Abstract
Streptomyces are among the most prolific bacterial producers of specialized metabolites, including antibiotics. The linear chromosome is partitioned into a central region harboring core genes and two extremities enriched in specialized metabolite biosynthetic gene clusters (SMBGCs). The molecular mechanisms governing structure and function of these compartmentalized genomes remain mostly unknown. Here we show that in exponential phase, chromosome structure correlates with genetic compartmentalization: conserved, large and highly transcribed genes form boundaries that segment the central part of the chromosome into domains, whereas the terminal ends are transcriptionally, largely quiescent compartments with different structural features. Onset of metabolic differentiation is accompanied by remodeling of chromosome architecture from an ‘open’ to a rather ‘closed’ conformation, in which the SMBGCs are expressed forming new boundaries. Altogether, our results reveal that S. ambofaciens’ linear chromosome is partitioned into structurally distinct entities, indicating a link between chromosome folding, gene expression and genome evolution.
Competing Interest Statement
The authors have declared no competing interest.
List of abbreviations
- 3C
- Chromosome Conformation Capture
- “Actino. Sign.”
- Actinobacterial Signature
- BGC
- Biosynthetic Gene Cluster
- CDS
- coding sequence
- CID
- Chromosome Interacting Domain
- GI
- Genomic island
- IGV
- Integrative Genomics Viewer
- LHEG
- long and highly expressed genes
- NAP
- Nucleoid Associated Protein
- NAPSFs
- Nucleoid Associated Proteins and structural factors
- PCA
- Principal Component Analysis
- rDNA
- ribosomal RNA encoding DNA
- RPK
- Read per kb
- SARTools
- Statistical Analysis of RNA-Seq data Tools
- SMBGC
- Specialized Metabolite Biosynthetic Gene Cluster
- TIR
- Terminal inverted repeat
- VST
- Variance Stabilizing Transformation