SynBio, Volume 1, Issue 1 (December 2022) – 6 articles

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Review
Proteins in Synthetic Biology with Agricultural and Environmental Applications
SynBio 2022, 1(1), 77-88; https://doi.org/10.3390/synbio1010006 - 21 Nov 2022
Viewed by 212
Abstract
Synthetic biology tools have become increasingly prevalent as we look to nature for biological approaches to complex problems. With an ever-growing global population, issues of food safety and security, as well as addressing pollution and striving for sustainability are of the utmost importance. [...] Read more.
Synthetic biology tools have become increasingly prevalent as we look to nature for biological approaches to complex problems. With an ever-growing global population, issues of food safety and security, as well as addressing pollution and striving for sustainability are of the utmost importance. In this review, we first highlight synthetic biology techniques such as directed evolution as a toolset for protein engineering and show direct applications for food safety and security. Moreover, we offer an introduction to creative approaches for biosensor design and development and spotlight a few innovative examples. Finally, we address biomanufacturing with direct applications, as well as biomanufacturing to improve natural processes. Full article
(This article belongs to the Special Issue Programmable Proteins in Synthetic Biology)
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Review
Programmable Proteins: Target Specificity, Programmability and Future Directions
SynBio 2022, 1(1), 65-76; https://doi.org/10.3390/synbio1010005 - 28 Oct 2022
Viewed by 322
Abstract
Programmable proteins to detect, visualize, modulate, or eliminate proteins of selection in vitro and in vivo are essential to study the targets recognized and the biology that follows. The specificity of programmable proteins can be easily altered by designing their sequences and structures. [...] Read more.
Programmable proteins to detect, visualize, modulate, or eliminate proteins of selection in vitro and in vivo are essential to study the targets recognized and the biology that follows. The specificity of programmable proteins can be easily altered by designing their sequences and structures. The flexibility and modularity of these proteins are currently pivotal for synthetic biology and various medical applications. There exist numerous reviews of the concept and application of individual programmable proteins, such as programmable nucleases, single-domain antibodies, and other protein scaffolds. This review proposes an expanded conceptual framework of such programmable proteins based on their programmable principle and target specificity to biomolecules (nucleic acids, proteins, and glycans) and overviews their advantages, limitations, and future directions. Full article
(This article belongs to the Special Issue Programmable Proteins in Synthetic Biology)
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Review
Biotechnological Application of Cutinase: A Powerful Tool in Synthetic Biology
SynBio 2022, 1(1), 54-64; https://doi.org/10.3390/synbio1010004 - 25 Aug 2022
Cited by 1 | Viewed by 495
Abstract
Cutinases (EC 3.1.1.74) are widely distributed in fungi, bacteria and plants with diversified structures and properties. Besides acting on the natural substrate cutin, cutinases are the first line of natural biocatalysts to hydrolyze artificial polyesters and toxic xenobiotics such as polyethylene terephthalate (PET), [...] Read more.
Cutinases (EC 3.1.1.74) are widely distributed in fungi, bacteria and plants with diversified structures and properties. Besides acting on the natural substrate cutin, cutinases are the first line of natural biocatalysts to hydrolyze artificial polyesters and toxic xenobiotics such as polyethylene terephthalate (PET), polycaprolactone (PCL), polylactic acid (PLA), polyhydroxybutyl succinate (PBS), phthalate and malathion esters. Moreover, cutinases can act as promising stereoselective catalysts in esterification and transesterification reactions and present better selectivities than lipases. These pioneering studies indicate that the biotechnological application of cutinase as a powerful tool in synthetic biology deserves further investigation, for both degradation and biosynthesis towards a broader range of ester bond-containing substrates. This review summarizes the classifications and properties of cutinases from different sources and insights into the structure–function relationship of different cutinases. It also highlights the uniqueness and advantages of representative cutinases in biodegradation and biosynthesis, and then prospects the future application of natural and engineered cutinases in synthetic biology. Full article
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Article
Trends in Synthetic Biology in the Bioeconomy of Non-Food-Competing Biofuels
SynBio 2022, 1(1), 33-53; https://doi.org/10.3390/synbio1010003 - 31 May 2022
Viewed by 671
Abstract
Despite the acknowledged relevance of renewable energy sources, biofuel production supported by food-related agriculture has faced severe criticism. One way to minimize the considered negative impacts is the use of sources of non-food biomass or wastes. Synthetic biology (SB) embraces a promising complex [...] Read more.
Despite the acknowledged relevance of renewable energy sources, biofuel production supported by food-related agriculture has faced severe criticism. One way to minimize the considered negative impacts is the use of sources of non-food biomass or wastes. Synthetic biology (SB) embraces a promising complex of technologies for biofuel production from non-edible and sustainable raw materials. Therefore, it is pertinent to identify the global evolution of investments, concepts, and techniques underlying the field in support of policy formulations for sustainable bioenergy production. We mapped the SB scientific knowledge related to biofuels using software that combines information visualization methods, bibliometrics, and data mining algorithms. The United States and China have been the leading countries in developing SB technologies. The Technical University of Denmark and Tsinghua University are institutions with higher centrality and have played prominent roles besides UC Los Angeles and Delft University Technology. We identified six knowledge clusters under the terms: versatile sugar dehydrogenase, redox balance principle, sesquiterpene production, Saccharomyces cerevisiae, recombinant xylose-fermenting strain, and Clostridium saccharoperbutylacetonicum N1-4. The emerging trends refer to specific microorganisms, processes, and products. Yarrowia lipolytica, Oleaginous yeast, E. coli, Klebsiella pneumoniae, Phaeodactylum tricornutum, and Microalgae are the most prominent microorganisms, mainly from the year 2016 onward. Anaerobic digestion, synthetic promoters, and genetic analysis appear as the most relevant platforms of new processes. Improved biofuels, bioethanol, and N-butanol are at the frontier of the development of SB-derived products. Synthetic biology is a dynamic interdisciplinary field in environmentally friendly bioenergy production pushed by growing social concerns and the emergent bioeconomy. Full article
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Review
Heterologous Production of Acrylic Acid: Current Challenges and Perspectives
SynBio 2022, 1(1), 3-32; https://doi.org/10.3390/synbio1010002 - 30 May 2022
Viewed by 680
Abstract
Acrylic acid (AA) is a chemical with high market value used in industry to produce diapers, paints, adhesives and coatings, among others. AA available worldwide is chemically produced mostly from petroleum derivatives. Due to its economic relevance, there is presently a need for [...] Read more.
Acrylic acid (AA) is a chemical with high market value used in industry to produce diapers, paints, adhesives and coatings, among others. AA available worldwide is chemically produced mostly from petroleum derivatives. Due to its economic relevance, there is presently a need for innovative and sustainable ways to synthesize AA. In the past decade, several semi-biological methods have been developed and consist in the bio-based synthesis of 3-hydroxypropionic acid (3-HP) and its chemical conversion to AA. However, more recently, engineered Escherichia coli was demonstrated to be able to convert glucose or glycerol to AA. Several pathways have been developed that use as precursors glycerol, malonyl-CoA or β-alanine. Some of these pathways produce 3-HP as an intermediate. Nevertheless, the heterologous production of AA is still in its early stages compared, for example, to 3-HP production. So far, only up to 237 mg/L of AA have been produced from glucose using β-alanine as a precursor in fed-batch fermentation. In this review, the advances in the production of AA by engineered microbes, as well as the hurdles hindering high-level production, are discussed. In addition, synthetic biology and metabolic engineering approaches to improving the production of AA in industrial settings are presented. Full article
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Editorial
SynBio: A Progressive Open Access Journal Publishing New Horizons in the Synthetic Biology
SynBio 2022, 1(1), 1-2; https://doi.org/10.3390/synbio1010001 - 08 Nov 2021
Viewed by 1224
Abstract
It is my pleasure to inaugurate the new open access journal, SynBio (ISSN: 2673-9259) [...] Full article
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