating samples from the continuous cultures on nonselective and selective agar medium containing neomycin. The plasmid was lost from the host strain under all conditions tested. However, the kinetics of the plasmid segregation from the chemostat populations were dependent on the growth-limiting substrate of the medium, the dilution rate of the continuous culture and the cultivation temperature. Size differences between the original plasmid and plasmid DNA isolated from neomycin-resistant clones after long-term chemostat cultivation were not observed. In neomycin-sensitive clones no extrachromosomal DNA was found.