Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany.
Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany.
Nat Microbiol. 2020 Oct;5(10):1202-1206. doi: 10.1038/s41564-020-0774-1. Epub 2020 Aug 17.
Bacteria respond to changes in their environment with specific transcriptional programmes, but even within genetically identical populations these programmes are not homogenously expressed. Such transcriptional heterogeneity between individual bacteria allows genetically clonal communities to develop a complex array of phenotypes, examples of which include persisters that resist antibiotic treatment and metabolically specialized cells that emerge under nutrient-limiting conditions. Fluorescent reporter constructs have played a pivotal role in deciphering heterogeneous gene expression within bacterial populations but have been limited to recording the activity of single genes in a few genetically tractable model species, whereas the vast majority of bacteria remain difficult to engineer and/or even to cultivate. Single-cell transcriptomics is revolutionizing the analysis of phenotypic cell-to-cell variation in eukaryotes, but technical hurdles have prevented its robust application to prokaryotes. Here, using an improved poly(A)-independent single-cell RNA-sequencing protocol, we report the faithful capture of growth-dependent gene expression patterns in individual Salmonella and Pseudomonas bacteria across all RNA classes and genomic regions. These transcriptomes provide important reference points for single-cell RNA-sequencing of other bacterial species, mixed microbial communities and host-pathogen interactions.
细菌会针对其环境变化做出特定的转录程序响应，但即使在遗传上完全相同的种群中，这些程序也不会均匀表达。这种单个细菌之间的转录异质性使遗传克隆群落能够发展出一系列复杂的表型，其中包括对抗生素治疗有抵抗力的持久性细菌和在营养限制条件下出现的代谢特化细胞。荧光报告基因构建体在破译细菌种群中的异质基因表达方面发挥了关键作用，但它们仅限于在少数遗传上可操作的模式物种中记录单个基因的活性，而绝大多数细菌仍然难以进行工程改造和/或甚至难以培养。单细胞转录组学正在彻底改变真核生物中表型细胞间变异性的分析，但技术障碍阻止了其在原核生物中的稳健应用。在这里，我们使用改进的聚（A）独立的单细胞 RNA 测序方案，报告了在单个沙门氏菌和假单胞菌细菌中所有 RNA 类和基因组区域的与生长相关的基因表达模式的忠实捕获。这些转录组为其他细菌物种、混合微生物群落和宿主-病原体相互作用的单细胞 RNA 测序提供了重要的参考点。
