scholarly journals Functional Genomic Study of Exogenous n-Butanol Stress in Escherichia coli

2010 ◽  
Vol 76 (6) ◽  
pp. 1935-1945 ◽  
Author(s):  
Becky J. Rutherford ◽  
Robert H. Dahl ◽  
Richard E. Price ◽  
Heather L. Szmidt ◽  
Peter I. Benke ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Escherichia Coli ◽  
Stress Responses ◽  
Fluorescent Dyes ◽  
Cell Envelope ◽  
High Titer ◽  
Stress Protein ◽  
Response Analysis ◽  
Genomic Study ◽  
Butanol Stress

ABSTRACT n-Butanol has been proposed as an alternative biofuel to ethanol, and several industrially used microbes, including Escherichia coli, have been engineered to produce it. Unfortunately, n-butanol is more toxic than ethanol to these organisms. To understand the basis for its toxicity, cell-wide studies were conducted at the transcript, protein, and metabolite levels to obtain a global view of the n-butanol stress response. Analysis of the data indicates that n-butanol stress has components common to other stress responses, including perturbation of respiratory functions (nuo and cyo operons), oxidative stress (sodA, sodC, and yqhD), heat shock and cell envelope stress (rpoE, clpB, htpG, cpxR, and cpxP), and metabolite transport and biosynthesis (malE and opp operon). Assays using fluorescent dyes indicated a large increase in reactive oxygen species during n-butanol stress, confirming observations from the microarray and proteomics measurements. Mutant strains with mutations in several genes whose products changed most dramatically during n-butanol stress were examined for increased sensitivity to n-butanol. Results from these analyses allowed identification of key genes that were recruited to alleviate oxidative stress, protein misfolding, and other causes of growth defects. Cellular engineering based on these cues may assist in developing a high-titer, n-butanol-producing host.

scholarly journals Genome-scale target identification in Escherichia coli for high-titer production of free fatty acids

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Lixia Fang ◽  
Jie Fan ◽  
Shulei Luo ◽  
Yaru Chen ◽  
Congya Wang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Fatty Acids ◽  
Free Fatty Acids ◽  
Stress Responses ◽  
Metabolic Networks ◽  
Target Identification ◽  
High Titer ◽  
Cell Factory ◽  
Microbial Cell Factory ◽  
Ffa Metabolism

AbstractTo construct a superior microbial cell factory for chemical synthesis, a major challenge is to fully exploit cellular potential by identifying and engineering beneficial gene targets in sophisticated metabolic networks. Here, we take advantage of CRISPR interference (CRISPRi) and omics analyses to systematically identify beneficial genes that can be engineered to promote free fatty acids (FFAs) production in Escherichia coli. CRISPRi-mediated genetic perturbation enables the identification of 30 beneficial genes from 108 targets related to FFA metabolism. Then, omics analyses of the FFAs-overproducing strains and a control strain enable the identification of another 26 beneficial genes that are seemingly irrelevant to FFA metabolism. Combinatorial perturbation of four beneficial genes involving cellular stress responses results in a recombinant strain ihfAL−-aidB+-ryfAM−-gadAH−, producing 30.0 g L−1 FFAs in fed-batch fermentation, the maximum titer in E. coli reported to date. Our findings are of help in rewiring cellular metabolism and interwoven intracellular processes to facilitate high-titer production of biochemicals.

scholarly journals Appropriate Regulation of the σE-Dependent Envelope Stress Response Is Necessary To Maintain Cell Envelope Integrity and Stationary-Phase Survival in Escherichia coli

2017 ◽  
Vol 199 (12) ◽  
Author(s):  
Hervé Nicoloff ◽  
Saumya Gopalkrishnan ◽  
Sarah E. Ades
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Outer Membrane ◽  
Stress Responses ◽  
Cell Envelope ◽  
Membrane Integrity ◽  
Point Mutations ◽  
Content Type ◽  
Envelope Stress ◽  
Outer Membrane Porins

ABSTRACT The alternative sigma factor σE is a key component of the Escherichia coli response to cell envelope stress and is required for viability even in the absence of stress. The activity of σE increases during entry into stationary phase, suggesting an important role for σE when nutrients are limiting. Elevated σE activity has been proposed to activate a pathway leading to the lysis of nonculturable cells that accumulate during early stationary phase. To better understand σE-directed cell lysis and the role of σE in stationary phase, we investigated the effects of elevated σE activity in cultures grown for 10 days. We demonstrate that high σE activity is lethal for all cells in stationary phase, not only those that are nonculturable. Spontaneous mutants with reduced σE activity, due primarily to point mutations in the region of σE that binds the −35 promoter motif, arise and take over cultures within 5 to 6 days after entry into stationary phase. High σE activity leads to large reductions in the levels of outer membrane porins and increased membrane permeability, indicating membrane defects. These defects can be counteracted and stationary-phase lethality delayed significantly by stabilizing membranes with Mg2+ and buffering the growth medium or by deleting the σE-dependent small RNAs (sRNAs) MicA, RybB, and MicL, which inhibit the expression of porins and Lpp. Expression of these sRNAs also reverses the loss of viability following depletion of σE activity. Our results demonstrate that appropriate regulation of σE activity, ensuring that it is neither too high nor too low, is critical for envelope integrity and cell viability. IMPORTANCE The Gram-negative cell envelope and cytoplasm differ significantly, and separate responses have evolved to combat stress in each compartment. An array of cell envelope stress responses exist, each of which is focused on different parts of the envelope. The σE response is conserved in many enterobacteria and is tuned to monitor pathways for the maturation and delivery of outer membrane porins, lipoproteins, and lipopolysaccharide to the outer membrane. The activity of σE is tightly regulated to match the production of σE regulon members to the needs of the cell. In E. coli, loss of σE results in lethality. Here we demonstrate that excessive σE activity is also lethal and results in decreased membrane integrity, the very phenotype the system is designed to prevent.

scholarly journals The BaeSR Two-Component Regulatory System Mediates Resistance to Condensed Tannins in Escherichia coli

2007 ◽  
Vol 74 (2) ◽  
pp. 535-539 ◽  
Author(s):  
Erwin G. Zoetendal ◽  
Alexandra H. Smith ◽  
Monica A. Sundset ◽  
Roderick I. Mackie
Keyword(s):  
Escherichia Coli ◽  
Cell Envelope ◽  
Expression Profiles ◽  
Stress Protein ◽  
Gene Expression Profiles ◽  
Regulatory System ◽  
Multidrug Transporter ◽  
Resistance Strategies ◽  
Envelope Stress ◽  
Two Component

ABSTRACT The gene expression profiles of Escherichia coli strains grown anaerobically with or without Acacia mearnsii (black wattle) extract were compared to identify tannin resistance strategies. The cell envelope stress protein gene spy and the multidrug transporter-encoding operon mdtABCD, both under the control of the BaeSR two-component regulatory system, were significantly up-regulated in the presence of tannins. BaeSR mutants were more tannin sensitive than their wild-type counterparts.

scholarly journals Genome-Wide Transcriptional Responses of Escherichia coli K-12 to Continuous Osmotic and Heat Stresses

2008 ◽  
Vol 190 (10) ◽  
pp. 3712-3720 ◽  
Author(s):  
Thusitha S. Gunasekera ◽  
Laszlo N. Csonka ◽  
Oleg Paliy
Keyword(s):  
Oxidative Stress ◽  
Escherichia Coli ◽  
High Temperature ◽  
Osmotic Stress ◽  
Stress Responses ◽  
Transcriptional Responses ◽  
High Osmolarity ◽  
Genome Wide ◽  
K 12 ◽  
And Oxidative Stress

ABSTRACT Osmotic stress is known to increase the thermotolerance and oxidative-stress resistance of bacteria by a mechanism that is not adequately understood. We probed the cross-regulation of continuous osmotic and heat stress responses by characterizing the effects of external osmolarity (0.3 M versus 0.0 M NaCl) and temperature (43°C versus 30°C) on the transcriptome of Escherichia coli K-12. Our most important discovery was that a number of genes in the SoxRS and OxyR oxidative-stress regulons were up-regulated by high osmolarity, high temperature, or a combination of both stresses. This result can explain the previously noted cross-protection of osmotic stress against oxidative and heat stresses. Most of the genes shown in previous studies to be induced during the early phase of adaptation to hyperosmotic shock were found to be also overexpressed under continuous osmotic stress. However, there was a poorer overlap between the heat shock genes that are induced transiently after high temperature shifts and the genes that we found to be chronically up-regulated at 43°C. Supplementation of the high-osmolarity medium with the osmoprotectant glycine betaine, which reduces the cytoplasmic K+ pool, did not lead to a universal reduction in the expression of osmotically induced genes. This finding does not support the hypothesis that K+ is the central osmoregulatory signal in Enterobacteriaceae.

scholarly journals Stress Reduction, Bacterial Style

2017 ◽  
Vol 199 (20) ◽  
Author(s):  
Susan Gottesman
Keyword(s):  
Escherichia Coli ◽  
Stress Reduction ◽  
Stress Responses ◽  
Cell Envelope ◽  
Content Type ◽  
E Coli ◽  
Envelope Stress ◽  
Multiple Cell ◽  
As Stress ◽  
Sigma E

ABSTRACT Bacteria have robust responses to a variety of stresses. In particular, bacteria like Escherichia coli have multiple cell envelope stress responses, and generally we evaluate what these responses are doing by the repair systems they induce. However, probably at least as important in interpreting what is being sensed as stress are the genes that these stress systems downregulate, directly or indirectly. This is discussed here for the Cpx and sigma E systems of E. coli.

scholarly journals Helical Disposition of Proteins and Lipopolysaccharide in the Outer Membrane of Escherichia coli

2005 ◽  
Vol 187 (6) ◽  
pp. 1913-1922 ◽  
Author(s):  
Anindya S. Ghosh ◽  
Kevin D. Young
Keyword(s):  
Escherichia Coli ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Fluorescent Dyes ◽  
Cell Envelope ◽  
Outer Membrane Proteins ◽  
E Coli ◽  
Physiological Processes ◽  
Side Walls

ABSTRACT In bacteria, several physiological processes once thought to be the products of uniformly dispersed reactions are now known to be highly asymmetric, with some exhibiting interesting geometric localizations. In particular, the cell envelope of Escherichia coli displays a form of subcellular differentiation in which peptidoglycan and outer membrane proteins at the cell poles remain stable for generations while material in the lateral walls is diluted by growth and turnover. To determine if material in the side walls was organized in any way, we labeled outer membrane proteins with succinimidyl ester-linked fluorescent dyes and then grew the stained cells in the absence of dye. Labeled proteins were not evenly dispersed in the envelope but instead appeared as helical ribbons that wrapped around the outside of the cell. By staining the O8 surface antigen of E. coli 2443 with a fluorescent derivative of concanavalin A, we observed a similar helical organization for the lipopolysaccharide (LPS) component of the outer membrane. Fluorescence recovery after photobleaching indicated that some of the outer membrane proteins remained freely diffusible in the side walls and could also diffuse into polar domains. On the other hand, the LPS O antigen was virtually immobile. Thus, the outer membrane of E. coli has a defined in vivo organization in which a subfraction of proteins and LPS are embedded in stable domains at the poles and along one or more helical ribbons that span the length of this gram-negative rod.

scholarly journals Differential Roles of the Universal Stress Proteins of Escherichia coli in Oxidative Stress Resistance, Adhesion, and Motility

2005 ◽  
Vol 187 (18) ◽  
pp. 6265-6272 ◽  
Author(s):  
Laurence Nachin ◽  
Ulf Nannmark ◽  
Thomas Nyström
Keyword(s):  
Oxidative Stress ◽  
Escherichia Coli ◽  
Stress Resistance ◽  
Stress Proteins ◽  
Stress Protein ◽  
Physiological Role ◽  
Cellular Growth ◽  
Yeast Cells ◽  
Phenotypic Characterization ◽  
Oxidative Stress Resistance

ABSTRACT The universal stress protein (UspA) superfamily encompasses a conserved group of proteins that are found in bacteria, archaea, and eukaryotes. Escherichia coli harbors six usp genes—uspA, -C, -D, -E, -F, and -G—the expression of which is triggered by a large variety of environmental insults. The uspA gene is important for survival during cellular growth arrest, but the exact physiological role of the Usp proteins is not known. In this work we have performed phenotypic characterization of mutants with deletions of the six different usp genes. We report on hitherto unknown functions of these genes linked to motility, adhesion, and oxidative stress resistance, and we show that usp functions are both overlapping and distinct. Both UspA and UspD are required in the defense against superoxide-generating agents, and UspD appears also important in controlling intracellular levels of iron. In contrast, UspC is not involved in stress resistance or iron metabolism but is essential, like UspE, for cellular motility. Electron microscopy demonstrates that uspC and uspE mutants are devoid of flagella. In addition, the function of the uspC and uspE genes is linked to cell adhesion, measured as FimH-mediated agglutination of yeast cells. While the UspC and UspE proteins promote motility at the expense of adhesion, the UspF and UspG proteins exhibit the exact opposite effects. We suggest that the Usp proteins have evolved different physiological functions that reprogram the cell towards defense and escape during cellular stress.

scholarly journals NfiS, a species-specific regulatory noncoding RNA of Pseudomonas stutzeri, enhances oxidative stress tolerance in Escherichia coli

AMB Express ◽  
2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Guihua Hu ◽  
Tao Hu ◽  
Yuhua Zhan ◽  
Wei Lu ◽  
Min Lin ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Escherichia Coli ◽  
Stress Responses ◽  
Noncoding Rna ◽  
Regulatory Networks ◽  
Target Genes ◽  
Pseudomonas Stutzeri ◽  
Bacterial Strains ◽  
E Coli ◽  
Species Specific

Abstract Noncoding RNAs (ncRNAs) can finely control the expression of target genes at the posttranscriptional level in prokaryotes. Regulatory small RNAs (sRNAs) designed to control target gene expression for applications in metabolic engineering and synthetic biology have been successfully developed and used. However, the effect on the heterologous expression of species- or strain-specific ncRNAs in other bacterial strains remains poorly understood. In this work, a Pseudomonas stutzeri species-specific regulatory ncRNA, NfiS, which has been shown to play an important role in the response to oxidative stress as well as osmotic stress in P. stutzeri A1501, was cloned and transferred to the Escherichia coli strain Trans10. Recombinant NfiS-expressing E. coli, namely, Trans10-nfiS, exhibited significant enhancement of tolerance to oxidative stress. To map the possible gene regulatory networks mediated by NfiS in E. coli under oxidative stress, a microarray assay was performed to delineate the transcriptomic differences between Trans10-nfiS and wild-type E. coli under H2O2 shock treatment conditions. In all, 1184 genes were found to be significantly altered, and these genes were divided into mainly five functional categories: stress response, regulation, metabolism related, transport or membrane protein and unknown function. Our results suggest that the P. stutzeri species-specific ncRNA NfiS acts as a regulator that integrates adaptation to H2O2 with other cellular stress responses and helps protect E. coli cells against oxidative damage.

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