Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, Villeurbanne, France.
mBio. 2022 Jun 28;13(3):e0052422. doi: 10.1128/mbio.00524-22. Epub 2022 May 2.
Dickeya dadantii is a phytopathogenic bacterium that causes soft rot in a wide range of plant hosts worldwide and a model organism for studying virulence gene regulation. The present study provides a comprehensive and annotated transcriptomic map of obtained by a computational method combining five independent transcriptomic data sets: (i) paired-end RNA sequencing (RNA-seq) data for a precise reconstruction of the RNA landscape; (ii) DNA microarray data providing transcriptional responses to a broad variety of environmental conditions; (iii) long-read Nanopore native RNA-seq data for isoform-level transcriptome validation and determination of transcription termination sites; (iv) differential RNA sequencing (dRNA-seq) data for the precise mapping of transcription start sites; (v) DNA microarray data for a comparison of gene expression profiles between experiments and the early stages of plant infection. Our results show that transcription units sometimes coincide with predicted operons but are generally longer, most of them comprising internal promoters and terminators that generate alternative transcripts of variable gene composition. We characterize the occurrence of transcriptional read-through at terminators, which might play a basal regulation role and explain the extent of transcription beyond the scale of operons. We finally highlight the presence of noncontiguous operons and excludons in the genome, novel genomic arrangements that might contribute to the basal coordination of transcription. The highlighted transcriptional organization may allow to finely adjust its gene expression program for a rapid adaptation to fast-changing environments. This is the first transcriptomic map of a species. It may therefore significantly contribute to further progress in the field of phytopathogenicity. It is also one of the first reported applications of long-read Nanopore native RNA-seq in prokaryotes. Our findings yield insights into basal rules of coordination of transcription that might be valid for other bacteria and may raise interest in the field of microbiology in general. In particular, we demonstrate that gene expression is coordinated at the scale of transcription units rather than operons, which are larger functional genomic units capable of generating transcripts with variable gene composition for a fine-tuning of gene expression in response to environmental changes. In line with recent studies, our findings indicate that the canonical operon model is insufficient to explain the complexity of bacterial transcriptomes.
戴克氏土壤杆菌是一种植物病原菌，可引起全球范围内广泛植物宿主的软腐病，是研究毒力基因调控的模式生物。本研究通过结合五个独立转录组数据集的计算方法提供了 的综合注释转录组图谱：（i） 为精确重建 RNA 图谱的配对末端 RNA 测序（RNA-seq）数据；（ii） 提供对各种环境条件转录响应的 DNA 微阵列数据；（iii） 用于同工型转录组验证和转录终止位点确定的长读长纳米孔天然 RNA-seq 数据；（iv） 用于精确绘制转录起始位点的差异 RNA 测序（dRNA-seq）数据；（v） 用于比较 实验和植物感染早期阶段基因表达谱的 DNA 微阵列数据。我们的结果表明，转录单元有时与预测的操纵子重合，但通常更长，其中大多数包含内部启动子和终止子，它们生成可变基因组成的替代转录本。我们描述了终止子处转录通读的发生情况，这可能发挥基础调控作用，并解释了超出操纵子范围的转录程度。我们最后强调了 在 基因组中存在非连续操纵子和 excludons，这是新的基因组排列，可能有助于转录的基础协调。突出的转录组织可能使 能够精细地调整其基因表达程序，以快速适应快速变化的环境。这是第一个 物种的转录组图谱。因此，它可能会极大地促进植物病理学领域的进一步发展。它也是第一个在原核生物中报道的长读长纳米孔天然 RNA-seq 应用之一。我们的研究结果深入了解了转录协调的基本规则，这些规则可能对其他细菌有效，并且可能引起一般微生物学领域的兴趣。特别是，我们证明基因表达是在转录单元而不是操纵子的尺度上协调的，操纵子是更大的功能基因组单元，能够生成具有可变基因组成的转录本，以精细调节基因表达以响应环境变化。与最近的研究一致，我们的研究结果表明，经典的操纵子模型不足以解释细菌转录组的复杂性。
