Sphingomonas wittichii strain RW1 genome-wide gene expression shifts in response to dioxins and clay

Sphingomonas wittichii strain RW1 (RW1) is one of 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 (SAP), an important geosorbent of toxicants in soil, 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 and 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 by 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 changes 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 (SAP) 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 environmentally important finding because clay is a major component of soil microbes' microenvironment influencing local chemistry and may serve as geosorbent for toxic pollutants. Similar to clay, DD and DF also affect motility and chemotaxis. Overall design: Differential expression analysis of transcriptomes sequnenced from two replicates from succinate (SUC, control), three from succinate in the presence of clay (SAP), three from DD, and three from DF.

威奇鞘氨醇单胞菌RW1菌株（Sphingomonas wittichii strain RW1，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。本研究采用RNA测序（RNA-Seq）对RW1开展转录组学研究，旨在阐明其在以琥珀酸盐为碳源时，暴露于DD、二苯并呋喃（dibenzofuran，DF）以及土壤中重要的有毒物质天然吸附剂——蒙脱石族黏土矿物皂石（smectite clay mineral saponite，SAP）后的转录响应模式。相较于化学结构相似的DF，RW1能够利用DD生长的能力较为罕见，尽管二者的初始氧化过程可能由同一双加氧酶介导。据此，本研究提出假说：该生长差异的根源不仅限于分解代谢途径，还可能涉及细胞-底物互作相关过程的基因，例如底物识别、转运与解毒相关基因。以琥珀酸盐（SUC）作为对照碳源时，DF诱导了超过240个蛋白编码基因发生差异表达，而DD则导致超过300个蛋白编码基因出现差异表达。DD与DF均可上调应激响应基因，且DD的诱导效果强于DF，提示DD的毒性高于DF。两种底物均会改变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与DF培养条件下也呈现特异性。DD与DF分别诱导了儿茶酚邻位裂解途径与水杨酸/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途径。皂石（SAP）可导致细胞运动与趋化相关基因全域下调，尤其是鞭毛合成、组装及功能相关基因。该发现具有重要的环境学意义：黏土是土壤微生物微环境的核心组成部分，可调控局部化学环境，并可作为有毒污染物的天然吸附介质。与黏土类似，DD与DF同样会影响细菌的运动性与趋化性。实验整体设计：对琥珀酸盐（SUC，对照组）的2次生物学重复、添加皂石（SAP）的琥珀酸盐培养基的3次生物学重复、DD培养基的3次生物学重复以及DF培养基的3次生物学重复的转录组样本开展差异表达分析。