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

By Zasha Weinberg, Jeffrey E. Barrick, Zizhen Yao, Adam Roth, Jane N. Kim, J. Gore, J. Wang, Elaine R. Lee, Kirsten F. Block, Narasimhan Sudarsan and 4 more. Nucleic Acids Research, 2007

311 citations recorded by the source corpus.

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 ε-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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/07d3e3f21251644846a1162b30a5398a27f8e4e1

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In Molecular Biology

1. Derek R. Lovley
2. Kelly P. Nevin
3. Ashley E. Franks
4. N. Malvankar
5. L. Waters
6. G. Storz
7. B. Logan
8. M. Lozano

Citations in the corpus

• Regulatory RNAs in Bacteria (2009, background): “Enabled by recent technical advances, including multilayered computational searches (Livny et al., 2008; Weinberg et al., 2007), deep sequencing (Sittka et al.”
• Geobacter: the microbe electric's physiology, ecology, and practical applications. (2011, background): “membranes and motility) (Weinberg et al., 2007), which have been shown to sense c-di-GMP in other bacteria (Sudarsan et al.”