scholarly journals Streamlining Natural Products Biomanufacturing With Omics and Machine Learning Driven Microbial Engineering

2020 ◽  
Vol 8 ◽  
Author(s):  
Ahmad Bazli Ramzi ◽  
Syarul Nataqain Baharum ◽  
Hamidun Bunawan ◽  
Nigel S. Scrutton
Keyword(s):  
Machine Learning ◽  
Natural Products ◽  
Metabolic Engineering ◽  
Synthetic Biology ◽  
Production Capacity ◽  
Biosynthetic Pathways ◽  
Biosynthetic Genes ◽  
Bioactive Natural Products ◽  
Beneficial Uses ◽  
Analytical Tools

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.

Biosynthesis of bioactive natural products from Basidiomycota

2019 ◽  
Vol 17 (5) ◽  
pp. 1027-1036 ◽  
Author(s):  
Hsiao-Ching Lin ◽  
Ranuka T. Hewage ◽  
Yuan-Chun Lu ◽  
Yit-Heng Chooi
Keyword(s):  
Natural Products ◽  
Bioactive Compounds ◽  
Biosynthetic Pathways ◽  
Bioactive Natural Products ◽  
Wide Range

The club fungi, Basidioycota, produce a wide range of bioactive compounds. Here, we describe recent studies on the biosynthetic pathways and enzymes of bioactive natural products from these fungi.

Facilitate Collaborations among Synthetic Biology, Metabolic Engineering and Machine Learning

2016 ◽  
Vol 3 (2) ◽  
pp. 45-54 ◽  
Author(s):  
Stephen Gang Wu ◽  
Kazuyuki Shimizu ◽  
Joseph Kuo-Hsiang Tang ◽  
Yinjie J. Tang
Keyword(s):  
Machine Learning ◽  
Metabolic Engineering ◽  
Synthetic Biology

scholarly journals Natural product biosyntheses in cyanobacteria: A treasure trove of unique enzymes

2011 ◽  
Vol 7 ◽  
pp. 1622-1635 ◽  
Author(s):  
Jan-Christoph Kehr ◽  
Douglas Gatte Picchi ◽  
Elke Dittmann
Keyword(s):  
Natural Products ◽  
Synthetic Biology ◽  
Natural Product ◽  
Bioactive Compounds ◽  
Polyketide Synthase ◽  
Biosynthetic Pathways ◽  
Peptide Synthetase ◽  
Biochemical Studies ◽  
Terrestrial Habitats ◽  
The Individual

Cyanobacteria are prolific producers of natural products. Investigations into the biochemistry responsible for the formation of these compounds have revealed fascinating mechanisms that are not, or only rarely, found in other microorganisms. In this article, we survey the biosynthetic pathways of cyanobacteria isolated from freshwater, marine and terrestrial habitats. We especially emphasize modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) pathways and highlight the unique enzyme mechanisms that were elucidated or can be anticipated for the individual products. We further include ribosomal natural products and UV-absorbing pigments from cyanobacteria. Mechanistic insights obtained from the biochemical studies of cyanobacterial pathways can inspire the development of concepts for the design of bioactive compounds by synthetic-biology approaches in the future.

scholarly journals Genome Mining as New Challenge in Natural Products Discovery

Marine Drugs ◽  
2020 ◽  
Vol 18 (4) ◽  
pp. 199 ◽  
Author(s):  
Luisa Albarano ◽  
Roberta Esposito ◽  
Nadia Ruocco ◽  
Maria Costantini
Keyword(s):  
Natural Products ◽  
Drug Discovery ◽  
Synthetic Biology ◽  
Anticancer Agents ◽  
Genome Mining ◽  
Bioactive Natural Products ◽  
Advantages And Disadvantages ◽  
A Genome ◽  
Living Organisms ◽  
Natural Drugs

Drug discovery is based on bioactivity screening of natural sources, traditionally represented by bacteria fungi and plants. Bioactive natural products and their secondary metabolites have represented the main source for new therapeutic agents, used as drug leads for new antibiotics and anticancer agents. After the discovery of the first biosynthetic genes in the last decades, the researchers had in their hands the tool to understand the biosynthetic logic and genetic basis leading to the production of these compounds. Furthermore, in the genomic era, in which the number of available genomes is increasing, genome mining joined to synthetic biology are offering a significant help in drug discovery. In the present review we discuss the importance of genome mining and synthetic biology approaches to identify new natural products, also underlining considering the possible advantages and disadvantages of this technique. Moreover, we debate the associated techniques that can be applied following to genome mining for validation of data. Finally, we review on the literature describing all novel natural drugs isolated from bacteria, fungi, and other living organisms, not only from the marine environment, by a genome-mining approach, focusing on the literature available in the last ten years.

scholarly journals Metabolic engineering for plant natural products biosynthesis: new procedures, concrete achievements and remaining limits

2021 ◽  
Author(s):  
Vincent Courdavault ◽  
Sarah E. O'Connor ◽  
Michael K. Jensen ◽  
Nicolas Papon
Keyword(s):  
Natural Products ◽  
Metabolic Engineering ◽  
Biosynthetic Pathways ◽  
Plant Natural Products ◽  
New Procedures

The recent achievements in the transfer of biosynthetic pathways of plant natural products in heterologous organisms offer new perspectives towards the supply of these compounds through metabolic engineering approaches.

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