Ribosomal RNA operons define a central functional compartment in the Streptomyces chromosome

Area of Science:

• Microbiology
• Genomics
• Molecular Biology

Background:

• Streptomyces bacteria produce valuable specialized metabolites for medicine and agriculture.
• Their large linear chromosomes exhibit genetic compartmentalization, with core genes centrally located and variable genes at the termini.
• Previous studies identified ribosomal RNA (rrn) operons as chromosome conformation boundaries in growing cells.

Purpose of the Study:

• To investigate the relationship between ribosomal RNA (rrn) operon distribution and genetic compartmentalization in Streptomyces.
• To establish a new nomenclature for Streptomyces genomes and analyze their rrn-based evolutionary history.
• To understand the functional implications of this compartmentalization, particularly regarding gene expression.

Main Methods:

• Comparative genomic analysis of a diverse panel of Streptomyces species.
• Identification of rrn operons and core genes within the analyzed genomes.
• Tracing the evolutionary history based on rrn operon distribution and pericentric inversions.

Main Results:

• Ribosomal RNA (rrn) operons and core genes form a conserved central genetic skeleton across Streptomyces.
• The central compartment, defined by rrn operons, is gene-dense and contains largely invariant core genes.
• Genes within this central compartment exhibit the highest expression levels, irrespective of their persistence or distance from the replication origin.

Conclusions:

• Ribosomal RNA (rrn) operons act as key structural organizers, defining a central functional compartment in Streptomyces chromosomes.
• This central compartment is characterized by high gene density and preferential high-level transcription.
• The findings provide insights into the genome architecture and regulatory mechanisms of Streptomyces.