An equation for biomimicking macromolecular crowding using Escherichia coli MG1655 strain

2019 ◽  
Vol 254 ◽  
pp. 106244 ◽  
Author(s):  
Khushal Khambhati ◽  
Nisarg Gohil ◽  
Gargi Bhattacharjee ◽  
Happy Panchasara ◽  
Vijai Singh
Keyword(s):  
Escherichia Coli ◽  
Macromolecular Crowding ◽  
Mg1655 Strain

scholarly journals Multiple optimal phenotypes overcome redox and glycolytic intermediate metabolite imbalances inEscherichia coli pgiknockout evolutions

2018 ◽  
Author(s):  
Douglas McCloskey ◽  
Sibei Xu ◽  
Troy E. Sandberg ◽  
Elizabeth Brunk ◽  
Ying Hefner ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gene Product ◽  
Major Gene ◽  
Regulatory Function ◽  
Second Step ◽  
Valuable Insight ◽  
Adaptive Laboratory Evolution ◽  
Laboratory Evolution ◽  
K 12 ◽  
Mg1655 Strain

AbstractA mechanistic understanding of how new phenotypes develop to overcome the loss of a gene product provides valuable insight on both the metabolic and regulatory function of the lost gene. Thepgigene, whose product catalyzes the second step in glycolysis, was deleted in a growth optimizedEscherichia coliK-12 MG1655 strain. The knock-out (KO) strain exhibited an 80% drop in growth rate, that was largely recovered in eight replicate, but phenotypically distinct, cultures after undergoing adaptive laboratory evolution (ALE). Multi omic data sets showed that the loss ofpgisubstantially shifted pathway usage leading to a redox and sugar phosphate stress response. These stress responses were overcome by unique combinations of innovative mutations selected for by ALE. Thus, we show the coordinated mechanisms from genome to metabolome that lead to multiple optimal phenotypes after loss of a major gene product.ImportanceA mechanistic understanding of how new phenotypes develop to overcome the loss of a gene product provides valuable insight on both the metabolic and regulatory function of the lost gene. Thepgigene, whose product catalyzes the second step in glycolysis, was deleted in a growth optimizedEscherichia coliK-12 MG1655 strain. Eight replicate adaptive laboratory evolution (ALE) resulted in eight phenotypically distinct endpoints that were able to overcome the gene loss. Utilizing multi-omics analysis, we show the coordinated mechanisms from genome to metabolome that lead to multiple optimal phenotypes after loss of a major gene product.

scholarly journals Decreased Effective Macromolecular Crowding in Escherichia coli Adapted to Hyperosmotic Stress

2019 ◽  
Vol 201 (10) ◽  
Author(s):  
Boqun Liu ◽  
Zarief Hasrat ◽  
Bert Poolman ◽  
Arnold J. Boersma
Keyword(s):  
Escherichia Coli ◽  
Osmotic Stress ◽  
Cell Volume ◽  
Volume Fraction ◽  
Macromolecular Crowding ◽  
Metabolic Energy ◽  
Content Type ◽  
Energy Limitation ◽  
General Response ◽  
In Cells

ABSTRACT Escherichia coli adapts to changing environmental osmolality to survive and maintain growth. It has been shown that the diffusion of green fluorescent protein (GFP) in cells adapted to osmotic upshifts is higher than expected from the increase in biopolymer volume fraction. To better understand the physicochemical state of the cytoplasm in adapted cells, we now follow the macromolecular crowding during adaptation with fluorescence resonance energy transfer (FRET)-based sensors. We apply an osmotic upshift and find that after an initial increase, the apparent crowding decreases over the course of hours to arrive at a value lower than that before the osmotic upshift. Crowding relates to cell volume until cell division ensues, after which a transition in the biochemical organization occurs. Analysis of single cells by microfluidics shows that changes in cell volume, elongation, and division are most likely not the cause for the transition in organization. We further show that the decrease in apparent crowding upon adaptation is similar to the apparent crowding in energy-depleted cells. Based on our findings in combination with literature data, we suggest that adapted cells have indeed an altered biochemical organization of the cytoplasm, possibly due to different effective particle size distributions and concomitant nanoscale heterogeneity. This could potentially be a general response to accommodate higher biopolymer fractions yet retaining crowding homeostasis, and it could apply to other species or conditions as well. IMPORTANCE Bacteria adapt to ever-changing environmental conditions such as osmotic stress and energy limitation. It is not well understood how biomolecules reorganize themselves inside Escherichia coli under these conditions. An altered biochemical organization would affect macromolecular crowding, which could influence reaction rates and diffusion of macromolecules. In cells adapted to osmotic upshift, protein diffusion is indeed faster than expected on the basis of the biopolymer volume fraction. We now probe the effects of macromolecular crowding in cells adapted to osmotic stress or depleted in metabolic energy with a genetically encoded fluorescence-based probe. We find that the effective macromolecular crowding in adapted and energy-depleted cells is lower than in unstressed cells, indicating major alterations in the biochemical organization of the cytoplasm.

Macromolecular Crowding in the Escherichia coli Periplasm Maintains α-Synuclein Disorder

2006 ◽  
Vol 355 (5) ◽  
pp. 893-897 ◽  
Author(s):  
Brian C. McNulty ◽  
Gregory B. Young ◽  
Gary J. Pielak
Keyword(s):  
Escherichia Coli ◽  
Macromolecular Crowding

scholarly journals Localization of Protein Aggregation in Escherichia coli Is Governed by Diffusion and Nucleoid Macromolecular Crowding Effect

2013 ◽  
Vol 9 (4) ◽  
pp. e1003038 ◽  
Author(s):  
Anne-Sophie Coquel ◽  
Jean-Pascal Jacob ◽  
Mael Primet ◽  
Alice Demarez ◽  
Mariella Dimiccoli ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein Aggregation ◽  
Macromolecular Crowding ◽  
Crowding Effect

The Escherichia coli CitT transporter can be used as a succinate exporter for succinate production

2020 ◽  
Author(s):  
Sousuke Takahashi ◽  
Mayu Miyachi ◽  
Hisanori Tamaki ◽  
Hideyuki Suzuki
Keyword(s):  
Escherichia Coli ◽  
Culture Medium ◽  
Isocitrate Lyase ◽  
Aerobic Condition ◽  
Coli Strain ◽  
Succinate Production ◽  
E Coli ◽  
Citrate Transporter ◽  
Fed Batch Culture ◽  
Mg1655 Strain

ABSTRACT Escherichia coli strain, whose gene is one of the subunits of succinate dehydrogenase (sdhA), and gene of the transcriptional repressor of isocitrate lyase (iclR) were disrupted, accumulated 6.6 times as much intracellular succinate as the wild-type MG1655 strain in aerobic growth, but succinate was not found in the culture medium. E. coli citT gene that encodes a citrate transporter was cloned under the control of the lacI promoter in pBR322-based plasmid and the above strain was transformed. This transformant, grown under aerobic condition in M9-tryptone medium with citrate, accumulated succinate in the medium while no succinate was found in the medium without citrate. CitT was active as a succinate transporter for 168 h by changing the culture medium or for 24 h in fed-batch culture. This study suggests that the CitT transporter functions as a succinate exporter in E. coli for succinate production in the presence of citrate.

Structural organization of escherichia coli ribosomes as determined by immuno electron microscopy

1978 ◽  
Vol 36 (2) ◽  
pp. 166-167 ◽  
Author(s):  
G. Stöffler ◽  
R.W. Bald ◽  
J. Dieckhoff ◽  
H. Eckhard ◽  
R. Lührmann ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Escherichia Coli ◽  
Ribosomal Proteins ◽  
Structural Organization ◽  
Three Dimensional ◽  
Ribosomal Subunit ◽  
Spatial Arrangement ◽  
Small Subunit ◽  
Antibody Binding ◽  
Immuno Electron Microscopy

A central step towards an understanding of the structure and function of the Escherichia coli ribosome, a large multicomponent assembly, is the elucidation of the spatial arrangement of its 54 proteins and its three rRNA molecules. The structural organization of ribosomal components has been investigated by a number of experimental approaches. Specific antibodies directed against each of the 54 ribosomal proteins of Escherichia coli have been performed to examine antibody-subunit complexes by electron microscopy. The position of the bound antibody, specific for a particular protein, can be determined; it indicates the location of the corresponding protein on the ribosomal surface.The three-dimensional distribution of each of the 21 small subunit proteins on the ribosomal surface has been determined by immuno electron microscopy: the 21 proteins have been found exposed with altogether 43 antibody binding sites. Each one of 12 proteins showed antibody binding at remote positions on the subunit surface, indicating highly extended conformations of the proteins concerned within the 30S ribosomal subunit; the remaining proteins are, however, not necessarily globular in shape (Fig. 1).

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