Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay

Sphingomonas wittichii strain RW1 (RW1) is one of the few strains that can grow on dibenzo-p-dioxin (DD). We conducted a transcriptomic study of RW1 using RNA-Seq to outline transcriptional responses to DD, dibenzofuran (DF), and the smectite clay mineral saponite with succinate as carbon source. The ability to grow on DD is rare compared to growth on the chemically similar DF even though the same initial dioxygenase may be involved in oxidation of both substrates. Therefore, we hypothesized the reason for this lies beyond catabolic pathways and may concern genes involved in processes for cell-substrate interactions such as substrate recognition, transport, and detoxification. Compared to succinate (SUC) as control carbon source, DF caused over 240 protein-coding genes to be differentially expressed, whereas more than 300 were differentially expressed with DD. Stress response genes were up-regulated in response to both DD and DF. This effect was stronger with DD than DF, suggesting a higher toxicity of DD compared to DF. Both DD and DF caused changes in expression of genes involved in active cross-membrane transport such as TonB-dependent receptor proteins, but the patterns of change differed between the two substrates. Multiple transcription factor genes also displayed expression patterns distinct to DD and DF growth. DD and DF induced the catechol ortho- and the salicylate/gentisate pathways, respectively. Both DD and DF induced the shared down-stream aliphatic intermediate compound pathway. Clay caused category-wide down-regulation of genes for cell motility and chemotaxis, particularly those involved in the synthesis, assembly and functioning of flagella. This is an environmentally important finding because clay is a major component of soil microbes’ microenvironment influencing local chemistry and may serve as a geosorbent for toxic pollutants. Similar to clay, DD and DF also affected expression of genes involved in motility and chemotaxis.威氏鞘氨醇单胞菌RW1菌株（Sphingomonas wittichii strain RW1，以下简称RW1）是少数能够以二苯并对二噁英（dibenzo-p-dioxin，DD）为唯一碳源生长的菌株之一。本研究通过RNA测序（RNA-Seq）对RW1开展转录组学分析，以解析其在以琥珀酸盐为碳源的培养条件下，分别暴露于DD、二苯并呋喃（dibenzofuran，DF）及蒙脱石族黏土矿物皂石后的转录响应特征。相较于化学结构相似的DF，RW1以DD为碳源生长的能力更为罕见，尽管二者的氧化过程可能涉及同一初始双加氧酶。据此我们提出假说：二者代谢能力的差异并非仅由分解代谢通路决定，可能还涉及底物识别、转运及解毒等细胞-底物互作相关过程的基因调控。以琥珀酸盐（SUC）作为对照碳源时，DF处理使超过240个蛋白编码基因呈现差异表达，而DD处理则诱导超过300个蛋白编码基因发生差异表达。应激反应基因在DD和DF处理下均出现上调，且DD诱导的上调效应更为显著，提示DD的毒性高于DF。DD与DF均可调控主动跨膜转运相关基因的表达，例如TonB依赖型受体蛋白（TonB-dependent receptor proteins）编码基因，但二者的表达变化模式存在显著差异。多个转录因子基因的表达模式在DD和DF培养条件下也呈现特异性。DD与DF分别诱导邻苯二酚邻位裂解途径及水杨酸/龙胆酸代谢途径，二者均可激活共享的下游脂肪族中间产物代谢通路。皂石处理可全域下调细胞运动与趋化相关基因的表达，尤其是参与鞭毛合成、组装及功能发挥的基因。这一发现具有重要环境意义：黏土是土壤微生物微环境的核心组成成分，可影响局部化学环境，并可作为有毒污染物的地质吸附剂。与皂石处理类似，DD与DF也可调控细胞运动及趋化相关基因的表达。