Lee Zarraz May-Ping, Bussema Carl, Schmidt Thomas M
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
Nucleic Acids Res. 2009 Jan;37(Database issue):D489-93. doi: 10.1093/nar/gkn689. Epub 2008 Oct 23.
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.
细菌和古菌基因组中单拷贝基因的一般模式有一个显著例外，即每个核糖体RNA编码基因存在1至15个拷贝。核糖体RNA数据库（rrnDB）的最初版本编录了16S rRNA编码基因数量的估计值；该数据库现在包括编码每种rRNA（5S、16S和23S）的基因数量、一个内部转录间隔区以及tRNA基因的数量。微生物学家大量使用rrnDB来预测微生物群体对有利生长条件作出反应的相对速率，并解读基于16S rRNA的微生物群落调查。为了扩展rrnDB（http://ribosome.mmg.msu.edu/rrndb/index.php）的功能，搜索引擎已重新设计，允许基于16S rRNA基因拷贝数、特定生物体或生物体的分类子集进行数据库搜索。改进后的数据库还能计算所选任何条目的平均基因拷贝数。管理工具现在允许快速更新，从而使数据库得以扩展，纳入了785种细菌和69种古菌菌株的数据。rrnDB仍然是记录微生物基因组中rRNA和tRNA基因系统发育分布的权威、经过整理的来源。
