Rewriting the Metabolic Blueprint: Advances in Pathway Diversification in Microorganisms

Hossain, Gazi Sakir; Nadarajan, Sivakumar; Zhang, Lei; Ng, Tee-Kheang; Foo, Jee Loon; Ling, Hua; Choi, Won Jae

doi:10.3389/fmicb.2018.00155

Cited by 9 publications

(2 citation statements)

References 66 publications

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“…Accessing new‐to‐Nature products through metabolic engineering is not only desirable but an actual necessity in a rapidly changing world in which access to natural, fossil‐based resources is becoming critical. Redesigning the biochemical palate of bacterial chassis is the way forward to access these novel products, and rewriting the metabolic blueprint to broaden the chemical repertoire achievable by engineered cells is a condition to access novel products (Hossain et al ., ). Note that such ambitious objective calls for deepening our current understanding of the very core metabolic wiring in bacteria, a subject that has recently gained much attention after quite some time of (undeserved) ostracism (Aslan et al ., ).…”

Section: Outlook and The Challenges Aheadmentioning

confidence: 99%

Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non‐traditional microorganisms

Calero

Nikel

2018

Microbial Biotechnology

223

184

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The last few years have witnessed an unprecedented increase in the number of novel bacterial species that hold potential to be used for metabolic engineering. Historically, however, only a handful of bacteria have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction - and only for the synthesis of very few, structurally simple compounds. One of the reasons for this unfortunate circumstance has been the dearth of tools for targeted genome engineering of bacterial chassis, and, nowadays, synthetic biology is significantly helping to bridge such knowledge gap. Against this background, in this review, we discuss the state of the art in the rational design and construction of robust bacterial chassis for metabolic engineering, presenting key examples of bacterial species that have secured a place in industrial bioproduction. The emergence of novel bacterial chassis is also considered at the light of the unique properties of their physiology and metabolism, and the practical applications in which they are expected to outperform other microbial platforms. Emerging opportunities, essential strategies to enable successful development of industrial phenotypes, and major challenges in the field of bacterial chassis development are also discussed, outlining the solutions that contemporary synthetic biology-guided metabolic engineering offers to tackle these issues.

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Section: Outlook and The Challenges Aheadmentioning

confidence: 99%

Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non‐traditional microorganisms

Calero

Nikel

2018

Microbial Biotechnology

223

184

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“…Living organisms have evolved over millions of years to build a complex metabolic network containing thousands of enzymatic reactions for their survival [ 1 ]. Enzymes are spatially organized in the cell to implement specific sequential reactions via the strategies of compartmentalization [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

Mechanistic Aspects for the Modulation of Enzyme Reactions on the DNA Scaffold

et al. 2022

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Cells have developed intelligent systems to implement the complex and efficient enzyme cascade reactions via the strategies of organelles, bacterial microcompartments and enzyme complexes. The scaffolds such as the membrane or protein in the cell are believed to assist the co-localization of enzymes and enhance the enzymatic reactions. Inspired by nature, enzymes have been located on a wide variety of carriers, among which DNA scaffolds attract great interest for their programmability and addressability. Integrating these properties with the versatile DNA–protein conjugation methods enables the spatial arrangement of enzymes on the DNA scaffold with precise control over the interenzyme distance and enzyme stoichiometry. In this review, we survey the reactions of a single type of enzyme on the DNA scaffold and discuss the proposed mechanisms for the catalytic enhancement of DNA-scaffolded enzymes. We also review the current progress of enzyme cascade reactions on the DNA scaffold and discuss the factors enhancing the enzyme cascade reaction efficiency. This review highlights the mechanistic aspects for the modulation of enzymatic reactions on the DNA scaffold.

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Evolutionary Approaches for Engineering Industrially Relevant Phenotypes in Bacterial Cell Factories

Fernández-Cabezón

Cros

Nikel

2019

Biotechnology Journal

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The bio‐based production of added‐value compounds (with applications as pharmaceuticals, biofuels, food ingredients, and building blocks) using bacterial platforms is a well‐established industrial activity. The design and construction of microbial cell factories (MCFs) with robust and stable industrially relevant phenotypes, however, remains one of the biggest challenges of contemporary biotechnology. In this review, traditional and cutting‐edge approaches for optimizing the performance of MCFs for industrial bioprocesses, rooted on the engineering principle of natural evolution (i.e., genetic variation and selection), are discussed. State‐of‐the‐art techniques to manipulate and increase genetic variation in bacterial populations and to construct combinatorial libraries of strains, both globally (i.e., genome level) and locally (i.e., individual genes or pathways, and entire sections and gene clusters of the bacterial genome) are presented. Cutting‐edge screening and selection technologies applied to isolate MCFs displaying enhanced phenotypes are likewise discussed. The review article is closed by presenting future trends in the design and construction of a new generation of MCFs that will contribute to the long‐sought‐after transformation from a petrochemical industry to a veritable sustainable bio‐based industry.

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Rewriting the Metabolic Blueprint: Advances in Pathway Diversification in Microorganisms

Cited by 9 publications

References 66 publications

Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non‐traditional microorganisms

Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non‐traditional microorganisms

Mechanistic Aspects for the Modulation of Enzyme Reactions on the DNA Scaffold

Evolutionary Approaches for Engineering Industrially Relevant Phenotypes in Bacterial Cell Factories

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