Genome-wide discovery of structured noncoding RNAs in bacteria

Stav, Shira; Atilho, Ruben M; Arachchilage, Gayan Mirihana; Nguyen, Giahoa; Higgs, Gadareth; Breaker, Ronald R.

doi:10.1186/s12866-019-1433-7

Cited by 53 publications

(89 citation statements)

References 73 publications

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“…A recently developed computational pipeline has been used to identify novel classes of ncRNA candidates in several bacterial genomes [34]. Among the 30 ncRNA candidates discovered, a putative RS was found associated with genes involved in the biosynthesis of TPP, in particular with thiS (encoding for a sulphur carrier protein involved in the synthesis of thiamine), and therefore termed thiS motif.…”

Section: Discussionmentioning

confidence: 99%

Characterization of a transcriptional TPP riboswitch in the human pathogen Neisseria meningitidis

et al. 2020

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Increasing evidence has demonstrated that regulatory RNA elements such as riboswitches (RS) play a pivotal role in the fine-tuning of bacterial gene expression. In this study, we investigated and characterized a novel transcriptional thiamine pyrophosphate (TPP) RS in the obligate human pathogen N. meningitidis MC58 (serogroup B). This RS is located in the 5´untranslated region upstream of thiC gene, encoding a protein involved in TPP biosynthesis, an essential cofactor for all living beings. Primer extension revealed the transcriptional start site of thiC. Northern blot analysis of thiC mRNA and reporter gene studies confirmed the presence of an active TPP-sensing RS. Expression patterns of the wild-type RS and site-specific mutants showed that it is an OFF switch that controls transcription elongation of thiC mRNA. Interestingly, the regulatory mechanism of the meningococcal thiC RS resembles the Grampositive Bacillus subtilis thiC RS rather than the Gram-negative Escherichia coli thiC RS. Therefore, the meningococcal thiC RS represents a rare example of transcriptional RS in a Gram-negative bacterium. We further observed that the RS is actively involved in modulating gene expression in response to different growth media and to supplemented bacterial and eukaryotic cell lysates as possible sources of nutrients in the nasopharynx. Our results suggest that RS-mediated gene regulation could influence meningococcal fitness, through the fine-tuning of biosynthesis and scavenging of nutrients and cofactors, such as thiamine. ARTICLE HISTORY

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Section: Discussionmentioning

confidence: 99%

Characterization of a transcriptional TPP riboswitch in the human pathogen Neisseria meningitidis

et al. 2020

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“…4). One exception was a riboswitch candidate originally called thiS (Stav et al 2019). Representatives of this class are always associated with genes coding for enzymes that synthesize the TPP biosynthetic intermediate hydroxyethyl-thiazole phosphate (HET-P) (Begley et al 1999).…”

Section: This Motif Rnas: Riboswitches For Hmp-ppmentioning

confidence: 99%

“…Despite these clues, ligand binding assays initially failed to reveal the natural ligand for this riboswitch class. However, the use of riboswitch reporter-fusion constructs and bacterial strains with knockouts of genes in the TPP biosynthetic pathway revealed that another intermediate, HMP-PP, was the ligand (Stav et al 2019;Atilho et al 2019). The riboswitch senses the build-up of HMP-PP to activate the expression of genes involved in producing HET-P, which together form the final coenzyme product.…”

Section: This Motif Rnas: Riboswitches For Hmp-ppmentioning

confidence: 99%

“…Thus, almost without exception, expression platforms exhibit considerable Cold Spring Harbor Laboratory Press on July 31, 2020 -Published by rnajournal.cshlp.org Downloaded from sequence diversity because the base-pair identities can drift over evolutionary time. One prominent exception is the riboswitch class for hydroxymethyl-pyrimidine pyrophosphate (HMP-PP), a thiamin pyrophosphate (TPP) biosynthetic intermediate Stav et al 2019). As discussed in more detail later, the aptamer of this unusual riboswitch class almost entirely overlaps the expression platform, which requires most of the riboswitch to remain highly conserved.…”

Section: Introductionmentioning

confidence: 99%

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

Sherlock

Breaker

2020

RNA

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Cold Spring Harbor Laboratory Press on July 31, 2020 -Published by rnajournal.cshlp.org Downloaded from Sherlock and Breaker Orphan Riboswitches 2 ABSTRACT Comparative sequence analyses have been used to discover numerous classes of structured noncoding RNAs, some of which are riboswitches that specifically recognize small-molecule or elemental ion ligands and influence expression of adjacent downstream genes. Determining the correct identity of the ligand for a riboswitch candidate typically is aided by an understanding of the genes under its regulatory control. Riboswitches whose ligands were straightforward to identify have largely been associated with well-characterized metabolic pathways, such as coenzyme or amino acid biosynthesis. Riboswitch candidates whose ligands resist identification, collectively known as orphan riboswitches, are often associated with genes coding for proteins of unknown function, or genes for various proteins with no established link to one another. The cognate ligands for 16 former orphan riboswitch motifs have been identified to date. The successful pursuit of the ligands for these classes has provided insight into areas of biology thatare not yet fully explored, such as ion homeostasis, signaling networks, and other previously underappreciated biochemical or physiological processes. Herein we discuss the strategies and methods used to match ligands with orphan riboswitch classes, and overview the lessons learned to inform and motivate ongoing efforts to identify ligands for the many remaining candidates.

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“…For instance, RNA switches belonging to just one type of bacteria or without a conserved sequence or known regulatory mechanism may be missed using this methodology. Thus, there is the potential that additional novel RNA switches exist, especially considering the vast number of molecules within a cell (Stav et al, 2019). Since known RNA switches have been found predominately within the 5′UTR of transcripts, we chose to first perform a search for new candidates within the 5′UTRs.…”

Section: Discovery Of a Transcription Attenuation Mechanism Via Strucmentioning

confidence: 99%

Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches inBacillus subtilis

Ritchey

Tack

Yakhnin

et al. 2020

Preprint

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RNA structure influences numerous processes in all organisms. In bacteria, these processes include transcription termination and attenuation, small RNA and protein binding, translation initiation, and mRNA stability, and can be regulated via metabolite availability and other stresses. Here we use Structure-seq2 to probe the in vivo RNA structurome of Bacillus subtilis grown in the presence and absence of amino acids. Our results reveal that amino acid starvation results in lower overall dimethyl sulfate (DMS) reactivity of the transcriptome, indicating enhanced protection owing to protein binding or RNA structure. Starvation-induced changes in DMS reactivity correlated inversely with transcript abundance changes. This correlation was particularly pronounced in genes associated with the stringent response and CodY regulons, which are involved in adaptation to nutritional stress, suggesting that RNA structure contributes to transcript abundance change in regulons involved in amino acid metabolism.Structure-seq2 accurately reported on four known amino acid-responsive riboswitches: T-box, SAM, glycine, and lysine riboswitches. Additionally, we discovered a transcription attenuation mechanism that reduces yfmG expression when amino acids are added to the growth medium. We also found that translation of a leader peptide (YfmH) encoded just upstream of yfmG regulates yfmG expression. Our results are consistent with a model in which a slow rate of yfmH translation caused by limitation of the amino acids encoded in YfmH prevents transcription termination in the yfmG leader region by favoring formation of an overlapping antiterminator structure. This novel RNA switch offers a way to simultaneously monitor the levels of multiple amino acids. Ritchey -3

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Genome-wide discovery of structured noncoding RNAs in bacteria

Cited by 53 publications

References 73 publications

Characterization of a transcriptional TPP riboswitch in the human pathogen Neisseria meningitidis

Characterization of a transcriptional TPP riboswitch in the human pathogen Neisseria meningitidis

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

Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches inBacillus subtilis

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