Challenges of ligand identification for the second wave of orphan riboswitch candidates

Abstract

Orphan riboswitch candidates are noncoding RNA motifs whose representatives are believed to function as genetic regulatory elements, but whose target ligands have yet to be identified. The study of certain orphans, particularly classes that have resisted experimental validation for many years, has led to the discovery of important biological pathways and processes once their ligands were identified. Previously, we highlighted details for four of the most common and intriguing orphan riboswitch candidates. This facilitated the validation of riboswitches for the signaling molecules c-di-AMP, ZTP, and ppGpp, the metal ion Mn, and the metabolites guanidine and PRPP. Such studies also yield useful linkages between the ligands sensed by the riboswitches and numerous biochemical pathways. In the current report, we describe the known characteristics of 30 distinct classes of orphan riboswitch candidates - some of which have remained unsolved for over a decade. We also discuss the prospects for uncovering novel biological insights via focused studies on these RNAs. Lastly, we make recommendations for experimental objectives along the path to finding ligands for these mysterious RNAs.

Point-of-Use Detection of Environmental Fluoride via a Cell-Free Riboswitch-Based Biosensor

“…The strategies we present here could be applied to optimize the performance of a large number of natural riboswitches for the detection of metabolites and ions relevant to environmental and human health monitoring (24). Additionally, the compatibility of CFE reactions for high-throughput screening (25) and the simple format of our DNA expression construct could be used to characterize the thousands of "orphan" riboswitches that have been bioinformatically identified but bind to unknown ligands (26). We imagine that these strategies could even be used to reengineer riboswitches to have novel function (27)(28)(29).…”

In silico prediction and expression profile analysis of small non-coding RNAs in Herbaspirillum seropedicae SmR1

“…In our work we observed the sucA RNA motif (Hsnc006) is highly expressed in the presence of nitrate (10 mmol/L) when compared to the control (20 mml/L NH 4 Cl) (Additional file 1). Since this motif typically appears at 5′ end of βproteobacteria sucA genes [46,47] this could indicate a unique adaptation of the energetic metabolism of this bacterial Class to the changes in nitrogen sources. This hypothesis should be investigated.…”

“…This result suggests that most of the H. seropedicae SmR1 sRNAs may be new or present low level of identity with those deposited in the Rfam database. Among the sRNAs identified the Toxic small RNA (tsRNA) and sucA RNA motif were found essentially in β-proteobacteria [46,47] whereas YkkC/YxkD leader is present in some Cyanobacteria and Proteobacteria [48]. The sRNAs belonging to the family of small toxic RNAs in H. seropedicae SmR1 were Hsnc59, Hsnc63, Hsnc86 and Hsnc107 (Table 1).…”

Former orphan riboswitches reveal unexplored areas of bacterial metabolism, signaling, and gene control processes

“…5) and include the key challenges discussed in detail below. There are currently dozens of orphan riboswitch candidates remaining to be analyzed (Corbino et al 2005;Weinberg et al 2007Weinberg et al , 2010Weinberg et al , 2017aWeinberg et al , 2017bGreenlee et al 2017), and therefore new strategies to overcome these limitations would help drive forward riboswitch validation research.…”