rrnDB about us

Lee Z.M., Bussema C. 3rd and Schmidt, T.M.(2008) rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res. pp1-5.

Klappenbach, J.A., P.R. Saxman, J.R. Cole and T.M. Schmidt (2001) rrnDB: the Ribosomal RNA Operon Copy Number Database. Nucleic Acids Res. 29(1):181-4.

The rrnDB is a curated database that catalogs the numbers of genes that encode for 16S, 23S and 5S ribosomal RNAs in Bacteria and Archaea. Typically, a single copy of each of these genes is clustered into a rRNA operon, with as many as 15 rRNA operons present per genome. The genomic locus for any of the rRNA encoding genes is “rrn” – hence the name of this database. Because the number of genes encoding tRNAs is positively correlated with the number of rRNA-encoding genes (1), tRNA gene copy number is also cataloged in the rrnDB. Data are gathered both from sequenced genomes and from published articles that include estimates of the number of rRNA encoding genes.

These are important data to microbiologists because the number of ribosomal RNA genes is indicative of where a bacterium lies on a spectrum of ecological strategies between oligotrophy (few rRNA genes) and copiotrophy (many rRNA genes) (3,4). The demand for rapid synthesis of ribosomes in copiotrophic bacteria is proposed to be the selective pressure driving the maintenance of multiple copies of rRNA genes per genome.

Measurement of the macromolecular composition of phylogenetically diverse bacteria suggests that the variation in the translational machinery of bacteria mirrors the number of rRNA operons. This variation is in the form of a fundamental tradeoff between power and efficiency, with more rapid translation of mRNA in copiotrophs and slower but more efficient translation of mRNA in oligotrophs (1).

While redundancy in rRNA genes forms the basis of ecological models to explain the distibution of microbes in nature, the difference in the number of rRNA genes poses challenges for those who use 16S or 23S rRNA gene as a tool to study microbial diversity. These challenges arise when the number of rRNA genes is used as a proxy measure for the number of organisms present (difficult to do unless the number of rRNA gene/genome is known), or when variation in the sequence of multiple rRNA genes/genome are used to design specific primers or probes (2). Data presented in the rrnDB can help address these challenges by providing easy access to data about rRNA gene copy number.

If you know of additional data that should be added to the rrnDB, please use the “Contact Us” information to let us know.

References:

1. Dethlefsen, L. and T.M. Schmidt (2007) The performance of the translational apparatus varies with the ecological strategies of bacteria. Journal of Bacteriology 189:3237-45.

2. Hashimoto, J.G., B. S. Stevenson and T.M. Schmidt (2003) Rates and consequences of recombination between ribosomal RNA operons. Journal of Bacteriology 185:966-972.