Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene.
Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene.
复制标题
DOI：
10.1371/journal.pgen.1001186
复制
发表时间：
2010-11-04
期刊：
影响因子：
4.5
通讯作者：
Palsson BØ
中科院分区：
文献类型：
--
作者：
Charusanti P;Conrad TM;Knight EM;Venkataraman K;Fong NL;Xie B;Gao Y;Palsson BØ
细菌的生存需要适应不同的环境扰动，如暴露于抗生素，温度或氧气水平的变化，DNA损伤和替代营养源。在适应过程中，细菌通常会发生有益的突变，从而增加新环境中的适应性。然而，对一种主要的非必需基因产物的丧失的适应性还没有在全基因组水平上进行过研究。我们通过自适应进化10个重复的E. coli K-12 MG 1655来研究其克服磷酸葡萄糖异构酶（pgi）丢失的能力。在葡萄糖M9基本培养基中培养缺乏pgi的大肠杆菌50天，并通过全基因组重测序和表型分析来表征终点克隆。我们发现：1）所有10个终点克隆的生长速率在50天内增加了约3倍; 2）在适应过程中出现了2 - 5个突变，最常见的是NADH/NADPH转氢酶udhA和pntAB以及与应激相关的σ因子rpoS;和3）尽管生长速率相似，但如乙酸盐和甲酸盐分泌的不同速率所定义的，发展出至少三种不同的终点表型。这些结果表明E.大肠杆菌可以适应一个主要的代谢基因产物的损失，只有少数突变，这种适应可以导致多种，替代表型。细菌必须不断适应许多不同的环境挑战，但当它们失去一个关键的基因产物时，它们如何适应呢？我们使用缺乏pgi（一种参与糖利用的主要代谢基因）的大肠杆菌解决了这个问题，通过连续传递缺乏pgi基因的复制品50天，并对从9个复制品中分离的终点克隆的整个基因组进行重测序。我们反复发现了rpoS的突变，rpoS是一种在稳定期最活跃的基因，但在指数期生长期间调节了大约50个基因的表达，还有udhA和pntAB，这三个基因参与维持细胞中的氧化还原平衡。我们还发现了多个不同的终点表型;根据其乙酸盐和甲酸盐分泌速率，在适应后，重复可分为三个不同的组。这些结果支持了E.大肠杆菌是健壮的，并且可以以替代方式调整主要代谢基因的丢失。
Bacterial survival requires adaptation to different environmental perturbations such as exposure to antibiotics, changes in temperature or oxygen levels, DNA damage, and alternative nutrient sources. During adaptation, bacteria often develop beneficial mutations that confer increased fitness in the new environment. Adaptation to the loss of a major non-essential gene product that cripples growth, however, has not been studied at the whole-genome level. We investigated the ability of Escherichia coli K-12 MG1655 to overcome the loss of phosphoglucose isomerase (pgi) by adaptively evolving ten replicates of E. coli lacking pgi for 50 days in glucose M9 minimal medium and by characterizing endpoint clones through whole-genome re-sequencing and phenotype profiling. We found that 1) the growth rates for all ten endpoint clones increased approximately 3-fold over the 50-day period; 2) two to five mutations arose during adaptation, most frequently in the NADH/NADPH transhydrogenases udhA and pntAB and in the stress-associated sigma factor rpoS; and 3) despite similar growth rates, at least three distinct endpoint phenotypes developed as defined by different rates of acetate and formate secretion. These results demonstrate that E. coli can adapt to the loss of a major metabolic gene product with only a handful of mutations and that adaptation can result in multiple, alternative phenotypes. Bacteria must constantly adapt to many different environmental challenges, but how do they adapt when they lose a key gene product? We addressed this question using Escherichia coli lacking pgi, a major metabolic gene involved in sugar utilization, by serially passing replicates lacking the pgi gene for 50 days and resequencing the entire genome from endpoint clones isolated from nine of the replicates. We repeatedly found mutations in rpoS, a gene mostly active during stationary phase but one that regulates the expression of about fifty genes during exponential phase growth, and udhA and pntAB, three genes involved in maintaining redox balance in the cell. We also found multiple distinct endpoint phenotypes; the replicates could be stratified into three different groups after adaptation based on their rates of acetate and formate secretion. These results support the view that the metabolic network in E. coli is robust and can adjust to loss of a major metabolic gene in alternative ways.
登录
查看更多内容
DOI：
10.1099/00221287-65-1-57
发表时间：
1971-01-01
期刊：
JOURNAL OF GENERAL MICROBIOLOGY
影响因子：
--
作者：
HOLMS, WH;BENNETT, PM
通讯作者：
BENNETT, PM
影响因子：
4.8
作者：
Fong, SS;Nanchen, A;Sauer, U
通讯作者：
Sauer, U
影响因子：
3.2
作者：
Harris, Dennis R.;Pollock, Steve V.;Battista, John R.
通讯作者：
Battista, John R.
影响因子：
9.9
作者：
通讯作者：
--
DOI：
10.1073/pnas.120163297
发表时间：
2000-06-06
影响因子：
11.1
作者：
Datsenko, KA;Wanner, BL
通讯作者：
Wanner, BL