High-throughput comparison of gene fitness among related bacteria.
High-throughput comparison of gene fitness among related bacteria.
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DOI：
10.1186/1471-2164-13-212
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发表时间：
2012-05-30
期刊：
影响因子：
4.4
通讯作者：
McClelland M
中科院分区：
文献类型：
--
作者：
Canals R;Xia XQ;Fronick C;Clifton SW;Ahmer BM;Andrews-Polymenis HL;Porwollik S;McClelland M
一个基因对细菌适应性的贡献可以通过该细菌是否以及在何种程度上耐受该基因中的转座子插入来测定。我们利用这一事实来比较相关沙门氏菌菌株之间同线性同源基因的适应性，从而揭示在基因序列水平上不明显的差异。
一种转座子Tn5衍生物被用于在鼠伤寒沙门氏菌ATCC14028（STM1）和伤寒沙门氏菌Ty2（STY1）中构建突变体，然后这些突变体在丰富培养基中生长。分别对234,152个和53,556个整合位点的位置进行了测序定位。这些数据与来自不同Ty2分离株（STY2）以及在大肠杆菌K - 12（ECO）中鉴定的必需基因的类似数据进行了比较。在ECO中被认为是必需的277个基因中，所有基因在STM1、STY1和STY2中都有同线性同源基因，并且除了9个基因外，所有基因要么没有转座子插入，要么插入很少。对于这9个基因中的3个，部分注释基因缺乏转座子整合（yejM、ftsN和murB）。其他6个基因中的至少一个，trpS，在沙门氏菌的其他位置编码有一个潜在功能冗余的基因，但在ECO中没有。另外165个基因在所检测的所有3种沙门氏菌菌株中几乎完全没有转座子整合，包括许多与蛋白质和DNA合成相关的基因。其中4个基因（STM14_1498、STM14_2872、STM14_3360和STM14_5442）在大肠杆菌中未被发现。在3种不同的沙门氏菌分离株之间也观察到基因选择程度的显著差异。例如，hns中的突变在STM1中被选择淘汰，但在两种STY菌株中则不然，这两种STY菌株在rpoS上有缺陷，使得hns非必需。
对在相似条件下生长的一个物种的不同成员以及相关物种之间的转座子整合图谱进行比较，可以确定同线性同源基因对适应性贡献的差异。在其他选择环境中，共享基因之间的适应性图谱可能会有进一步的差异，这对比较系统生物学具有潜在的相关性。
The contribution of a gene to the fitness of a bacterium can be assayed by whether and to what degree the bacterium tolerates transposon insertions in that gene. We use this fact to compare the fitness of syntenic homologous genes among related Salmonella strains and thereby reveal differences not apparent at the gene sequence level. A transposon Tn5 derivative was used to construct mutants in Salmonella Typhimurium ATCC14028 (STM1) and Salmonella Typhi Ty2 (STY1), which were then grown in rich media. The locations of 234,152 and 53,556 integration sites, respectively, were mapped by sequencing. These data were compared to similar data available for a different Ty2 isolate (STY2) and essential genes identified in E. coli K-12 (ECO). Of 277 genes considered essential in ECO, all had syntenic homologs in STM1, STY1, and STY2, and all but nine genes were either devoid of transposon insertions or had very few. For three of these nine genes, part of the annotated gene lacked transposon integrations (yejM, ftsN and murB). At least one of the other six genes, trpS, had a potentially functionally redundant gene encoded elsewhere in Salmonella but not in ECO. An additional 165 genes were almost entirely devoid of transposon integrations in all three Salmonella strains examined, including many genes associated with protein and DNA synthesis. Four of these genes (STM14_1498, STM14_2872, STM14_3360, and STM14_5442) are not found in E. coli. Notable differences in the extent of gene selection were also observed among the three different Salmonella isolates. Mutations in hns, for example, were selected against in STM1 but not in the two STY strains, which have a defect in rpoS rendering hns nonessential. Comparisons among transposon integration profiles from different members of a species and among related species, all grown in similar conditions, identify differences in gene contributions to fitness among syntenic homologs. Further differences in fitness profiles among shared genes can be expected in other selective environments, with potential relevance for comparative systems biology.
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影响因子：
7
作者：
Langridge, Gemma C.;Phan, Minh-Duy;Turner, A. Keith
通讯作者：
Turner, A. Keith
影响因子：
46.9
作者：
Badarinarayana, V;Estep, PW;Church, GM
通讯作者：
Church, GM
DOI：
10.1073/pnas.95.18.10716
发表时间：
1998-09-01
影响因子：
11.1
作者：
Goryshin, IY;Miller, JA;Reznikoff, WS
通讯作者：
Reznikoff, WS
大肠杆菌K-12的构造框架，单基因敲除突变体：Keio Collection。
影响因子：
9.9
作者：
通讯作者：
--
影响因子：
4.4
作者：
Hamilton S;Bongaerts RJ;Mulholland F;Cochrane B;Porter J;Lucchini S;Lappin-Scott HM;Hinton JC
通讯作者：
Hinton JC