Plasmid transfer in Streptomyces lividans: identification of a kil-kor system associated with the transfer region of pIJ101

Mutational and functional analysis of the korA and korB gene products of Streptomyces plasmid pIJ101

The korA and korB loci of Streptomyces lividans plasmid pIJ101 have previously been shown to control expression of the pIJ101 tra (formerly kilA) and kilB genes at the transcriptional level. We show here that mutations in translational open reading frames (ORFs) that map within the kor loci abolish repression of the S. lividans lac gene directed by the tra and kilB promoters. Introduction of the korA and korB ORFs into Escherichia coli maxicells under control of an E. coli promoter gave rise to 31 kDa and 10 kDa proteins that correspond in size to the products expected from the sequences of the respective ORFs; these proteins controlled transcription from the pIJ101 tra and kilB promoters in the E. coli host. Mutations that affected the KorA or KorB phenotype altered the structure of, or eliminated, the protein products of the korA and korB ORFs, further demonstrating that these ORFs encode the functional repressors of the pIJ101 kil/kor gene system.

Characterization of the genetic elements required for site-specific integration of plasmid pSE211 in Saccharopolyspora erythraea

The 18.1-kilobase plasmid pSE211 integrates into the chromosome of Saccharopolyspora erythraea at a specific attB site. Restriction analysis of the integrated plasmid, pSE211int, and adjacent chromosomal sequences allowed identification of attP, the plasmid attachment site. Nucleotide sequencing of attP, attB, attL, and attR revealed a 57-base-pair sequence common to all sites with no duplications of adjacent plasmid or chromosomal sequences in the integrated state, indicating that integration takes place through conservative, reciprocal strand exchange. An analysis of the sequences indicated the presence of a putative gene for Phe-tRNA at attB which is preserved at attL after integration has occurred. A comparison of the attB site for a number of actinomycete plasmids is presented. Integration at attB was also observed when a 2.4-kilobase segment of pSE211 containing attP and the adjacent plasmid sequence was used to transform a pSE211- host. Nucleotide sequencing of this segment revealed the presence of two complete open reading frames (ORFs) and a segment of a third ORF. The ORF adjacent to attP encodes a putative polypeptide 437 amino acids in length that shows similarity, at its C-terminal domain, to sequences of site-specific recombinases of the integrase family. The adjacent ORF encodes a putative 98-amino-acid basic polypeptide that contains a helix-turn-helix motif at its N terminus which corresponds to domains in the Xis proteins of a number of bacteriophages. A proposal for the function of this polypeptide is presented. The deduced amino acid sequence of the third ORF did not reveal similarities to polypeptide sequences in the current data banks.

Identification and analysis of transcriptional regulatory signals for the kil and kor loci of Streptomyces plasmid pIJ101

Four regulated promoters that direct the transcription of genes (i.e., korA, tra, kilB, and korB) involved in the transfer of the Streptomyces plasmid pIJ101 were isolated following the in vitro fusion of plasmid DNA fragments to a promoterless gene encoding the S. lividans extracellular enzyme beta-galactosidase. Introduction of pIJ101 into cells carrying each of these promoter-lac fusions resulted in decreased lac expression. The sites of initiation of transcription by the promoter sequences were identified by primer extension experiments, and the DNA sequences specifically required for promoter activity and regulation by pIJ101-encoded functions were determined by deletion analysis. The data obtained indicate that the korB locus encodes a repressor that regulates its own transcription, as well as transcription of the kilB promoter; korA and tra are transcribed from overlapping divergent promoters that are coregulated by the korA gene product. Common DNA sequence domains within coregulated promoters allowed the identification of putative binding sites for each of the kor gene products.

"Strong incompatibility" between derivatives of the Streptomyces multi-copy plasmid pIJ101

Some derivatives of pIJ101, a 8.9 kb Streptomyces multi-copy plasmid, can co-exist with each other at similar copy numbers but others are strongly incompatible. The DNA sequence, sti, which causes this "strong incompatibility" was localised on a DNA segment of about 200 bp which is not part of the essential replication region of pIJ101. The sti function is active only when the DNA fragment carrying it is present in the natural orientation with respect to the basic replicon region of pIJ101. Pairs of plasmids which either both possess sti in the correct orientation (Sti+) or both lack sti or carry it in reverse orientation (Sti-) can co-exist, but Sti+ and Sti- plasmids cannot; in this case the Sti+ plasmid is retained and the Sti- plasmid is lost. This phenomenon is called strong incompatibility to distinguish it from classical incompatibility where identical or related plasmids are incompatible and dissimilar plasmids are compatible. pIJ101 probably replicates via a single-stranded intermediate; sti would be a site where the synthesis of the second (lagging) DNA strand is initiated because Sti- plasmids accumulate more single-stranded plasmid DNA than Sti+ plasmids. The copy number of pIJ101 and its derivatives is influenced by sti and by an additional trans-acting function (cop).

Complete nucleotide sequence of the Streptomyces lividans plasmid pIJ101 and correlation of the sequence with genetic properties

The complete nucleotide sequence of the multicopy Streptomyces plasmid pIJ101 has been determined and correlated with previously published genetic data. The circular DNA molecule is 8,830 nucleotides in length and has a G+C composition of 72.98%. The use of a computer program, FRAME, enabled identification in the sequence of seven open reading frames, four of which, tra (621 amino acids [aa]), spdA (146 aa), spdB (274 aa), and kilB (177 aa), appear to be genes involved in plasmid transfer. At least two of the above genes are predicted to be transcribed by known promoters that are regulated in trans by the products of the korA (241 aa) and korB (80 aa) loci on the plasmid. The segment of the plasmid capable of autonomous replication contains one large open reading frame (rep; 450 aa) and a noncoding region presumed to be the origin of replication. Four other small (less than 90 aa) open reading frames are also present on the plasmid, although no function can be attributed to them. The sequence of the pIJ101 replication segment present in several widely used cloning vectors (e.g., pIJ350 and pIJ702) has also been determined, so that the complete nucleotide sequences of these vectors are now known.

Site-specific insertion of biologically functional adventitious genes into the Streptomyces lividans chromosome

We report that transformation of Streptomyces lividans with cloned DNA of the SLP1 genetic element results in integration of the element at the same chromosomal locus (attB) normally occupied by SLP1 in its original host, Streptomyces coelicolor, and in S. lividans that has received SLP1 by mating. We constructed SLP1 derivatives that can integrate foreign DNA at the attB site and used these to introduce adventitious DNA sequences into the S. lividans chromosome. We also identified three regions of SLP1 essential for its integration and demonstrated that integration of the SLP1 element does not require expression of functions necessary for stable maintenance or transfer of extrachromosomal forms of SLP1.

The impact of genetic engineering on the commercial production of antibiotics by Streptomyces and related bacteria

Developments in Streptomyces genetics that have laid a foundation for this field over the past ten years are reviewed and discussed to suggest how this knowledge might useful for improving the commercial production of antibiotics. This brief analysis predicts a bright future for the application of Streptomyces genetics in antibiotic production.