Bilateral symmetry of linear streptomycete chromosomes

Abstract

Here, we characterize an uncommon set of telomeres from Streptomyces rimosus ATCC 10970, the parental strain of a lineage of one of the earliest-discovered antibiotic producers. Following the closure of its genome sequence, we compared unusual telomeres from this organism with the other five classes of replicon ends found amongst streptomycetes. Closed replicons of streptomycete chromosomes were organized with respect to their phylogeny and physical orientation, which demonstrated that different telomeres were not associated with particular clades and are likely shared amongst different strains by plasmid-driven horizontal gene transfer. Furthermore, we identified a ~50 kb origin island with conserved synteny that is located at the core of all streptomycete chromosomes and forms an axis around which symmetrical chromosome inversions can take place. Despite this chromosomal bilateral symmetry, a bias in parS sites to the right of oriC is maintained across the family Streptomycetaceae and suggests that the formation of ParB/parS nucleoprotein complexes on the right replichore is a conserved feature in streptomycetes. Consequently, our studies reveal novel features of linear bacterial replicons that, through their manipulation, may lead to improvements in growth and productivity of this important industrial group of bacteria.

Reference-Grade Genome and Large Linear Plasmid of Streptomyces rimosus: Pushing the Limits of Nanopore Sequencing

“…The only difference was in the estimated fragment sizes; the published lengths of Pandza et al differed for the larger bands (>500 kb), which is likely to be a consequence of the high GC content and more complex estimation of fragment length when using DNA size markers ( 35 ). Our PFGE analysis was also consistent with recently published PFGE data ( 6 ). We obtained the same number of fragments after in silico restriction, and the visible DNA fragments on the PFGE gel correlated strongly.…”

“…Compared to the GenBank accession no. GCF_000331185.2 genome assembly ( 6 ), our assembly lacked the complete telomere sequences at both ends of the chromosome (324 bp of missing sequence on the right and a 1,771-bp fragment on the left side). Regarding the linear plasmid telomeres, the plasmid from our ATCC 10970 assembly had the right arm containing a complete telomere sequence, while the left arm was missing a 20-bp fragment at the end, which was present on the plasmid sequence of GCF_000331185.2 ( 6 ).…”

“…2A ) revealed that only the aforementioned assembly of strain ATCC 10970 (GenBank accession no. GCF_000331185.2 ) ( 6 ) had a comparable plasmid sequence. Several contig-level assemblies had complete coverage of the plasmid sequence, but the contigs were not connected at certain regions.…”

“…The whole-genome assembly of ATCC 10970 was validated by its PFGE digestion profile and compared with two previously published PFGE results ( 34 , 35 ). The restriction of the chromosomal DNA obtained from the ATCC 10970 (R7) strain, performed by Pandza et al, yielded 14 visible fragments after AseI digestion.…”

“…GCF_006229535.1 ). Using a similar approach, a group from the Korea Advanced Institute of Science and Technology (KAIST) ( GCF_008704655.1 ) and a group from the University of Strathclyde ( GCF_000331185.2 ) recently also obtained the genome sequence for this strain ( 5 , 6 ).…”