Microbiology Department, Institut Pasteur, Université Paris Cité, Biology of Spirochetes Unit, Paris, France.
INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec H7V 1B7, Canada.
Mol Biol Evol. 2024 Apr 2;41(4). doi: 10.1093/molbev/msae066.
Transcriptomic analyses across large scales of evolutionary distance have great potential to shed light on regulatory evolution but are complicated by difficulties in establishing orthology and limited availability of accessible software. We introduce here a method and a graphical user interface wrapper, called Annotator-RNAtor, for performing interspecies transcriptomic analysis and studying intragenus evolution. The pipeline uses third-party software to infer homologous genes in various species and highlight differences in the expression of the core-genes. To illustrate the methodology and demonstrate its usefulness, we focus on the emergence of the highly virulent Leptospira subclade known as P1+, which includes the causative agents of leptospirosis. Here, we expand on the genomic study through the comparison of transcriptomes between species from P1+ and their related P1- counterparts (low-virulent pathogens). In doing so, we shed light on differentially expressed pathways and focused on describing a specific example of adaptation based on a differential expression of PerRA-controlled genes. We showed that P1+ species exhibit higher expression of the katE gene, a well-known virulence determinant in pathogenic Leptospira species correlated with greater tolerance to peroxide. Switching PerRA alleles between P1+ and P1- species demonstrated that the lower repression of katE and greater tolerance to peroxide in P1+ species was solely controlled by PerRA and partly caused by a PerRA amino-acid permutation. Overall, these results demonstrate the strategic fit of the methodology and its ability to decipher adaptive transcriptomic changes, not observable by comparative genome analysis, that may have been implicated in the emergence of these pathogens.
跨大规模进化距离的转录组分析具有阐明调控进化的巨大潜力，但由于同源基因的确定困难和可访问软件的有限可用性而变得复杂。我们在这里介绍一种方法和一个图形用户界面包装器，称为 Annotator-RNAtor，用于进行种间转录组分析和研究属内进化。该流水线使用第三方软件推断各种物种中的同源基因，并突出核心基因表达的差异。为了说明方法学并展示其有用性，我们专注于高度毒力的 Leptospira 亚群 P1+的出现，其中包括导致钩端螺旋体病的病原体。在这里，我们通过比较 P1+和它们相关的 P1-对应物（低毒力病原体）之间的转录组，扩展了基因组研究。通过这种方式，我们揭示了差异表达的途径，并重点描述了基于 PerRA 控制基因差异表达的特定适应示例。我们表明，P1+物种表现出 katE 基因的更高表达，katE 基因是致病性 Leptospira 物种中众所周知的毒力决定因素，与对过氧化物的更大耐受性相关。在 P1+和 P1-物种之间切换 PerRA 等位基因表明，P1+物种中 katE 的抑制作用降低和对过氧化物的耐受性增加仅由 PerRA 控制，部分原因是 PerRA 氨基酸置换。总的来说，这些结果表明该方法的战略适应性及其能够破译通过比较基因组分析无法观察到的适应性转录组变化，这些变化可能与这些病原体的出现有关。
