Small non-coding RNA SraG regulates the operon YPK_1206-1205 in Yersinia pseudotuberculosis

Lu, Pei Jung; Zhang, Yong; Li, Lamei; Hu, Yangbo; Huang, Li; Li, Yunlong; Rayner, Simon; Chen, Shiyun

doi:10.1111/j.1574-6968.2012.02548.x

Cited by 15 publications

(20 citation statements)

References 21 publications

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“…The function of SraG was studied in Yersinia pseudotuberculosis. While no effect on pnp was reported, SraG was shown to negatively regulate the YPK_1206-1205 operon, which encodes genes that have no homologs outside the Yersinia genus (Lu et al 2012). Other potential candidates were identified by proteomic analysis of the wt and ΔsraG mutant in this species but without further confirmation.…”

Section: Discussionmentioning

confidence: 99%

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The small RNA SraG participates in PNPase homeostasis

Fontaine

Gasiorowski

Gracia

et al. 2016

RNA

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The rpsO-pnp operon encodes ribosomal protein S15 and polynucleotide phosphorylase, a major 3 ′ -5 ′ exoribonuclease involved in mRNA decay in Escherichia coli. The gene for the SraG small RNA is located between the coding regions of the rpsO and pnp genes, and it is transcribed in the opposite direction relative to the two genes. No function has been assigned to SraG. Multiple levels of post-transcriptional regulation have been demonstrated for the rpsO-pnp operon. Here we show that SraG is a new factor affecting pnp expression. SraG overexpression results in a reduction of pnp expression and a destabilization of pnp mRNA; in contrast, inhibition of SraG transcription results in a higher level of the pnp transcript. Furthermore, in vitro experiments indicate that SraG inhibits translation initiation of pnp. Together, these observations demonstrate that SraG participates in the post-transcriptional control of pnp by a direct antisense interaction between SraG and PNPase RNAs. Our data reveal a new level of regulation in the expression of this major exoribonuclease.

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Section: Discussionmentioning

confidence: 99%

“…SraG of Yersinia pseudotuberculosis has been shown to regulate the YPK_1206-1205 operon (Lu et al 2012). We investigated a possible role of SraG on RNA targets transcribed from elsewhere on the E. coli chromosome by using various strategies.…”

Section: Does Srag Have Any Other Roles?mentioning

confidence: 99%

The small RNA SraG participates in PNPase homeostasis

Fontaine

Gasiorowski

Gracia

et al. 2016

RNA

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“…Naturally occurring antisense small noncoding RNAs (sRNA) have been reported to repress genes downstream of the targeted ORF. Two examples are sRNAs of the phoPQ operon in E. coli (37) and the YPK_1206-1205 operon in Yersinia pseudotuberculosis (38), where sRNAs silence the target and downstream genes. It will be interesting to see if upstream silencing exists in nature as more sRNAs are identified and characterized.…”

Section: Discussionmentioning

confidence: 99%

Silencing of Essential Genes within a Highly Coordinated Operon in Escherichia coli

Goh

Hohmeier

Stone

et al. 2015

Appl Environ Microbiol

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Essential bacterial genes located within operons are particularly challenging to study independently because of coordinated gene expression and the nonviability of knockout mutants. Essentiality scores for many operon genes remain uncertain. Antisense RNA (asRNA) silencing or in-frame gene disruption of genes may help establish essentiality but can lead to polar effects on genes downstream or upstream of the target gene. Here, the Escherichia coli ribF-ileS-lspA-fkpB-ispH operon was used to evaluate the possibility of independently studying an essential gene using expressed asRNA and target gene overexpression to deregulate coupled expression. The gene requirement for growth in conditional silencing strains was determined by the relationship of target mRNA reduction with growth inhibition as the minimum transcript level required for 50% growth (MTL 50 ). Mupirocin and globomycin, the protein inhibitors of IleS and LspA, respectively, were used in sensitization assays of strains containing both asRNA-expressing and open reading frame-expressing plasmids to examine deregulation of the overlapping ileS-lspA genes. We found upstream and downstream polar silencing effects when either ileS or lspA was silenced, indicating coupled expression. Weighted MTL 50 values (means and standard deviations) of ribF, ileS, and lspA were 0.65 ؎ 0.18, 0.64 ؎ 0.06, and 0.76 ؎ 0.10, respectively. However, they were not significantly different (P ‫؍‬ 0.71 by weighted one-way analysis of variance). The gene requirement for ispH could not be determined due to insufficient growth reduction. Mupirocin and globomycin sensitization experiments indicated that ileS-lspA expression could not be decoupled. The results highlight the inherent challenges associated with genetic analyses of operons; however, coupling of essential genes may provide opportunities to improve RNA-silencing antimicrobials.

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“…Sequences within the coding region of YPK_1206 are necessary and sufficient for negative regulation of both YPK_1206 and the downstream YPK_1205. 36 Although a direct binding site between SraG and YPK_1206-1205 has not been identified, truncation analyses revealed that a region between +9-+63 of the YPK_1206 coding region is required for coordinate regulation of the operon. 36 Whether SraG affects only translation or both translation and mRNA stability by binding at one site is currently unknown.…”

Section: New Developments In Post-transcriptional Regulation Of Operomentioning

confidence: 99%

“…35 While very little is known about the physiological function of SraG, a recent study showed that Yersinia pseudotuberculosis SraG regulates a polycistronic mRNA, YPK_1206-1205. 36 While the functions of the YPK_1205 and the iscS, iscU and iscA genes encode the biogenesis and assembly machinery, IscR is a transcription factor and autorepresses iscRSUA. 31 IscR exists in the Holo-form bound by Fe-S clusters or in the unbound Apo-form.…”

Section: New Developments In Post-transcriptional Regulation Of Operomentioning

confidence: 99%

New developments in post-transcriptional regulation of operons by small RNAs

Balasubramanian

Vanderpool

2013

RNA Biology

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Small regulatory RNAs (sRNAs) are influential post-transcriptional modulators of gene expression in bacteria. They regulate gene expression by base pairing to target mRNAs, leading to inhibition of translation and/or alteration of mRNA stability. Recently, several sRNAs have been discovered to regulate genes encoded in operons. In some cases, these sRNAs regulate all the genes encoded by the polycistronic mRNA (coordinate regulation) while in other cases, only a select subset of cistrons is controlled by the sRNA (discoordinate regulation). In this point of view, mechanisms of regulation and characteristics of sRNA-mRNA interactions involving polycistronic mRNAs are described. The diversity in mechanisms represented by these few characterized examples suggests that we still have much to learn about sRNA regulation of long polycistronic messages.

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Small non-coding RNA SraG regulates the operon YPK_1206-1205 in Yersinia pseudotuberculosis

Cited by 15 publications

References 21 publications

The small RNA SraG participates in PNPase homeostasis

The small RNA SraG participates in PNPase homeostasis

Silencing of Essential Genes within a Highly Coordinated Operon in Escherichia coli

New developments in post-transcriptional regulation of operons by small RNAs

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