Transcription Antitermination by a Phosphorylated Response Regulator and Cobalamin-Dependent Termination at a B
            <sub>12</sub>
            Riboswitch Contribute to Ethanolamine Utilization in Enterococcus faecalis

Baker, Kris Ann; Perego, Marta

doi:10.1128/jb.00217-11

Cited by 21 publications

(26 citation statements)

References 42 publications

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“…Alignment of multiple RNAs targeted by EutV shows a 13-nt shared conserved sequence (AGCAANGRRGCUY) (19); this sequence overlaps with the left stem of the terminator hairpin and the right stem of a putative low-stability antitermination hairpin (2). This conserved feature led to the hypothesis that binding of EutV to the conserved sequence increases the stability of the antiterminator structure, preventing the formation of a terminator hairpin (2).…”

Section: Discussionmentioning

confidence: 99%

NasT-Mediated Antitermination Plays an Essential Role in the Regulation of the Assimilatory Nitrate Reductase Operon in Azotobacter vinelandii

Wang

Pierson

Rensing

et al. 2012

Appl Environ Microbiol

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ABSTRACTAzotobacter vinelandiiis a well-studied model system for nitrogen fixation in bacteria. Regulation of nitrogen fixation inA. vinelandiiis independent of NtrB/NtrC, a conserved nitrogen regulatory system in proteobacteria. Previous work showed that anntrCmutation inA. vinelandiiresulted in a loss of induction of assimilatory nitrate and nitrite reductases encoded by thenasABoperon. In addition to NtrC, several other proteins, including NasT, a protein containing a potential RNA-binding domain ANTAR (AmiR andNasRtranscriptionantiterminationregulators), have been implicated innasABregulation. In this work, we characterize the sequence upstream ofnasAand identify several DNA sequence elements, including two potential NtrC binding sites and a putative intrinsic transcriptional terminator upstream ofnasAthat are potentially involved innasABregulation. Our analyses confirm that thenasABpromoter,PnasA, is under NtrC control. However, unlike NtrC-regulated promoters in enteric bacteria,PnasAshows high activity in the presence of ammonium; in addition, thePnasAactivity is altered in thenifAgene mutation background. We discuss the implication of these results on NtrC-mediated regulation inA. vinelandii. Our study provides direct evidence that induction ofnasABis regulated by NasT-mediated antitermination, which occurs within the leader region of the operon. The results also support the hypothesis that NasT binds the promoter proximal hairpin ofnasABfor its regulatory function, which contributes to the understanding of the regulatory mechanism of ANTAR-containing antiterminators.

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Section: Discussionmentioning

confidence: 99%

NasT-Mediated Antitermination Plays an Essential Role in the Regulation of the Assimilatory Nitrate Reductase Operon in Azotobacter vinelandii

Wang

Pierson

Rensing

et al. 2012

Appl Environ Microbiol

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“…The ethanolamine deamination systems of Escherichia coli and Klebsiella aerogenes are cobalamin dependent (62). Moreover, adenosyl-cobalamine is a cofactor required in the first enzymatic step of ethanolamine catabolism (62), and in Enterococcus faecalis the ethanolamine utilization (eut) locus, containing at least 19 genes distributed over four polycistronic messenger RNAs, appears to be regulated by a single adenosyl-cobalamine-responsive riboswitch that controls gene expression by sequestration of a response regulator (63,64).…”

Section: Discussionmentioning

confidence: 99%

Small RNA Transcriptome of the Oral Microbiome during Periodontitis Progression

Duran-Pinedo¹,

Yost²,

Frias-Lopez

2015

Appl Environ Microbiol

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The oral microbiome is one of the most complex microbial communities in the human body, and due to circumstances not completely understood, the healthy microbial community becomes dysbiotic, giving rise to periodontitis, a polymicrobial inflammatory disease. We previously reported the results of community-wide gene expression changes in the oral microbiome during periodontitis progression and identified signatures associated with increasing severity of the disease. Small noncoding RNAs (sRNAs) are key players in posttranscriptional regulation, especially in fast-changing environments such as the oral cavity. Here, we expanded our analysis to the study of the sRNA metatranscriptome during periodontitis progression on the same samples for which mRNA expression changes were analyzed. We observed differential expression of 12,097 sRNAs, identifying a total of 20 Rfam sRNA families as being overrepresented in progression and 23 at baseline. Gene ontology activities regulated by the differentially expressed (DE) sRNAs included amino acid metabolism, ethanolamine catabolism, signal recognition particle-dependent cotranslational protein targeting to membrane, intron splicing, carbohydrate metabolism, control of plasmid copy number, and response to stress. In integrating patterns of expression of protein coding transcripts and sRNAs, we found that functional activities of genes that correlated positively with profiles of expression of DE sRNAs were involved in pathogenesis, proteolysis, ferrous iron transport, and oligopeptide transport. These findings represent the first integrated sequencing analysis of the community-wide sRNA transcriptome of the oral microbiome during periodontitis progression and show that sRNAs are key regulatory elements of the dysbiotic process leading to disease. Bacterial small noncoding RNAs (sRNAs) encompass a large and diverse group of RNA molecules that do not result in the translation of a protein product. They show high heterogeneity in size and structure and many are used in regulatory roles or other functional capacities upon transcription. sRNAs are important in bacteria because they can be used to adapt rapidly to changing environmental conditions, especially in an environment such as the oral cavity, which is exposed daily to regular changes in amount and quality of nutrients available for use by the oral biofilms. Most of these sRNAs are encoded in the 5= and 3= untranslated regions, as well as in intergenic regions (IGRs) of the genome (1).sRNAs display a wide variety of mechanisms of action. sRNAs repress translation of mRNA by attaching to the ribosome binding site (RBS) competing with the ribosome and leading to the rapid degradation of the mRNA (2). Other noncanonical mechanisms of translation repression have been also described, such as binding cis-acting antisense RNA to a ribosome standby site upstream of the RBS (3). In addition, sRNAs can also activate the translations of mRNAs (4, 5) or can modulate gene expression by varying the level of transcript stability (6). sRNA ca...

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“…Phosphorylated EutV dimerizes, which increases the affinity for the dual hairpin, which prevents the formation of the terminator structure and thereby induces gene expression (fig. S1A) (4, 5, 8, 9). A fourth promoter was detected just upstream of the AdoCbl riboswitch (8).…”

mentioning

confidence: 99%

“…S1A) (4, 5, 8, 9). A fourth promoter was detected just upstream of the AdoCbl riboswitch (8). Moreover, we discovered that another two-hairpin motif (P3/P4) is located downstream of the AdoCbl riboswitch (fig.…”

mentioning

confidence: 99%

A riboswitch-containing sRNA controls gene expression by sequestration of a response regulator

DebRoy

Gebbie

Ramesh

et al. 2014

Science

128

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The ethanolamine utilization (eut) locus of Enterococcus faecalis, containing at least 19 genes distributed over four polycistronic messenger RNAs, appears to be regulated by a single adenosyl cobalamine (AdoCbl)–responsive riboswitch. We report that the AdoCbl-binding riboswitch is part of a small, transacting RNA, EutX, which additionally contains a dual-hairpin substrate for the RNA binding–response regulator, EutV. In the absence of AdoCbl, EutX uses this structure to sequester EutV. EutV is known to regulate the eut messenger RNAs by binding dual-hairpin structures that overlap terminators and thus prevent transcription termination. In the presence of AdoCbl, EutV cannot bind to EutX and, instead, causes transcriptional read through of multiple eut genes. This work introduces riboswitch-mediated control of protein sequestration as a posttranscriptional mechanism to coordinately regulate gene expression.

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Transcription Antitermination by a Phosphorylated Response Regulator and Cobalamin-Dependent Termination at a B ₁₂ Riboswitch Contribute to Ethanolamine Utilization in Enterococcus faecalis

Cited by 21 publications

References 42 publications

NasT-Mediated Antitermination Plays an Essential Role in the Regulation of the Assimilatory Nitrate Reductase Operon in Azotobacter vinelandii

NasT-Mediated Antitermination Plays an Essential Role in the Regulation of the Assimilatory Nitrate Reductase Operon in Azotobacter vinelandii

Small RNA Transcriptome of the Oral Microbiome during Periodontitis Progression

A riboswitch-containing sRNA controls gene expression by sequestration of a response regulator

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Transcription Antitermination by a Phosphorylated Response Regulator and Cobalamin-Dependent Termination at a B 12 Riboswitch Contribute to Ethanolamine Utilization in Enterococcus faecalis

Cited by 21 publications

References 42 publications

NasT-Mediated Antitermination Plays an Essential Role in the Regulation of the Assimilatory Nitrate Reductase Operon in Azotobacter vinelandii

NasT-Mediated Antitermination Plays an Essential Role in the Regulation of the Assimilatory Nitrate Reductase Operon in Azotobacter vinelandii

Small RNA Transcriptome of the Oral Microbiome during Periodontitis Progression

A riboswitch-containing sRNA controls gene expression by sequestration of a response regulator

Contact Info

Product

Resources

About

Transcription Antitermination by a Phosphorylated Response Regulator and Cobalamin-Dependent Termination at a B ₁₂ Riboswitch Contribute to Ethanolamine Utilization in Enterococcus faecalis