Special Issue "Metabolic Engineering and Synthetic Biology Volume 2"
Deadline for manuscript submissions: 31 August 2020.
Interests: synthetic biology; metabolomics; metabolic engineering; metabolic flux analysis; bioeconomy
Interests: Ustilago; metabolomics; metabolic engineering; metabolic flux analysis; mass spectrometry
In times of ever-increasing demand for chemicals and the subsequent increase of CO2 in the atmosphere, we have to intensify our efforts to establish a circular (bio)economy. To reduce fossil resource use, alternative carbon sources including biomass and CO2 itself need to be used. The (bio)catalysts of choice that are able to convert these carbon sources into valuable chemicals often have to be tailored to meet the industrial requirements in titer, rate, and yield, and, hence, ultimately in cost. While exciting examples exist, from vitamins to plastic monomers and bioplastics, the metabolic engineering of such biocatalysts is still time and cost consuming. With the improvement of genetic tools and ideas for genetic standardization, creating and/or building new whole-cell biocatalysts becomes an ever more rapid task. However, the two other aspects of the design/build/test cycle are to some extent still very cumbersome. While computational tools support whole-cell biocatalyst design, parallelization and miniaturization speed up the characterization of mutants. Still, the goal has to be a knowledge-based design and a high information content phenotyping.
In this Special Issue, we ask for contributions of metabolic engineering and synthetic biology that are driven by flux and/or metabolome approaches. We would like to emphasize the importance of sample preparation and data evaluation. Fluxes of all intracellular biochemical reaction steps are the ultimate outcome of genetic and environmental alterations. We are convinced that quantitative approaches in metabolite analysis will help to reduce the time required to establish an efficient whole-cell biocatalyst. While the concentrations of intracellular metabolites can highlight enzymatic bottlenecks, the intracellular fluxes might help decipher redox cofactor imbalances, futile cycles, and the use of alternative pathways. Thermodynamically feasible reaction conditions can not only explain the phenotype observed but may also lead to genetic targets for further strain improvement and to new biochemical network designs.
Prof. Dr. Lars M. Blank
Dr. An N. T. Phan
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 papers will be 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. Metabolites 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 1600 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.
- metabolic engineering
- synthetic biology
- metabolic flux analysis
- cell factory
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Title: Analysis of Dynamic Labeling Patterns to Debottleneck L-Histidine Production in C. glutamicum
Authors: Ralf Takors
Affiliation: Institute of Biochemical Engineering, University of Stuttgart, Germany
Title: Assessing the in vivo rate of formaldehyde condensation with tetrahydrofolate
Authors: Arren Bar-Even
Affiliation: Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm-Potsdam, Germany
Title: Comparative fluxome and metabolome analysis of trehalose-mediated metabolic response in glucose‐limited cultivation of Penicillium chrysogenum
Authors: Guan Wang
Affiliation: East China University Of Science And Technology Shanghai, China
Abstract: Trehalose cycling has been confirmed as a double-edged sword in the high-yielding Penicillium chrysogenum strain; this cycling helps to cope with sudden glucose availability, facilitating the maintenance of metabolic balanced state, but it consumes extra amount of ATP responsible for repeated breakdown and formation of trehalose molecule in response to extracellular glucose perturbations. This loss of ATP would be in competition with the high ATP-demanding penicillin biosynthesis. Hence, it is of great importance to study the role of trehalose metabolism. Through interfering with the genes (tps1 and tps2) in the trehalose metabolism, our latest findings have shown that trehalose metabolism plays an important role in metabolic regulation and is central to maintaining higher penicillin productivity under glucose-limited chemostat cultures. However, due to insufficient mass transfer and mixing issues, cells in the industrial-scale bioreactor are forced to experience glucose feast/famine cycles, mostly resulting in the reduced commercial metrics (titer, yield and productivity). In this upcoming paper, the metabolite levels and fluxes in response to continuous feeding (control) and intermittent feeding (mimicking glucose gradients present in an industrial-scale fermentor) in glucose‐limited chemostat cultures at the dilution rate (D) of 0.05 h−1 are determined to evaluate the quantitative impact of trehalose cycling on the physiology of a high‐yielding P. chrysogenum strain. Based on this, we will as a whole evaluate the role of trehalose cycling in both steady state and dynamic conditions.
Title: Pathway enzymes assembly for metabolic flux control and optimization
Authors: Long Liu
Affiliation: Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, China
Abstract: Enzyme assembling by ligand binding or physically sequestrating enzymes, substrates or metabolites into the isolated compartments can bring the key molecules closer to enhance metabolic pathway flux. The emergence of enzymatic assembly provides both opportunities and challenges for metabolic engineering. In recent years, enzyme assembly via the synthetic scaffold strategy involving in nucleic acid, proteins or micro-compartments and scaffold-free self-assembly strategy has been explored and applied to the synthesis of various important bio-based products, and has also achieved varying degrees of success. Despite some achievements, the pathway enzyme assembly, especially in vivo, still has many problems that have attracted wide attention of researchers. Here, we review recent research on the scaffold-free self-assembly and synthetic scaffold strategy for enzyme assembly and discuss their notable advances. In addition, the potential applications and the challenges in the applications are also highlighted.
Title: Metabolic engineering design strategies for increasing acetyl-CoA flux
Authors: Ethan I Lan
Affiliation: Department of Biological Science and Technology, NCTU
Title: Heterologous production of 6-deoxyerythronolide B in Escherichia coli through the Wood Werkman cycle
Authors: Ricardo Axayacatl Gonzalez-Garcia, Lars K. Nielsen, Esteban Marcellin*
Affiliation: 1 Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia. 2 Queensland Node of Metabolomics Australia, The University of Queensland, Brisbane, QLD, Australia *Corresponding author: Dr Esteban Marcellin, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia. Phone: +61 7 334 64298, Fax: +61 7 3346 3973, Email: [email protected]