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Data-driven rational biosynthesis design: from molecules to cell factories.

Fu Chen1,2,3, Le Yuan2,4, Shaozhen Ding3

  • 1College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China.

Briefings in Bioinformatics
|June 28, 2019
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Summary
This summary is machine-generated.

Data-driven rational biosynthesis design leverages big data and computational tools to engineer cell factories. This approach enables automated design for biosynthesizing target molecules from biomass.

Keywords:
cell factory designdata-driven biosynthesis designenzyme function predictiongene construction and assemblytarget selection

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Area of Science:

  • Synthetic biology
  • Metabolic engineering
  • Bioinformatics

Background:

  • Recent advancements in chemical, reaction, and enzyme databases, alongside computational tools, facilitate data-driven rational biosynthesis design.
  • The era of big data, especially in biomedicine, presents opportunities for designing target-oriented chassis organisms through data-driven approaches.
  • Cell factory design aims to engineer complex metabolic systems for biosynthesizing target molecules from inexpensive biomass.

Purpose of the Study:

  • To outline the steps involved in data-driven rational biosynthesis design.
  • To provide an overview of computational tools and methods for each step of cell factory design.
  • To highlight the potential of a one-stop cell factory system for automated design.

Main Methods:

  • Target molecule selection and metabolic pathway design.
  • Prediction of novel enzymes using protein domain and structure analysis.
  • Large-scale DNA construction, assembly methods, and visualization tools.

Main Results:

  • Emergence of numerous databases and computational tools supporting data-driven biosynthesis.
  • Identification of key steps in data-driven cell factory design, from molecule selection to chassis engineering.
  • Development of integrated systems for automated design from molecule to chassis level.

Conclusions:

  • Data-driven rational biosynthesis design is a powerful approach for constructing engineered organisms.
  • The integration of various computational tools and databases streamlines the cell factory design process.
  • Automated, one-stop cell factory systems hold significant promise for future biotechnological applications.