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Bioengineering
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Bio-Applications of Engineered Escherichia coli
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Bio-Applications of Engineered Escherichia coli

A special issue of Bioengineering (ISSN 2306-5354). This special issue belongs to the section "Biochemical Engineering".

Deadline for manuscript submissions: 30 April 2024 | Viewed by 6687

Special Issue Editors

Dr. Joana Rodrigues

E-Mail Website
Guest Editor
Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
Interests: synthetic biology; molecular biology; heterologous production; biosynthetic pathways; biosensors
Dr. Debora Ferreira

E-Mail Website
Guest Editor
1. CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
2. LABBELS-Associate Laboratory, 4710-057 Braga, Portugal
Interests: biosurfactants; synthetic biology; industrial biotechnology; bioprocess development; biomarkers
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The model organism Escherichia coli has several interesting properties and molecular tools available that make it preferable for synthetic biology applications. Some of the desired properties include small genome size, high product yield, fast growth in cheap media, cost-effectiveness and being easy to scale up. Therefore, engineered E. coli has been explored in recent decades to produce a vast number of value-added compounds, such as industrial chemicals and even drugs and food ingredients. Indeed, most of the heterologous proteins for therapeutic use are industrially produced using this chassis. In addition, engineered E. coli is frequently used as chassis in the development of whole-cell biosensors in the detection of several analytes, including proteins. These biosensors have been exploited in different areas, from the detection of pollutants to the development of diagnostic tools. Moreover, engineered E. coli is also being explored as delivery method of therapeutic agents.

This Special Issue on “Bio-Applications of engineered Escherichia coli” will focus on original research papers, comprehensive reviews and communications on the use of engineered E. coli to solve several of mankind’s problems. We welcome engineered E. coli applications related to the production of value-added compounds that promote sustainable and economically viable industrial processes, the development of new diagnosis tools and treatments, and ways to fight global warming, among other topics.

Areas of interest for this Special Issue include, but are not limited to, the following:

  • E. coli as chassis for the expression of heterologous pathway for value-added compound production;
  • E. coli as chassis for the production of therapeutic proteins and/or molecules;
  • Development of improved E.coli strains to overcome limitations (e.g., post-translational modifications absence);
  • Development of tools to improve E.coli engineering;
  • E. coli as a whole-cell biosensor in diagnostic tools, pollution detection, etc.;
  • Engineered E. coli as therapeutic agent.

Dr. Joana Rodrigues
Dr. Débora Ferreira
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Bioengineering is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Escherichia coli
  • heterologous production
  • biosynthetic pathways
  • value-added compounds
  • microbial chassis
  • microbial host
  • biosensors
  • whole-cell biosensors
  • diagnosis tools
  • therapeutic tools

Published Papers (4 papers)

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Research

21 pages, 4566 KiB  
Article
A Novel Bio-Purification Process Employing an Engineered E. coli Strain for Downstream Processing of Lactic Acid Solutions from the Fermentation of Agro-Industrial by-Products
by Alexandra Nastouli, Alexandra Moschona, Panagiotis A. Bizirtsakis, Joseph Sweeney, Irini Angelidaki, Michael Harasek, Anastasios J. Karabelas and Sotiris I. Patsios
Bioengineering 2024, 11(5), 412; https://doi.org/10.3390/bioengineering11050412 - 23 Apr 2024
Viewed by 232
Abstract
This study aims to integrate a novel bio-purification process employing an engineered E. coli strain in the downstream processing of lactic acid (LA) fermentation broths from low-cost renewable biological feedstocks. Fermentation broth of candy waste and digestate mixture was used as a real [...] Read more.
This study aims to integrate a novel bio-purification process employing an engineered E. coli strain in the downstream processing of lactic acid (LA) fermentation broths from low-cost renewable biological feedstocks. Fermentation broth of candy waste and digestate mixture was used as a real biological feedstock. An engineered E. coli strain that selectively catabolize impurities without catabolizing LA was initially adapted on the biological feedstock, followed by shake flask experiments to prove the bio-purification concept. Scale-up and validation in a bench-scale bioreactor followed, before developing a semi-continuous membrane bioreactor (MBR) bio-purification process. The MBR bio-purification was assessed with biological feedstocks which simulated ultrafiltration or nanofiltration permeates. Incomplete removal of impurities and increased fouling was observed in the case of the ultrafiltration permeate. Contrarily, the nanofiltration permeate was successfully treated with MBR bio-purification, since low membrane fouling, 100% maltose and acetic acid removal, and no LA catabolism was achieved. MBR bio-purification as a post-treatment step in the downstream processing of LA was demonstrated as a promising technology for increasing the purity of LA solutions. Full article
(This article belongs to the Special Issue Bio-Applications of Engineered Escherichia coli)
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14 pages, 1429 KiB  
Article
Engineering Escherichia coli for Poly-β-hydroxybutyrate Production from Methanol
by Jiaying Wang, Zhiqiang Chen, Xiaogui Deng, Qianqian Yuan and Hongwu Ma
Bioengineering 2023, 10(4), 415; https://doi.org/10.3390/bioengineering10040415 - 26 Mar 2023
Cited by 5 | Viewed by 1944
Abstract
The naturally occurring one-carbon assimilation pathways for the production of acetyl-CoA and its derivatives often have low product yields because of carbon loss as CO2. We constructed a methanol assimilation pathway to produce poly-3-hydroxybutyrate (P3HB) using the MCC pathway, which included [...] Read more.
The naturally occurring one-carbon assimilation pathways for the production of acetyl-CoA and its derivatives often have low product yields because of carbon loss as CO2. We constructed a methanol assimilation pathway to produce poly-3-hydroxybutyrate (P3HB) using the MCC pathway, which included the ribulose monophosphate (RuMP) pathway for methanol assimilation and non-oxidative glycolysis (NOG) for acetyl-CoA (precursor for PHB synthesis) production. The theoretical product carbon yield of the new pathway is 100%, hence no carbon loss. We constructed this pathway in E. coli JM109 by introducing methanol dehydrogenase (Mdh), a fused Hps–phi (hexulose-6-phosphate synthase and 3-phospho-6-hexuloisomerase), phosphoketolase, and the genes for PHB synthesis. We also knocked out the frmA gene (encoding formaldehyde dehydrogenase) to prevent the dehydrogenation of formaldehyde to formate. Mdh is the primary rate-limiting enzyme in methanol uptake; thus, we compared the activities of three Mdhs in vitro and in vivo and then selected the one from Bacillus methanolicus MGA3 for further study. Experimental results indicate that, in agreement with the computational analysis results, the introduction of the NOG pathway is essential for improving PHB production (65% increase in PHB concentration, up to 6.19% of dry cell weight). We demonstrated that PHB can be produced from methanol via metabolic engineering, which provides the foundation for the future large-scale use of one-carbon compounds for biopolymer production. Full article
(This article belongs to the Special Issue Bio-Applications of Engineered Escherichia coli)
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20 pages, 3097 KiB  
Article
Aptasensor for the Detection of Moraxella catarrhalis Adhesin UspA2
by Maria G. Sande, Débora Ferreira, Joana L. Rodrigues, Luís D. R. Melo, Athanasios Saragliadis, Dirk Linke, Felismina T. C. Moreira, Maria Goreti F. Sales and Ligia R. Rodrigues
Bioengineering 2023, 10(2), 178; https://doi.org/10.3390/bioengineering10020178 - 31 Jan 2023
Cited by 3 | Viewed by 1862
Abstract
Innovative point-of-care (PoC) diagnostic platforms are desirable to surpass the deficiencies of conventional laboratory diagnostic methods for bacterial infections and to tackle the growing antimicrobial resistance crisis. In this study, a workflow was implemented, comprising the identification of new aptamers with high affinity [...] Read more.
Innovative point-of-care (PoC) diagnostic platforms are desirable to surpass the deficiencies of conventional laboratory diagnostic methods for bacterial infections and to tackle the growing antimicrobial resistance crisis. In this study, a workflow was implemented, comprising the identification of new aptamers with high affinity for the ubiquitous surface protein A2 (UspA2) of the bacterial pathogen Moraxella catarrhalis and the development of an electrochemical biosensor functionalized with the best-performing aptamer as a bioreceptor to detect UspA2. After cell-systematic evolution of ligands by exponential enrichment (cell-SELEX) was performed, next-generation sequencing was used to sequence the final aptamer pool. The most frequent aptamer sequences were further evaluated using bioinformatic tools. The two most promising aptamer candidates, Apt1 and Apt1_RC (Apt1 reverse complement), had Kd values of 214.4 and 3.4 nM, respectively. Finally, a simple and label-free electrochemical biosensor was functionalized with Apt1_RC. The aptasensor surface modifications were confirmed by impedance spectroscopy and cyclic voltammetry. The ability to detect UspA2 was evaluated by square wave voltammetry, exhibiting a linear detection range of 4.0 × 104–7.0 × 107 CFU mL−1, a square correlation coefficient superior to 0.99 and a limit of detection of 4.0 × 104 CFU mL−1 at pH 5.0. The workflow described has the potential to be part of a sensitive PoC diagnostic platform to detect and quantify M. catarrhalis from biological samples. Full article
(This article belongs to the Special Issue Bio-Applications of Engineered Escherichia coli)
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11 pages, 2200 KiB  
Article
Modification of Fatty Acid Composition of Escherichia coli by Co-Expression of Fatty Acid Desaturase and Thioesterase from Arabidopsis thaliana
by Yihan Pu, Yujin Cao and Mo Xian
Bioengineering 2022, 9(12), 771; https://doi.org/10.3390/bioengineering9120771 - 06 Dec 2022
Cited by 2 | Viewed by 1550
Abstract
Fatty acid composition has an important influence on the fluidity of biological membranes, which is a key factor for the survival of Escherichia coli. With the aim to modify fatty acid composition in this experimentally friendly microorganism, the AtFab2 gene, encoding the [...] Read more.
Fatty acid composition has an important influence on the fluidity of biological membranes, which is a key factor for the survival of Escherichia coli. With the aim to modify fatty acid composition in this experimentally friendly microorganism, the AtFab2 gene, encoding the Arabidopsis thaliana fatty acid desaturase, was expressed separately and jointly with AtFatA, a fatty acid thioesterase of the same plant origin. The expression of ATFab2 desaturase resulted in an enhancement of cis-vaccenic acid (18:1Δ11) contents, while amounts of palmitioleic acid (16:1Δ9) accumulated by E. coli were increased by 130% for the expression of the AtFatA thioesterase. In the final engineered strain co-expressing AtFab2 and AtFatA, the percentage of palmitic acid (16:0), the most abundant saturated fatty acid found in E. coli, was reduced to 29.9% and the ratio of unsaturated fatty acid to saturated fatty acid reached 2:1. Free fatty acids accounted for about 40% of total fatty acid profiles in the recombinant strain expressing both two genes, and the unsaturated fatty acid contents reached nearly 75% in the free fatty acid profiles. The increase of unsaturated fatty acid level might provide some implication for the construction of cold tolerant strains. Full article
(This article belongs to the Special Issue Bio-Applications of Engineered Escherichia coli)
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