Issue 3, Volume 1 – 5 articles

Metabolic Engineering of Microorganisms Towards the Biomanufacturing of Non-Natural C5 and C6 Chemicals

Five-carbon (C5) and six-carbon (C6) chemicals are essential components in the manufacturing of a variety of pharmaceuticals, fuels, polymers, and other materials. However, the predominant reliance on chemical synthesis methods and unsustainable feedstock sources has placed significant strain on Earth’s finite fossil resources and the environment. To address this challenge and promote sustainability, significant efforts have been undertaken to re-program microorganisms through metabolic engineering and synthetic biology approaches allowing for bio-based manufacturing of these compounds. This review provides a comprehensive overview of the advancements in microbial production of commercially significant non-natural C5 chemicals, including 1-pentanol, 1,5-pentanediol, cadaverine, δ-valerolactam, glutaric acid, glutaconic acid, and 5-hydroxyvaleric acid, as well as C6 chemicals, including cis, cis-muconic acid, adipic acid, 1,6-hexamethylenediamine, 6-aminocaproic acid, β-methyl-δ-valerolactone, 1-hexanol, ε-caprolactone, 6-hydroxyhexanoic acid, and 1,6-hexanediol.

Time-efficient and Semi-automated Production and Screening of Proteins

Fast, flexible and non-randomized modification, production and screening of proteins in fully automated system are of high interest in biological research and applications. The conventional methods for protein engineering and screening, especially for mutations of multiple residues. are time consuming and often unreliable. We demonstrate here a new, fast and flexible protein production and screening method which combines linear expression template (LET) based cell free protein synthesis (CFPS) with specific screening methods. This approach is demonstrated using green fluorescence protein, phosphoserine aminotransferase (serC) and aspartokinase III (AKIII) as model systems. The results show that mutants with changes in different protein properties upon multiple point mutations can be produced and screened within 6 to 15 h. This method can be used further to generate mutants of enzymes and multi-enzyme complexes and be implemented within the workflow of a feedback-guided protein optimization and screening system.

Serine Integrase-based Recombination Enables Direct Plasmid Assembly In Vivo

Serine integrases are emerging as one of the powerful tools for synthetic biology. They have been widely developed across genome engineering, biological part construction, genetic circuit design, and in vitro DNA assembly. However, the strategy of in vivo DNA assembly by serine integrases has not yet been reported. To address this opportunity, here we developed a serine integrase-based in vivo DNA (plasmid) assembly approach. First, we demonstrated that the engineered “Acceptor” plasmids could be assembled with diverse “Donor” plasmids by serine integrases (Bxb1 and phiC31) in Escherichia coli (E. coli). Then, by programming the “Donor” plasmids and the host E. coli cells, we established an assembly cascade procedure and finally constructed plasmids that could constitutively express three different fluorescent proteins. Moreover, we used this approach to assemble different chromoprotein genes and generated colored E. coli cells. We anticipate that this approach will enrich the serine integrase-based biotechnology toolbox, and accelerate multiple plasmid assembly for synthetic biology with broad applications.

Deciphering the Code of Pattern Formation: Integrating In Silico and Wet Lab Approaches in Synthetic Biology

Pattern formation is a fundamental process in biological development, enabling the transformation of initially uniform or random states into spatially ordered structures. A comprehensive understanding of the formation and function of these patterns is crucial for unraveling the underlying principles of biological design and engineering. In recent years, synthetic biology has emerged as a powerful discipline for investigating and manipulating pattern formation in biological systems, involving the design and construction of novel biological components, circuits, and networks with specific functionalities. The integration of computational simulations (in silico) and experimental techniques (wet lab) in synthetic biology has significantly advanced our knowledge of pattern formation and its implications in biological design and engineering. This review provides an overview of the computational simulations employed in studying pattern formation and introduces the representative and cutting-edge experimental methods utilized in wet labs.

A Perspective in Future Biomanufacturing: Challenges in Industrial Fermentation—Understanding and Controlling Microbial Lifespan and Aging