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

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 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.

Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria

“…This narrow distribution has precedent, as SAM-III also appears limited to the same group of bacteria (Fuchs et al 2006). However, the bioinformatics searches that identified the preQ 1 -II riboswitch candidate did not uncover SAM-III Weinberg et al 2007), suggesting that there may be other RNA elements unique to this family that have yet to be identified. As genomic information continues to become available, however, bioinformatics searches could be used to discover additional rare structured RNA elements of which some could function as metabolite-sensing riboswitches.…”

“…The aptamer of each riboswitch class usually is well conserved due to constraints imposed by the ligand binding site. This conservation of aptamer sequences and structures makes bioinformatics analyses of genomic sequences an effective tool for identifying new riboswitch candidates (e.g., Rodionov et al 2002Rodionov et al , 2003Barrick et al 2004;AbreuGoodger and Merino 2005;Corbino et al 2005;Weinberg et al 2007). In contrast, expression platforms may vary considerably and utilize diverse genetic regulatory mechanisms such as transcription termination and translation inhibition (Mandal and Breaker 2004b).…”

Challenges of ligand identification for riboswitch candidates

“…The mini-ykkC 10 and ykkC-III 13 RNAs are structurally distinct from the ykkC RNA and both these RNAs are hypothesized to respond to the same biological conditions or stresses as the ykkC RNA. These structured RNA motifs are positioned as if they serve a common gene control function, which is similar to the multiple riboswitch classes that bind S-adenosylmethionine, 21 prequeuosine-1, 3 and cyclic-di-GMP.…”

“…The extensive conservation of aptamer domains makes them readily identifiable through comparative sequence analysis, which has become the predominant method of riboswitch discovery. [10][11][12][13] Riboswitches identified to date bind a variety of ligands including amino acids, coenzymes and even second messengers such as c-di-GMP. 3,14 Ligands are typically inferred from the open reading frames (ORFs) appearing immediately 3' of candidate riboswitches.…”

TPP riboswitch characterization in Alishewanella tabrizica and Alishewanella aestuarii and comparison with other TPP riboswitches

“…Until now about 30 different classes of riboswitches have been identified. However, many candidate riboswitches identified by bioinformatics still await ligand-assignment (Weinberg et al, 2007(Weinberg et al, , 2010.…”