Research Center for Infectious Diseases (ZINF), University of Würzburg, Würzburg, Germany.
PLoS Genet. 2013 May;9(5):e1003495. doi: 10.1371/journal.pgen.1003495. Epub 2013 May 16.
Campylobacter jejuni is currently the leading cause of bacterial gastroenteritis in humans. Comparison of multiple Campylobacter strains revealed a high genetic and phenotypic diversity. However, little is known about differences in transcriptome organization, gene expression, and small RNA (sRNA) repertoires. Here we present the first comparative primary transcriptome analysis based on the differential RNA-seq (dRNA-seq) of four C. jejuni isolates. Our approach includes a novel, generic method for the automated annotation of transcriptional start sites (TSS), which allowed us to provide genome-wide promoter maps in the analyzed strains. These global TSS maps are refined through the integration of a SuperGenome approach that allows for a comparative TSS annotation by mapping RNA-seq data of multiple strains into a common coordinate system derived from a whole-genome alignment. Considering the steadily increasing amount of RNA-seq studies, our automated TSS annotation will not only facilitate transcriptome annotation for a wider range of pro- and eukaryotes but can also be adapted for the analysis among different growth or stress conditions. Our comparative dRNA-seq analysis revealed conservation of most TSS, but also single-nucleotide-polymorphisms (SNP) in promoter regions, which lead to strain-specific transcriptional output. Furthermore, we identified strain-specific sRNA repertoires that could contribute to differential gene regulation among strains. In addition, we identified a novel minimal CRISPR-system in Campylobacter of the type-II CRISPR subtype, which relies on the host factor RNase III and a trans-encoded sRNA for maturation of crRNAs. This minimal system of Campylobacter, which seems active in only some strains, employs a unique maturation pathway, since the crRNAs are transcribed from individual promoters in the upstream repeats and thereby minimize the requirements for the maturation machinery. Overall, our study provides new insights into strain-specific transcriptome organization and sRNAs, and reveals genes that could modulate phenotypic variation among strains despite high conservation at the DNA level.
空肠弯曲菌是目前人类细菌性胃肠炎的主要致病菌。对多种空肠弯曲菌菌株的比较显示出高度的遗传和表型多样性。然而，对于转录组组织、基因表达和小 RNA（sRNA）谱的差异知之甚少。在这里，我们首次基于 4 株空肠弯曲菌的差异 RNA-seq（dRNA-seq）进行了比较性初级转录组分析。我们的方法包括一种新颖的、通用的转录起始位点（TSS）自动注释方法，该方法使我们能够在分析的菌株中提供全基因组启动子图谱。通过将多个菌株的 RNA-seq 数据映射到一个共同的坐标系统中，该系统是从全基因组比对中衍生出来的，从而对这些全局 TSS 图谱进行了精细的整合，这使得比较 TSS 注释成为可能。考虑到 RNA-seq 研究的数量不断增加，我们的自动 TSS 注释不仅将促进更广泛的原核和真核生物的转录组注释，而且还可以适应不同生长或应激条件下的分析。我们的比较 dRNA-seq 分析表明，大多数 TSS 是保守的，但启动子区域也存在单核苷酸多态性（SNP），这导致了菌株特异性的转录输出。此外，我们还鉴定了菌株特异性的 sRNA 谱，这些 sRNA 可能有助于菌株间的差异基因调控。此外，我们在空肠弯曲菌的 II 型 CRISPR 亚型中发现了一个新的最小 CRISPR 系统，该系统依赖于宿主因子 RNase III 和一个反式编码的 sRNA 来成熟 crRNA。这种空肠弯曲菌的最小系统似乎只在一些菌株中活跃，它采用了一种独特的成熟途径，因为 crRNA 是从上游重复序列中的单个启动子转录而来的，从而最大限度地减少了成熟机制的需求。总的来说，我们的研究提供了关于菌株特异性转录组组织和 sRNA 的新见解，并揭示了尽管在 DNA 水平上高度保守，但可以调节菌株间表型变异的基因。
