Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria
Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria
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DOI：
10.1038/s41564-020-0774-1
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发表时间：
2020-08-17
影响因子：
28.3
通讯作者：
Vogel, Joerg
中科院分区：
文献类型：
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作者：
Imdahl, Fabian;Vafadarnejad, Ehsan;Vogel, Joerg
细菌通过特定的转录程序对其环境变化做出反应，但即使在基因相同的群体中，这些程序也不是同质表达的 (1)。个体细菌之间的这种转录异质性使得基因克隆群落能够形成一系列复杂的表型(1)，其中的例子包括抵抗抗生素治疗的持续细胞和在营养限制条件下出现的代谢特化细胞(2)。荧光报告基因构建体在破译细菌群体内的异质基因表达方面发挥了关键作用(3)，但仅限于记录一些遗传上易处理的模型物种中单个基因的活性，而绝大多数细菌仍然难以改造和/或什至培养。单细胞转录组学正在彻底改变真核生物表型细胞间变异的分析，但技术障碍阻碍了其在原核生物中的稳健应用。在这里，我们使用改进的不依赖于 Poly(A) 的单细胞 RNA 测序方案，报告了跨所有 RNA 类别和基因组区域的单个沙门氏菌和假单胞菌中生长依赖性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。本研究报告了一种改进的不依赖于 Poly(A) 的单细胞 RNA 测序方案，用于捕获单个沙门氏菌和假单胞菌中生长依赖性基因表达模式。
Bacteria respond to changes in their environment with specific transcriptional programmes, but even within genetically identical populations these programmes are not homogenously expressed(1). Such transcriptional heterogeneity between individual bacteria allows genetically clonal communities to develop a complex array of phenotypes(1), examples of which include persisters that resist antibiotic treatment and metabolically specialized cells that emerge under nutrient-limiting conditions(2). Fluorescent reporter constructs have played a pivotal role in deciphering heterogeneous gene expression within bacterial populations(3)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 individualSalmonellaandPseudomonasbacteria 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.This study reports an improved poly(A)-independent single-cell RNA-sequencing protocol to capture growth-dependent gene expression patterns in individualSalmonellaandPseudomonasbacteria.