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

Abstract

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.

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

“…The association between deletion and genetic instability was frequently reported in Streptomyces species (2,5,6). In S. glaucescens, for example, the double mutant phenotype Str-Mel-was ascribed to deletions whose sizes were estimated to range from 270 to over 800 kb (2).…”

Genome rearrangement and genetic instability in Streptomyces spp

“…Interestingly, in this species the resulting genetic map (20) could not easily be reconciled with subsequently obtained physical linkage data, which clearly showed that the two loci are 350 kb apart (7). Although both map to the chromosome, the apparent map interval derived from recombination frequencies suggested a substantially larger distance than this, indicating that even apparently reliable mapping data must be viewed with the utmost caution when unstable traits are involved.…”

“…22,23,28). Additionally, analyses involving DNA surrounding unstable genes demonstrated that extensive flanking sequences were also absent, implicating large chromosomal deletion events in the instabilities (6,7,18). In S. glaucescens, deletions which were responsible for the loss of the unstable genes coding for tyrosinase (melC) and hydroxystreptomycin phosphotransferase (strS) were initially characterized (22,23).…”

“…For S. glaucescens, evidence is available to support a model in which deletion precedes amplification (7,21). Amplifications were found exclusively in strains possessing the most extensive deletions, and though strains carrying only deletions were frequently characterized, in no case was amplification detected in the absence of an accompanying deletion.…”

“…The majority of these instabilities are the result of extensive chromosomal deletions which, interestingly, are frequently accompanied by intense DNA amplifications that take place in the absence of any obvious selection pressure. The deletions can extend to in excess of 800 kb (7), and the physically linked amplified arrays can extend to 3,000 kb (20,21), constituting 18 and 45% of the chromosome, respectively.…”