Overexpression of an antisense RNA, ArrS, increases the acid resistance of Escherichia coli

Aiso, Toshiko; Kamiya, Shigeru; Yonezawa, Hideo; Gamou, Shinobu

doi:10.1099/mic.0.075994-0

Cited by 35 publications

(35 citation statements)

References 40 publications

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“…We identified three of the five cleavage sites in ncRNA targets, but did not detect any of the reported cleavage sites in the ncRNAs (Table 1 and Supplementary Table S2c ). We did, however, identify one cleavage site in the ArrS ncRNA (which was not explicitly determined before), in agreement with the suggestion that ArrS binds in cis to gadE mRNA and regulates its stability in an RNase III-dependent manner ( 25 ).…”

Section: Resultssupporting

confidence: 87%

In vivo cleavage rules and target repertoire of RNase III in Escherichia coli

Altuvia

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Reiss

et al. 2018

Nucleic Acids Research

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Bacterial RNase III plays important roles in the processing and degradation of RNA transcripts. A major goal is to identify the cleavage targets of this endoribonuclease at a transcriptome-wide scale and delineate its in vivo cleavage rules. Here we applied to Escherichia coli grown to either exponential or stationary phase a tailored RNA-seq-based technology, which allows transcriptome-wide mapping of RNase III cleavage sites at a nucleotide resolution. Our analysis of the large-scale in vivo cleavage data substantiated the established cleavage pattern of a double cleavage in an intra-molecular stem structure, leaving 2-nt-long 3′ overhangs, and refined the base-pairing preferences in the cleavage site vicinity. Intriguingly, we observed that the two stem positions between the cleavage sites are highly base-paired, usually involving at least one G-C or C-G base pair. We present a clear distinction between intra-molecular stem structures that are RNase III substrates and intra-molecular stem structures randomly selected across the transcriptome, emphasizing the in vivo specificity of RNase III. Our study provides a comprehensive map of the cleavage sites in both intra-molecular and inter-molecular duplex substrates, providing novel insights into the involvement of RNase III in post-transcriptional regulation in the bacterial cell.

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Section: Resultssupporting

confidence: 87%

In vivo cleavage rules and target repertoire of RNase III in Escherichia coli

Altuvia

Bar

Reiss

et al. 2018

Nucleic Acids Research

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“…6B, “striped” bars). Enhanced acid resistance for ArrS-producing strains was observed previously and was attributed to ArrS positively regulating gadE expression (Aiso et al, 2014). Our data suggest that ArrS-dependent activation of cfa might also contribute to enhanced acid resistance of ArrS-producing cells.…”

Section: Resultssupporting

confidence: 60%

“…6B, 7), indicating that ArrS may not play a role in acid stress under the conditions tested. ArrS has been characterized as an activator of the transcriptional activator GadE and ectopic expression of ArrS increases acid resistance though its activation of gadE but a deletion phenotype has not been reported (Aiso et al, 2014, Aiso et al, 2011). ArrS may activate cfa under another condition where CFAs in the membrane contribute to stress resistance (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…ArrS is an antisense sRNA that is encoded upstream of gadE (encoding the major acid resistance transcription factor) and is complementary to the 5’ UTR of the longest of three gadE transcripts (Aiso, Murata et al, 2011). ArrS expression is induced by low pH through σ s and GadE, and overexpression of ArrS increases survival of cells exposed to acidic pH (Aiso, Kamiya et al, 2014). A second sRNA associated with the gadE locus is GadF, which is liberated from the 3’ UTR of gadE mRNA by endonucleolytic cleavage (Melamed et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

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Bacterial cyclopropane fatty acid synthase mRNA is targeted by activating and repressing small RNAs

Bianco

Fröhlich

Vanderpool

2018

Preprint

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36Altering membrane protein and lipid composition is an important strategy for maintaining 37 membrane integrity during environmental stress. Many bacterial small RNAs (sRNAs) 38 control membrane protein production, but sRNA-mediated regulation of membrane fatty 39 acid composition is less understood. The sRNA RydC was previously shown to stabilize 40 cfa (cyclopropane fatty acid synthase) mRNA, resulting in higher levels of cyclopropane 41 fatty acids in the cell membrane. Here, we report that three additional sRNAs, ArrS, 42CpxQ, and GadF also regulate cfa post-transcriptionally. RydC, ArrS, and GadF act 43 through masking an RNase E cleavage site in the cfa mRNA 5' untranslated region 44 (UTR), and all three sRNAs post-transcriptionally activate cfa. In contrast, CpxQ binds to 45 a different site in the cfa mRNA 5' UTR and represses cfa. Alteration of membrane lipid 46 composition is a key mechanism for bacteria to survive low pH environments, and we 47show that cfa translation increases in an sRNA-dependent manner when cells are 48 subjected to mild acid stress. This work suggests an important role for sRNAs in the acid 49 stress response through regulation of cfa mRNA. 50 51

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“…Two of these, GadY and ArrS, strongly bind Hfq. While GadY has been shown to downregulate the antisense-encoded gadXW mRNA by directing RNase III-mediated cleavage (47,48) and ArrS is required for RNase III-dependent processing of one form of the antisense-encoded gadE mRNA (49), it also appears that both of these sRNAs form pairs with trans-encoded targets (20). These observations suggest that they are not simply antisense RNAs but may be better considered Hfq-dependent basepairing RNAs that happen to be antisense to one of their targets.…”

Section: General Srna Categoriesmentioning

confidence: 99%

Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica

et al. 2020

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The last few decades have led to an explosion in our understanding of the major roles that small regulatory RNAs (sRNAs) play in regulatory circuits and the responses to stress in many bacterial species. Much of the foundational work was carried out with Escherichia coli and Salmonella enterica serovar Typhimurium. The studies of these organisms provided an overview of how the sRNAs function and their impact on bacterial physiology, serving as a blueprint for sRNA biology in many other prokaryotes. They also led to the development of new technologies. In this chapter, we first summarize how these sRNAs were identified, defining them in the process. We discuss how they are regulated and how they act and provide selected examples of their roles in regulatory circuits and the consequences of this regulation. Throughout, we summarize the methodologies that were developed to identify and study the regulatory RNAs, most of which are applicable to other bacteria. Newly updated databases of the known sRNAs in E. coli K-12 and S. enterica Typhimurium SL1344 serve as a reference point for much of the discussion and, hopefully, as a resource for readers and for future experiments to address open questions raised in this review.

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Overexpression of an antisense RNA, ArrS, increases the acid resistance of Escherichia coli

Cited by 35 publications

References 40 publications

In vivo cleavage rules and target repertoire of RNase III in Escherichia coli

In vivo cleavage rules and target repertoire of RNase III in Escherichia coli

Bacterial cyclopropane fatty acid synthase mRNA is targeted by activating and repressing small RNAs

Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica

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