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Current advancements in systems and synthetic biology studies of Saccharomyces cerevisiae

Ting TY, Li Y, Bunawan H, Ramzi AB, Goh HH

J Biosci Bioeng, 2023 Apr;135(4):259-265.
PMID: 36803862 DOI: 10.1016/j.jbiosc.2023.01.010

Saccharomyces cerevisiae has a long-standing history of biotechnological applications even before the dawn of modern biotechnology. The field is undergoing accelerated advancement with the recent systems and synthetic biology approaches. In this review, we highlight the recent findings in the field with a focus on omics studies of S. cerevisiae to investigate its stress tolerance in different industries. The latest advancements in S. cerevisiae systems and synthetic biology approaches for the development of genome-scale metabolic models (GEMs) and molecular tools such as multiplex Cas9, Cas12a, Cpf1, and Csy4 genome editing tools, modular expression cassette with optimal transcription factors, promoters, and terminator libraries as well as metabolic engineering. Omics data analysis is key to the identification of exploitable native genes/proteins/pathways in S. cerevisiae with the optimization of heterologous pathway implementation and fermentation conditions. Through systems and synthetic biology, various heterologous compound productions that require non-native biosynthetic pathways in a cell factory have been established via different strategies of metabolic engineering integrated with machine learning.

Matched MeSH terms: Synthetic Biology*
Metabolic Engineering and Synthetic Biology

Ramzi AB

Adv Exp Med Biol, 2018 11 2;1102:81-95.
PMID: 30382570 DOI: 10.1007/978-3-319-98758-3_6

In the modern era of next-generation genomics and Fourth Industrial Revolution, there is a growing demand for translational research that brings about not only impactful research but also potential commercialisation of R- and D-based products. Advancement of metabolic engineering and synthetic biology has put forward a viable and innovative biotechnological platform for bioproduct development especially using microbial chassis. In this chapter, readers will be introduced on the concepts of metabolic engineering, synthetic biology and microbial chassis and the applications of these biological engineering (BioE) components in the advancement of industrial and agricultural biotechnology. Main strategies in employing BioE platform are discussed especially for waste bioconversion and value-added product development. More importantly, this chapter will also discuss current endeavours in integrating systems and synthetic biology for microbial production of natural products by introducing flavonoid biosynthesis genes of Polygonum minus, a medicinally important tropical plant in engineered yeast.

Matched MeSH terms: Synthetic Biology*
Prospects and progress in the production of valuable carotenoids: Insights from metabolic engineering, synthetic biology, and computational approaches

Sankari M, Rao PR, Hemachandran H, Pullela PK, Doss C GP, Tayubi IA, et al.

J Biotechnol, 2018 Jan 20;266:89-101.
PMID: 29247672 DOI: 10.1016/j.jbiotec.2017.12.010

Carotenoids are isoprenoid pigments synthesized exclusively by plants and microorganisms and play critical roles in light harvesting, photoprotection, attracting pollinators and phytohormone production. In recent years, carotenoids have been used for their health benefits due to their high antioxidant activity and are extensively utilized in food, pharmaceutical, and nutraceutical industries. Regulation of carotenoid biosynthesis occurs throughout the life cycle of plants, with vibrant changes in composition based on developmental needs and responses to external environmental stimuli. With advancements in metabolic engineering techniques, there has been tremendous progress in the production of industrially valuable secondary metabolites such as carotenoids. Application of metabolic engineering and synthetic biology has become essential for the successful and improved production of carotenoids. Synthetic biology is an emerging discipline; metabolic engineering approaches may provide insights into novel ideas for biosynthetic pathways. In this review, we discuss the current knowledge on carotenoid biosynthetic pathways and genetic engineering of carotenoids to improve their nutritional value. In addition, we investigated synthetic biological approaches for the production of carotenoids. Theoretical biology approaches that may aid in understanding the biological sciences are discussed in this review. A combination of theoretical knowledge and experimental strategies may improve the production of industrially relevant secondary metabolites.

Matched MeSH terms: Synthetic Biology/methods*
Fulltext Streamlining Natural Products Biomanufacturing With Omics and Machine Learning Driven Microbial Engineering

Ramzi AB, Baharum SN, Bunawan H, Scrutton NS

Front Bioeng Biotechnol, 2020;8:608918.
PMID: 33409270 DOI: 10.3389/fbioe.2020.608918

Increasing demands for the supply of biopharmaceuticals have propelled the advancement of metabolic engineering and synthetic biology strategies for biomanufacturing of bioactive natural products. Using metabolically engineered microbes as the bioproduction hosts, a variety of natural products including terpenes, flavonoids, alkaloids, and cannabinoids have been synthesized through the construction and expression of known and newly found biosynthetic genes primarily from model and non-model plants. The employment of omics technology and machine learning (ML) platforms as high throughput analytical tools has been increasingly leveraged in promoting data-guided optimization of targeted biosynthetic pathways and enhancement of the microbial production capacity, thereby representing a critical debottlenecking approach in improving and streamlining natural products biomanufacturing. To this end, this mini review summarizes recent efforts that utilize omics platforms and ML tools in strain optimization and prototyping and discusses the beneficial uses of omics-enabled discovery of plant biosynthetic genes in the production of complex plant-based natural products by bioengineered microbes.

Matched MeSH terms: Synthetic Biology
Current progress in production of flavonoids using systems and synthetic biology platforms

Ku Nurul Aqmar Ku Bahaudin, Ahmad Bazli Ramzi, Syarul Nataqain Baharum, Suriana Sabri, Adam Leow Thean Chor, Tewin Tencomnao

Sains Malaysiana, 2018;47:3077-3084.

Flavonoid is an industrially-important compound due to its high pharmaceutical and cosmeceutical values. However,
conventional methods in extracting and synthesizing flavonoids are costly, laborious and not sustainable due to small
amount of natural flavonoids, large amounts of chemicals and space used. Biotechnological production of flavonoids
represents a viable and sustainable route especially through the use of metabolic engineering strategies in microbial
production hosts. In this review, we will highlight recent strategies for the improving the production of flavonoids
using synthetic biology approaches in particular the innovative strategies of genetically-encoded biosensors for in
vivo metabolite analysis and high-throughput screening methods using fluorescence-activated cell sorting (FACS).
Implementation of transcription factor based-biosensor for microbial flavonoid production and integration of systems
and synthetic biology approaches for natural product development will also be discussed.

Matched MeSH terms: Synthetic Biology
Fulltext Bacterial Biopolymer: Its Role in Pathogenesis to Effective Biomaterials

Ghosh S, Lahiri D, Nag M, Dey A, Sarkar T, Pathak SK, et al.

Polymers (Basel), 2021 Apr 12;13(8).
PMID: 33921239 DOI: 10.3390/polym13081242

Bacteria are considered as the major cell factories, which can effectively convert nitrogen and carbon sources to a wide variety of extracellular and intracellular biopolymers like polyamides, polysaccharides, polyphosphates, polyesters, proteinaceous compounds, and extracellular DNA. Bacterial biopolymers find applications in pathogenicity, and their diverse materialistic and chemical properties make them suitable to be used in medicinal industries. When these biopolymer compounds are obtained from pathogenic bacteria, they serve as important virulence factors, but when they are produced by non-pathogenic bacteria, they act as food components or biomaterials. There have been interdisciplinary studies going on to focus on the molecular mechanism of synthesis of bacterial biopolymers and identification of new targets for antimicrobial drugs, utilizing synthetic biology for designing and production of innovative biomaterials. This review sheds light on the mechanism of synthesis of bacterial biopolymers and its necessary modifications to be used as cell based micro-factories for the production of tailor-made biomaterials for high-end applications and their role in pathogenesis.

Matched MeSH terms: Synthetic Biology
Recombinant LipL32 Protein Developed Using a Synthetic Gene Detects Leptospira-specific Antibodies in Human Serum Samples

Yaakob Y, Rodrigues KF, Opook F, William T, John DV

Malays J Med Sci, 2017 Oct;24(5):44-51.
PMID: 29386971 DOI: 10.21315/mjms2017.24.5.5

Background: Synthetic biology is emerging as a viable alternative for the production of recombinant antigens for diagnostic applications. It offers a safe alternative for the synthesis of antigenic principles derived from organisms that pose a high biological risk.
Methods: Here, we describe an enzyme-linked immunosorbent assay (ELISA) using the synthetic recombinant LipL32 (rLipL32) protein expressed in Escherichia coli for the detection of Leptospira-specific antibodies in human serum samples. The rLipL32-based ELISA was compared with a microscopic agglutination test (MAT), which is currently used as the gold standard for the diagnosis of leptospirosis.
Results: Our results showed that all the MAT-positive serum samples were positive for Leptospira-specific IgG in an ELISA, while 65% (n = 13) of these samples were also positive for Leptospira-specific IgM. In the MAT-negative serum samples, 80% and 55% of the samples were detected as negative by an ELISA for Leptospira-specific IgM and IgG, respectively.
Conclusion: An ELISA using the synthetic rLipL32 antigen was able to distinguish Leptospira-specific IgM (sensitivity 65% and specificity 80%) and IgG (sensitivity 100% and specificity 55%) in human serum samples and has the potential to serve as a rapid diagnostic test for leptospirosis.

Matched MeSH terms: Synthetic Biology
Recent advancements in high-level synthesis of the promising clinical drug, prodigiosin

Yip CH, Yarkoni O, Ajioka J, Wan KL, Nathan S

Appl Microbiol Biotechnol, 2019 Feb;103(4):1667-1680.
PMID: 30637495 DOI: 10.1007/s00253-018-09611-z

Prodigiosin, a red linear tripyrrole pigment and a member of the prodiginine family, is normally secreted by the human pathogen Serratia marcescens as a secondary metabolite. Studies on prodigiosin have received renewed attention as a result of reported immunosuppressive, antimicrobial and anticancer properties. High-level synthesis of prodigiosin and the bioengineering of strains to synthesise useful prodiginine derivatives have also been a subject of investigation. To exploit the potential use of prodigiosin as a clinical drug targeting bacteria or as a dye for textiles, high-level synthesis of prodigiosin is a prerequisite. This review presents an overview on the biosynthesis of prodigiosin from its natural host Serratia marcescens and through recombinant approaches as well as highlighting the beneficial properties of prodigiosin. We also discuss the prospect of adopting a synthetic biology approach for safe and cost-effective production of prodigiosin in a more industrially compliant surrogate host.

Matched MeSH terms: Synthetic Biology/methods
Fulltext Optimization: Molecular Communication Networks for Viral Disease Analysis Using Deep Leaning Autoencoder

Junejo AR, Kaabar MKA, Li X

Comput Math Methods Med, 2021;2021:9949328.
PMID: 34938362 DOI: 10.1155/2021/9949328

Developing new treatments for emerging infectious diseases in infectious and noninfectious diseases has attracted a particular attention. The emergence of viral diseases is expected to accelerate; these data indicate the need for a proactive approach to develop widely active family specific and cross family therapies for future disease outbreaks. Viral disease such as pneumonia, severe acute respiratory syndrome type 2, HIV infection, and Hepatitis-C virus can cause directly and indirectly cardiovascular disease (CVD). Emphasis should be placed not only on the development of broad-spectrum molecules and antibodies but also on host factor therapy, including the reutilization of previously approved or developing drugs. Another new class of therapeutics with great antiviral therapeutic potential is molecular communication networks using deep learning autoencoder (DL-AEs). The use of DL-AEs for diagnosis and prognosis prediction of infectious and noninfectious diseases has attracted a particular attention. MCN is map to molecular signaling and communication that are found inside and outside the human body where the goal is to develop a new black box mechanism that can serve the future robust healthcare industry (HCI). MCN has the ability to characterize the signaling process between cells and infectious disease locations at various levels of the human body called point-to-point MCN through DL-AE and provide targeted drug delivery (TDD) environment. Through MCN, and DL-AE healthcare provider can remotely measure biological signals and control certain processes in the required organism for the maintenance of the patient's health state. We use biomicrodevices to promote the real-time monitoring of human health and storage of the gathered data in the cloud. In this paper, we use the DL-based AE approach to design and implement a new drug source and target for the MCN under white Gaussian noise. Simulation results show that transceiver executions for a given medium model that reduces the bit error rate which can be learned. Then, next development of molecular diagnosis such as heart sounds is classified. Furthermore, biohealth interface for the inside and outside human body mechanism is presented, comparative perspective with up-to-date current situation about MCN.

Matched MeSH terms: Synthetic Biology