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Metabolites
Special Issues
Cellular and Metabolic Engineering
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Cellular and Metabolic Engineering

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Cell Metabolism".

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 2946

Special Issue Editors

Dr. Shouyong Jiang

E-Mail Website
Guest Editor
School of Computer Science, University of Lincoln, Lincoln LN6 7TS, UK
Interests: optimisation methods; systems biology, industrial biotechnology; smart energy; intelligent greenhouses; maching learning; data science; computational intelligence; evolutionary computation
Special Issues, Collections and Topics in MDPI journals
Dr. Ashish Misra

E-Mail Website
Guest Editor
Department of Biochemical Engineering and Biotechnology, IIT Delhi, New Delhi, India
Interests: metabolic analyses and engineering

Special Issue Information

Dear Collegues,

Cellular and metabolic engineering refers to the purposeful modification of cell properties and/or metabolic phenotypes to achieve various engineering goals, such as the improved production of native chemicals, the formation of non-native chemicals, the addition of new catabolic activities for the degradation of toxic chemicals, and the alteration of cell properties for new cellular functions. In recent years, this field has quickly received growing amounts of attention from both academia and industry due to cells’ great potential to boost biomanufacturing as a sustainable alternative to petrochemical-based production processes. New methodologies and techniques have been developed to provide a better understanding of cell physiology, metabolic functions, and the cost-effective modification of cells. The aim of this Special Issue is to collect state-of-the-art research on the topic of cellular and metabolic engineering. It welcomes any relevant topics, methods, and applications of the research and manipulation of cells for various purposes.

Dr. Shouyong Jiang
Dr. Ashish Misra
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. 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 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

  • synthetic biology methodologies
  • systems biology methodologies
  • bioinformatics methodologies and tools for metabolic engineering
  • development of genetic tools
  • data curation, database creation, and analysis
  • artificial intelligence/machine learning for metabolic engineering
  • carbon recycling in microbial and plant cells
  • metabolic flux modeling and analysis
  • biosynthetic pathway design
  • microbial community interactions
  • human metabolism and metabolic disease therapies

Published Papers (2 papers)

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Research

17 pages, 2530 KiB  
Article
Metabolic Modeling of Hermetia illucens Larvae Resource Allocation for High-Value Fatty Acid Production
by Kristina Grausa, Shahida A. Siddiqui, Norbert Lameyer, Karin Wiesotzki, Sergiy Smetana and Agris Pentjuss
Metabolites 2023, 13(6), 724; https://doi.org/10.3390/metabo13060724 - 3 Jun 2023
Cited by 1 | Viewed by 1771
Abstract
All plant and animal kingdom organisms use highly connected biochemical networks to facilitate sustaining, proliferation, and growth functions. While the biochemical network details are well known, the understanding of the intense regulation principles is still limited. We chose to investigate the Hermetia illucens [...] Read more.
All plant and animal kingdom organisms use highly connected biochemical networks to facilitate sustaining, proliferation, and growth functions. While the biochemical network details are well known, the understanding of the intense regulation principles is still limited. We chose to investigate the Hermetia illucens fly at the larval stage because this stage is a crucial period for the successful accumulation and allocation of resources for the subsequent organism’s developmental stages. We combined iterative wet lab experiments and innovative metabolic modeling design approaches to simulate and explain the H. illucens larval stage resource allocation processes and biotechnology potential. We performed time-based growth and high-value chemical compound accumulation wet lab chemical analysis experiments on larvae and the Gainesville diet composition. We built and validated the first H. illucens medium-size, stoichiometric metabolic model to predict the effects of diet-based alterations on fatty acid allocation potential. Using optimization methods such as flux balance and flux variability analysis on the novel insect metabolic model, we predicted that doubled essential amino acid consumption increased the growth rate by 32%, but pure glucose consumption had no positive impact on growth. In the case of doubled pure valine consumption, the model predicted a 2% higher growth rate. In this study, we describe a new framework for researching the impact of dietary alterations on the metabolism of multi-cellular organisms at different developmental stages for improved, sustainable, and directed high-value chemicals. Full article
(This article belongs to the Special Issue Cellular and Metabolic Engineering)
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15 pages, 2163 KiB  
Article
Control Analysis of Cooperativity and Complementarity in Metabolic Regulations: The Case of NADPH Homeostasis
by Benjamin Pfeuty, Julien Hurbain and Quentin Thommen
Metabolites 2023, 13(4), 485; https://doi.org/10.3390/metabo13040485 - 28 Mar 2023
Viewed by 881
Abstract
Complex feedback regulation patterns shape the cellular metabolic response to external or internal perturbations. We propose here a framework consisting of a sampling-based metabolic control analysis of kinetic models to investigate the modes of regulatory interplay in metabolic functions. NADPH homeostasis, for instance [...] Read more.
Complex feedback regulation patterns shape the cellular metabolic response to external or internal perturbations. We propose here a framework consisting of a sampling-based metabolic control analysis of kinetic models to investigate the modes of regulatory interplay in metabolic functions. NADPH homeostasis, for instance in a context of oxidative stress, is an example of metabolic function that involves multiple feedback regulations which raises the issue of their concerted action. Our computational framework allows us to characterize both respective and combined effects of regulations, distinguishing between synergistic versus complementary modes of regulatory crosstalk. Synergistic regulation of G6PD enzymes and PGI enzymes is mediated by congruent effects between concentration sensitivities and reaction elasticities. Complementary regulation of pentose phosphate pathway and lower glycolysis relates to metabolic state-dependent range of regulation efficiency. These cooperative effects are shown to significantly improve metabolic flux response to support NADPH homeostasis, providing a rationale for the complex feedback regulation pattern at work. Full article
(This article belongs to the Special Issue Cellular and Metabolic Engineering)
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