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

DEAD-box RNA-helicases catalyze the reorganization of structured RNAs and the formation of RNP complexes. The cyanobacterium <i>Synechocystis</i> 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 <i>Synechocystis</i>.DEAD盒RNA解旋酶（DEAD-box RNA-helicase）可催化结构化RNA的重排过程与核糖核蛋白（RNP）复合物的形成。蓝细菌集胞藻（Synechocystis）sp. PCC 6803仅编码一种DEAD盒RNA解旋酶CrhR（Slr0083），其表达受多种可改变光合电子传递链氧化还原电位的非生物胁迫调控，其中包括温度骤降。尽管已有研究推测CrhR参与RNA代谢调控，且已知其与低温胁迫适应密切相关，但此前关于CrhR基因敲除对集胞藻转录组低温适应影响的报道，仅鉴定出8个受影响的基因。本研究利用定制化基因芯片，探究了非低温胁迫条件下CrhR RNA解旋酶活性缺失对集胞藻转录组的影响。CrhR截短突变会影响一类RNA子集，该子集约占非编码RNA（ncRNA）总量的10%，同时也约占信使RNA（mRNA）转录本总量的10%。尽管丰度上调和下调的mRNA数量相当，但在CrhR缺失的情况下，超过90%的ncRNA表达量均出现上调，这表明CrhR对ncRNA的转录或稳定性具有负调控作用。本研究进一步针对响应显著的RNA，验证了CrhR对其稳定性的调控作用，由此揭示了转录后调控与转录调控的具体案例。实验数据表明，CrhR可对集胞藻内RNA代谢的多个环节产生调控作用。