Gene expression during citramalate production by E. coli
ABSTRACT: Citramalate is a chemical of potential industrial importance. Efficient fermentations have been developed using recombinant E. coli as the chassis. The experiments explore the transcriptional reprogramming that occurs upon induction of citramalate production.
Project description:Interaction between the host and invading pathogen determines the fate of both organisms during the infectious state. The host is equipped with a battery of immune reactions, while the pathogen displays a variety of mechanisms to compromise host immunity. Although bacteria alter their pattern of gene expression when they enter host organisms, studies to elucidate the mechanism behind this are only in their infancy. In the present study, we examined the possibility that host immune proteins directly participate in the change of gene expression in bacteria. To this end, Escherichia coli was treated with a mixture of the extracellular region of membrane-bound peptidoglycan recognition protein LC (PGRP-LC) and the antimicrobial peptide attacin of Drosophila, and subsequently subjected to DNA microarray analysis for the repertoire of mRNA. We identified nearly 200 genes whose mRNA increased after the treatment, and at least four of them were induced in response to PGRP-LC. One such gene, lipoprotein-encoding nlpI, showed a transient increase of its mRNA level in adult flies depending on PGRP-LC, and NlpI-lacking E. coli had a smaller pathogenic effect with lowered growth/viability than the parental strain in adult flies. These results suggest that a host immune receptor triggers a change of gene expression in bacteria simultaneously to their recognition of the invader and induction of immune responses. The E. coli strain BW25113 (2 x 10^9) suspended with insect saline (0.13 M NaCl, 4.7 mM KCl, 1.9 mM CaCl2), was incubated with a mixture of GST-attacin (0.125 μM), GST-PGRP-LCa (0.5 μM), GST-PGRP-LCx (1 μM), and GST-PGRP-LCy (0.5 μM) for 10 min at room temperature. As a negative control, incubation of E. coli was done in the presence of GST alone (3 μM).
Project description:Comparison of gene expression profile in E. coli BW25113 wild type and ldhA-pflB- double mutant growing microaerobically in M9 media containing 10 g/L Glucose two samples: wild type and mutant
Project description:Measuring precise concentrations of proteins can provide insights into biological processes. Here we use efficient protein extraction and sample fractionation, as well as state-of-the-art quantitative mass spectrometry techniques to generate a comprehensive, condition-dependent protein-abundance map for Escherichia coli. We measure cellular protein concentrations for 55% of predicted E. coli genes (>2,300 proteins) under 22 different experimental conditions and identify methylation and N-terminal protein acetylations previously not known to be prevalent in bacteria. We uncover system-wide proteome allocation, expression regulation and post-translational adaptations. These data provide a valuable resource for the systems biology and broader E. coli research communities.
Project description:Transcriptome analysis of isolated mutants using the method Visualizing Evolution in Real-Time (VERT) for the study of n-butanol tolerance. The samples were isolated from an evolution experiment picking samples at different times based in the evolution dynamics obtained with VERT. Mutants were grown in chemostats at 0.8% (v/v) of n-butanol and compared with the expression of wild-type to the same concentration of solvent. Three biological replicas. Each sample represents an isolated mutant. The reference for each mutant corresponds to wild-type, both exposed to the same concentration of n-butanol (0.8% (v/v)).
Project description:To determine whether c-di-GMP could affect CobB-dependent deacetylation in a global setting, we applied Stable Isotope Labeling with Amino acids in Cell culture (SILAC) coupled with MS to quantitatively compare the levels of protein acetylation in WT, ΔcobB and ΔdgcZ cells.
Project description:Description To determine whether c-di-GMP could affect CobB-dependent deacetylation in a global setting, we applied Stable Isotope Labeling with Amino acids in Cell culture (SILAC) coupled with MS to quantitatively compare the levels of protein acetylation in WT, ΔcobB and ΔdgcZ cells. Before that, we determined the labeling efficiency for these samples.
Project description:This dataset contains the gene expression signature in triplicates of Escherichia coli BW25113 growing exponentially on eight different environments: minimal medium supplemented with 5 g/L of Glucose, Galactose, Glycerol, Gluconate, Fructose, Pyruvate, Succinate or Acetate as the sole carbon source.
Project description:RNA-seq of C.elegans strain N2 (wt) with and without sfa-1 RNAi at adult day 3 and day 15, C. elegans strain DA1116 (eat-2(ad1116)) with and without sfa-1 RNAi at adult day 3, day 15, and day 27, C. elegans strain SS104 (glp-4(bn2)) with and without hrp-2 RNAi at adult day 1, and HeLa cells with and without SF1 siRNA.
Project description:Dihydroxyacetone (DHA) is an attractive molecule produced in a wide range of industries . DHA is found among all the kingdoms as an intermediate of various metabolic pathways and can be used as a carbon source by many organisms. The bacterium Escherichia coli is able to grow on DHA as the sole carbon source albeit at a low growth rate (0.1 h-1). If the topology of DHA metabolic network has been characterized, the function and regulation of the metabolic pathways involved in DHA metabolism remain unsolved. Here, we aimed to better understand DHA metabolism in E. coli BW25113 by exploring its transcriptional pattern on DHA versus glucose. We also studied the pattern of three DHA pathway mutants (dhaKLM, ptsA and glpK).
Project description:Genes clustered into polycistronic operons was thought a characteristic of bacteria and many other species. More than half protein-coding genes are organized in polycistronic operons composed of two or more than ten genes in bacterial genomes. Although the structure of operons have been studied precisely, how the member genes within operon maintain their stoichiometry expression is remain unknown. Using a highly accurate label-free absolute quantification method DIA (data-independent acquisition), we present a global analysis of Escherichia coli proteome, quantified 1607 proteins, including 59.1% of the known polycistronic operons. We found shorter operons tend to be more tightly controlled than longer operons, and those operons for metabolic pathways are less controlled for stoichiometry balance than those operons for protein complexes. Our results thus reveal the two-level regulation mode involving transcription and translation of operons would balance the stoichiometry expression of genes in polycistronic operons in different time-scale.