Microbial Metabolic Engineering

1. Front Matter

   Pages i-x

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2. Pathway and Gene Discovery from Natural Hosts and Organisms

   • Jing Ke, Yasuo Yoshikuni

   Pages 1-9

3. Metabolic In Silico Network Expansions to Predict and Exploit Enzyme Promiscuity

   • James Jeffryes, Jonathan Strutz, Chris Henry, Keith E. J. Tyo

   Pages 11-21

4. Antisense RNA Elements for Downregulating Expression

   • Yaping Yang, Jian Wang, Ruihua Zhang, Yajun Yan

   Pages 23-35

5. Chemically Inducible Chromosomal Evolution (CIChE) for Multicopy Metabolic Pathway Engineering

   • Aaron M. Love, Bradley W. Biggs, Keith E. J. Tyo, Parayil Kumaran Ajikumar

   Pages 37-45

6. Bacterial Expression of Membrane-Associated Cytochrome P450s and Their Activity Assay in Nanodiscs

   • Demetrios Maroutsos, Hannah Huff, Aditi Das

   Pages 47-72

7. Delta Integration CRISPR-Cas (Di-CRISPR) in Saccharomyces cerevisiae

   • Shuobo Shi, Youyun Liang, Ee Lui Ang, Huimin Zhao

   Pages 73-91

8. Assembly of Complex Pathways Using Type IIs Restriction Enzymes

   • Sylvestre Marillonnet, Stefan Werner

   Pages 93-109

9. Combinatorial Assembly of Multigene Pathways by Combining Single-Strand Assembly with Golden Gate Assembly

   • D. Bauwens, P. Coussement, J. Maertens, Marjan De Mey

   Pages 111-123

10. Checks and Balances with Use of the Keio Collection for Phenotype Testing

    • Sandra J. Aedo, Helena R. Ma, Mark P. Brynildsen

    Pages 125-138

11. Genetic Engineering of Cyanobacteria: Design, Implementation, and Characterization of Recombinant Synechocystis sp. PCC 6803

    • Jacob Sebesta, Allison Werner, Christie Ann Marie Peebles

    Pages 139-154

12. Genetic Tools for Streamlined and Accelerated Pathway Engineering in Yarrowia lipolytica

    • Lynn Wong, Benjamin Holdridge, Jake Engel, Peng Xu

    Pages 155-177

13. Gas Chromatography–Mass Spectrometry Microbial Metabolomics for Applications in Strain Optimization

    • McKenzie L. Smith, April M. Miguez, Mark P. Styczynski

    Pages 179-189

14. Targeted Mass Spectrometry-Based Proteomics Tools for Strain Optimization

    • Hsien-Chung Tseng, Christine Nicole S. Santos

    Pages 191-201

15. A Protocol for the Construction and Curation of Genome-Scale Integrated Metabolic and Regulatory Network Models

    • Sriram Chandrasekaran

    Pages 203-214

16. 13C-Fingerprinting and Metabolic Flux Analysis of Bacterial Metabolisms

    • Whitney Hollinshead, Lian He, Yinjie J. Tang

    Pages 215-230

17. A Genetic Screen for the Isolation of Mutants with Increased Flux in the Isoprenoid Pathway of Yeast

    • Manisha Wadhwa, Anand K. Bachhawat

    Pages 231-246

18. Back Matter

    Pages 247-252

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This volume covers a wide array of topics that will aid researchers in the task of engineering complex biological systems. This book is divided into three parts: Part One discusses the discovery and identification of relevant biosynthetic pathways for engineering; Part Two looks at the development of genetic tools for manipulating enzymes, biosynthetic pathways, and whole genomes; and Part Three covers the characterization of engineered microbes using targeted and global systems biology tools, as well as in silico models. Chapters explore topics such as leveraging enzyme promiscuity to construct novel biosynthetic pathways; assembling combinatorial multigene pathways for rapid strain optimization; applying 'omics technologies for identifying bottlenecks; and engineering nontraditional host organisms like cyanobacterium and Yarrowia lipolytica. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.


Cutting edge and authoritative, Microbial Metabolic Engineering: Methods and Protocols is a valuable resource for researchers and scientists interested in engineering and optimizing microbes for a variety of biotechnological applications.

• biochemical pathways
• promoter libraries
• ribosome binding site design
• CLIVA
• genome editing

• Manus Bio, Cambridge, USA

  Christine Nicole S. Santos, Parayil Kumaran Ajikumar

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