rrn

rrn, short for ribosomal RNA operon, denotes the genetic loci that encode ribosomal RNA in bacteria, archaea, and some organelles. In most bacteria, rrn operons contain tandem rRNA genes—typically 16S, 23S, and 5S rRNA—often with one or more tRNA genes between them. A single operon is transcribed as a precursor rRNA and processed into mature rRNAs that form ribosomes. The number of rrn operons per genome varies by species; copy number ranges from one to more than a dozen, with a well-studied example being seven operons in Escherichia coli.

Copy number and promoter strength influence the capacity for ribosome production and growth rate. rrn transcription is regulated by the growth state: rapid growth favors high transcription by RNA polymerase with sigma-70, while nutrient limitation triggers the stringent response, in which ppGpp and DksA suppress rrn transcription and shift resources elsewhere.

Because 16S rRNA sequences are highly conserved, they are widely used for taxonomic identification and phylogeny; however, variation in rrn copy number among organisms affects abundance estimates in metagenomics and ecology studies. The repetitive nature of rrn loci also complicates genome assembly from short reads.

In mitochondria and chloroplasts, rrn genes reflect bacterial ancestry; mitochondria commonly carry 12S and 16S rRNA genes, while plastids carry 16S, 23S, 4.5S, and 5S rRNA genes in operon-like clusters.

RrnDB is a public resource that catalogs rrn operon copy numbers across bacteria and archaea and the 16S rRNA gene sequences used in taxonomic analyses.