rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea

By Z. M. Lee, Carl Bussema, Thomas M. Schmidt. Nucleic Acids Res., 2008

449 citations recorded by the source corpus.

A dramatic exception to the general pattern of single-copy genes in bacterial and archaeal genomes is the presence of 1–15 copies of each ribosomal RNA encoding gene. The original version of the Ribosomal RNA Database (rrnDB) cataloged estimates of the number of 16S rRNA-encoding genes; the database now includes the number of genes encoding each of the rRNAs (5S, 16S and 23S), an internally transcribed spacer region, and the number of tRNA genes. The rrnDB has been used largely by microbiologists to predict the relative rate at which microbial populations respond to favorable growth conditions, and to interpret 16S rRNA-based surveys of microbial communities. To expand the functionality of the rrnDB (http://ribosome.mmg.msu.edu/rrndb/index.php), the search engine has been redesigned to allow database searches based on 16S rRNA gene copy number, specific organisms or taxonomic subsets of organisms. The revamped database also computes average gene copy numbers for any collection of entries selected. Curation tools now permit rapid updates, resulting in an expansion of the database to include data for 785 bacterial and 69 archaeal strains. The rrnDB continues to serve as the authoritative, curated source that documents the phylogenetic distribution of rRNA and tRNA genes in microbial genomes.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7149bea88717104db682fed694887c6fafd08567

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Citations in the corpus

Differential Growth Responses of Soil Bacterial Taxa to Carbon Substrates of Varying Chemical Recalcitrance (2011, methodology): “We hypothesized that the soil bacterial community is comprised of relatively distinct phylogenetic subsets that are either metabolically versatile with regard to their C substrate preferences or display specific C substrate utilization profiles and that response to substrates can be related to rRNA ”
A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing (2016, background): “…we de ﬁ ne cell abundances in this manuscript as 16S rRNA gene abundances, although we recognize that the conversion from 16S rRNA gene numbers to bacterial cell abundances should be done with caution as the number of 16S rRNA gene copies per cell can vary from one to ﬁ fteen (Lee et al., 2009).”
Constraints on the Biological Source(s) of the Orphan Branched Tetraether Membrane Lipids (2009, methodology): “As cells can contain more than one copy of the 16S rRNA gene, gene copy numbers have been translated in to numbers of cells using a correction factor obtained from the Ribosomal RNA Database (rrnDB, Lee et al. 2009).”
Bacterial Communities Associated with the Leaves and the Roots of Arabidopsis thaliana (2013, background): “16S rRNA copies range from 1 to 15 depending on the bacterial species [45].”
Insights from 20 years of bacterial genome sequencing (2015, background): “In addition, there is evidence that an increased number of tRNAs and rRNAs is correlated with a faster growth rate (Lee et al. 2009).”
Culture-independent molecular techniques for soil microbial ecology (2010, background): “php (Lee et al., 2009).”
Fundamentals of Microbial Community Resistance and Resilience (2012, background): “By contrast, microorganisms with fewer copies of rRNAencoding genes maximize efficiency of resource use (progeny per mole substrate; Lee et al., 2009), and may increase community resistance to press disturbances that result in long-term resource limitation.”
Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance (2012, methodology): “We assessed the accuracy of our method for estimating genomic 16S copy number by comparing our estimates of copy number with estimates for the same strains in another database of genomic 16S copy number estimates (the rrnDB database [15]).”
rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development (2014, methodology): “The rrnDB holds 216 organism-based records that use rrn copy number estimates from various empirical methods (19).”