A Haloarchaeal Small Regulatory RNA (sRNA) Is Essential for Rapid Adaptation to Phosphate Starvation Conditions

Abstract

The haloarchaeon Haloferax volcanii contains nearly 2800 small non-coding RNAs (sRNAs). One intergenic sRNA, sRNA132, was chosen for a detailed characterization. A deletion mutant had a growth defect and thus underscored the importance of sRNA132. A microarray analysis identified the transcript of an operon for a phosphate-specific ABC transporter as a putative target of sRNA132. Both the sRNA132 and the operon transcript accumulated under low phosphate concentrations, indicating a positive regulatory role of sRNA132. A kinetic analysis revealed that sRNA132 is essential shortly after the onset of phosphate starvation, while other regulatory processes take over after several hours. Comparison of the transcriptomes of wild-type and the sRNA132 gene deletion mutant 30 min after the onset of phosphate starvation revealed that sRNA132 controls a regulon of about 40 genes. Remarkably, the regulon included a second operon for a phosphate-specific ABC transporter, which also depended on sRNA132 for rapid induction in the absence of phosphate. Competitive growth experiments of the wild-type and ABC transporter operon deletion mutants underscored the importance of both transporters for growth at low phosphate concentrations. Northern blot analyses of four additional members of the sRNA132 regulon verified that all four transcripts depended on sRNA132 for rapid regulation after the onset of phosphate starvation. Importantly, this is the first example for the transient importance of a sRNA for any archaeal and bacterial species. In addition, this study unraveled the first sRNA regulon for haloarchaea.

Biological functions, genetic and biochemical characterization, and NMR structure determination of the small zinc finger protein HVO_2753 from Haloferax volcanii

“…Northern blot analyses were essentially performed as described [59]. In short, H. volcanii cultures were grown in complex medium to mid-exponential growth phase.…”

A small RNA is linking CRISPR-Cas and zinc transport

“…IntaRNA prediction reveals that the 3’ end of the s479 interacts with the coding region of znu C1. The energy gain predicted for the interaction implies a stable sRNA-target pairing (Kliemt et al, 2019). The few examples of archaeal sRNA-target pairs described to date suggest a non-universal mode of action and a wide variability in the site of target contact (Buddeweg et al, 2018b; Gomes-Filho et al, 2018).…”

“…It is well established that intergenic sRNAs of H. volcanii are differentially expressed in response to growth phase or environmental stimuli including temperature, salinity, as well as oxidative stress (Straub et al, 2009; Babski et al, 2011; Fischer et al, 2011; Gelsinger and DiRuggiero, 2018a). Their profound biological role is unquestioned as growth phenotypes have been demonstrated for sRNA deletion mutants in response to temperature, salt, alternative carbon-sources, phosphate availability and oxidative stress (Straub et al, 2009; Fischer et al, 2011; Heyer et al, 2012; Jaschinski et al, 2014; Kliemt et al, 2019). Besides growth, swarming behaviour or cell shape have been affected by sRNA deletions as well (Jaschinski et al, 2014).…”

A Novel Noncoding RNA dsr11 Involved in Heat Stress Tolerance in Deinococcus radiodurans

“…For example, hundreds of differentially expressed ncRNAs in response to oxidative stress were identified in H. volcanii [22]. In H. volcanii, sRNA132 is important for rapid adaptation to phosphate starvation [23]. Recently, Tsai et al [24] identified 41 ncRNA candidates in D. radiodurans by the genome-wide RNA sequencing approach but the functional roles of these ncRNAs are still poorly understood.…”