Riboswitch diversity and distribution

McCown, Phillip J.; Corbino, Keith A.; Stav, Shira; Sherlock, Madeline E.; Breaker, Ronald R.

doi:10.1261/rna.061234.117

Cited by 381 publications

(487 citation statements)

References 129 publications

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“…Several types of small ncRNAs perform regulatory functions, for example, microRNA (miRNA) and piwi-interacting RNA (piRNA) act as key regulators of gene expression in higher eukaryotes. Several types of ncRNAs, including riboswitches (McCown, Corbino, Stav, Sherlock, & Breaker, 2017) and RNA thermometers (Kortmann & Narberhaus, 2012), are found in bacteria where they play roles in gene expression, virulence, and stress response.…”

Section: Commentarymentioning

confidence: 99%

Non‐Coding RNA Analysis Using the Rfam Database

Kalvari

Nawrocki

Argasinska

et al. 2018

CP in Bioinformatics

306

194

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Rfam is a database of non-coding RNA families in which each family is represented by a multiple sequence alignment, a consensus secondary structure, and a covariance model. Using a combination of manual and literature-based curation and a custom software pipeline, Rfam converts descriptions of RNA families found in the scientific literature into computational models that can be used to annotate RNAs belonging to those families in any DNA or RNA sequence. Valuable research outputs that are often locked up in figures and supplementary information files are encapsulated in Rfam entries and made accessible through the Rfam Web site. The data produced by Rfam have a broad application, from genome annotation to providing training sets for algorithm development. This article gives an overview of how to search and navigate the Rfam Web site, and how to annotate sequences with RNA families. The Rfam database is freely available at http://rfam.org. © 2018 by John Wiley & Sons, Inc.

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Section: Commentarymentioning

confidence: 99%

Non‐Coding RNA Analysis Using the Rfam Database

Kalvari

Nawrocki

Argasinska

et al. 2018

CP in Bioinformatics

306

194

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“…Among the most common functions for the highly-structured ncRNA classes, which excludes less structured classes such as bacterial sRNAs (26), are RNA self-cleavage (24, 25, 27) and riboswitch-mediated ligand binding and gene control (28). Most representatives of these natural self-cleaving ribozyme and riboswitch classes are shorter than 200 nucleotides.…”

Section: Large Ncrnas With Unknown Functionsmentioning

confidence: 99%

Large Noncoding RNAs in Bacteria

Harris

Breaker

2018

Microbiol Spectr

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Bacterial noncoding RNA (ncRNA) classes longer than 200 nucleotides are rare, but are responsible for performing some of the most fundamental tasks in living cells. RNAs such as 16S and 23S ribosomal RNA, group I and group II introns, RNase P ribozymes, tmRNAs, and coenzyme B12 riboswitches, are diverse in structure and accomplish biochemical functions that rival the activities of proteins. Over the last decade, a number of new classes of large ncRNAs have been uncovered in bacteria. A total of 21 classes with no established functions have been identified through the use of bioinformatics search strategies. Based on precedents for bacterial large ncRNAs performing sophisticated functions, it seems likely that some of these structured ncRNAs also will prove to carry out complex functions. Thus, determining their roles will provide a better understanding of fundamental biological processes. A few studies have produced data that provide clues to the purposes of some of these recently-found classes, but the true functions of most classes remain mysterious.

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“…[2] Bacteria modulate expression of certain genes to survive and replicate in low Mg 2+ environments. [2,6] Although Mg 2+ -sensing riboswitches are well-studied, [6] the effects of aM g 2+ -depleted environment on metabolite-sens-ing riboswitches, [7] which regulate the genes essential for survival and growth during bacterial pathogenesis,a re not characterized. [4] TheMg 2+ ion is crucial for RNAfunctions as it neutralizes the phosphate backbone to stabilize RNAt ertiary structure formation.…”

mentioning

confidence: 99%

“…[4] TheMg 2+ ion is crucial for RNAfunctions as it neutralizes the phosphate backbone to stabilize RNAt ertiary structure formation. [2,6] Although Mg 2+ -sensing riboswitches are well-studied, [6] the effects of aM g 2+ -depleted environment on metabolite-sens-ing riboswitches, [7] which regulate the genes essential for survival and growth during bacterial pathogenesis,a re not characterized. [2,6] Although Mg 2+ -sensing riboswitches are well-studied, [6] the effects of aM g 2+ -depleted environment on metabolite-sens-ing riboswitches, [7] which regulate the genes essential for survival and growth during bacterial pathogenesis,a re not characterized.…”

mentioning

confidence: 99%

Crowding Shifts the FMN Recognition Mechanism of Riboswitch Aptamer from Conformational Selection to Induced Fit

Rode¹,

Endoh²,

Sugimoto

2018

Angewandte Chemie

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In bacteria, the binding between the riboswitch aptamer domain and ligand is regulated by environmental cues,such as lowMg 2+ in macrophages during pathogenesis to ensure spatiotemporal expression of virulence genes.B inding was investigated between the flavin mononucleotide (FMN) riboswitch aptamer and its anionic ligand in the presence of molecular crowding agent without Mg 2+ ion, whichm imics pathogenic conditions.Structural, kinetic, and thermodynamic analyses under the crowding revealed more dynamic conformational rearrangements of the FMN riboswitch aptamer compared to dilute Mg 2+ -containing solution. It is hypothesized that under crowding conditions FMN binds through an induced fit mechanism in contrast to the conformational selection mechanism previously demonstrated in dilute Mg 2+ solution. Since these two mechanisms involve different conformational intermediates and rate constants,these findings have practical significance in areas such as drug design and RNAengineering.Bacteria must survive in various extracellular and intracellular environments during infection. [1] Fore xample,t he divalent magnesium cation (Mg 2+ )c oncentration is significantly lower during intramacrophage survival and growth of bacteria than it is during in vitro culture. [2] Bacteria modulate expression of certain genes to survive and replicate in low Mg 2+ environments. [2,3] Bacteria sense the decrease in Mg 2+ levels to achieve temporal and spatial expression of virulence genes. [4] TheMg 2+ ion is crucial for RNAfunctions as it neutralizes the phosphate backbone to stabilize RNAt ertiary structure formation. [5] Thus,t he fluctuation of intracellular Mg 2+ concentration during bacterial pathogenesis will have significant impacts on regulatory RNAc onformations and functions.Indeed, Mg 2+ -sensing riboswitches modulate expression of genes responsible for magnesium transport across the membrane as well as of genes involved in virulence. [2,6] Although Mg 2+ -sensing riboswitches are well-studied, [6] the effects of aM g 2+ -depleted environment on metabolite-sens-ing riboswitches, [7] which regulate the genes essential for survival and growth during bacterial pathogenesis,a re not characterized. Metabolite-sensing riboswitches depend on Mg 2+ to stabilize tertiary structures indispensable for function. [5] Affinities of riboswitches for their anionic ligands such as thiamine pyrophosphate, [8] glucosamine-6-phosphate, [9] and flavin mono nucleotide (FMN) [10] are decreased by up to 1000-fold upon disruption of the Mg 2+ -mediated interactions.S ince metabolite-sensing riboswitches are promising antibacterial drug targets, [11] understanding how riboswitchligand interactions respond to Mg 2+ concentration fluctuations is crucial for development of antibacterial drugs.Most structural and ligand binding studies of riboswitches have been performed in dilute solutions [12] that substantially differ from the intracellular environment in which riboswitches function. [13] Living cells contain between 20 and 40 wt % protein, nucleic...

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Riboswitch diversity and distribution

Cited by 381 publications

References 129 publications

Non‐Coding RNA Analysis Using the Rfam Database

Non‐Coding RNA Analysis Using the Rfam Database

Large Noncoding RNAs in Bacteria

Crowding Shifts the FMN Recognition Mechanism of Riboswitch Aptamer from Conformational Selection to Induced Fit

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