Reiterated DNA sequences in a mutant strain of Streptomyces glaucescens and cloning of the sequence in Escherichia coli

DNA amplification affects protease production and sporulation in Streptomyces fradiae

Chloramphenicol resistance is an unstable character in Streptomyces fradiae, since spontaneous chloramphenicol-sensitive (Cmls) mutants arose at very high frequencies. One such Cmls mutant, DM14, showed DNA amplification as well. Extracellular protease activity was tenfold higher in DM14 when compared with its wild-type parent. Protease activity decreased considerably in DM14 when treated with spectinomycin, a treatment that reduces the copy number of amplified units of DNA. Sporulation in DM14 was delayed in the presence of spectinomycin at a concentration of 5 micrograms/ml, whereas the wild type was unaffected at that concentration. The results strongly indicated that the amplified DNA affected the two secondary metabolic functions, viz., protease production and the onset of sporulation in the mutant.

Stabilization of Streptomyces lividans by homologous recombinational insertion

We have developed a system for the introduction and maintenance of novel tandem repeats in the chromosome of Streptomyces lividans 66. This was achieved by introducing, via transformation, Escherichia coli "suicide" vectors carrying manipulated S. lividans DNA fragments. Selection for antibiotic resistance markers carried on such plasmids permitted the isolation and maintenance of mutant strains containing novel tandem repeats formed by the integration into the chromosome of the plasmids, via homologous recombination between plasmid-borne chromosomal sequences and identical sequences on the chromosome. When novel repeats were introduced, and maintained, in regions of the chromosome which become deleted in unstable strains of S. lividans, those deletion events were blocked. Surprisingly, such strains were also 10 to 20-fold more stable than the parent even in the absence of selection. In stable regions of the chromosome, the maintenance of novel repeats had no obvious effect on the deletion events. This strategy could be generally applicable to industrial strains of Streptomyces, where instability is a common problem.

Extremely large chromosomal deletions are intimately involved in genetic instability and genomic rearrangements in Streptomyces glaucescens

Genetic instability in Streptomyces glaucescens characteristically involves the occurrence of gross genomic rearrangements including high-level sequence amplification and extensive deletion. We investigated the relationship of the unstable melC and strS loci and a 100 kb region of the chromosome which frequently gives rise to intense heterogeneous DNA amplification. Standard chromosome walking using a cosmid bank in conjunction with a "reverse-blot" procedure enabled us to construct a contiguous genomic BamHI map of the unstable region exceeding 900 kb. The unstable genes and the amplifiable region (AUD locus) are physically linked within a 600 kb segment of the chromosome. The previously characterized deletions which affect these loci are merely components of much larger deletions ranging from 270 to over 800 kb which are polar in nature, effecting the sequential loss of the strS and melC loci. The more extensive deletions terminate either adjacent to, or in the vicinity of DNA reiterations at the AUD locus. Additionally, a deletion junction fragment and the corresponding deletion ends were cloned and analysed at the sequence level.

Heterogeneous genomic amplification in Streptomyces glaucescens: structure, location and junction sequence analysis

Certain chromosomal markers in Streptomyces glaucescens behave unstably, being lost at high frequency as a result of extensive genomic deletion. Additionally, mutant strains possessing such deletions frequently display intense DNA amplification. With the help of a wild-type cosmid library we investigated the structure of the amplified DNA sequences (ADS) and the corresponding wild-type amplifiable units of DNA (AUD). The reiterations were heterogeneous in location, copy number and sequences involved and originated predominantly from a single 100 kb region of the chromosome called the AUD locus. All strains bearing reiterations possessed associated deletions which terminated either close to or at the ADS. The termini of four AUDs were sequenced in order to gain more knowledge about these heterogeneous amplifications. In three of the four cases investigated small, interrupted homologies were found bordering the AUDs. With the help of orthogonal-field-alternation gel electrophoresis (OFAGE) we were able to visualize a tandem reiteration of more than 1,500 kb in length.

Hypervariability, a new phenomenon of genetic instability, related to DNA amplification in Streptomyces ambofaciens

The wild-type strain Streptomyces ambofaciens DSM 40697 exhibits a high degree of genetic instability. Pigment-defective colonies were observed in the progeny of wild-type colonies at a frequency of about 0.01. While only 13% of these pigment-defective colonies gave rise to homogeneous progeny exhibiting the mutant parental phenotype, 87% of the mutant colonies gave rise to hetergeneous progeny without a preponderant phenotype. This new phenomenon of instability was called hypervariability. In addition, 21% of the mutant strains arising in hypervariable progeny contained highly reiterated DNA sequences, while amplified DNA sequences could be detected in neither stable pigment-defective mutant clones nor in wild-type clones. These results indicate a frequent association between genetic instability and hypervariability and a frequent association between hypervariability and amplification of DNA sequences.

Reiterated DNA sequences in Rhizobium and Agrobacterium spp

Repeated DNA sequences are a general characteristic of eucaryotic genomes. Although several examples of DNA reiteration have been found in procaryotic organisms, only in the case of the archaebacteria Halobacterium halobium and Halobacterium volcanii [C. Sapienza and W. F. Doolittle, Nature (London) 295:384-389, 1982], has DNA reiteration been reported as a common genomic feature. The genomes of two Rhizobium phaseoli strains, one Rhizobium meliloti strain, and one Agrobacterium tumefaciens strain were analyzed for the presence of repetitive DNA. Rhizobium and Agrobacterium spp. are closely related soil bacteria that interact with plants and that belong to the taxonomical family Rhizobiaceae. Rhizobium species establish a nitrogen-fixing symbiosis in the roots of legumes, whereas Agrobacterium species is a pathogen in different plants. The four strains revealed a large number of repeated DNA sequences. The family size was usually small, from 2 to 5 elements, but some presented more than 10 elements. Rhizobium and Agrobacterium spp. contain large plasmids in addition to the chromosomes. Analysis of the two Rhizobium strains indicated that DNA reiteration is not confined to the chromosome or to some plasmids but is a property of the whole genome.

Intraplasmid recombination in Streptomyces lividans 66

An Escherichia coli-Streptomyces shuttle plasmid pIF132 containing two direct mel repeats was constructed. While pIF132 replicated relatively stably in E. coli (Rec+ or recA), its structure was unstable in S. lividans: recombination between the mel repeats resulted in a smaller plasmid, pIF138. Furthermore, pIF132 formed oligomers extensively in E. coli but not in S. lividans.

Two families of repeated DNA sequences in Thiobacillus ferrooxidans

The genome of Thiobacillus ferrooxidans ATCC 19859 is about 2.8 X 10(6) base pairs as determined by analysis of reassociation kinetics of sheared DNA. This is 70% of the size of the genome of Escherichia coli. About 6% of the genome of T. ferrooxidans consists of moderately repetitive DNA sequences that are repeated an average of 20 times per genome. Two distinct repeated sequences, designated family 1 and family 2, have been analyzed in more detail. Both families are approximately 1 kilobase in length and are repeated 20 to 30 times per genome. Preliminary evidence from restriction enzyme analysis, Southern blotting experiments, and thermal melting analysis indicates that members of both families are conserved and are interspersed with single-copy DNA. Six copies of one family are present on the 45-kilobase-pair plasmid of strain ATCC 19859.

DNA deletions in spontaneous chloramphenicol-sensitive mutants of Streptomyces coelicolor A 3(2) and Streptomyces lividans 66

A mutant of Streptomyces coelicolor A 3(2) highly resistant to chloramphenicol was selected. It had amplified some chromosomal DNA fragments to a copy number of 20-50. Some of the amplified fragments were cloned and used as hybridisation probes to investigate the spontaneous chloramphenicol-sensitive mutants which occur at high frequency in this species and the closely related species Streptomyces lividans 66. These investigations demonstrated that chloramphenicol sensitivity in both species is associated with large deletions that are at least 40 kb in length.

A plausible mechanism for large-scale chromosomal DNA amplification in streptomycetes

Recent advances in our understanding of the structure of highly amplified DNA sequences in Streptomyces fradiae and lividans have enabled us to formulate a possible mechanism by which amplification may occur. An essential feature of the model is the generation of an amplification precursor, which comprises a circularised copy of the DNA to be amplified, attached to one arm of the chromosome by a replication fork. Multiple copies of the amplifiable DNA are generated by rolling circle replication. The model adequately accounts for many features of gene amplification in these two species, including the tendency for deletions to occur to one side, but not the other, of the amplified DNA.

DNA rearrangements associated with instability of an arginine gene in Streptomyces coelicolor A3(2)

Streptomyces coelicolor A3(2) gives rise to spontaneous chloramphenicol sensitive mutants at a frequency of about 0.3% per spore. These mutants are often genetically unstable and give rise to arginine auxotrophs (Arg-) at frequencies of 1-7% per spore. These Arg- mutants usually lack the enzyme argininosuccinate synthetase (one exception was found that lacked ornithine carbamoyltransferase) and were shown to have deleted the corresponding argG gene by hybridisation analysis using a cloned S. cattleya argG gene. The Arg- strains also showed a variety of different DNA amplification and deletion events in a region homologous to an amplified DNA sequence found in spontaneous Arg- mutants in S. lividans 66.

Genetic rearrangements of a Rhizobium phaseoli symbiotic plasmid

Different structural changes of the Sym plasmid were found in a Rhizobium phaseoli strain that loses its symbiotic phenotype at a high frequency. These rearrangements affected both nif genes and Tn5 mob insertions in the plasmid, and in some cases they modified the expression of the bacterium's nodulation ability. One of the rearrangements was more frequent in heat-treated cells, but was also found under standard culture conditions; other structural changes appeared to be related to the conjugal transfer of the plasmid.

Amplification of the amyE-tmrB region on the chromosome in tunicamycin-resistant cells of Bacillus subtilis

In a class of tunicamycin-resistant mutants (tmrA7) of Bacillus subtilis, the production of extracellular alpha-amylase is increased by about five fold. The tmrA7 characteristics (tunicamycin resistance and hyperproduction of extracellular alpha-amylase) can be transferred to recipient cells by transformation. In the transformants and the original tmrA7 mutant, typical amplification of the region from 4 kb upstream of the amyE gene to the tmrB gene on the chromosome was detected. The repeating unit, 16 kb in size, repeats tandemly about five and ten times in the mutant and transformants, respectively, and the alpha-amylase production is proportional to the copy number of the amyE gene. Simultaneous amplification of the tmrB gene, which is responsible for tunicamycin resistance in the multicopy state, and the alpha-amylase structural gene (amyE) seems to be the cause of the pleiotropy of the tmrA7 mutation.

Directed selection of differentiation mutants of Streptomyces noursei using chemostat cultivation

A nourseothricin-producing Streptomyces noursei strain was continuously cultivated in a chemostat equipped with a stirrer for mechanical fractionation of the mycelium. Different cultivation conditions allowed the selection of six types of differentiation mutants after the culture had reached a population genetically stationary state. The mutants showed an altered control pattern of sporulation as well as altered antibiotic biosynthesis and antibiotic resistance. In addition, the stability of the recombinant plasmid pIJ385 in several differentiation type mutants as host strains was tested. The results suggest that there exists a strong correlation between the cultivation conditions employed and the type of differentiation mutants selected.

Structure of an amplifiable DNA sequence in Streptomyces lividans 66

Spontaneous chloramphenicol-sensitive mutants of Streptomyces lividans 66 had previously been shown to be very unstable and to yield arginine auxotrophic mutants at a frequency of 25% of spores; the Arg- mutants had amplified a particular 5.7 kb DNA sequence to over one hundred tandem copies per genome. In this paper we report the cloning of the amplifiable region from amplified and wild-type strains. This showed that the amplifiable fragment is already present as a duplication in wild type cells. Hybridisation experiments also demonstrated that in the amplified strains there was a deletion of neighbouring DNA sequences to one side of the amplifiable element; sequences to the other side remain intact.

Determination of the molecular mass of bacterial genomic DNA and plasmid copy number by high-pressure liquid chromatography

Relatively rapid methods for the determination of relative genome molecular mass (Mr) and the estimation of plasmid copy number have been developed. These methods are based on the ability of the Bio-Rad high-pressure liquid chromatography hydroxylapatite column to separate and quantify single-stranded DNA, double-stranded DNA, and plasmid DNA. Genome Mr values were calculated from reassociation kinetics of single-stranded DNA as measured with the hydroxylapatite column. Bacteriophage T4 DNA was used to establish a C0t (moles of nucleotides times seconds per liter), or standard reassociation value. From this C0t value, C0t values for Escherichia coli B, Beggiatoa alba B18LD, and Streptomyces coelicolor were determined by comparative calculations. From those calculated C0t values, the Mr values of 1.96 X 10(9) for E. coli, 2.02 X 10(9) for B. alba, and 3.28 X 10(9) for S. coelicolor were estimated. Plasmid concentration was determined from cleared lysates by comparing the integrated area under the phosphate buffer-eluted plasmid peak to values obtained with known amounts of plasmid. The plasmid copy number was estimated by multiplying the ratio between the amounts of plasmid and chromosomal DNA by the ratio between the Mr values of the chromosome and the plasmid. A copy number of 29 was obtained from a culture of E. coli HB101 harboring pBR322 grown to a culture density of 1.6 X 10(9) CFU . ml-1.

Mutagenic and error-free DNA repair in Streptomyces

Two mutants of Streptomyces fradiae defective in DNA repair have been characterized for their responses to the mutagenic and lethal effects of several chemical mutagens and ultraviolet (UV) light. S. fradiae JS2 (mcr-2) was more sensitive than wild type to agents which produce bulky lesions resulting in large distortions of the double helix [i.e. UV-light, 4-nitroquinoline-1-oxide (NQO), and mitomycin C (MC)] but not to agents which produce small lesions [i.e. hydroxylamine (HA), methyl methanesulfonate (MMS), ethyl methanesulfonate (EMS) and N-methyl-N'-nitro-N-nitrosoguanidine (MNNG)]. JS2 expressed a much higher frequency of mutagenesis induced by UV-light at low doses and thus appeared to be defective in an error-free excision repair pathway for bulky lesions analogous to the uvr ABC pathway of Escherichia coli. S. fradiae JS4 (mcr-4) was defective in repair of damage by most agents which produce small or bulky lesions (i.e., HA, NQO, MMS, MNNG, MC, and UV, but not EMS). JS4 was slightly hypermutable by EMS and MMS but showed reduced mutagenesis by NQO and HA. This unusual phenotype suggests that the mcr-4+ protein plays some role in error-prone repair in S. fradiae.

Certain chromosomal regions in Streptomyces glaucescens tend to carry amplifications and deletions

Streptomycetes are subject to a high degree of genetic instability. One manifestation of this phenomenon is the occurrence of tandemly reiterated DNA stretches within the chromosome. We describe the analysis of ten reiterated sequences observed in various ethidium bromide-treated streptomycin-sensitive and melanin-negative mutant strains of Streptomyces glaucescens. The repeated DNA units were 2.9 to 35 kb in length. No two sequences were identical. The amplified sequences occupied up to 45% of the total genomic DNA. Structural analysis of the cloned repeated DNA stretches by means of restriction enzymes and by cross hybridization revealed the presence of two chromosomal areas rich in DNA reiterations. In some cases reiterated regions were accompanied by nearby rearrangements.

Mutagenic DNA repair in Streptomyces

Streptomyces fradiae JS6 (mcr-6) is defective in the repair of potentially lethal damage to DNA induced by mitomycin C (MC), hydroxylamine (NH2OH), methyl methanesulfonate (MMS), 4-nitroquinoline 1-oxide (NQO), N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), and ultraviolet light (UV), but it exhibits nearly normal sensitivity to ethyl methanesulfonate (EMS)-induced lethality. JS6 is substantially less mutable by MNNG, MMS, NQO, UV, NH2OH, and also EMS than is the parental strain. A spontaneous revertant of JS6 showed wild-type levels of resistance to all of these agents and wild-type levels of induced mutagenesis, indicating that a single mutation caused the multiple traits displayed by JS6. The mcr-6 gene product thus appears to control an error-prone (mutagenic) DNA repair system. Mediation of EMS mutagenesis by an error-prone repair pathway in S. fradiae, rather than by direct mispairing as in Escherichia coli, suggests that the streptomycetes have evolved more efficient error-avoidance mechanisms than those commonly observed in the single-celled eubacteria.

A 2.2-kilobase repeated DNA segment is associated with DNA amplification in Streptomyces fradiae

We have previously identified a 10.5-kilobase DNA sequence which is highly amplified and tandemly repeated in the mutant Streptomyces fradiae JS85. A library of DNA was prepared from S. fradiae T776, which does not contain amplified DNA. The library was screened by plaque hybridization to identify phage clones containing the unamplified 10.5-kilobase DNA sequence. Four phage isolates were identified which contained DNA homology to the amplified DNA sequence. This sequence was designated the amplifiable unit of DNA. None of the clones carried an entire amplifiable unit of DNA, and so overlapping regions were aligned to create a map of the entire region. Detailed restriction mapping identified a 2.2-kilobase direct repeat at the ends of the amplifiable unit of DNA. Analysis by Southern hybridization confirmed that the direct repeats were homologous to each other. The DNA of S. fradiae contained at least two additional copies of DNA that was homologous to the repeat sequence.

Streptomyces contain Escherichia coli-type A + T-rich promoters having novel structural features

We describe here the isolation and characterization of a class of A + T-rich transcriptionally active sequences in the filamentous antibiotic-producing Gram-positive bacterial genus Streptomyces. These regions, which digress dramatically in base composition from the 73% G + C composition characteristic of the Streptomyces genome, promote gene expression in both Escherichia coli and Streptomyces lividans and contain the major elements that determine promoter strength in E. coli. The Streptomyces-E. coli-type promoters (SEP) also show novel structural features that include multiple direct repeats within the promoter region as well as a specific hexameric sequence in the vicinity of the mRNA start point.

Plasmids in different strains of Streptomyces ambofaciens: free and integrated form of plasmid pSAM2

Five strains of Streptomyces ambofaciens were examined for their plasmid content. Among these strains, four belong to the same lineage (strains B) and the other was isolated independently (strain A). A large plasmid (ca. 80 kb), called pSAM1 in this paper and already described, was present in all B strains, and absent in strain A. A second plasmid, not described before, was found as covalently closed circular DNA in two of the four B strains. This plasmid with a size of 11.1 kb was called pSAM2. A restriction map for 14 enzymes was established. Hybridization experiments showed that a unique sequence homologous to this plasmid is integrated in a larger replicon, which is not pSAM1 and is probably the chromosome, in all B strains and not in strain A. It seems probable that the integrated sequence is the origin of the free plasmid found in two strains of the B family. It is noteworthy that the integrated form and the free plasmid may be found together. Transformation experiments proved that pSAM2 may be maintained autonomously in S. ambofaciens strain A and in S. lividans. pSAM2 is a self-transmissible plasmid, able to elicit the lethal zygosis reaction. pSAM2 was compared to the plasmids SLP1, pIJ110 and pIJ408, which all come from integrated sequences in three Streptomyces species and are found as autonomous plasmids after transfer to S. lividans. If pSAM2 resembles these plasmids in its origin, it does not appear to be related directly to them. Concerning their plasmid content, the two isolates of S. ambofaciens are very different.(ABSTRACT TRUNCATED AT 250 WORDS)

Inverted repeats in the DNA of Streptomyces plasmids pMG110 and pMG120

Two cryptic plasmids pMG110 (10.5 kb) and pMG120 (14.5 kb) isolated from Streptomyces luteolutescens were cleaved by restriction endonucleases Bg/II, KpnI, and SalGI. A physical map was constructed for pMG110. After denaturation and intrastrand reannealing, two types of snap-back structures were identified by electron microscopy, differing in the size of the loop (type 1, 1 kb; type 2, 1.6 kb), whereas the stem of both structures was about 190 bp long. Stem-loop structures of similar size were also observed in pMG120. In rare cases, both types of elements were present on the same DNA molecule. The analysis of Bg/II- and KpnI-generated fragments allowed the localization of the elements at two alternative positions on the physical map of pMG110.

DNA amplification and an unstable arginine gene in Streptomyces lividans 66

Streptomyces lividans 66 produced spontaneous chloramphenicol-sensitive mutants (CmlS) at a frequency of about 1% of spores. The CmlS mutant strains were very unstable, giving Arg- mutants at frequencies of about 25% of spores. All the Arg- mutants had amplified a particular 5.75 kb DNA fragment into tandem repeats of 250-500 copies per chromosome.

Recombination between short direct repeats in Streptomyces lavendulae plasmid DNA

Streptomyces lavendulae S985 carried two plasmids, pSL1 and pSL2. pSL2 contained all of the pSL1 sequences plus a tandem duplication of 900 base pairs from a region of pSL1. Sequence analysis of the duplication junction suggested that the duplication occurred by recombination between short direct repeats of as little as 5 base pairs.

Evidence for the wide distribution of repetitive DNA sequences in the genus Streptomyces

Repeated DNA sequences were detected as rapidly reannealing sequences in the chromosomal DNA of 13 out of 14 Streptomyces species using either hypochromicity measurements or hydroxyapatite chromatography. These sequences made up between approximately 4% and 11% of the total DNA of these species; only in Streptomyces rimosus were repeated DNA sequences not detected. The repeated sequences fall into a number of distinct percentage G + C (%G + C) classes, many being of rather low %G + C. Analytical density ultracentrifugation of the DNA of these species indicated satellite bands of low %G + C, and high-resolution thermal denaturation profiles indicated the presence of blocks of DNA of low G + C content too. No such satellite band could be found in Streptomyces coelicolor and no low-%G + C DNA could be detected in its thermal denaturation profile. The possible relationship of this repeated DNA, an unusual occurrence in a procaryote, to genetic instability and genetic control mechanisms in Streptomyces is discussed.

Amplified DNA in Streptomyces fradiae

A spontaneous mutant of Streptomyces fradiae contained an amplifiable unit of DNA with a sequence length of approximately 10.5 kilobases that was amplified to approximately 500 copies per chromosome. The amplified DNA appears to be cryptic. SalI fragments of the amplified DNA were cloned into Escherichia coli to construct a restriction map and characterize the amplified DNA. The amplified DNA contained tandem repeats of the amplifiable unit of DNA. The unit had an average base composition of 71% guanine plus cytosine, similar to the chromosomal DNA of Streptomyces species. At least a portion of the amplifiable unit of DNA was present at a low copy number in the wild-type strain. The phenotype of amplified DNA was designated Ads1SF for amplified DNA sequence 1 in S. fradiae.

Deletion and amplification of DNA sequences in melanin-negative variants of Streptomyces reticuli

The sporulating wild type of Streptomyces reticuli produces the pigment melanin. Though the ability to synthesize tyrosinase is frequently lost, it was demonstrated, that the structural gene coding for this enzyme is not located on the extrachromosomal DNA of the wild type strain or melanin-positive variants. Melanin negative variants were found to have lost this gene and to contain amplified nucleotide sequences within their genomes.