Genetic instability and hypervariability in <i>Streptomyces ambofaciens</i>: towards an understanding of a mechanism of genome plasticity

Leblond, Pierre; Demuyter, Philippe; Simonet, Jean-Marc; Decaris, Bernard

doi:10.1111/j.1365-2958.1990.tb00641.x

Cited by 59 publications

(36 citation statements)

References 35 publications

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“…The exact sizes of the deletions are not known. It is not clear how these deletions occurred, but in the studied genetic instability of the Streptomyces chromosomes, tandem amplifications frequently accompany spontaneous deletions at the termini (Cullum et al, 1988;Schrempf et al, 1989;Birch et al, 1990;Leblond et al, 1990).…”

Section: Discussionmentioning

confidence: 99%

“…Deletions of tens to hundreds of kilobases occur spontaneously at frequencies of about 5 × 10 ¹3 and are often accompanied by extensive tandem amplifications of specific sequences (reviewed in Cullum et al, 1988;Schrempf et al, 1989;Birch et al, 1990;Leblond et al, 1990). In S. lividans, one of the most frequently deleted markers is the chloramphenicol (Cm) resistance gene, cmr (Altenbuchner and Cullum, 1984;Dyson and Schrempf, 1987), which was located near one end of the chromosome (Redenbach et al, 1993).…”

Section: Introductionmentioning

confidence: 99%

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Instability of artificially circularized chromosomes of Streptomyces lividans

Lin¹,

Chen²

1997

Molecular Microbiology

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SummaryThe chromosomes of Streptomyces species are linear molecules, containing long terminal inverted repeats and covalently bound terminal proteins. These chromosomes undergo spontaneous deletions of the terminal sequences at high frequencies and become circularized in several cases examined. Artificial circularization of the Streptomyces lividans chromosome was also achieved by targeted recombination in vivo, in which the terminal inverted repeats of the chromosome were connected by a kanamycin resistance gene (aphII ). Under kanamycin selection, the circularized chromosomes harboured tandem amplifications of a 20.2 kb sequence that included the aphII gene flanked by direct repeats and deletions nearby. On release from kanamycin selection, the aphII amplifications and the neighbouring sequences were deleted from the chromosomes, rendering all the cultures kanamycin sensitive. The chloramphenicol resistance gene, which was prone to deletion in wild-type S. lividans, became much more stable in the kanamycin-sensitive derivatives. These results indicate that the telomeres and/or certain terminal sequences may be involved in the structural instability of Streptomyces chromosomes.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Instability of artificially circularized chromosomes of Streptomyces lividans

Lin¹,

Chen²

1997

Molecular Microbiology

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“…These deletions affected the DNA region overlapping both amplifiable loci. PFGE also allowed us to localize the amplified DNA sequences and to establish their structure: amplification takes place at the AUD locus as a tandem array of the wild-type AUD sequence.The Streptomyces genome exhibits a high degree of genome plasticity, consisting of large deletions and amplified DNA sequences (ADS) associated with instability of many characteristics (1,11,13). In Streptomyces ambofaciens DSM40697 (9), two levels of genetic instability were characterized: (i) a basic genetic instability similar to that reported for other Streptomyces spp.…”

mentioning

confidence: 89%

“…The Streptomyces genome exhibits a high degree of genome plasticity, consisting of large deletions and amplified DNA sequences (ADS) associated with instability of many characteristics (1,11,13). In Streptomyces ambofaciens DSM40697 (9), two levels of genetic instability were characterized: (i) a basic genetic instability similar to that reported for other Streptomyces spp.…”

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confidence: 89%

Genetic instability and associated genome plasticity in Streptomyces ambofaciens: pulsed-field gel electrophoresis evidence for large DNA alterations in a limited genomic region

et al. 1991

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Using pulsed-field gel electrophoresis (PFGE) analysis, the amplifiable units of DNA (AUD) loci AUD6 and AUD90 of Streptomyces ambofaciens DSM40697 could be mapped in the wild-type genome within two adjacent AseI restriction fragments estimated to be about 75 and 850 kb. In addition, the genetic instability and formation of very large deletions were strictly correlated. Their sizes were estimated to range from 250 to more than 2,000 kb. These deletions affected the DNA region overlapping both amplifiable loci. PFGE also allowed us to localize the amplified DNA sequences and to establish their structure: amplification takes place at the AUD locus as a tandem array of the wild-type AUD sequence.The Streptomyces genome exhibits a high degree of genome plasticity, consisting of large deletions and amplified DNA sequences (ADS) associated with instability of many characteristics (1,11,13). In Streptomyces ambofaciens DSM40697 (9), two levels of genetic instability were characterized: (i) a basic genetic instability similar to that reported for other Streptomyces spp. and (ii) hypervariability, closely related to the first phenomenon, generating a phenotypic variability from mutant clones (12). At least two DNA regions undergo amplification in close association with hypervariability (3, 12). In addition, an amplifiable locus was recently characterized as a rearrangement hotspot, mainly for deletions (4). An analogous situation implying successive mutational events associated with changes in DNA structure is well documented in Streptomyces lividans (5). Using pulsed-field gel electrophoresis (PFGE), we investigated the localization of the amplifiable units of DNA (AUD) on large restriction fragments generated from the wild-type (WT) genome and the size of the deletions associated with genetic instability. We then studied the structure and the physical localization of the ADS in the mutant genome.Physical relationship between the AUD regions on the WT genome. Forty-eight ADSs, whose sizes ranged from 5.2 to 105 kb, generated through independent genetic instability events were considered. Three probes were used in hybridization experiments: S1, consisting of the cloned extremities of ADS6 (Fig. 1); S120, consisting of a 1.95-kb BamHI fragment of ADS120 (12) (Fig. 1). The relative intensity of the signals could be explained by the fact that the 75-kb fragment contained two homologous stretches (i.e., the right side of the AUD and the internal homologous sequence). On the other hand, the 850-kb fragment contained only the left side of AUD6. Both the S120 and S55 (from an ADS belonging to a region other than AUD90 or AUD6) probes revealed the 850-kb fragment. Faint signals could be detected that corresponded to almost all restriction fragments generated by AseI, particularly the 200-kb doublet (14)

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“…The 4.3 kb AUD is not flanked by repeats and its amplification has been observed only in S. lividans TKIII-1OT. Other examples of type 1 AUD lacking repeated sequences or carrying only short microhomologies within very short imperfect repeats have been detected within Streptomyces glaucescens (Hausler et al, 1989) and S. ambofaciens (Leblond et al, 1990). In contrast, two tandem copies of AUDl (consisting of three 1 kb repeats which flank two 4.7 kb parts) reside in the 'silent' region of S. lividans wild-type chromosome (Altenbuchner & Cullum, 1985 ;Piendl et af., 1994).…”

Section: Discussionmentioning

confidence: 99%

Identification of genes in Rhizobium leguminosarum bv. trifolii whose products are homologues to a family of ATP-binding proteins

1997

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The wild-type Streptomyces lividans 66 genome contains a 4 3 kb amplifiable DNA unit (AUD), and its four ORFs encode proteins that could not be identified by sequence comparison with databases. One of the gene products (encoded by orf-2) was purified and determined to be a novel 23 kDa protein. This protein is synthesized by the wild-type strain, absent in a variant lacking the AUD and overproduced in a variant in which the AUD is amplified (ADS). Immunological studies and analyses by confocal laser microscopy showed that the 23 kDa protein is associated with the substrate hyphae of the wild-type and the ADS-containing variant. Examination by microscopy revealed that the strain carrying the ADS forms bulges within the substrate hyphae and apical vesicles. These bulges have high levels of associated 23 kDa protein and contain storage-I i ke material.

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Genetic instability and hypervariability in Streptomyces ambofaciens: towards an understanding of a mechanism of genome plasticity

Cited by 59 publications

References 35 publications

Instability of artificially circularized chromosomes of Streptomyces lividans

Instability of artificially circularized chromosomes of Streptomyces lividans

Genetic instability and associated genome plasticity in Streptomyces ambofaciens: pulsed-field gel electrophoresis evidence for large DNA alterations in a limited genomic region

Identification of genes in Rhizobium leguminosarum bv. trifolii whose products are homologues to a family of ATP-binding proteins

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