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SynBio, Volume 2, Issue 1 (March 2024) – 6 articles

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27 pages, 5369 KiB  
Review
Expanding the Biosynthetic Toolbox: The Potential and Challenges of In Vitro Type II Polyketide Synthase Research
by Max A. J. Rivers and Andrew N. Lowell
SynBio 2024, 2(1), 85-111; https://doi.org/10.3390/synbio2010006 - 07 Mar 2024
Viewed by 783
Abstract
Type II polyketide synthase (PKS) systems are a rich source of structurally diverse polycyclic aromatic compounds with clinically relevant antibiotic and chemotherapeutic properties. The enzymes responsible for synthesizing the polyketide core, known collectively as the minimal cassette, hold potential for applications in synthetic [...] Read more.
Type II polyketide synthase (PKS) systems are a rich source of structurally diverse polycyclic aromatic compounds with clinically relevant antibiotic and chemotherapeutic properties. The enzymes responsible for synthesizing the polyketide core, known collectively as the minimal cassette, hold potential for applications in synthetic biology. The minimal cassette provides polyketides of different chain lengths, which interact with other enzymes that are responsible for the varied cyclization patterns. Additionally, the type II PKS enzyme clusters offer a wide repertoire of tailoring enzymes for oxidations, glycosylations, cyclizations, and rearrangements. This review begins with the variety of chemical space accessible with type II PKS systems including the recently discovered highly reducing variants that produce polyalkenes instead of the archetypical polyketide motif. The main discussion analyzes the previous approaches with an emphasis on further research that is needed to characterize the minimal cassette enzymes in vitro. Finally, the potential type II PKS systems hold the potential to offer new tools in biocatalysis and synthetic biology, particularly in the production of novel antibiotics and biofuels. Full article
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15 pages, 3284 KiB  
Article
Pangenome-Scale Mathematical Modelling of ANAMMOX Bacteria Metabolism
by Roman G. Bielski and M. Ahsanul Islam
SynBio 2024, 2(1), 70-84; https://doi.org/10.3390/synbio2010005 - 08 Feb 2024
Viewed by 549
Abstract
Removal of fixed nitrogen compounds such as ammonium and nitrite from wastewater is of critical importance for balancing the nitrogen cycle and protecting aquatic environments from eutrophication. ANaerobic AMMonium OXidising (ANAMMOX) bacteria have recently been employed for fixed nitrogen removal purposes in wastewater [...] Read more.
Removal of fixed nitrogen compounds such as ammonium and nitrite from wastewater is of critical importance for balancing the nitrogen cycle and protecting aquatic environments from eutrophication. ANaerobic AMMonium OXidising (ANAMMOX) bacteria have recently been employed for fixed nitrogen removal purposes in wastewater treatment processes. These specialised bacteria convert ammonium and nitrite into nitrogen gas anaerobically, thereby reducing the amount of energy required for aeration in conventional wastewater treatment processes. However, slow growth rates of ANAMMOX remain a major obstacle towards their widespread use in industrial wastewater treatment processes. Thus, a pangenome-scale, constraint-based metabolic model, iRB399, of ANAMMOX bacteria has been developed to design strategies for accelerating their growth. The main metabolic limitation was identified in the energy metabolism of these bacteria, concerning the production of ATP. The extremely low efficiency of the electron transport chain combined with very high growth-associated maintenance energy is likely to be responsible for the slow growth of ANAMMOX. However, different ANAMMOX species were found to conserve energy using a variety of different redox couples, and the modelling simulations revealed their comparative advantages under different growth conditions. iRB399 also identified dispensable catabolic reactions that have demonstrably beneficial effects on enhancing the growth rates of ANAMMOX bacteria. Thus, the pangenome-scale model will not only help identify and overcome metabolic limitations of ANNAMOX bacteria, but also provide a valuable resource for designing efficient ANNAMOX-based wastewater treatment processes. Full article
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14 pages, 5276 KiB  
Article
Transcriptomic Investigation in CRISPR/Cas9-Mediated GRIK1-, GRIK2-, and GRIK4-Gene-Knockout Human Neuroblastoma Cells
by Tsung-Ming Hu, Shih-Hsin Hsu, Hsin-Yao Tsai and Min-Chih Cheng
SynBio 2024, 2(1), 56-69; https://doi.org/10.3390/synbio2010004 - 05 Feb 2024
Viewed by 392
Abstract
The glutamate ionotropic kainate receptors, encoded by the GRIK gene family, are composed of four subunits and function as ligand-activated ion channels. They play a critical role in regulating synaptic transmission and various synaptic receptors’ processes, as well as in the pathophysiology of [...] Read more.
The glutamate ionotropic kainate receptors, encoded by the GRIK gene family, are composed of four subunits and function as ligand-activated ion channels. They play a critical role in regulating synaptic transmission and various synaptic receptors’ processes, as well as in the pathophysiology of schizophrenia. However, their functions and mechanisms of action need to be better understood and are worthy of exploration. To further understand the exact role of the kainate receptors in vitro, we generated kainate-receptor-knockout (KO) isogenic SH-SY5Y cell lines using the CRISPR/Cas9-mediated gene editing method. We conducted RNA sequencing (RNA-seq) to determine the differentially expressed genes (DEGs) in the isogenic edited cells and used rhodamine-phalloidin staining to quantitate filamentous actin (F-actin) in differentiated edited cells. The RNA-seq and the Gene Ontology enrichment analysis revealed that the genetic deletion of the GRIK1, GRIK2, and GRIK4 genes disturbed multiple genes involved in numerous signal pathways, including a converging pathway related to the synaptic membrane. An enrichment analysis of gene–disease associations indicated that DEGs in the edited cell lines were associated with several neuropsychiatric disorders, especially schizophrenia. In the morphology study, fluorescent images show that less F-actin was expressed in differentiated SH-SY5Y cells with GRIK1, GRIK2, or GRIK4 deficiency than wild-type cells. Our data indicate that kainate receptor deficiency might disturb synaptic-membrane-associated genes, and elucidating these genes should shed some light on the pathophysiology of schizophrenia. Furthermore, the transcriptomic profiles for kainate receptor deficiency of SH-SY5Y cells contribute to emerging evidence for the novel mechanisms underlying the effect of kainate receptors and the pathophysiology of schizophrenia. In addition, our data suggest that kainate-receptor-mediated F-actin remodeling may be a candidate mechanism underlying schizophrenia. Full article
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25 pages, 9296 KiB  
Article
Generation of New Glycoanalogues of Polyene Antibiotics by Synthetic Biology—Testing Current Technical Boundaries
by Mark Hogan, Yuhao Song, Jimmy Muldoon and Patrick Caffrey
SynBio 2024, 2(1), 31-55; https://doi.org/10.3390/synbio2010003 - 04 Jan 2024
Cited by 1 | Viewed by 948
Abstract
A number of antifungal drugs are based on polyene macrolides that cause severe side effects. Most of these compounds contain a single aminodeoxysugar, D-mycosamine. Toxicity can be reduced by increasing the extent of glycosylation. The aromatic heptaene 67-121C and two analogues of the [...] Read more.
A number of antifungal drugs are based on polyene macrolides that cause severe side effects. Most of these compounds contain a single aminodeoxysugar, D-mycosamine. Toxicity can be reduced by increasing the extent of glycosylation. The aromatic heptaene 67-121C and two analogues of the degenerate heptaene nystatin have a second sugar attached to the C4′ hydroxyl of mycosamine. Another nystatin analogue has L-digitoxose as a second sugar attached to C35 on the macrolactone ring. The pentaene selvamicin has 4-O-methyl-L-digitoxose at C27, the equivalent position. To assist the production of new antifungals by synthetic biology, we explore further the utility of three classes of polyene glycosyltransferase: extending glycosyltransferases that form disaccharide-containing polyenes, glycosyltransferases that add the L-digitoxose sugars of nystatin A3 and selvamicin, and mycosaminyltransferases that add the primary aminodeoxysugar. In addition, we combine enzymatic hyperglycosylation with a known chemical method for adding sugars to the C3′ amino group of mycosamine. This was used to convert the disaccharide-containing 67-121C heptaene to forms containing branched trisaccharide or tetrasaccharide chains. These analogues are of interest for testing as anti-Leishmania drugs. Full article
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10 pages, 7987 KiB  
Article
Chemo-Enzymatic Synthesis of Bioactive Carbazole Derivatives
by Saad Alrashdi, Federica Casolari, Kwaku Kyeremeh and Hai Deng
SynBio 2024, 2(1), 21-30; https://doi.org/10.3390/synbio2010002 - 04 Jan 2024
Viewed by 612
Abstract
Carbazoles are key scaffolds of either antimicrobial/antiviral alkaloid natural products or therapeutics. As such, access to structurally diverse indole-containing carbazoles has attracted considerable attention. In this report, a pilot study is described using biotransformation to provide carbazoles that contain various acyl substituents. The [...] Read more.
Carbazoles are key scaffolds of either antimicrobial/antiviral alkaloid natural products or therapeutics. As such, access to structurally diverse indole-containing carbazoles has attracted considerable attention. In this report, a pilot study is described using biotransformation to provide carbazoles that contain various acyl substituents. The biotransformation system contains the thiamine-diphosphate (ThDP)-dependent enzyme NzsH, the FabH-like 3-ketoacyl-ACP synthase NzsJ, and the aromatase/cyclase NzsI, encoded in the biosynthetic gene cluster (nzs) of the bacterial carbazole alkaloid natural product named neocarazostatin A. The utilization of a range of acyl-SNACs (synthetic acyl-thioester analogues of the native substrate) together with indole-3-pyruvate and pyruvate in the designed biotransformation system allows production of carbazole derivatives. Our results demonstrate that this three-enzyme system displays a considerable substrate profile toward acyl donors for production of carbazoles with different acyl substituents. Finally, two more enzymes were included in the biotransformation system: the tryptophan synthase stand-alone β-subunit variant, PfTrpB, generated from directed evolution in the literature, and a commercially available L-amino acid oxidase (LAAO). The addition of these two enzymes allows the transformation to start with indole building blocks to provide carbazoles with modifications in the indole ring system. Full article
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20 pages, 2409 KiB  
Review
Synthetic Proteins in Dental Applications
by Christian Andrea Lopez-Ayuso, Benjamin Aranda-Herrera, Dulce Guzman-Rocha, Patricia Alejandra Chavez-Granados and Rene Garcia-Contreras
SynBio 2024, 2(1), 1-20; https://doi.org/10.3390/synbio2010001 - 27 Dec 2023
Viewed by 777
Abstract
Biotechnology and artificial intelligence have sparked a revolution in dentistry, with a focus on restoring natural tissue functions. This transformation has given rise to bioactive materials, inspired by biomimetics, aimed at replicating the processes found in nature. As synthetic biology advances, there is [...] Read more.
Biotechnology and artificial intelligence have sparked a revolution in dentistry, with a focus on restoring natural tissue functions. This transformation has given rise to bioactive materials, inspired by biomimetics, aimed at replicating the processes found in nature. As synthetic biology advances, there is a heightened focus on signaling systems crucial for bio-based diagnostics and therapeutics. Dentistry now harnesses synthetic proteins for tissue regeneration and dental material enhancement. A current research priority is bacterial biofilm inhibition, vital for dental health. Given the role of Streptococcus mutans in dental caries, the development of synthetic antimicrobial peptides targeting this bacterium is underway. The balance of dental enamel between demineralization and remineralization impacts caries formation. Factors such as the presence of hydroxyapatite and salivary peptides influence enamel health. Recent studies have spotlighted salivary protein-inspired peptides for enhanced remineralization. In the realm of bone regeneration, synthetic proteins like bone morphogenetic proteins (BMP) have been spotlighted, earning FDA approval. Research is currently delving into peptides such as cementum protein 1 peptide (CEMP-1-p1) and parathyroid hormone variants like PTH (1-34), underscoring their potential in advancing dental and bone health. Full article
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