Inactivation of the RNA helicase CrhR impacts a specific subset of the transcriptome in the cyanobacterium Synechocystis sp. PCC 6803

ABSTRACT

DEAD-box RNA-helicases catalyze the reorganization of structured RNAs and the formation of RNP complexes. The cyanobacterium Synechocystis sp. PCC 6803 encodes a single DEAD-box RNA helicase, CrhR (Slr0083), whose expression is regulated by abiotic stresses that alter the redox potential of the photosynthetic electron transport chain, including temperature downshift. Despite its proposed effect on RNA metabolism and its known relevance in cold-stress adaptation, the reported impact of a CrhR knockout on the cold adaption of the transcriptome only identified eight affected genes. Here, we utilized a custom designed microarray to assess the impact of the absence of CrhR RNA helicase activity on the transcriptome, independent of cold stress. CrhR truncation impacts an RNA subset comprising ~10% of the ncRNA and also ~10% of the mRNA transcripts. While equal numbers of mRNAs showed increased as well as decreased abundance, more than 90% of the ncRNAs showed enhanced expression in the absence of CrhR, indicative of a negative effect on ncRNA transcription or stability. We further tested the effect of CrhR on the stability of strongly responding RNAs that identify examples of post-transcriptional and transcriptional regulation. The data suggest that CrhR impacts multiple aspects of RNA metabolism in Synechocystis.

KEYWORDS:

• Small regulatory RNA
• cyanobacteria
• gene expression regulation
• CrhR RNA helicase
• RNA:RNA interaction

Acknowledgments

We thank Loubna Youssar for support in the calculation of RNA half lives.

Author contributions

GWO, WRH and JG designed the study; JG, ARRR, DC, AM performed experiments; AM, GWO, JG, WRH analyzed data; JG, GWO and WRH wrote the paper with contributions from all authors.

Disclosure of Potential Conflicts of Interest

No potential conflict of interest was reported by the authors.

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Funding

This work was supported by a grant from the Baden-Wuerttemberg Foundation BWST_NCRNA_008 to WRH and by the Natural Sciences and Engineering Research Council of Canada (NSERC), grant number 171319, to GWO.