The structural features of the ligand-free moaA riboswitch and its ion-dependent folding

Amadei, Fabio; Reichenbach, María; Gallo, Sofia; Sigel, Roland K. O.

doi:10.1016/j.jinorgbio.2023.112153

Cited by 2 publications

(2 citation statements)

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“…The moaA motif was identified as Moco riboswitch in 2008 [ 41 ], however, few studies have been reported due to its highly oxygen sensitivity. The latest researches have revealed specific Mg 2+ -binding pockets, indicating that the phosphate group of Moco is involved in ligand recognition [ 42 ]. Surprisingly, the absence of P3 element in Moco riboswitch causes it to bind Tungsten cofactor (Wco), which is almost identical in structure and function to Moco [ 9 , 41 ].…”

Section: The Diversity Of Riboswitchesmentioning

confidence: 99%

“…The coenzymes, nucleotide derivatives and signaling molecules could be regarded as RNA or RNA precursors derivatives. Information sources, SAM [ 146 ], TPP [ 3 ], FMN [ 144 ], NAD + [ 32 ], THF [ 38 ], Moco [ 42 ], Wco [ 42 ], theophylline [ 43 ], guanine [ 44 ], adenine [ 21 ], xanthine [ 49 ], preQ1 [ 45 ], c-di-AMP [ 36 ], c-di-GMP [ 54 ], c-AMP-GMP [ 56 ], lysine [ 64 ], glycine [ 67 ], glutamine [ 70 ], guanidine [ 72 ]. …”

Section: Introductionmentioning

confidence: 99%

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Riboswitches, from cognition to transformation

Hou

Ding

et al. 2023

Synthetic and Systems Biotechnology

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Section: The Diversity Of Riboswitchesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Riboswitches, from cognition to transformation

Hou

Ding

et al. 2023

Synthetic and Systems Biotechnology

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TaRTLEt: Transcriptionally-active Riboswitch Tracer Leveraging Edge deTection

Kshatriya,

Bagby

2024

Preprint

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Structured RNAs have emerged as a major component of cellular regulatory systems, but their mechanism of action is often poorly understood. Riboswitches are structured RNAs that allosterically regulate gene expression through any of several different mechanisms. In vitro approaches to characterizing mechanism are costly, low-throughput, and must be repeated for each individual riboswitch locus of interest. Bioinformatic methods promise higher throughput; despite robust computational identification of riboswitches, however, computational classification of riboswitch mechanism has so far been both model-bound, relying on identification of sequence motifs known to be required for specific models of riboswitch activity, and empirically untested, with predictions far outpacing biological validation. Here, we introduce TaRTLEt (Transcriptionally-active Riboswitch Tracer Leveraging Edge deTection), a new high-throughput tool that recovers in vivo patterns of riboswitch-mediated transcription termination from paired-end RNA-seq data using edge detection methods. TaRTLEt successfully extracts transcription termination signals despite numerous sources of biological and technical noise. We tested the effectiveness of TaRTLEt on riboswitches identified from a wide range of sequenced bacterial taxa by utilizing publicly available paired-end RNA-seq readsets, finding broad agreement with previously published in vitro characterization results. In addition, we use TaRTLEt to infer the in vivo regulatory mechanism of uncharacterized riboswitch loci from existing public data. TaRTLEt is available on GitHub and can be applied to paired-end RNA-seq datasets from isolates or complex communities.

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The structural features of the ligand-free moaA riboswitch and its ion-dependent folding

Cited by 2 publications

References 53 publications

Riboswitches, from cognition to transformation

Riboswitches, from cognition to transformation

TaRTLEt: Transcriptionally-active Riboswitch Tracer Leveraging Edge deTection

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