Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany.
DNA Res. 2018 Oct 1;25(5):489-497. doi: 10.1093/dnares/dsy019.
Prochlorococcus is a marine picocyanobacterium with a streamlined genome that is adapted to different ecological niches in the oligotrophic oceans. There are currently >20 regulatory small RNAs (sRNAs) that have been identified in the model strain Prochlorococcus MED4. While most of these sRNAs are ecotype-specific, sRNA homologs of Yfr1 and of the Yfr2 family are widely found throughout the cyanobacterial phylum. Although they were identified 13 yrs ago, the functions of Yfr1 and Yfr2 have remained unknown. We observed a strong induction of two Yfr2 sRNA homologs of Prochlorococcus MED4 during high light stress and nitrogen starvation. Several Prochlorococcus and marine Synechococcus yfr2 promoter regions contain a conserved motif we named CGRE1 (cyanobacterial GntR family transcriptional regulator responsive element 1). Using the conserved promoter region as bait in a DNA affinity pull-down assay we identified the GntR family transcriptional regulator PMM1637 as a binding partner. Similar to Yfr2, homologs of PMM1637 are universally and exclusively found in cyanobacteria. We suggest that PMM1637 governs the induction of gene expression of Yfr2 homologs containing CGRE1 in their promoters under nitrogen-depleted and high-light stress conditions.
聚球藻是一种海洋型的微微型蓝藻，具有精简的基因组，能够适应贫营养海洋中的不同生态位。目前在模式菌株聚球藻 MED4 中已经鉴定出超过 20 种调控性小 RNA（sRNA）。虽然大多数 sRNA 具有生态型特异性，但 Yfr1 和 Yfr2 家族的 sRNA 同源物在整个蓝藻门中广泛存在。尽管它们在 13 年前就被鉴定出来了，但 Yfr1 和 Yfr2 的功能仍然未知。我们观察到在高光胁迫和氮饥饿时，聚球藻 MED4 中的两个 Yfr2 sRNA 同源物会强烈诱导。几个聚球藻和海洋聚球藻的 yfr2 启动子区域含有一个保守的基序，我们将其命名为 CGRE1（蓝细菌 GntR 家族转录调节因子响应元件 1）。我们使用保守的启动子区域作为 DNA 亲和下拉测定中的诱饵，鉴定出 GntR 家族转录调节因子 PMM1637 是其结合伴侣。与 Yfr2 类似，PMM1637 的同源物普遍且专门存在于蓝细菌中。我们认为，PMM1637 调控含有 CGRE1 的启动子中 Yfr2 同源物的基因表达诱导，这一过程发生在氮饥饿和高光胁迫条件下。
