Small RNAs in the Genus<i>Clostridium</i>

Chen, Yili; Indurthi, Dinesh C.; Jones, Shawn W.; Papoutsakis, Eleftherios T.

doi:10.1128/mbio.00340-10

Cited by 79 publications

(86 citation statements)

References 63 publications

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“…Furthermore, in this work, we show that Tn916 preferentially targets intergenic regions which have been shown to have an important regulatory role in bacterial metabolism, an observation which could be useful if one wished to disrupt noncoding RNA sequences (3). In support of this notion, Chen et al (8) have undertaken a systematic search of small noncoding RNA (sRNA) sequences in the clostridia, and the C. difficile sRNA sequences contained 2,134 Tn916 insertion motifs entirely within the sRNA sequences and a further 739 motifs that overlap into/out of an sRNA. In addition, Tn916 has been used to generate a metabolic mutant in a noncoding region of Clostridium proteoclasticum (33).…”

Section: Discussionsupporting

confidence: 65%

Behavior and Target Site Selection of Conjugative Transposon Tn 916 in Two Different Strains of Toxigenic Clostridium difficile

Mullany

Williams

Langridge

et al. 2012

Appl Environ Microbiol

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ABSTRACTThe insertion sites of the conjugative transposon Tn916in the anaerobic pathogenClostridium difficilewere determined using Illumina Solexa high-throughput DNA sequencing of Tn916insertion libraries in two different clinical isolates: 630ΔE, an erythromycin-sensitive derivative of 630 (ribotype 012), and the ribotype 027 isolate R20291, which was responsible for a severe outbreak ofC. difficiledisease. A consensus 15-bp Tn916insertion sequence was identified which was similar in both strains, although an extended consensus sequence was observed in R20291. A search of theC. difficile630 genome showed that the Tn916insertion motif was present 100,987 times, with approximately 63,000 of these motifs located in genes and 35,000 in intergenic regions. To test the usefulness of Tn916as a mutagen, a functional screen allowed the isolation of a mutant. This mutant contained Tn916inserted into a gene involved in flagellar biosynthesis.

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Section: Discussionsupporting

confidence: 65%

Behavior and Target Site Selection of Conjugative Transposon Tn 916 in Two Different Strains of Toxigenic Clostridium difficile

Mullany

Williams

Langridge

et al. 2012

Appl Environ Microbiol

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“…This RNase also affects toxin production and secretion, cell adhesion, and cell proliferation in C. perfringens. Furthermore, a number of sRNAs have been predicted in the genus Clostridium, and these sRNAs are potentially involved in physiological functions (42). RNase Y is more likely to have an important role in sRNA function, because this enzyme is involved in posttranscriptional colA regulation by VR-RNA, an sRNA in C. perfringens.…”

Section: Discussionmentioning

confidence: 99%

“…colA regulation by VR-RNA and RNase Y is the first example of trans-acting sRNAs and endoribonucleases functioning in concert in clostridia. RNase Y may be an important factor for sRNA-dependent posttranscriptional regulation in Clostridium and Bacillus (41,42).…”

Section: Discussionmentioning

confidence: 99%

Role of RNase Y in Clostridium perfringens mRNA Decay and Processing

2017

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RNase Y is a major endoribonuclease that plays a crucial role in mRNA degradation and processing. We study the role of RNase Y in the Gram-positive anaerobic pathogen Clostridium perfringens, which until now has not been well understood. Our study implies an important role for RNase Y-mediated RNA degradation and processing in virulence gene expression and the physiological development of the organism. We began by constructing an RNase Y conditional knockdown strain in order to observe the importance of RNase Y on growth and virulence. Our resulting transcriptome analysis shows that RNase Y affects the expression of many genes, including toxin-producing genes. We provide data to show that RNase Y depletion repressed several toxin genes in C. perfringens and involved the virR-virS twocomponent system. We also observe evidence that RNase Y is indispensable for processing and stabilizing the transcripts of colA (encoding a major toxin collagenase) and pilA2 (encoding a major pilin component of the type IV pili). Posttranscriptional regulation of colA is known to be mediated by cleavage in the 5= untranslated region (5=UTR), and we observe that RNase Y depletion diminishes colA 5=UTR processing. We show that RNase Y is also involved in the posttranscriptional stabilization of pilA2 mRNA, which is thought to be important for host cell adherence and biofilm formation.IMPORTANCE RNases have important roles in RNA degradation and turnover in all organisms. C. perfringens is a Gram-positive anaerobic spore-forming bacterial pathogen that produces numerous extracellular enzymes and toxins, and it is linked to digestive disorders and disease. A highly conserved endoribonuclease, RNase Y, affects the expression of hundreds of genes, including toxin genes, and studying these effects is useful for understanding C. perfringens specifically and RNases generally. Moreover, RNase Y is involved in processing specific transcripts, and we observed that this processing in C. perfringens results in the stabilization of mRNAs encoding a toxin and bacterial extracellular apparatus pili. Our study shows that RNase activity is associated with gene expression, helping to determine the growth, proliferation, and virulence of C. perfringens.

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“…We followed the recommended convention for naming of small RNAs, which is to begin with the letter "s," then the three-letter genome identifier (ID) used in the KEGG database, "ava," and then the number that indicates its genomic location to the nearest kilobase plus 1 (55). As recommended by the Bacterial Small Regulatory RNA Database (BSRD), we added a period and the number "1" at the end to indicate the number of small RNAs (sRNAs) identified in this location (which is currently one).…”

Section: Table 2 Primersmentioning

confidence: 99%

Role of RNA Secondary Structure and Processing in Stability of the nifH1 Transcript in the Cyanobacterium Anabaena variabilis

2015

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In the cyanobacterium Anabaena variabilis ATCC 29413, aerobic nitrogen fixation occurs in micro-oxic cells called heterocysts. Synthesis of nitrogenase in heterocysts requires expression of the large nif1 gene cluster, which is primarily under the control of the promoter for the first gene, nifB1. Strong expression of nifH1 requires the nifB1 promoter but is also controlled by RNA processing, which leads to increased nifH1 transcript stability. The processing of the primary nifH1 transcript occurs at the base of a predicted stem-loop structure that is conserved in many heterocystous cyanobacteria. Mutations that changed the predicted secondary structure or changed the sequence of the stem-loop had detrimental effects on the amount of nifH1 transcript, with mutations that altered or destabilized the structure having the strongest effect. Just upstream from the transcriptional processing site for nifH1 was the promoter for a small antisense RNA, sava4870.1. This RNA was more strongly expressed in cells grown in the presence of fixed nitrogen and was downregulated in cells 24 h after nitrogen step down. A mutant strain lacking the promoter for sava4870.1 showed delayed nitrogen fixation; however, that phenotype might have resulted from an effect of the mutation on the processing of the nifH1 transcript. The nifH1 transcript was the most abundant and most stable nif1 transcript, while nifD1 and nifK1, just downstream of nifH1, were present in much smaller amounts and were less stable. The nifD1 and nifK1 transcripts were also processed at sites just upstream of nifD1 and nifK1. IMPORTANCEIn the filamentous cyanobacterium Anabaena variabilis, the nif1 cluster, encoding the primary Mo nitrogenase, functions under aerobic growth conditions in specialized cells called heterocysts that develop in response to starvation for fixed nitrogen. The large cluster comprising more than a dozen nif1 genes is transcribed primarily from the promoter for the first gene, nifB1; however, this does not explain the large amount of transcript for the structural genes nifH1, nifD1, and nifK1, which are also under the control of the distant nifB1 promoter. Here, we demonstrate the importance of a predicted stem-loop structure upstream of nifH1 that controls the abundance of nifH1 transcript through transcript processing and stabilization and show that nifD1 and nifK1 transcripts are also controlled by transcript processing.A nabaena variabilis is a filamentous cyanobacterium that fixes nitrogen under oxic growth conditions in cells called heterocysts. Heterocysts, which are specialized micro-oxic cells that develop in a semiregular pattern in the filament in response to nitrogen stress, fix atmospheric dinitrogen to ammonium using the enzyme nitrogenase (1-3). The micro-oxic conditions of the heterocyst result from the glycolipid layer that may restrict oxygen diffusion into the cell, the absence of oxygen-evolving photosystem II, and increased respiration, all of which serve to protect nitrogenase from oxygen (4-6). While all heter...

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Small RNAs in the GenusClostridium

Cited by 79 publications

References 63 publications

Behavior and Target Site Selection of Conjugative Transposon Tn 916 in Two Different Strains of Toxigenic Clostridium difficile

Behavior and Target Site Selection of Conjugative Transposon Tn 916 in Two Different Strains of Toxigenic Clostridium difficile

Role of RNase Y in Clostridium perfringens mRNA Decay and Processing

Role of RNA Secondary Structure and Processing in Stability of the nifH1 Transcript in the Cyanobacterium Anabaena variabilis

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