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Synthetic Enzymology – Enzymology for Purposeful Engineering of Biology
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Synthetic Enzymology – Enzymology for Purposeful Engineering of Biology

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Molecular Structure".

Deadline for manuscript submissions: closed (31 March 2021) | Viewed by 18254

Special Issue Editor

Prof. Dr. Wen Shan YEW

E-Mail Website
Guest Editor
Synthetic Biology for Clinical and Technological Innovation, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
Interests: rational design and directed evolution of enzymatic activities; drug design and therapeutics against infectious diseases, metabolic disorders, cancer and aging; synthetic enzymology for biomedical and bioremediation applications; deciphering enzyme specificity; mechanistic enzymology of enzymes of pharmaceutical and industrial importance; discovery of new enzymatic functions

Special Issue Information

Dear Colleagues,

Synthetic biology or engineering biology refers to the design and engineering of biologically based parts, novel devices and systems, as well as the redesign of existing biological systems, for purposeful function. It is enriched by a multitude of foundational disciplines, including synthetic enzymology, defined as the use of enzymological principles such as mechanistic enzymology, rational and directed enzyme engineering, combinatorial biosynthesis, and genomic and functional enzymology, in the intentional design and engineering of biological systems for purposeful function. The utility of synthetic enzymology is wide and varied, including for the purposeful and sustainable production and development of therapeutics, functional food and food ingredients, nutraceuticals, and high-value (bio)chemicals. The main focus of this Special Issue on “Synthetic Enzymology—Enzymology for Purposeful Engineering of Biology” is to serve as an open forum where researchers may share their investigations and findings in this exciting field and, thanks to the open access platform, increase their visibility and the chances to interact with colleagues in industries and academia. Contributions to this issue, both in the form of original research or review articles, may cover all aspects of synthetic enzymology; studies with multidisciplinary input, offering new methodologies or insights, are particularly welcome.

Prof. Wen Shan YEW
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 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. Molecules is an international peer-reviewed open access semimonthly 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

  • Engineering biology
  • Synthetic biology
  • Synthetic enzymology
  • Protein engineering
  • Directed evolution
  • Synthetic compartments
  • Metabolic engineering
  • Computational design
  • Sustainable solutions
  • Bioproduction and biotransformation
  • Circuit biodesign
  • Biosensors and devices
  • Biotechnology
  • Environmental sustainability
  • Human health and nutrition

Published Papers (5 papers)

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Research

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13 pages, 4511 KiB  
Communication
Elucidation of Gram-Positive Bacterial Iron(III) Reduction for Kaolinite Clay Refinement
by Hao Jing, Zhao Liu, Seng How Kuan, Sylvia Chieng and Chun Loong Ho
Molecules 2021, 26(11), 3084; https://doi.org/10.3390/molecules26113084 - 21 May 2021
Cited by 4 | Viewed by 2241
Abstract
Recently, microbial-based iron reduction has been considered as a viable alternative to typical chemical-based treatments. The iron reduction is an important process in kaolin refining, where iron-bearing impurities in kaolin clay affects the whiteness, refractory properties, and its commercial value. In recent years, [...] Read more.
Recently, microbial-based iron reduction has been considered as a viable alternative to typical chemical-based treatments. The iron reduction is an important process in kaolin refining, where iron-bearing impurities in kaolin clay affects the whiteness, refractory properties, and its commercial value. In recent years, Gram-negative bacteria has been in the center stage of iron reduction research, whereas little is known about the potential use of Gram-positive bacteria to refine kaolin clay. In this study, we investigated the ferric reducing capabilities of five microbes by manipulating the microbial growth conditions. Out of the five, we discovered that Bacillus cereus and Staphylococcus aureus outperformed the other microbes under nitrogen-rich media. Through the biochemical changes and the microbial behavior, we mapped the hypothetical pathway leading to the iron reduction cellular properties, and found that the iron reduction properties of these Gram-positive bacteria rely heavily on the media composition. The media composition results in increased basification of the media that is a prerequisite for the cellular reduction of ferric ions. Further, these changes impact the formation of biofilm, suggesting that the cellular interaction for the iron(III)oxide reduction is not solely reliant on the formation of biofilms. This article reveals the potential development of Gram-positive microbes in facilitating the microbial-based removal of metal contaminants from clays or ores. Further studies to elucidate the corresponding pathways would be crucial for the further development of the field. Full article
(This article belongs to the Special Issue Synthetic Enzymology – Enzymology for Purposeful Engineering of Biology)
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12 pages, 2567 KiB  
Communication
Substrate Specificity of Chimeric Enzymes Formed by Interchange of the Catalytic and Specificity Domains of the 5′-Nucleotidase UshA and the 3′-Nucleotidase CpdB
by Alicia Cabezas, Iralis López-Villamizar, María Jesús Costas, José Carlos Cameselle and João Meireles Ribeiro
Molecules 2021, 26(8), 2307; https://doi.org/10.3390/molecules26082307 - 16 Apr 2021
Cited by 4 | Viewed by 1552
Abstract
The 5′-nucleotidase UshA and the 3′-nucleotidase CpdB from Escherichia coli are broad-specificity phosphohydrolases with similar two-domain structures. Their N-terminal domains (UshA_Ndom and CpdB_Ndom) contain the catalytic site, and their C-terminal domains (UshA_Cdom and CpdB_Cdom) contain a substrate-binding site responsible [...] Read more.
The 5′-nucleotidase UshA and the 3′-nucleotidase CpdB from Escherichia coli are broad-specificity phosphohydrolases with similar two-domain structures. Their N-terminal domains (UshA_Ndom and CpdB_Ndom) contain the catalytic site, and their C-terminal domains (UshA_Cdom and CpdB_Cdom) contain a substrate-binding site responsible for specificity. Both enzymes show only partial overlap in their substrate specificities. So, it was decided to investigate the catalytic behavior of chimeras bearing the UshA catalytic domain and the CpdB specificity domain, or vice versa. UshA_Ndom–CpdB_Cdom and CpdB_Ndom–UshA_Cdom were constructed and tested on substrates specific to UshA (5′-AMP, CDP-choline, UDP-glucose) or to CpdB (3′-AMP), as well as on 2′,3′-cAMP and on the common phosphodiester substrate bis-4-NPP (bis-4-nitrophenylphosphate). The chimeras did show neither 5′-nucleotidase nor 3′-nucleotidase activity. When compared to UshA, UshA_Ndom–CpdB_Cdom conserved high activity on bis-4-NPP, some on CDP-choline and UDP-glucose, and displayed activity on 2′,3′-cAMP. When compared to CpdB, CpdB_Ndom–UshA_Cdom conserved phosphodiesterase activities on 2′,3′-cAMP and bis-4-NPP, and gained activity on the phosphoanhydride CDP-choline. Therefore, the non-nucleotidase activities of UshA and CpdB are not fully dependent on the interplay between domains. The specificity domains may confer the chimeras some of the phosphodiester or phosphoanhydride selectivity displayed when associated with their native partners. Contrarily, the nucleotidase activity of UshA and CpdB depends strictly on the interplay between their native catalytic and specificity domains. Full article
(This article belongs to the Special Issue Synthetic Enzymology – Enzymology for Purposeful Engineering of Biology)
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Graphical abstract

11 pages, 4166 KiB  
Article
Zymography for Picogram Detection of Lipase and Esterase Activities
by Andre Mong Jie Ng, Hongfang Zhang and Giang Kien Truc Nguyen
Molecules 2021, 26(6), 1542; https://doi.org/10.3390/molecules26061542 - 11 Mar 2021
Cited by 5 | Viewed by 4128
Abstract
Lipases and esterases are important catalysts with wide varieties of industrial applications. Although many methods have been established for detecting their activities, a simple and sensitive approach for picogram detection of lipolytic enzyme quantity is still highly desirable. Here we report a lipase [...] Read more.
Lipases and esterases are important catalysts with wide varieties of industrial applications. Although many methods have been established for detecting their activities, a simple and sensitive approach for picogram detection of lipolytic enzyme quantity is still highly desirable. Here we report a lipase detection assay which is 1000-fold more sensitive than previously reported methods. Our assay enables the detection of as low as 5 pg and 180 pg of lipolytic activity by direct spotting and zymography, respectively. Furthermore, we demonstrated that the detection sensitivity was adjustable by varying the buffering capacity, which allows for screening of both high and low abundance lipolytic enzymes. Coupled with liquid chromatography-mass spectrometry, our method provides a useful tool for sensitive detection and identification of lipolytic enzymes. Full article
(This article belongs to the Special Issue Synthetic Enzymology – Enzymology for Purposeful Engineering of Biology)
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Review

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14 pages, 16262 KiB  
Review
Directed Evolution Methods for Enzyme Engineering
by Saurabh Rajendra Nirantar
Molecules 2021, 26(18), 5599; https://doi.org/10.3390/molecules26185599 - 15 Sep 2021
Cited by 20 | Viewed by 5266
Abstract
Enzymes underpin the processes required for most biotransformations. However, natural enzymes are often not optimal for biotechnological uses and must be engineered for improved activity, specificity and stability. A rich and growing variety of wet-lab methods have been developed by researchers over decades [...] Read more.
Enzymes underpin the processes required for most biotransformations. However, natural enzymes are often not optimal for biotechnological uses and must be engineered for improved activity, specificity and stability. A rich and growing variety of wet-lab methods have been developed by researchers over decades to accomplish this goal. In this review such methods and their specific attributes are examined. Full article
(This article belongs to the Special Issue Synthetic Enzymology – Enzymology for Purposeful Engineering of Biology)
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33 pages, 7544 KiB  
Review
Genetically Encodable Scaffolds for Optimizing Enzyme Function
by Yong Quan Tan, Bo Xue and Wen Shan Yew
Molecules 2021, 26(5), 1389; https://doi.org/10.3390/molecules26051389 - 4 Mar 2021
Cited by 5 | Viewed by 4359
Abstract
Enzyme engineering is an indispensable tool in the field of synthetic biology, where enzymes are challenged to carry out novel or improved functions. Achieving these goals sometimes goes beyond modifying the primary sequence of the enzyme itself. The use of protein or nucleic [...] Read more.
Enzyme engineering is an indispensable tool in the field of synthetic biology, where enzymes are challenged to carry out novel or improved functions. Achieving these goals sometimes goes beyond modifying the primary sequence of the enzyme itself. The use of protein or nucleic acid scaffolds to enhance enzyme properties has been reported for applications such as microbial production of chemicals, biosensor development and bioremediation. Key advantages of using these assemblies include optimizing reaction conditions, improving metabolic flux and increasing enzyme stability. This review summarizes recent trends in utilizing genetically encodable scaffolds, developed in line with synthetic biology methodologies, to complement the purposeful deployment of enzymes. Current molecular tools for constructing these synthetic enzyme-scaffold systems are also highlighted. Full article
(This article belongs to the Special Issue Synthetic Enzymology – Enzymology for Purposeful Engineering of Biology)
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