Enhanced organic solvent tolerance of Escherichia coli by 3-hydroxyacid dehydrogenase family genes

The Hfq regulon of Neisseria meningitidis

The conserved RNA‐binding protein, Hfq, has multiple regulatory roles within the prokaryotic cell, including promoting stable duplex formation between small RNAs and mRNAs, and thus hfq deletion mutants have pleiotropic phenotypes. Previous proteome and transcriptome studies of Neisseria meningitidis have generated limited insight into differential gene expression due to Hfq loss. In this study, reversed‐phase liquid chromatography combined with data‐independent alternate scanning mass spectrometry (LC‐MS^E) was utilized for rapid high‐resolution quantitative proteomic analysis to further elucidate the differentially expressed proteome of a meningococcal hfq deletion mutant. Whole‐cell lysates of N. meningitidis serogroup B H44/76 wild‐type (wt) and H44/76Δhfq (Δhfq) grown in liquid growth medium were subjected to tryptic digestion. The resulting peptide mixtures were separated by liquid chromatography (LC) prior to analysis by mass spectrometry (MS^E). Differential expression was analyzed by Student's t‐test with control for false discovery rate (FDR). Reliable quantitation of relative expression comparing wt and Δhfq was achieved with 506 proteins (20%). Upon FDR control at q ≤ 0.05, 48 up‐ and 59 downregulated proteins were identified. From these, 81 were identified as novel Hfq‐regulated candidates, while 15 proteins were previously found by SDS/PAGE/MS and 24 with microarray analyses. Thus, using LC‐MS^E we have expanded the repertoire of Hfq‐regulated proteins. In conjunction with previous studies, a comprehensive network of Hfq‐regulated proteins was constructed and differentially expressed proteins were found to be involved in a large variety of cellular processes. The results and comparisons with other gram‐negative model systems, suggest still unidentified sRNA analogs in N. meningitidis.

Significantly improved solvent tolerance of Escherichia coli by global transcription machinery engineering

BACKGROUND

Escherichia coli has emerged as a promising platform microorganism to produce biofuels and fine chemicals of industrial interests. Certain obstacles however remain to be overcome, among which organic-solvent tolerance is a crucial one.

RESULTS

We used global transcription machinery engineering (gTME) to improve the organic-solvent tolerance (OST) of E. coli JM109. A mutant library of σ(70) encoded by rpoD was screened under cyclohexane pressure. E. coli JM109 strain harboring σ(70) mutant C9 was identified with capability of tolerating 69 % cyclohexane. The rpoD mutant contains three amino-acid substitutes and a stop-codon mutation, resulting a truncated sequence containing regions σ(1.1) and σ(1.2). Total protein difference produced by E. coli JM109 strain harboring C9 was examined with 2D-PAGE, and 204 high-abundant proteins showed over twofold variation under different solvent stress.

CONCLUSIONS

Our results show that several genes (gapA, sdhB, pepB and dppA) play critical roles in enhanced solvent tolerance of E. coli, mainly involving in maintaining higher intracellular energy level under solvent stress. Global transcription machinery engineering is therefore a feasible and efficient approach for engineering strain with enhanced OST-phenotype.