title: Tailoring of global transcription sigma D factor by random mutagenesis to improve Escherichia coli tolerance towards low-pHs.
abstract: Bioconversion processes of organic acid or acid hydrolysis of raw material for microbial metabolism often suffer limitations as a result of microbial sensitivity in low-pH conditions. We adopted a three-step method called RAndom Insertional-deletional Strand Exchange mutagenesis (RAISE) to engineer the components of global regulator Sigma D factor (RpoD) of Escherichia coli to improve its acid tolerance. The best strain Mutant VII was identified from random mutagenesis libraries based on the growth performance, which exhibited much higher growth rate than the control (0.22h(-1) vs. 0.15h(-1)) at pH as low as 3.17. Combined transcriptome and phenome analysis of E. coli was carried out to better understand the global effects of RpoD on the regulatory networks. Our analysis showed that 95 (2.1%) of all E. coli genes were induced and 178 (4.0%) genes were repressed, including those for trehalose biosynthesis, nucleotides biosynthesis, carbon metabolism, amino acid utilization, except for acid resistance. Also regulated were the master regulators (ArcA, EvgA, H-NS and RpoS) and gene/operon-specific transcription factors (GadX, GadW, AppY, YdeO, KdgR). These results demonstrated that RpoD acts as global regulator in the growth phase of E. coli and consequently improves acid tolerances.
authors.affiliation: College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, PR China. Electronic address: melindag@yeah.net.
authors.forename: Xi
authors.initials: X
authors.lastname: Gao
authors.affiliation: College of Food Science and Light Industry, Nanjing Tech University, Nanjing 210009, PR China. Electronic address: jiangling@njtech.edu.cn.
authors.forename: Ling
authors.initials: L
authors.lastname: Jiang
authors.affiliation: College of Sciences, Nanjing Tech University, Nanjing 210009, PR China. Electronic address: zlyhappy@njtech.edu.cn.
authors.forename: Liying
authors.initials: L
authors.lastname: Zhu
authors.affiliation: College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, PR China. Electronic address: xuqing357@njtech.edu.cn.
authors.forename: Qing
authors.initials: Q
authors.lastname: Xu
authors.affiliation: College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, PR China. Electronic address: xuxian@njtech.edu.cn.
authors.forename: Xian
authors.initials: X
authors.lastname: Xu
authors.affiliation: College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, PR China. Electronic address: biotech@njtech.edu.cn.
authors.forename: He
authors.initials: H
authors.lastname: Huang
mesh_terms: D000222:Adaptation, Physiological; D012321:DNA-Directed RNA Polymerases / Q000235:genetics* / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000254:growth & development*; D029968:Escherichia coli Proteins / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D006863:Hydrogen-Ion Concentration; D016296:Mutagenesis; D012808:Sigma Factor / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D029968:Escherichia coli Proteins; D012808:Sigma Factor; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases
keywords: Acid tolerance; Escherichia coli; Phenotype microarray; RNA-seq; RpoD