rRNAGene

Ribosomal RNA genes, commonly abbreviated as rRNA genes or rDNA, are DNA sequences that encode the RNA components of ribosomes, the molecular machines that synthesize proteins. In all domains of life, ribosomes contain ribosomal RNA that forms a large part of the catalytic core and structural framework. In bacteria and archaea, the main rRNA species are 16S rRNA in the small subunit and 23S and 5S rRNAs in the large subunit. In eukaryotes, the small subunit contains 18S rRNA, while the large subunit contains 28S, 5.8S, and 5S rRNAs. Organelles such as mitochondria and chloroplasts also carry their own rRNA genes that resemble bacterial counterparts.

Organization and genomic arrangement differ between domains. In bacteria and archaea, rRNA genes are typically arranged in operons that encode 16S-23S-5S rRNA genes in a single transcriptional unit, with multiple operons present per genome. In eukaryotes, the 18S-5.8S-28S rRNA genes are arranged in tandem repeats within ribosomal DNA (rDNA) clusters, known as nucleolar organizer regions; the 5S rRNA genes are often located in separate arrays. Eukaryotic rDNA transcription is mainly by RNA polymerase I for the 18S-28S-5.8S unit, while 5S rRNA is transcribed by RNA polymerase III.

Function and evolution. rRNA genes are highly conserved, with conserved regions suitable for universal primer binding and variable regions useful for phylogenetic analysis. They are central to ribosome function, and their sequence variation underpins taxonomic identification and evolutionary studies. In practical use, the 16S rRNA gene is a standard marker for bacteria and archaea, while eukaryotic counterparts rely on 18S rRNA and related markers. Copy number and sequence variation among repeats can affect expression and complicate comparative analyses.