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Special Issue "Design in Synthetic Biology"

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

Deadline for manuscript submissions: closed (1 August 2018)

Special Issue Editors

Guest Editor
Dr. Jiantao Guo

Department of Chemistry, University of Nebraska-Lincoln, 634AA Hamilton Hall, Lincoln, USA
Website | E-Mail
Interests: synthetic biology; chemical biology; bioorganic chemistry; protein engineering; unnatural amino acid; genetic code; directed evolution; metabolic engineering
Guest Editor
Dr. Wei Niu

Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, USA
Website | E-Mail
Interests: synthetic biology; metabolic engineering; protein engineering; codon expansion; systems biology

Special Issue Information

Dear Colleagues,

As a young multidisciplinary research field, Synthetic Biology has been enjoying rapid growth over recent years. It combines fundamental principles of science and engineering in order to achieve a precision design and an efficient construction of useful biological functions and systems. Synthetic Biology attracts interests from the fields of Biology, Chemistry, Mathematics, Chemical Engineering, Biomedical Engineering, Material Engineering, Computer Engineering, Electrical Engineering, etc. Applications of Synthetic Biology serve a very broad spectrum of goals, ranging from making basic scientific discoveries to solving practical problems, such as producing drugs and bio-based chemicals/fuels, improving traits of crops, and optimizing gene therapy.

The present Special Issue is aimed at bringing the most recent and exciting advances in Synthetic Biology to its audience. It covers, but is not limited to, new methods and novel applications in genetic circuit design, genetic code engineering, genome editing, DNA/genome synthesis, natural product discover/synthesis, novel pathway design/construction, metabolic engineering, biosensing, protein design/engineering, and mathematical modelling.

As Guest Editors, we cordially invite researchers to submit their recent advances in the field to this Special Issue of Molecules.

With best regards,

Dr. Jiantao Guo
Dr. Wei Niu
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 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. Molecules 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 1800 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
  • Chemical Biology
  • Natural Product Biosynthesis
  • Protein Engineering
  • Genetic Code
  • Metabolic Engineering
  • Biocatalysis

Published Papers (8 papers)

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Research

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Open AccessArticle Improved l-Leucine Production in Corynebacterium glutamicum by Optimizing the Aminotransferases
Molecules 2018, 23(9), 2102; https://doi.org/10.3390/molecules23092102
Received: 12 July 2018 / Revised: 17 August 2018 / Accepted: 20 August 2018 / Published: 21 August 2018
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Abstract
The production of branched-chain amino acids (BCAAs) is still challenging, therefore we rationally engineered Corynebacterium glutamicum FA-1 to increase the l-leucine production by optimizing the aminotransferases. Based on this, we investigated the effects of the native aminotransferases, i.e., branched-chain amino acid aminotransferase
[...] Read more.
The production of branched-chain amino acids (BCAAs) is still challenging, therefore we rationally engineered Corynebacterium glutamicum FA-1 to increase the l-leucine production by optimizing the aminotransferases. Based on this, we investigated the effects of the native aminotransferases, i.e., branched-chain amino acid aminotransferase (BCAT; encoded by ilvE) and aspartate aminotransferase (AspB; encoded by aspB) on l-leucine production in C. glutamicum. The strain FA-1△ilvE still exhibited significant growth without leucine addition, while FA-1△ilvEaspB couldn’t, which indicated that AspB also contributes to L-leucine synthesis in vivo and the yield of leucine reached 20.81 ± 0.02 g/L. It is the first time that AspB has been characterized for l-leucine synthesis activity. Subsequently, the aromatic aminotransferase TyrB and the putative aspartate aminotransferases, the aspC, yhdR, ywfG gene products, were cloned, expressed and characterized for leucine synthesis activity in FA-1△ilvEaspB. Only TyrB was able to synthesize l-leucine and the l-leucine production was 18.55 ± 0.42 g/L. The two putative branched-chain aminotransferase genes, ybgE and CaIlvE, were also cloned and expressed. Both genes products function efficiently in BCAAs biosynthesis. This is the first report of a rational modification of aminotransferase activity that improves the l-leucine production through optimizing the aminotransferases. Full article
(This article belongs to the Special Issue Design in Synthetic Biology)
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Open AccessArticle (2E,5E)-2,5-Bis(3-hydroxy-4-methoxybenzylidene) cyclopentanone Exerts Anti-Melanogenesis and Anti-Wrinkle Activities in B16F10 Melanoma and Hs27 Fibroblast Cells
Molecules 2018, 23(6), 1415; https://doi.org/10.3390/molecules23061415
Received: 11 May 2018 / Revised: 8 June 2018 / Accepted: 11 June 2018 / Published: 11 June 2018
Cited by 1 | PDF Full-text (2260 KB) | HTML Full-text | XML Full-text
Abstract
Ultraviolet (UV) radiation exposure is the primary cause of extrinsic skin aging, which results in skin hyperpigmentation and wrinkling. In this study, we investigated the whitening effect of (2E,5E)-2,5-bis(3-hydroxy-4-methoxybenzylidene)cyclopentanone (BHCP) on B16F10 melanoma and its anti-wrinkle activity on Hs27
[...] Read more.
Ultraviolet (UV) radiation exposure is the primary cause of extrinsic skin aging, which results in skin hyperpigmentation and wrinkling. In this study, we investigated the whitening effect of (2E,5E)-2,5-bis(3-hydroxy-4-methoxybenzylidene)cyclopentanone (BHCP) on B16F10 melanoma and its anti-wrinkle activity on Hs27 fibroblasts cells. BHCP was found to potently inhibit tyrosinase, with 50% inhibition concentration (IC50) values of 1.10 µM and 8.18 µM for monophenolase (l-tyrosine) and diphenolase (l-DOPA), and the enzyme kinetics study revealed that BHCP is a competitive-type tyrosinase inhibitor. Furthermore, BHCP significantly inhibited melanin content and cellular tyrosinase activity, and downregulated the levels of microphthalmia-associated transcription factor (MITF), phosphorylated levels of cAMP response element-binding (CREB) protein, and tyrosinase in α-melanocyte stimulating hormone (α-MSH)-induced B16F10 melanoma cells. Moreover, BHCP inhibited the phosphorylation of p65 and expression of matrix metalloproteinases (MMP-1, MMP-9, MMP-12, and MMP-13) in Hs27 fibroblasts stimulated with UV radiation. Therefore, our results demonstrate that BHCP may be a good candidate for the development of therapeutic agents for diseases associated with hyperpigmentation and wrinkling. Full article
(This article belongs to the Special Issue Design in Synthetic Biology)
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Open AccessArticle Functional Characterisation of New Sesquiterpene Synthase from the Malaysian Herbal Plant, Polygonum Minus
Molecules 2018, 23(6), 1370; https://doi.org/10.3390/molecules23061370
Received: 23 March 2018 / Revised: 29 May 2018 / Accepted: 31 May 2018 / Published: 6 June 2018
PDF Full-text (4794 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Polygonum minus (syn. Persicaria minor) is a herbal plant that is well known for producing sesquiterpenes, which contribute to its flavour and fragrance. This study describes the cloning and functional characterisation of PmSTPS1 and PmSTPS2, two sesquiterpene synthase genes that
[...] Read more.
Polygonum minus (syn. Persicaria minor) is a herbal plant that is well known for producing sesquiterpenes, which contribute to its flavour and fragrance. This study describes the cloning and functional characterisation of PmSTPS1 and PmSTPS2, two sesquiterpene synthase genes that were identified from P. minus transcriptome data mining. The full-length sequences of the PmSTPS1 and PmSTPS2 genes were expressed in the E. coli pQE-2 expression vector. The sizes of PmSTPS1 and PmSTPS2 were 1098 bp and 1967 bp, respectively, with open reading frames (ORF) of 1047 and 1695 bp and encoding polypeptides of 348 and 564 amino acids, respectively. The proteins consist of three conserved motifs, namely, Asp-rich substrate binding (DDxxD), metal binding residues (NSE/DTE), and cytoplasmic ER retention (RxR), as well as the terpene synthase family N-terminal domain and C-terminal metal-binding domain. From the in vitro enzyme assays, using the farnesyl pyrophosphate (FPP) substrate, the PmSTPS1 enzyme produced multiple acyclic sesquiterpenes of β-farnesene, α-farnesene, and farnesol, while the PmSTPS2 enzyme produced an additional nerolidol as a final product. The results confirmed the roles of PmSTPS1 and PmSTPS2 in the biosynthesis pathway of P. minus, to produce aromatic sesquiterpenes. Full article
(This article belongs to the Special Issue Design in Synthetic Biology)
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Open AccessArticle Replacing Standard Reporters from Molecular Cloning Plasmids with Chromoproteins for Positive Clone Selection
Molecules 2018, 23(6), 1328; https://doi.org/10.3390/molecules23061328
Received: 24 April 2018 / Revised: 23 May 2018 / Accepted: 25 May 2018 / Published: 31 May 2018
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Abstract
Cloning and expression plasmids are the workhorses of modern molecular biology. Despite the pathway paved by synthetic biology, laboratories around the globe still relay on standard cloning techniques using plasmids with reporter proteins for positive clone selection, such as β-galactosidase alpha peptide complementation
[...] Read more.
Cloning and expression plasmids are the workhorses of modern molecular biology. Despite the pathway paved by synthetic biology, laboratories around the globe still relay on standard cloning techniques using plasmids with reporter proteins for positive clone selection, such as β-galactosidase alpha peptide complementation for blue/white screening or ccdB, which encodes for a toxic DNA gyrase. These reporters, when interrupted, serve as a positive clone detection system. In the present report, we show that molecular cloning plasmids bearing the coding sequence for a 25.4 kDa protein, AmilCP, encoded by a 685 bp gene, that is well expressed in Escherichia coli, render blue-purple colonies. Using this reporter protein, we developed and tested a cloning system based on the constitutive expression of the non-toxic AmilCP protein, that once interrupted, the loss of purple color serves to facilitate positive clone selection. The main advantage of this system is that is less expensive than other systems since media do not contain chromogenic markers such as X-gal, which is both expensive and cumbersome to prepare and use, or inductors such as IPTG. We also designed an inducible expression plasmid suitable for recombinant protein expression that also contains AmilCP cloning selection marker, a feature not commonly found in protein expression plasmids. The use of chromogenic reporters opens an important avenue for its application in other organisms besides E. coli for clone selection or even for mutant selection. Full article
(This article belongs to the Special Issue Design in Synthetic Biology)
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Open AccessArticle Multicomponent Domino Synthesis, Anticancer Activity and Molecular Modeling Simulation of Complex Dispirooxindolopyrrolidines
Molecules 2018, 23(5), 1094; https://doi.org/10.3390/molecules23051094
Received: 17 April 2018 / Revised: 29 April 2018 / Accepted: 3 May 2018 / Published: 5 May 2018
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Abstract
A series of spirooxindolopyrrolidine fused N-styrylpiperidone heterocyclic hybrids has been synthesized in excellent yield via a domino multicomponent protocol that involves one-pot three component 1,3-dipolar cycloaddition and concomitant enamine reactions performed in an inexpensive ionic liquid, namely 1-butyl-3-methylimidazolium bromide ([bmim]Br). Compounds thus
[...] Read more.
A series of spirooxindolopyrrolidine fused N-styrylpiperidone heterocyclic hybrids has been synthesized in excellent yield via a domino multicomponent protocol that involves one-pot three component 1,3-dipolar cycloaddition and concomitant enamine reactions performed in an inexpensive ionic liquid, namely 1-butyl-3-methylimidazolium bromide ([bmim]Br). Compounds thus synthesized were evaluated for their cytotoxicity against U-937 tumor cells. Interestingly; compounds 5i and 5m exhibited a better cytotoxicity than the anticancer drug bleomycin. In addition; the effect of the synthesized compounds on the nuclear morphology of U937 FaDu cells revealed that treatment with compounds 5am led to their apoptotic cell death. Full article
(This article belongs to the Special Issue Design in Synthetic Biology)
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Open AccessArticle Biochemical, Physiological and Transcriptomic Comparison between Burley and Flue-Cured Tobacco Seedlings in Relation to Carbohydrates and Nitrate Content
Molecules 2017, 22(12), 2126; https://doi.org/10.3390/molecules22122126
Received: 7 November 2017 / Revised: 21 November 2017 / Accepted: 28 November 2017 / Published: 2 December 2017
Cited by 2 | PDF Full-text (4590 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Burley tobacco is a genotype of chloroplast-deficient mutant with accumulates high levels of tobacco-specific nitrosamines (TSNAs) which would induce malignant tumors in animals. Nitrate is a principle precursor of tobacco-specific nitrosamines. Nitrate content in burley tobacco was significantly higher than that in flue-cured
[...] Read more.
Burley tobacco is a genotype of chloroplast-deficient mutant with accumulates high levels of tobacco-specific nitrosamines (TSNAs) which would induce malignant tumors in animals. Nitrate is a principle precursor of tobacco-specific nitrosamines. Nitrate content in burley tobacco was significantly higher than that in flue-cured tobacco. The present study investigated differences between the two tobacco types to explore the mechanisms of nitrate accumulation in burley tobacco. transcripts (3079) related to the nitrogen and carbon metabolism were observed. Expression of genes involved in carbon fixation, glucose and starch biosynthesis, nitrate translocation and assimilation were significantly low in burley tobacco than flue-cured tobacco. Being relative to flue-cured tobacco, burley tobacco was significantly lower at total nitrogen and carbohydrate content, nitrate reductase and glutamine synthetase activities, chlorophyll content and photosynthetic rate (Pn), but higher nitrate content. Burley tobacco required six-fold more nitrogen fertilizers than flue-cured tobacco, but both tobaccos had a similar leaf biomass. Reduced chlorophyll content and photosynthetic rate (Pn) might result in low carbohydrate formation, and low capacity of nitrogen assimilation and translocation might lead to nitrate accumulation in burley tobacco. Full article
(This article belongs to the Special Issue Design in Synthetic Biology)
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Review

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Open AccessReview Recent Development of Genetic Code Expansion for Posttranslational Modification Studies
Molecules 2018, 23(7), 1662; https://doi.org/10.3390/molecules23071662
Received: 25 June 2018 / Revised: 3 July 2018 / Accepted: 5 July 2018 / Published: 8 July 2018
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Abstract
Nowadays advanced mass spectrometry techniques make the identification of protein posttranslational modifications (PTMs) much easier than ever before. A series of proteomic studies have demonstrated that large numbers of proteins in cells are modified by phosphorylation, acetylation and many other types of PTMs.
[...] Read more.
Nowadays advanced mass spectrometry techniques make the identification of protein posttranslational modifications (PTMs) much easier than ever before. A series of proteomic studies have demonstrated that large numbers of proteins in cells are modified by phosphorylation, acetylation and many other types of PTMs. However, only limited studies have been performed to validate or characterize those identified modification targets, mostly because PTMs are very dynamic, undergoing large changes in different growth stages or conditions. To overcome this issue, the genetic code expansion strategy has been introduced into PTM studies to genetically incorporate modified amino acids directly into desired positions of target proteins. Without using modifying enzymes, the genetic code expansion strategy could generate homogeneously modified proteins, thus providing powerful tools for PTM studies. In this review, we summarized recent development of genetic code expansion in PTM studies for research groups in this field. Full article
(This article belongs to the Special Issue Design in Synthetic Biology)
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Open AccessFeature PaperReview Application of the Asymmetric Pictet–Spengler Reaction in the Total Synthesis of Natural Products and Relevant Biologically Active Compounds
Molecules 2018, 23(4), 943; https://doi.org/10.3390/molecules23040943
Received: 22 March 2018 / Revised: 7 April 2018 / Accepted: 12 April 2018 / Published: 18 April 2018
Cited by 1 | PDF Full-text (21275 KB) | HTML Full-text | XML Full-text
Abstract
Tetrahydroisoquinolines are the framework of numerous natural products predominantly alkaloids, an important and one of the most wide spread families of naturally occurring compounds in the plant kingdom. Tetrahydroisoquinolines are commonly constructed through an old reaction, the so-called Pictet–Spengler Reaction (PSR). In this
[...] Read more.
Tetrahydroisoquinolines are the framework of numerous natural products predominantly alkaloids, an important and one of the most wide spread families of naturally occurring compounds in the plant kingdom. Tetrahydroisoquinolines are commonly constructed through an old reaction, the so-called Pictet–Spengler Reaction (PSR). In this reaction, a β-aryl ethylamine undergoes an acid mediated condensation with a suitable aldehyde or ketone, followed by ring closure. In this review, we aim to highlight the applications of the asymmetric variant of this old name reaction in the total synthesis of natural products, chiefly, alkaloids, which exhibit significant biological properties. Full article
(This article belongs to the Special Issue Design in Synthetic Biology)
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