Special Issue "Metabolic Engineering and Synthetic Biology"

A special issue of Metabolites (ISSN 2218-1989).

Deadline for manuscript submissions: closed (30 October 2015)

Special Issue Editor

Guest Editor
Dr. Dirk Steinhauser

Department Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
Website | E-Mail
Phone: +49331 567 8218
Interests: metabolic diversity and evolution; systems metabolomics, synthetic biology; computational biology and bioinformatics

Special Issue Information

Dear Colleagues,

In bioengineering, observation and identification, analyzing and understanding (disassembling) as well as re-/design and evaluation (assembling) are crucial key components. The recent maturation and application of post-genomic technologies in biology provide novel opportunities for metabolic engineering and synthetic biology. On the one hand, biological functions can be studied within and between systems levels to acquire a rather holistic understanding of how complex biological systems are operating. This enables the extraction of functional and regulatory design principles for the optimization of existing and the establishment of novel and synthetic metabolic routes as well as for the construction of orthogonal biological systems. On the other hand, ‘-omics’ technologies can be utilized as fast and comprehensive readout to evaluate a rational or evolutionary engineered system towards the expected output, undesired side effects and to detect remaining constrains as targets for further optimizations. Moreover, the large quantities of accumulated ‘-omics’ level data, in particular genome information, may facilitate the identification of evolutionary conserved as well as unique and novel design principles via comparative computational approach.

In this special issue we encourage the submissions of original research papers and review articles focusing on bioengineering and synthetic biology with special emphasis on metabolism and metabolic as well as metabolite-associated regulatory pathways. Topics that will be covered by this special issue include (not exclusively): reverse metabolomics and engineering; rational and evolutionary engineering; metabolic design principles and chemical/regulatory circuit logic; computational and mathematic models; molecule and pathway design; tools and resources in metabolic engineering and synthetic biology. Furthermore, manuscripts related to exploiting metabolic diversity for metabolic engineering, for lead compound and pathway discovery or dealing with other challenging issues in metabolic engineering and synthetic biology are also welcome.

Dr. Dirk Steinhauser
Guest Editor

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 1000 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
  • reverse metabolomics and engineering
  • rational and evolutionary engineering
  • chemical engineering
  • molecule and pathway design and redesign
  • metabolic design principles
  • computational and mathematical models
  • tools and resources
  • variation and selection
  • metabolic diversity

Published Papers (3 papers)

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Research

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Open AccessArticle
Fermentative Production of the Diamine Putrescine: System Metabolic Engineering of Corynebacterium Glutamicum
Metabolites 2015, 5(2), 211-231; https://doi.org/10.3390/metabo5020211
Received: 26 February 2015 / Revised: 8 April 2015 / Accepted: 13 April 2015 / Published: 24 April 2015
Cited by 26 | PDF Full-text (1210 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Corynebacterium glutamicum shows great potential for the production of the glutamate-derived diamine putrescine, a monomeric compound of polyamides. A genome-scale stoichiometric model of a C. glutamicum strain with reduced ornithine transcarbamoylase activity, derepressed arginine biosynthesis, and an anabolic plasmid-addiction system for heterologous expression [...] Read more.
Corynebacterium glutamicum shows great potential for the production of the glutamate-derived diamine putrescine, a monomeric compound of polyamides. A genome-scale stoichiometric model of a C. glutamicum strain with reduced ornithine transcarbamoylase activity, derepressed arginine biosynthesis, and an anabolic plasmid-addiction system for heterologous expression of E. coli ornithine decarboxylase gene speC was investigated by flux balance analysis with respect to its putrescine production potential. Based on these simulations, enhancing glycolysis and anaplerosis by plasmid-borne overexpression of the genes for glyceraldehyde 3-phosphate dehydrogenase and pyruvate carboxylase as well as reducing 2-oxoglutarate dehydrogenase activity were chosen as targets for metabolic engineering. Changing the translational start codon of the chromosomal gene for 2-oxoglutarate dehydrogenase subunit E1o to the less preferred TTG and changing threonine 15 of OdhI to alanine reduced 2-oxoglutarate dehydrogenase activity about five fold and improved putrescine titers by 28%. Additional engineering steps improved further putrescine production with the largest contributions from preventing the formation of the by-product N-acetylputrescine by deletion of spermi(di)ne N-acetyltransferase gene snaA and from overexpression of the gene for a feedback-resistant N-acetylglutamate kinase variant. The resulting C. glutamicum strain NA6 obtained by systems metabolic engineering accumulated two fold more putrescine than the base strain, i.e., 58.1 ± 0.2 mM, and showed a specific productivity of 0.045 g·g−1·h−1 and a yield on glucose of 0.26 g·g−1. Full article
(This article belongs to the Special Issue Metabolic Engineering and Synthetic Biology)
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Review

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Open AccessReview
Advances in Metabolic Engineering of Cyanobacteria for Photosynthetic Biochemical Production
Metabolites 2015, 5(4), 636-658; https://doi.org/10.3390/metabo5040636
Received: 2 July 2015 / Revised: 30 September 2015 / Accepted: 22 October 2015 / Published: 27 October 2015
Cited by 23 | PDF Full-text (818 KB) | HTML Full-text | XML Full-text
Abstract
Engineering cyanobacteria into photosynthetic microbial cell factories for the production of biochemicals and biofuels is a promising approach toward sustainability. Cyanobacteria naturally grow on light and carbon dioxide, bypassing the need of fermentable plant biomass and arable land. By tapping into the central [...] Read more.
Engineering cyanobacteria into photosynthetic microbial cell factories for the production of biochemicals and biofuels is a promising approach toward sustainability. Cyanobacteria naturally grow on light and carbon dioxide, bypassing the need of fermentable plant biomass and arable land. By tapping into the central metabolism and rerouting carbon flux towards desirable compound production, cyanobacteria are engineered to directly convert CO2 into various chemicals. This review discusses the diversity of bioproducts synthesized by engineered cyanobacteria, the metabolic pathways used, and the current engineering strategies used for increasing their titers. Full article
(This article belongs to the Special Issue Metabolic Engineering and Synthetic Biology)
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Open AccessReview
Essences in Metabolic Engineering of Lignan Biosynthesis
Metabolites 2015, 5(2), 270-290; https://doi.org/10.3390/metabo5020270
Received: 26 February 2015 / Revised: 21 April 2015 / Accepted: 27 April 2015 / Published: 4 May 2015
Cited by 22 | PDF Full-text (1033 KB) | HTML Full-text | XML Full-text
Abstract
Lignans are structurally and functionally diverse phytochemicals biosynthesized in diverse plant species and have received wide attentions as leading compounds of novel drugs for tumor treatment and healthy diets to reduce of the risks of lifestyle-related non-communicable diseases. However, the lineage-specific distribution and [...] Read more.
Lignans are structurally and functionally diverse phytochemicals biosynthesized in diverse plant species and have received wide attentions as leading compounds of novel drugs for tumor treatment and healthy diets to reduce of the risks of lifestyle-related non-communicable diseases. However, the lineage-specific distribution and the low-amount of production in natural plants, some of which are endangered species, hinder the efficient and stable production of beneficial lignans. Accordingly, the development of new procedures for lignan production is of keen interest. Recent marked advances in the molecular and functional characterization of lignan biosynthetic enzymes and endogenous and exogenous factors for lignan biosynthesis have suggested new methods for the metabolic engineering of lignan biosynthesis cascades leading to the efficient, sustainable, and stable lignan production in plants, including plant cell/organ cultures. Optimization of light conditions, utilization of a wide range of elicitor treatments, and construction of transiently gene-transfected or transgenic lignan-biosynthesizing plants are mainly being attempted. This review will present the basic and latest knowledge regarding metabolic engineering of lignans based on their biosynthetic pathways and biological activities, and the perspectives in lignan production via metabolic engineering. Full article
(This article belongs to the Special Issue Metabolic Engineering and Synthetic Biology)
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