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Bioengineering
Special Issues
Bioengineering and Synthetic Biology Approaches for High-Value Compounds
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Bioengineering and Synthetic Biology Approaches for High-Value Compounds

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

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 8789

Special Issue Editors

Dr. Wei Liu

E-Mail Website
Guest Editor
CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
Interests: biosynthesis; enzymatic catalysis; metabolic engineering
Dr. Xinjun Feng

E-Mail Website
Guest Editor
CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
Interests: synthetic biology; metabolic engineering; biopolymers; bio-based chemicals
Dr. Min Liu

E-Mail Website
Guest Editor
State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
Interests: synthetic biology; metabolic engineering; protein modification; bio-based chemicals

Special Issue Information

Dear Colleagues,

High-value compounds have numerous applications in pharmaceutical, nutraceutical, and cosmetics industries, among others. Organisms have amazing manufacturing capabilities, and the biocatalytic synthesis of high-value compounds is an excellent complement to traditional chemical synthesis. However, the low productivity and high cost still remain, and restrict the popular application of biocatalytic synthesis. Moreover, the biosynthetic pathways of many high-value compounds are unclear, and cannot be synthesized by biological approaches.

This Special Issue on “Bioengineering and Synthetic Biology Approaches for High-Value Compounds”, will therefore focus on original research papers and comprehensive reviews dealing with cutting-edge experimental research for the multiscale investigation of the biosynthesis of high-value compounds. Topics of interest for this Special Issue include, but are not limited to, the following:

  • Modification and creation of chassis cells.
  • Metabolic engineering to improve high-value compounds productivity.
  • Design and assembly of biosynthetic pathways for target high-value compounds.
  • Enzymes that can catalyze new reactions.
  • Solutions to reduce the overall cost of high-value compounds production.

Dr. Wei Liu
Dr. Xinjun Feng
Dr. Min Liu
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

  • chassis cells
  • high-value compounds
  • biosynthetic pathways
  • enzymes
  • metabolic engineering

Published Papers (5 papers)

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Research

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13 pages, 3195 KiB  
Article
Photocatalytic Reduction of Methylene Blue by Surface-Engineered Recombinant Escherichia coli as a Whole-Cell Biocatalyst
by Ashokkumar Kumaravel, Vidhya Selvamani and Soon Ho Hong
Bioengineering 2023, 10(12), 1389; https://doi.org/10.3390/bioengineering10121389 - 04 Dec 2023
Viewed by 1108
Abstract
A novel Escherichia coli strain, created by engineering its cell surface with a cobalt-binding peptide CP1, was investigated in this study. The recombinant strain, pBAD30-YiaT-CP1, was structurally modeled to determine its cobalt-binding affinity. Furthermore, the effectiveness and specificity of pBAD30-CP1 in adsorbing and [...] Read more.
A novel Escherichia coli strain, created by engineering its cell surface with a cobalt-binding peptide CP1, was investigated in this study. The recombinant strain, pBAD30-YiaT-CP1, was structurally modeled to determine its cobalt-binding affinity. Furthermore, the effectiveness and specificity of pBAD30-CP1 in adsorbing and extracting cobalt from artificial wastewater polluted with the metal were investigated. The modified cells were subjected to cobalt concentrations (0.25 mM to 1 mM) and pH levels (pH 3, 5, 7, and 9). When exposed to a pH of 7 and a cobalt concentration of 1 mM, the pBAD30-CP1 strain had the best cobalt recovery efficiency, measuring 1468 mol/g DCW (Dry Cell Weight). Furthermore, pBAD30-CP1 had a higher affinity for cobalt than nickel and manganese. Field Emission Scanning Electron Microscopy (FE-SEM), Transmission Electron Microscopy (TEM), and Energy-Dispersive X-ray Spectroscopy (EDS) were used to examine the physiochemical parameters of the recombinant cells after cobalt adsorption. These approaches revealed the presence of cobalt in a bound state on the cell surface in the form of nanoparticles. In addition, the cobalt-binding recombinant strains were used in the photocatalytic reduction of methylene blue, which resulted in a 59.52% drop in the observed percentage. This study shows that modified E. coli strains have the potential for efficient cobalt recovery and application in environmental remediation operations. Full article
(This article belongs to the Special Issue Bioengineering and Synthetic Biology Approaches for High-Value Compounds)
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15 pages, 2238 KiB  
Article
A Single Active-Site Mutagenesis Confers Enhanced Activity and/or Changed Product Distribution to a Pentalenene Synthase from Streptomyces sp. PSKA01
by Hongshuang Liu, Senbiao Fang, Lin Zhao, Xiao Men and Haibo Zhang
Bioengineering 2023, 10(3), 392; https://doi.org/10.3390/bioengineering10030392 - 22 Mar 2023
Cited by 1 | Viewed by 1748
Abstract
Pentalenene is a ternary cyclic sesquiterpene formed via the ionization and cyclization of farnesyl pyrophosphate (FPP), which is catalyzed by pentalenene synthase (PentS). To better understand the cyclization reactions, it is necessary to identify more key sites and elucidate their roles in terms [...] Read more.
Pentalenene is a ternary cyclic sesquiterpene formed via the ionization and cyclization of farnesyl pyrophosphate (FPP), which is catalyzed by pentalenene synthase (PentS). To better understand the cyclization reactions, it is necessary to identify more key sites and elucidate their roles in terms of catalytic activity and product specificity control. Previous studies primarily relied on the crystal structure of PentS to analyze and verify critical active sites in the active cavity, while this study started with the function of PentS and screened a novel key site through random mutagenesis. In this study, we constructed a pentalenene synthetic pathway in E. coli BL21(DE3) and generated PentS variants with random mutations to construct a mutant library. A mutant, PentS-13, with a varied product diversity, was obtained through shake-flask fermentation and product identification. After sequencing and the functional verification of the mutation sites, it was found that T182A, located in the G2 helix, was responsible for the phenotype of PentS-13. The site-saturation mutagenesis of T182 demonstrated that mutations at this site not only affected the solubility and activity of the enzyme but also affected the specificity of the product. The other products were generated through different routes and via different carbocation intermediates, indicating that the 182 active site is crucial for PentS to stabilize and guide the regioselectivity of carbocations. Molecular docking and molecular dynamics simulations suggested that these mutations may induce changes in the shape and volume of the active cavity and disturb hydrophobic/polar interactions that were sufficient to reposition reactive intermediates for alternative reaction pathways. This article provides rational explanations for these findings, which may generally allow for the protein engineering of other terpene synthases to improve their catalytic efficiency or modify their specificities. Full article
(This article belongs to the Special Issue Bioengineering and Synthetic Biology Approaches for High-Value Compounds)
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14 pages, 2252 KiB  
Article
Development of a Transcriptional Factor PuuR-Based Putrescine-Specific Biosensor in Corynebacterium glutamicum
by Nannan Zhao, Jian Wang, Aiqing Jia, Ying Lin and Suiping Zheng
Bioengineering 2023, 10(2), 157; https://doi.org/10.3390/bioengineering10020157 - 24 Jan 2023
Viewed by 1544
Abstract
Corynebacterium glutamicum is regarded as an industrially important microbial cell factory and is widely used to produce various value-added chemicals. Because of the importance of C. glutamicum applications, current research is increasingly focusing on developing C. glutamicum synthetic biology platforms. Because of [...] Read more.
Corynebacterium glutamicum is regarded as an industrially important microbial cell factory and is widely used to produce various value-added chemicals. Because of the importance of C. glutamicum applications, current research is increasingly focusing on developing C. glutamicum synthetic biology platforms. Because of its ability to condense with adipic acid to synthesize the industrial plastic nylon-46, putrescine is an important platform compound of industrial interest. Developing a high-throughput putrescine biosensor can aid in accelerating the design–build–test cycle of cell factories (production strains) to achieve high putrescine-generating strain production in C. glutamicum. This study developed a putrescine-specific biosensor (pSenPuuR) in C. glutamicum using Escherichia coli-derived transcriptional factor PuuR. The response characteristics of the biosensor to putrescine were further improved by optimizing the genetic components of pSenPuuR, such as the response promoter, reporter protein, and promoter for controlling PuuR expression. According to the findings of the study, pSenPuuR has the potential to be used to assess putrescine production in C. glutamicum and is suitable for high-throughput genetic variant screening. Full article
(This article belongs to the Special Issue Bioengineering and Synthetic Biology Approaches for High-Value Compounds)
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Review

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15 pages, 2159 KiB  
Review
N-Amidation of Nitrogen-Containing Heterocyclic Compounds: Can We Apply Enzymatic Tools?
by Anran Yang, Xue Miao, Liu Yang, Chao Xu, Wei Liu, Mo Xian and Huibin Zou
Bioengineering 2023, 10(2), 222; https://doi.org/10.3390/bioengineering10020222 - 07 Feb 2023
Viewed by 1930
Abstract
Amide bond is often seen in value-added nitrogen-containing heterocyclic compounds, which can present promising chemical, biological, and pharmaceutical significance. However, current synthesis methods in the preparation of amide-containing N-heterocyclic compounds have low specificity (large amount of by-products) and efficiency. In this study, we [...] Read more.
Amide bond is often seen in value-added nitrogen-containing heterocyclic compounds, which can present promising chemical, biological, and pharmaceutical significance. However, current synthesis methods in the preparation of amide-containing N-heterocyclic compounds have low specificity (large amount of by-products) and efficiency. In this study, we focused on reviewing the feasible enzymes (nitrogen acetyltransferase, carboxylic acid reductase, lipase, and cutinase) for the amidation of N-heterocyclic compounds; summarizing their advantages and weakness in the specific applications; and further predicting candidate enzymes through in silico structure-functional analysis. For future prospects, current enzymes demand further engineering and improving for practical industrial applications and more enzymatic tools need to be explored and developed for a broader range of N-heterocyclic substrates. Full article
(This article belongs to the Special Issue Bioengineering and Synthetic Biology Approaches for High-Value Compounds)
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Other

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11 pages, 1227 KiB  
Brief Report
De Novo Synthesis of Poly(3-hydroxybutyrate-co-3-hydroxypropionate) from Oil by Engineered Cupriavidus necator
by Mengdi Li, Wei Li, Tongtong Zhang, Keyi Guo, Dexin Feng, Fengbing Liang, Chao Xu, Mo Xian and Huibin Zou
Bioengineering 2023, 10(4), 446; https://doi.org/10.3390/bioengineering10040446 - 06 Apr 2023
Cited by 2 | Viewed by 1389
Abstract
Poly(3-hydroxybutyrate-co-3-hydroxypropionate) [P(3HB-co-3HP)] is a biodegradable and biocompatible polyester with improved and expanded material properties compared with poly(3-hydroxybutyrate) (PHB). This study engineered a robust malonyl-CoA pathway in Cupriavidus necator for the efficient supply of a 3HP monomer, and could achieve [...] Read more.
Poly(3-hydroxybutyrate-co-3-hydroxypropionate) [P(3HB-co-3HP)] is a biodegradable and biocompatible polyester with improved and expanded material properties compared with poly(3-hydroxybutyrate) (PHB). This study engineered a robust malonyl-CoA pathway in Cupriavidus necator for the efficient supply of a 3HP monomer, and could achieve the production of [P(3HB-co-3HP)] from variable oil substrates. Flask level experiments followed by product purification and characterization found the optimal fermentation condition (soybean oil as carbon source, 0.5 g/L arabinose as induction level) in general consideration of the PHA content, PHA titer and 3HP molar fraction. A 5 L fed-batch fermentation (72 h) further increased the dry cell weight (DCW) to 6.08 g/L, the titer of [P(3HB-co-3HP)] to 3.11 g/L and the 3HP molar fraction to 32.25%. Further improving the 3HP molar fraction by increasing arabinose induction failed as the engineered malonyl-CoA pathway was not properly expressed under the high-level induction condition. With several promising advantages (broader range of economic oil substrates, no need for expensive supplementations such as alanine and VB12), this study indicated a candidate route for the industrial level production of [P(3HB-co-3HP)]. For future prospects, further studies are needed to further improve the strain and the fermentation process and expand the range of relative products. Full article
(This article belongs to the Special Issue Bioengineering and Synthetic Biology Approaches for High-Value Compounds)
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