Common themes and differences in SAM recognition among SAM riboswitches

Price, Ian R.; Grigg, J.C.; Ke, Ailong

doi:10.1016/j.bbagrm.2014.05.013

Cited by 32 publications

(32 citation statements)

References 54 publications

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“…These RNAs usually reside in 5′ untranslated regions (5′-UTRs) of mRNAs and regulate expression mainly by premature transcription termination or inhibition of translation initiation (Peselis and Serganov, 2014; Price et al, 2014; Serganov and Nudler, 2013). Other regulatory mechanisms have been demonstrated, including the control of mRNA degradation or alternative splicing (Caron et al, 2012; Li and Breaker, 2013).…”

Section: Introductionmentioning

confidence: 99%

Mn2+-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches

et al. 2015

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Summary Gene regulation in cis by riboswitches is prevalent in bacteria. The yybP-ykoY riboswitch family is quite widespread, yet its ligand and function remained unknown. Here we characterize the Lactococcus lactis yybP-ykoY riboswitch as a Mn2+-dependent transcription-ON riboswitch, with a ~30–40 μM affinity for Mn2+. We further determined its crystal structure at 2.7 Å to elucidate the metal sensing mechanism. The riboswitch resembles a hairpin, with two coaxially stacked helices tethered by a four-way junction and a tertiary docking interface. The Mn2+-sensing region, strategically located at the highly conserved docking interface, has two metal binding sites. Whereas the one site tolerates binding of both Mg2+ and Mn2+, the other site strongly prefers Mn2+ due to a direct contact from the N7 of an invariable adenosine. Mutagenesis and a Mn2+-free E. coli yybP-ykoY structure further reveal that Mn2+ binding is coupled with stabilization of the Mn2+-sensing region and the aptamer domain.

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Section: Introductionmentioning

confidence: 99%

Mn2+-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches

et al. 2015

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“…In their typical mechanism, structural changes of the aptamer domain directly modulate the secondary structure of the neighboring expression platform, structural changes of which then result in either translational control to mask or unmask the ribosome‐binding sequence (RBS) or transcriptional control to close or open the terminator (or antiterminator) stem‐loop. Such structural changes have been characterized or proposed for several riboswitches, including two adenine riboswitches ( ydhL and add , Serganov et al., ), xpt guanine riboswitch (Serganov et al., ), thiM TPP riboswitch (Winkler, Nahvi, & Breaker, ), yitJ SAM‐I riboswitch (Shahbabian, Jamalli, Zig, & Putzer, ), Enterococcus faecalis SAM‐III riboswitch (Price, Grigg, & Ke, ) and lysC lysine riboswitch (Sudarsan, Wickiser, Nakamura, Ebert, & Breaker, ), the expression platforms of which are all <40 nt in length. Putative riboswitches can also be identified through functional outcomes in expression of downstream ORFs or the confirmation of their aptamer domain structures.…”

Section: Introductionmentioning

confidence: 99%

Recognition of cyclic‐di‐GMP by a riboswitch conducts translational repression through masking the ribosome‐binding site distant from the aptamer domain

et al. 2018

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The riboswitch is a class of RNA-based gene regulatory machinery that is dependent on recognition of its target ligand by RNA tertiary structures. Ligand recognition is achieved by the aptamer domain, and ligand-dependent structural changes of the expression platform then usually mediate termination of transcription or translational initiation. Ligand-dependent structural changes of the aptamer domain and expression platform have been reported for several riboswitches with short (<40 nucleotides) expression platforms. In this study, we characterized structural changes of the Vc2 c-di-GMP riboswitch that represses translation of downstream open reading frames in a ligand-dependent manner. The Vc2 riboswitch has a long (97 nucleotides) expression platform, but its structure and function are largely unknown. Through mutational analysis and chemical probing, we identified its secondary structures that are possibly responsible for switch-OFF and switch-ON states of translational initiation.

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“…In the absence of SAM binding, an anti-terminator is formed and transcription of the downstream gene proceeds [26]. Presumably, the gonococcal SAM riboswitch functions in a similar manner by sensing SAM levels and disrupting methionine adenosyltransferase transcription as the ligand binds to the riboswitch.…”

Section: Resultsmentioning

confidence: 99%

Iron-regulated small RNA expression as Neisseria gonorrhoeae FA 1090 transitions into stationary phase growth

et al. 2017

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BackgroundFor most pathogens, iron (Fe) homeostasis is crucial for maintenance within the host and the ability to cause disease. The primary transcriptional regulator that controls intracellular Fe levels is the Fur (ferric uptake regulator) protein, which exerts its action on transcription by binding to a promoter-proximal sequence termed the Fur box. Fur-regulated transcriptional responses are often fine-tuned at the post-transcriptional level through the action of small regulatory RNAs (sRNAs). Consequently, identifying sRNAs contributing to the control of Fe homeostasis is important for understanding the Fur-controlled bacterial Fe-response network.ResultsIn this study, we sequenced size-selected directional libraries representing sRNA samples from Neisseria gonorrhoeae strain FA 1090, and examined the Fe- and temporal regulation of these sRNAs. RNA-seq data for all time points identified a pool of at least 340 potential sRNAs. Differential analysis demonstrated that expression appeared to be regulated by Fe availability for at least fifteen of these sRNAs. Fourteen sRNAs were induced in high Fe conditions, consisting of both cis and trans sRNAs, some of which are predicted to control expression of a known virulence factor, and one SAM riboswitch. An additional putative cis-acting sRNA was repressed by Fe availability. In the pathogenic Neisseria species, one sRNA that contributes to Fe-regulated post-transcriptional control is the Fur-repressible sRNA NrrF. The expression of five Fe-induced sRNAs appeared to be at least partially controlled by NrrF, while the remainder was expressed independently of NrrF. The expression of the 14 Fe-induced sRNAs also exhibited temporal control, as their expression levels increased dramatically as the bacteria entered stationary phase.ConclusionsHere we report the temporal expression of Fe-regulated sRNAs in N. gonorrhoeae FA 1090 with several appearing to be controlled by the Fe-repressible sRNA NrrF. Temporal regulation of these sRNAs suggests a regulatory role in controlling functions necessary for survival, and may be important for phenotypes often associated with altered growth rates, such as biofilm formation or intracellular survival. Future functional studies will be needed to understand how these regulatory sRNAs contribute to gonococcal biology and pathogenesis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3684-8) contains supplementary material, which is available to authorized users.

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Common themes and differences in SAM recognition among SAM riboswitches

Cited by 32 publications

References 54 publications

Mn2+-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches

Mn2+-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches

Recognition of cyclic‐di‐GMP by a riboswitch conducts translational repression through masking the ribosome‐binding site distant from the aptamer domain

Iron-regulated small RNA expression as Neisseria gonorrhoeae FA 1090 transitions into stationary phase growth

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