Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline

@article{WEINBERG2007, abstract = {We applied a computational pipeline based on comparative genomics to bacteria, and identified 22 novel candidate RNA motifs. We predicted six to be riboswitches, which are mRNA elements that regulate gene expression on binding a specific metabolite. In separate studies, we confirmed that two of these are novel riboswitches. Three other riboswitch candidates are upstream of either a putative transporter gene in the order Lactobacillales, citric acid cycle genes in Burkholderiales or molybdenum cofactor biosynthesis genes in several phyla. The remaining riboswitch candidate, the widespread Genes for the Environment, for Membranes and for Motility (GEMM) motif, is associated with genes important for natural competence in Vibrio cholerae and the use of metal ions as electron acceptors in Geobacter sulfurreducens. Among the other motifs, one has a genetic distribution similar to a previously published candidate riboswitch, ykkC/yxkD, but has a different structure. We identified possible non-coding RNAs in five phyla, and several additional cis-regulatory RNAs, including one in{varepsilon} -proteobacteria (upstream of purD, involved in purine biosynthesis), and one in Cyanobacteria (within an ATP synthase operon). These candidate RNAs add to the growing list of RNA motifs involved in multiple cellular processes, and suggest that many additional RNAs remain to be discovered. 10.1093/nar/gkm487}, author = {Weinberg, Zasha and Barrick, Jeffrey E. and Yao, Zizhen and Roth, Adam and Kim, Jane N. and Gore, Jeremy and Wang, Joy X. and Lee, Elaine R. and Block, Kirsten F. and Sudarsan, Narasimhan and Neph, Shane and Tompa, Martin and Ruzzo, Walter L. and Breaker, Ronald R. }, citeulike-article-id = {1869950}, doi = {10.1093/nar/gkm487}, journal = {Nucl. Acids Res.}, month = {July}, pages = {gkm487+}, posted-at = {2008-04-09 08:13:31}, priority = {2}, title = {Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline}, url = {http://dx.doi.org/10.1093/nar/gkm487}, year = {2007} }

TY - JOUR ID - WEINBERG2007 L3 - citeulike-article-id:1869950 TI - Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline JF - Nucl. Acids Res. SP - gkm487 N2 - We applied a computational pipeline based on comparative genomics to bacteria, and identified 22 novel candidate RNA motifs. We predicted six to be riboswitches, which are mRNA elements that regulate gene expression on binding a specific metabolite. In separate studies, we confirmed that two of these are novel riboswitches. Three other riboswitch candidates are upstream of either a putative transporter gene in the order Lactobacillales, citric acid cycle genes in Burkholderiales or molybdenum cofactor biosynthesis genes in several phyla. The remaining riboswitch candidate, the widespread Genes for the Environment, for Membranes and for Motility (GEMM) motif, is associated with genes important for natural competence in Vibrio cholerae and the use of metal ions as electron acceptors in Geobacter sulfurreducens. Among the other motifs, one has a genetic distribution similar to a previously published candidate riboswitch, ykkC/yxkD, but has a different structure. We identified possible non-coding RNAs in five phyla, and several additional cis-regulatory RNAs, including one in{varepsilon} -proteobacteria (upstream of purD, involved in purine biosynthesis), and one in Cyanobacteria (within an ATP synthase operon). These candidate RNAs add to the growing list of RNA motifs involved in multiple cellular processes, and suggest that many additional RNAs remain to be discovered. 10.1093/nar/gkm487 AU - Weinberg, Zasha AU - Barrick, Jeffrey AU - Yao, Zizhen AU - Roth, Adam AU - Kim, Jane AU - Gore, Jeremy AU - Wang, Joy AU - Lee, Elaine AU - Block, Kirsten AU - Sudarsan, Narasimhan AU - Neph, Shane AU - Tompa, Martin AU - Ruzzo, Walter AU - Breaker, Ronald PY - 2007/07/09/ UR - http://dx.doi.org/10.1093/nar/gkm487 ER -