Transcriptome profiling of Variovorax paradoxus EPS under different growth conditions reveals regulatory and structural novelty in biofilm formation.
Transcriptome profiling of Variovorax paradoxus EPS under different growth conditions reveals regulatory and structural novelty in biofilm formation.
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DOI：
10.1099/acmi.0.000121
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发表时间：
2020-01-01
影响因子：
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通讯作者：
Orwin, Paul M
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文献类型：
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作者：
Fredendall, Richard J;Stone, Jenny L;Orwin, Paul M
我们使用转录组分析配对末端链特异性RNA-seq来评估与根际植物生长促进细菌Variovorax paradoxus EPS中向静态生物膜生长过渡相关的基因表达的特异性变化。对指数生长期、稳定期和静态生物膜样品进行了检测。DESeq 2和跳岩企鹅用于鉴定每个生长阶段特异性基因表达的稳健和广泛的变化。我们使用DESeq 2鉴定了1711个蛋白质编码基因（28%），与指数生长相比，这些基因在生物膜中特异性地改变了两倍以上的表达。在静止期培养中特异性差异表达的基因较少（757，12%）。一小组基因（103/6020）在生物膜和稳定期以相反的方式差异表达，表明表型可能发生实质性变化。基因本体论分析表明，唯一一类的基因特异性上调生物膜与营养运输，突出了生物膜中的营养吸收的重要性。生物膜特异性基因没有重叠基本上与诱变研究确定的基因座，虽然有些是在这两个集。预测最高度上调的生物膜特异性基因是RNA降解体的一部分，这表明RNA稳定性用于调节生物膜表型。两个小的推定的蛋白质，Varpa_0407和Varpa_3832，是高度表达的生物膜中特异性，并被预测为分泌的DNA结合蛋白，这可能会稳定细胞外DNA作为生物膜基质的组成部分。flp/tad IV型菌毛基因座（Varpa_5148-60）在生物膜中特异性地被强烈下调，与来自这些皮利的其它系统的结果相反。突变证实，这个位点是重要的表面运动，而不是生物膜形成。这些实验结果表明，V. paradoxus EPS生物膜具有实质性的调节和结构新奇。
We used transcriptome analysis by paired-end strand-specific RNA-seq to evaluate the specific changes in gene expression associated with the transition to static biofilm growth in the rhizosphere plant growth-promoting bacterium Variovorax paradoxus EPS. Triplicate biological samples of exponential growth, stationary phase and static biofilm samples were examined. DESeq2 and Rockhopper were used to identify robust and widespread shifts in gene expression specific to each growth phase. We identified 1711 protein-coding genes (28%) using DESeq2 that had altered expression greater than twofold specifically in biofilms compared to exponential growth. Fewer genes were specifically differentially expressed in stationary-phase culture (757, 12%). A small set of genes (103/6020) were differentially expressed in opposing fashions in biofilm and stationary phase, indicating potentially substantial shifts in phenotype. Gene-ontology analysis showed that the only class of genes specifically upregulated in biofilms was associated with nutrient transport, highlighting the importance of nutrient uptake in the biofilm. The biofilm-specific genes did not overlap substantially with the loci identified by mutagenesis studies, although some were present in both sets. The most highly upregulated biofilm-specific gene is predicted to be a part of the RNA degradosome, which indicates that RNA stability is used to regulate the biofilm phenotype. Two small putative proteins, Varpa_0407 and Varpa_3832, are highly expressed specifically in biofilms and are predicted to be secreted DNA-binding proteins, which may stabilize extracellular DNA as a component of the biofilm matrix. An flp/tad type-IV pilus locus (Varpa_5148-60) is strongly downregulated specifically in biofilms, in contrast with results from other systems for these pili. Mutagenesis confirms that this locus is important in surface motility rather than biofilm formation. These experimental results suggest that V. paradoxus EPS biofilms have substantial regulatory and structural novelty.