Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
Nucleic Acids Res. 2013 Apr;41(8):4549-64. doi: 10.1093/nar/gkt148. Epub 2013 Mar 6.
Salmonella Typhi and Typhimurium diverged only ∼50 000 years ago, yet have very different host ranges and pathogenicity. Despite the availability of multiple whole-genome sequences, the genetic differences that have driven these changes in phenotype are only beginning to be understood. In this study, we use transposon-directed insertion-site sequencing to probe differences in gene requirements for competitive growth in rich media between these two closely related serovars. We identify a conserved core of 281 genes that are required for growth in both serovars, 228 of which are essential in Escherichia coli. We are able to identify active prophage elements through the requirement for their repressors. We also find distinct differences in requirements for genes involved in cell surface structure biogenesis and iron utilization. Finally, we demonstrate that transposon-directed insertion-site sequencing is not only applicable to the protein-coding content of the cell but also has sufficient resolution to generate hypotheses regarding the functions of non-coding RNAs (ncRNAs) as well. We are able to assign probable functions to a number of cis-regulatory ncRNA elements, as well as to infer likely differences in trans-acting ncRNA regulatory networks.
伤寒沙门氏菌和鼠伤寒沙门氏菌仅在大约 5 万年前发生分化，但它们具有非常不同的宿主范围和致病性。尽管有多种全基因组序列可用，但导致这些表型变化的遗传差异才刚刚开始被理解。在这项研究中，我们使用转座子定向插入位点测序来探测这两种密切相关血清型在丰富培养基中竞争生长的基因需求差异。我们确定了 281 个保守核心基因，这些基因是两种血清型生长所必需的，其中 228 个基因在大肠杆菌中是必需的。我们能够通过对其抑制剂的需求来识别活跃的噬菌体元件。我们还发现，参与细胞表面结构生物发生和铁利用的基因的需求存在明显差异。最后，我们证明转座子定向插入位点测序不仅适用于细胞的蛋白质编码内容，而且具有足够的分辨率，可以提出关于非编码 RNA（ncRNA）功能的假设。我们能够为许多顺式调控 ncRNA 元件分配可能的功能，并推断出反式作用 ncRNA 调控网络可能存在的差异。
