The response to individual deletion of two transptional repressor genes in Hyphomicrobium denitrificans

Bacteria use different strategies to sense and respond to reduced sulfur compounds such as sulfide or thiosulfate. In the methylotrophic Alphaproteobacterium Hyphomicrobium denitrificans, which uses thiosulfate as an accessory electron donor, this involves two distinct but related ArsR-type transcriptional repressors, sHdrR and SoxR. Here, we focused on identifying target genes regulated by these repressors. This was achieved by generating individual deletions of each regulator gene, and performing comparative RNA-seq analysis. To identify SoxR and sHdrR-regulated genes, we performed an RNA-sequencing transcriptomic analysis of strains H. denitrificans ΔtsdA ΔsoxR and H. denitrificans ΔtsdA ΔshdrR. In a previous project (accession number GSE278992), we have identified thiosulfate-inducible genes in the reference strain H. denitrificans ΔtsdA. This strain lacks the tetrathionate-forming enzyme thiosulfate dehydrogenase. Here, we identified SoxR and sHdrR regulated genes by comparing expression levels in the reference strain vs. the repressor-deficient strains grown on methanol-containing medium under aerobic conditions in the absence of thiosulfate.

细菌可通过多种策略感知并响应硫化物、硫代硫酸盐（thiosulfate）等还原态硫化合物。在以硫代硫酸盐作为辅助电子供体的甲基营养型α-变形菌（Alphaproteobacterium）脱氮生丝微菌（Hyphomicrobium denitrificans）中，该感知响应过程涉及两类功能独立但序列相关的ArsR型转录阻遏蛋白（ArsR-type transcriptional repressor）：sHdrR与SoxR。本研究聚焦于鉴定这两类阻遏蛋白的调控靶基因，具体通过分别构建各调控基因的单基因缺失突变株，并开展比较转录组RNA测序（RNA-seq）分析实现研究目标。为鉴定SoxR与sHdrR的调控靶基因，我们对菌株脱氮生丝微菌ΔtsdA ΔsoxR以及脱氮生丝微菌ΔtsdA ΔshdrR开展了RNA测序转录组分析。在前期项目（登录号：GSE278992）中，我们已在参考菌株脱氮生丝微菌ΔtsdA中鉴定出硫代硫酸盐诱导表达的基因；该菌株缺失催化四硫代酸盐合成的硫代硫酸盐脱氢酶（thiosulfate dehydrogenase）。本研究通过对比参考菌株与阻遏蛋白缺失菌株在不含硫代硫酸盐的有氧甲醇培养基中的基因表达水平，最终成功鉴定得到SoxR与sHdrR的调控靶基因。