SynBio

18 pages, 2623 KiB

Open AccessReview

Applications of Serine Integrases in Synthetic Biology over the Past Decade

by Fang Ba, Yufei Zhang, Luyao Wang, Wan-Qiu Liu and Jian Li

SynBio 2023, 1(2), 172-189; https://doi.org/10.3390/synbio1020012 - 11 Sep 2023

Cited by 1 | Viewed by 3885

Serine integrases are emerging as one of the most powerful biological tools for biotechnology. Over the past decade, many research papers have been published on the use of serine integrases in synthetic biology. In this review, we aim to systematically summarize the various studies ranging from structure and the catalytic mechanism to genetic design and interdisciplinary applications. First, we introduce the classification, structure, and catalytic model of serine integrases. Second, we present a timeline with milestones that describes the representative achievements. Then, we summarize the applications of serine integrases in genome engineering, genetic design, and DNA assembly. Finally, we discuss the potential of serine integrases for advancing interdisciplinary research. We anticipate that serine integrases will be further expanded as a versatile genetic toolbox for synthetic biology applications. Full article

(This article belongs to the Special Issue Feature Paper Collection in Synthetic Biology)

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14 pages, 2332 KiB

Open AccessReview

Mechanism-of-Action-Based Development of New Cyclophosphamides

by Georg Voelcker

SynBio 2023, 1(2), 158-171; https://doi.org/10.3390/synbio1020011 - 24 Aug 2023

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Abstract

Even more than 60 years after its introduction into the clinic, cyclophosphamide (CP), which belongs to the group of alkylating cytostatics, is indispensable for the treatment of cancer. This is despite the fact that its exact mechanism of action was unknown until a few years ago, and therefore, all attempts to improve the effectiveness of CP failed. The reason for not knowing the mechanism of action was the uncritical transfer of the chemical processes that lead to the formation of the actual alkylating CP metabolite phosphoreamide mustard (PAM) in vitro to in vivo conditions. In vitro—e.g., in cell culture experiments—PAM is formed by β-elimination of acrolein from the pharmacologically active CP metabolite aldophosphamide (ALD). In vivo, on the other hand, it is formed by enzymatic cleavage of ALD by phosphodiesterases (PDE) with the formation of 3-hydroxypropanal (HPA). The discovery of HPA as a cyclophosphamide metabolite, together with the discovery that HPA is a proapoptotic aldehyde and the discovery that the cell death event in therapy with CP is DNA-alkylation-initiated p53-controlled apoptosis, led to the formulation of a mechanism of action of CP and other oxazaphosphorine cytostatics (OX). This mechanism of action is presented here and is confirmed by newly developed CP-like compounds with lower toxicity and an order of magnitude better effectiveness. Full article

(This article belongs to the Special Issue Feature Paper Collection in Synthetic Biology)

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14 pages, 2119 KiB

Open AccessArticle

An Engineered Escherichia coli Community for Studying Quorum Sensing

by Yuwei Li, Justin E. Clarke, Alex J. O’Neill, Francisco M. Goycoolea and James Smith

SynBio 2023, 1(2), 144-157; https://doi.org/10.3390/synbio1020010 - 07 Jul 2023

Viewed by 1265

Abstract

In bacterial communities, quorum sensing (QS) is a process mediated via chemical signalling that individuals use to coordinate their collective phenotypes. It is closely associated with pathogenic traits such as virulence factor production and antibiotic resistance. In their natural habitats, bacteria live in small niches, forming intricate consortia, where the role of QS is little understood. This work aims to construct a tuneable, trackable, and reconfigurable model bacterial community for studying QS. To this end, three Escherichia coli fluorescent reporter strains were constructed based on the paradigm LuxI/LuxR QS system. The strains recreate the three major aspects of QS response: sensing (S), autoinducer production (P), and regulation (R). We found that the response of the S strain as a function of the N-(3-oxohexanoyl)-L-homoserine lactone (OHHL) concentration did not saturate and exhibited a concentration-dependent response (in the range 10⁻⁷ to 10⁻⁴ M). The P strain produced OHHL and showed the ability to activate the S response, while the R strain showed the ability to attenuate the response due to the expression of the lactonase AiiA. Monitoring the fluorescent signals of the strains permits tracking the activation and attenuation activities of the LuxI/LuxR QS system. Future studies can now also benefit from this straightforward subcloning strategy to study other QS systems. Full article

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SynBio, Volume 1, Issue 2 (September 2023) – 3 articles

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