Abstract
Bacteria are increasingly used for biotechnological applications such as bioremediation, biorecovery, bioproduction, and biosensing. The development of strains suited for such applications requires a thorough understanding of their behavior, with a key role for their transcriptomic landscape. We present a thorough analysis of the transcriptome of Cupriavidus metallidurans CH34 cells acutely exposed to copper by tagRNA-sequencing. C. metallidurans CH34 is a model organism for metal resistance, and its potential as a biosensor and candidate for metal bioremediation has been demonstrated in multiple studies. Several metabolic pathways were impacted by Cu exposure, and a broad spectrum of metal resistance mechanisms, not limited to copper-specific clusters, was overexpressed. In addition, several gene clusters involved in the oxidative stress response and the cysteine-sulfur metabolism were induced. In total, 7500 transcription start sites (TSSs) were annotated and classified with respect to their location relative to coding sequences (CDSs). Predicted TSSs were used to re-annotate 182 CDSs. The TSSs of 2422 CDSs were detected, and consensus promotor logos were derived. Interestingly, many leaderless messenger RNAs (mRNAs) were found. In addition, many mRNAs were transcribed from multiple alternative TSSs. We observed pervasive intragenic TSSs both in sense and antisense to CDSs. Antisense transcripts were enriched near the 5′ end of mRNAs, indicating a functional role in post-transcriptional regulation. In total, 578 TSSs were detected in intergenic regions, of which 35 were identified as putative small regulatory RNAs. Finally, we provide a detailed analysis of the main copper resistance clusters in CH34, which include many intragenic and antisense transcripts. These results clearly highlight the ubiquity of noncoding transcripts in the CH34 transcriptome, many of which are putatively involved in the regulation of metal resistance.
Highlights
Environmental pollution with toxic metals due to anthropogenic activities is an internationally growing concern [1,2,3]
In comparison with the previous microarray analysis (403 up and 373 down), the overlap was limited with 40 up- and 25 downregulated coding sequences (CDSs) shared between both analyses
In an effort to map the transcriptomic profile and the regulatory features of C. metallidurans CH34 in response to acute Cu stress, we performed tagRNA-Seq on C. metallidurans CH34 cultures exposed to Cu2+ and analyzed both differential gene expression and transcription start sites
Summary
Environmental pollution with toxic metals due to anthropogenic activities is an internationally growing concern [1,2,3]. The exposure and the risk of elevated concentrations of these pollutants in the environment can lead to bioaccumulation and harmful effects [4,5,6,7], which are facilitated by the high toxicity and recalcitrance of some metals [8,9]. Microorganisms show great promise as biosensors to quantify the bioavailable fraction of heavy metals such as copper [13], an essential trace. Microorganisms can be used to combat environmental contamination with heavy metals in a process called bioremediation [3,8,15,16]
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