PMID- 26971973 OWN - NLM STAT- MEDLINE DCOM- 20161214 LR - 20220330 IS - 1873-4863 (Electronic) IS - 0168-1656 (Linking) VI - 224 DP - 2016 Apr 20 TI - Tailoring of global transcription sigma D factor by random mutagenesis to improve Escherichia coli tolerance towards low-pHs. PG - 55-63 LID - S0168-1656(16)30110-9 [pii] LID - 10.1016/j.jbiotec.2016.03.012 [doi] AB - 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. CI - Copyright (c) 2016 Elsevier B.V. All rights reserved. FAU - Gao, Xi AU - Gao X AD - College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, PR China. Electronic address: melindag@yeah.net. FAU - Jiang, Ling AU - Jiang L AD - College of Food Science and Light Industry, Nanjing Tech University, Nanjing 210009, PR China. Electronic address: jiangling@njtech.edu.cn. FAU - Zhu, Liying AU - Zhu L AD - College of Sciences, Nanjing Tech University, Nanjing 210009, PR China. Electronic address: zlyhappy@njtech.edu.cn. FAU - Xu, Qing AU - Xu Q AD - College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, PR China. Electronic address: xuqing357@njtech.edu.cn. FAU - Xu, Xian AU - Xu X AD - College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, PR China. Electronic address: xuxian@njtech.edu.cn. FAU - Huang, He AU - Huang H AD - College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, PR China. Electronic address: biotech@njtech.edu.cn. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20160310 PL - Netherlands TA - J Biotechnol JT - Journal of biotechnology JID - 8411927 RN - 0 (Escherichia coli Proteins) RN - 0 (Sigma Factor) RN - EC 2.7.7.- (RNA polymerase sigma 70) RN - EC 2.7.7.6 (DNA-Directed RNA Polymerases) SB - IM MH - Adaptation, Physiological MH - DNA-Directed RNA Polymerases/*genetics/metabolism MH - Escherichia coli/genetics/*growth & development MH - Escherichia coli Proteins/genetics MH - Gene Expression Profiling/methods MH - Gene Expression Regulation, Bacterial MH - Gene Regulatory Networks MH - Hydrogen-Ion Concentration MH - *Mutagenesis MH - Sigma Factor/*genetics/metabolism MH - *Transcription, Genetic OTO - NOTNLM OT - Acid tolerance OT - Escherichia coli OT - Phenotype microarray OT - RNA-seq OT - RpoD EDAT- 2016/03/15 06:00 MHDA- 2016/12/15 06:00 CRDT- 2016/03/15 06:00 PHST- 2015/09/22 00:00 [received] PHST- 2016/03/02 00:00 [revised] PHST- 2016/03/08 00:00 [accepted] PHST- 2016/03/15 06:00 [entrez] PHST- 2016/03/15 06:00 [pubmed] PHST- 2016/12/15 06:00 [medline] AID - S0168-1656(16)30110-9 [pii] AID - 10.1016/j.jbiotec.2016.03.012 [doi] PST - ppublish SO - J Biotechnol. 2016 Apr 20;224:55-63. doi: 10.1016/j.jbiotec.2016.03.012. Epub 2016 Mar 10.