Isolation and characterization of plasmid DNAs in Actinomycetes

Characterization of a replication locus and formation of a higher-order complex between RepA protein and two inverted repeats in Streptomyces plasmid pSV1

We identified the minimal locus of 163-kb plasmid pSV1 of Streptomyces violaceoruber for the replication in S. lividans. This locus comprised a repA gene and an upstream 407-bp sequence containing two inverted repeats (IR-III and IR-IV) within an iteron, an AT-rich region and a 300-bp noncoding sequence (NCS). RepA protein bound specifically to a 94-bp sequence covering the intact IR-III and IR-IV to form multimers of DNA/protein complexes, but was unable to bind specifically to the NCS and the promoter of repA gene. Interestingly, this 'bound' region also leaves eight 1-bp 'unbound' spacers at 7-11-9-11-9-11-9-11-8-bp intervals. RepA protein-protein interaction could form dimers or trimers in vitro. These results suggest that a higher-order complex between pSV1 RepA protein and the long inverted repeats may be formed during the initiation of plasmid replication.

SCP1, a 356 023 bp linear plasmid adapted to the ecology and developmental biology of its host, Streptomyces coelicolor A3(2)

The sequencing of the entire genetic complement of Streptomyces coelicolor A3(2) has been completed with the determination of the 365,023 bp sequence of the linear plasmid SCP1. Remarkably, the functional distribution of SCP1 genes somewhat resembles that of the chromosome: predicted gene products/functions include ECF sigma factors, antibiotic biosynthesis, a gamma-butyrolactone signalling system, members of the actinomycete-specific Wbl class of regulatory proteins and 14 secreted proteins. Some of these genes are among the 18 that contain a TTA codon, making them targets for the developmentally important tRNA encoded by the bldA gene. RNA analysis and gene fusions showed that one of the TTA-containing genes is part of a large bldA-dependent operon, the gene products of which include three proteins isolated from the spore surface by detergent washing (SapC, D and E), and several probable metabolic enzymes. SCP1 shows much evidence of recombinational interactions with other replicons and transposable elements during its history. For example, it has two sets of partitioning genes (which may explain why an integrated copy of SCP1 partially suppressed the defective partitioning of a parAB-deleted chromosome during sporulation). SCP1 carries a cluster of probable transfer determinants and genes encoding likely DNA polymerase III subunits, but it lacks an obvious candidate gene for the terminal protein associated with its ends. This may be related to atypical features of its end sequences.

Limited regions of homology between linear and circular plasmids encoding methylenomycin biosynthesis in two independently isolated streptomycetes

pSV1 is a plasmid in Streptomyces violaceoruber SANK95570 that carries the methylenomycin biosynthetic (mmy) gene cluster. An ordered cosmid map and an EcoRI map have been constructed for pSV1, confirming that pSV1 is a 163 kb circular plasmid. The mmy gene cluster has been found on three different replicon structures; the circular plasmid pSV1, the 356 kb linear plasmid SCP1 and, via SCP1 integration, the linear chromosome of Streptomyces coelicolor A3(2). Comparison of pSV1 and SCP1 sequences revealed that the two plasmids have homology to each other only around the mmy and parAB regions, eliminating models in which pSV1 was generated by circularization of SCP1 or vice versa. It is likely that the mmy gene cluster was horizontally transferred as a set together with the parAB region in the comparatively recent evolutionary past.

Characterization of the Streptomyces violaceoruber SANK95570 plasmids pSV1 and pSV2

We have analyzed the structure of two extrachromosomal elements of the methylenomycin producing actinomycete Streptomyces violaceoruber SANK95570. The presence of the circular plasmid pSV1 which was supposed to contain the genes for methylenomycin biosynthesis could be verified. Physical mapping of pSV1 revealed a size of 175.35 kb for this plasmid. In addition we generated a restriction map for the 100-kb linear plasmid pSV2. Cloning and sequencing of the terminal ends of pSV2 indicated the presence of 426-bp terminal inverted repeats. Both pSV2 termini show significant homology to the chromosome ends of Streptomyces coelicolor A3(2) which is a closely related strain to S. violaceoruber SANK95570.

Genetic instability in Streptomyces niveus plasmid pSN2: in vivo formation of deletion derivatives

A plasmid designated pSN2 (molecular size 32.0 kb) was isolated from the wild type of Streptomyces niveus ATCC 19793. To permit phenotypic identification of pSN2 the 1.9 kb BclI fragment was replaced in vitro by the 1.1 kb BclI fragment of pIJ702 carrying the thiostrepton resistance (tsr) gene to form the plasmid pSN3. pSN3 transforms S. lividans to thiostrepton resistance at high frequency and is stably maintained. However, when used to transform S. niveus pSN3 was unstable and produced a 5.5 kb thiostrepton resistant deletion derivative pLG5. pLG5 is also stable and expresses thiostrepton resistance in S. lividans but on transformation of S. niveus was unstable and produced a further thiostrepton resistant derivative, pLG10, of 6.5 kb. pLG5 and pLG10 like pSN3 transform S. lividans at high frequency and produce pocks. DNA hybridizations with a probe derived from pLG5 confirm that pLG5 is derived from DNA sequences present on pSN2 and pSN3.

Isolation and characterization of a temperate bacteriophage from Streptomyces galilaeus

A new temperate actinophage from Streptomyces galilaeus ATCC 31133 was purified after that strain was crossed with S. peucetius ATCC 29050. Sensitive hosts became lysogenized and yielded turbid plaques of 2 to 3 mm in diameter. Host-range analysis indicated that 16 of 27 Streptomyces strains tested were sensitive to infection on solid medium. S. lividans and S. coelicolor A3(2) were among those not infected by this new actinophage. The new actinophage, designated phi SPK1, belongs to the Bradley group B morphological type, the pH optimum for infection is 6.75 to 7.0, it is not efficiently induced by mitomycin C or UV irradiation, it has a circular chromosome of 35.8 +/- 0.5 kilobase pairs in length containing overlapping (cohesive) ends, and the G+C content of its DNA was calculated from the buoyant density of 1.7240 to be 69 mol%. The DNA of phage phi SPK1 was cleaved by the restriction endonucleases ApaI, AluII, EcoRI, PvuII, and SalI, but, in all cases except that with EcoRI, treatment yielded greater than 20 restriction fragments. No sites were detected for BamHI, BclI, BglII, ClaI, HindIII, MluI, PstI, SmaI, SphI, SstI, XbaI, or XhoI.

Copy number mutants of the broad-host-range Streptomyces plasmid pMG200

pMG200, isolated from the bacteriocin-releasing strain Streptomyces chrysomallus, was further physically mapped. Variants of S. chrysomallus were isolated which inhibited the parental strain. Two types of plasmids, pMG210 and pMG220, were isolated from these variants, with copy numbers of 10-30 and 300, respectively, compared with 1-3 for pMG200. pMG210 is apparently physically identical to pMG200 but presumably differs at a level not detected by simple restriction mapping; pMG220 is deleted for 1.6 kb. Genes for thiostrepton and viomycin resistance were subcloned from pIJ364 on to pMG200 and a fragment containing the gene for nourseothricin resistance was subcloned on to pMG220. In this way nonessential sites were identified.

Factors affecting the isolation of CCC DNA from Streptomyces lividans and Escherichia coli

Based on the results of a systematic study of factors affecting plasmid yield and purity, a procedure suitable for the rapid screening for and isolation of covalently closed circular DNA from Streptomyces lividans and Escherichia coli was developed. The method consists of lysis of lysozyme-treated bacteria combined with alkaline denaturation of DNA at high temperature. Renaturation of CCC DNA and precipitation of single-stranded DNA together with protein is achieved by the addition of a minimal amount of phenol/chloroform. The screening procedure uses only a single tube and the samples can be analyzed by agarose gel electrophoresis about 30 min after lysis. Removal of phenol and further purification of the plasmid preparation is achieved by consecutive precipitations with isopropanol and spermine, followed by extraction with ethanol, producing samples suitable for restriction endonuclease digestion, ligation, and transformation of S. lividans protoplasts or competent E. coli cells in about 2 h. All steps of the procedure are explained in detail with information about the effects of changing parameters. This should help the experimenter to obtain reproducible results and may be useful if the method has to be adapted to new strains or plasmids.

pIJ101, a multi-copy broad host-range Streptomyces plasmid: functional analysis and development of DNA cloning vectors

Streptomyces lividans ISP 5434 contains four small high copy number plasmids: pIJ101 (8.9 kb), pIJ102 (4.0 kb), pIJ103 (3.9 kb) and pIJ104 (4.9 kb). The three smaller species appear to be naturally occurring deletion variants of pIJ101. pIJ101 and its in vivo and in vitro derivatives were studied after transformation into S. lividans 66. pIJ101 was found to be self-transmissible by conjugation, to elicit "lethal zygosis" and to promote chromosomal recombination at high frequency in both S. lividans 66 and S. coelicolor A3(2). A restriction endonuclease cleavage map of pIJ101 was constructed for 11 endonucleases; sites for five others were lacking. Many variants of pIJ101 were constructed in vitro by inserting DNA fragments determining resistance to neomycin, thiostrepton or viomycin, and having BamHI termini, into MboI or BclI sites on the plasmid, sometimes with deletion of segments of plasmid DNA. The physical maps of these plasmids were related to their phenotypes in respect of lethal zygosis and transfer properties. In vivo recombination tests between pairs of variant plasmids were also done. These physical and genetic studies indicated that determinants of conjugal transfer occupy less than 2.1 kb of the plasmid. A second segment is required for spread of the plasmid within a plasmid-free culture to produce the normal lethal zygosis phenotype: insertion of foreign DNA in this region caused a marked reduction in the diameter of lethal zygosis zones. The minimum replicon was deduced to be 2.1 kb or less in size; adjacent to this region is a 0.5 kb segment which may be required for stable inheritance of the plasmid. The copy number of several derivatives of pIJ101 in S. lividans 66 was between 40 and 300 per chromosome and appeared to vary with the age or physiological state of the culture. pIJ101 derivatives have a wide host range within the genus Streptomyces: 13 out of 18 strains, of diverse species, were successfully transformed. Knowledge of dispensable DNA segments and the availability of restriction sites for the insertion of DNA, deduced from the properties of plasmids carrying the E. coli plasmid pACYC184 introduced at various sites, was used in the construction of several derivatives of pIJ101 suitable as DNA cloning vectors. These were mostly designed to be non-conjugative and to carry pairs of resistance genes for selection. They include a bifunctional shuttle vector for E. coli and Streptomyces; a Streptomyces viomycin resistance gene of this plasmid is expressed in both hosts.

Excision of chromosomal DNA sequences from Streptomyces coelicolor forms a novel family of plasmids detectable in Streptomyces lividans

When strains of Streptomyces coelicolor A3(2) lacking the previously identified autonomous plasmids SCP1 and SCP2 are crossed with Streptomyces lividans 66, some of the S. lividans progeny are able to elicit zones of growth inhibition (lethal zygosis), previously associated with the transfer of conjugative Streptomyces plasmids, when grown in contact with S. lividans 66. Some such progeny yield covalently closed circular (CCC) plasmid DNA, the size and restriction endonuclease cleavage pattern of which is constant for a particular isolate, but varies among isolates. These plasmids, which have been named SLP1.1, SLP1.2, etc., all confer resistance to lethal zygosis elicited by the others. Genetic and molecular characterization of the plasmids reveals that they are derived from the strA region of the chromosome of S. coelicolor. It is proposed that, before or during mating with S. lividans, the SLP1 sequences are excised from the chromosome, bringing varying regions of the surrounding chromosome with them, and can circularize to yield the SLP1 family of plasmids. Autonomous SLP1 plasmids can also be generate by cleaving total DNA of S. coelicolor with certain restriction enzymes, ligating it, and transforming the DNA into S. lividans. The autonomous SLP1 plasmids exist within S. lividans in a few copies per chromosome, and act as fertility factors. They provide suitable vectors for DNA cloning since the segments of chromosomal DNA carried by the larger members of the family are dispensable.

Possible involvement of a plasmid in arginine auxotrophic mutation of Streptomyces kasugaensis

Streptomyces kasugaensis gave arginine auxotrophic mutants at high frequency, The coupled loss and reappearance of plasmid deoxyribonucleic acid with arginine auxotrophy suggested that the insertion of the plasmid into chromosomal deoxyribonucleic acid caused the arginine auxotrophy.