Genetic changes during a laboratory adaptive evolution process that allowed fast growth in glucose to an Escherichia coli strain lacking the major glucose transport system

BMC Genomics

Research Article

Francisco Bolívar¹  Ramón de Anda¹  Guillermo Gosset¹  César Aguilar¹  Adelfo Escalante¹  Enrique Morett¹  Noemí Flores¹  Fernando Riveros-McKay² 

[1] Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología. Universidad Nacional Autónoma de México (UNAM), 62210, Cuernavaca, Morelos, México;Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología. Universidad Nacional Autónoma de México (UNAM), 62210, Cuernavaca, Morelos, México;Winter Genomics, México D.F. 07300, 62210, Cuernavaca, Morelos, México;

关键词: PTS system;    Resequencing;    Laboratory evolution;    Mutation;    Deletion;    Adaptation;    rppH;    Glycolysis;   

DOI  :  10.1186/1471-2164-13-385

 received in 2012-04-10, accepted in 2012-08-02,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundEscherichia coli strains lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system (PTS), which is the major bacterial component involved in glucose transport and its phosphorylation, accumulate high amounts of phosphoenolpyruvate that can be diverted to the synthesis of commercially relevant products. However, these strains grow slowly in glucose as sole carbon source due to its inefficient transport and metabolism. Strain PB12, with 400% increased growth rate, was isolated after a 120 hours adaptive laboratory evolution process for the selection of faster growing derivatives in glucose. Analysis of the genetic changes that occurred in the PB12 strain that lacks PTS will allow a better understanding of the basis of its growth adaptation and, therefore, in the design of improved metabolic engineering strategies for enhancing carbon diversion into the aromatic pathways.ResultsWhole genome analyses using two different sequencing methodologies: the Roche NimbleGen Inc. comparative genome sequencing technique, and high throughput sequencing with Illumina Inc. GAIIx, allowed the identification of the genetic changes that occurred in the PB12 strain. Both methods detected 23 non-synonymous and 22 synonymous point mutations. Several non-synonymous mutations mapped in regulatory genes (arcB, barA, rpoD, rna) and in other putative regulatory loci (yjjU, rssA and ypdA). In addition, a chromosomal deletion of 10,328 bp was detected that removed 12 genes, among them, the rppH, mutH and galR genes. Characterization of some of these mutated and deleted genes with their functions and possible functions, are presented.ConclusionsThe deletion of the contiguous rppH, mutH and galR genes that occurred simultaneously, is apparently the main reason for the faster growth of the evolved PB12 strain. In support of this interpretation is the fact that inactivation of the rppH gene in the parental PB11 strain substantially increased its growth rate, very likely by increasing glycolytic mRNA genes stability. Furthermore, galR inactivation allowed glucose transport by GalP into the cell. The deletion of mutH in an already stressed strain that lacks PTS is apparently responsible for the very high mutation rate observed.

【 授权许可】

Unknown   
© Aguilar et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.