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 alsõ 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.

RNA helicase–regulated processing of the Synechocystis rimO–crhR operon results in differential cistron expression and accumulation of two sRNAs

“…The genes rimO and crhR are syntenic in many cyanobacteria (61), consistent with the idea that genomic context can indicate functional relatedness (62). It is therefore tempting to speculate that co-transcription of rimO and crhR may indicate that both proteins function in enhancing cellular fitness during cold stress.…”

Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803

“…This includes CrhR, an ortholog of Slr0083, known to be upregulated by cold stress in Synechocystis sp. PCC 6803 (Georg et al, 2019), which was indeed also the case for HLacclimated WH7803 cells.…”

The temperature-regulated DEAD-box RNA helicase CrhR interactome: Autoregulation and photosynthesis-related transcripts

“…The DEAD-box RNA helicase CrhR is one of the major cold shock proteins of Synechocystis (Kujat and Owttrim, 2000; Prakash et al ., 2010; Rowland et al ., 2011; Rosana et al ., 2012a,b; Sireesha et al ., 2012). Consistent with observations in many other organisms that shift to lower temperature increases expression of DEAD-box RNA helicases (Owttrim, 2013), we observed previously an increased crhR transcript abundance after temperature downshift to 20°C, with a log 2 FC of 1.4 in the wild type and 2.6 for the 5’ portion of the gene not deleted in a partial crhR inactivation mutant (Georg et al ., 2019). The higher induction in the partial crhR inactivation mutant pointed at a possible feedback effect of CrhR that was active in the wild type but absent in the mutant.…”

“…Although the molecular effects of crhR deletion or inactivation were studied at both the transcriptome (Prakash et al ., 2010; Georg et al ., 2019) and proteome level (Rowland et al ., 2011), the direct RNA targets of CrhR and interacting protein partners have not been identified. To monitor transcriptome-wide binding of CrhR, we immuno-precipitated the RNA species interacting with a FLAG-tagged version of the native RNA helicase expressed in a ΔcrhR background (subsequently called CrhR WT ).…”