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Book: Microbial metabolic engineering

Santos, Christine Nicole S. / Ajikumar, Parayil Kumaran

methods and protocols

(Methods in molecular biology ; 1927 ; Springer protocols)

2019

Author's details	edited by Christine Nicole S. Santos and Parayil Kumaran Ajikumar
Series title	Methods in molecular biology ; 1927 Springer protocols
Collection
Language	English
Size	x, 252 Seiten, Illustrationen
Publisher	Humana Press
Publishing place	New York, NY
Publishing country	United States
Document type	Book
HBZ-ID	HT019995897
ISBN	978-1-4939-9141-9 ; 9781493991426 ; 1-4939-9141-8 ; 1493991426
Database	Catalogue ZB MED Medicine, Health

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Shelf mark	Loan status	Location
Zs A 7042 -1927-	verfügbar in Königswinter	Königswinter

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Article ; Online: Enabling commercial success of industrial biotechnology.

Biggs, Bradley W / Alper, Hal S / Pfleger, Brian F / Tyo, Keith E J / Santos, Christine N S / Ajikumar, Parayil Kumaran / Stephanopoulos, Gregory

Science (New York, N.Y.)

2021 Volume 374, Issue 6575, Page(s) 1563–1565

Abstract: Commercial-scale research translation has been muted. ...

Abstract	Commercial-scale research translation has been muted.
MeSH term(s)	Biocatalysis ; Bioengineering/economics ; Biotechnology/economics ; Biotechnology/education ; Biotechnology/instrumentation ; Commerce ; Industry/economics ; Industry/instrumentation ; Metabolic Engineering/economics ; Policy ; Translational Research, Biomedical
Language	English
Publishing date	2021-12-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abj5040
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Zs.MG 77: Show issues

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Article ; Online: Chemically Inducible Chromosomal Evolution (CIChE) for Multicopy Metabolic Pathway Engineering.

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

Methods in molecular biology (Clifton, N.J.)

2019 Volume 1927, Page(s) 37–45

Abstract: Chemically inducible chromosomal evolution (CIChE) was developed for stable multicopy chromosomal integration of heterologous genes. In this technique, flanking an antibiotic selection marker and a gene of interest with identical regions of homology ... ...

Abstract	Chemically inducible chromosomal evolution (CIChE) was developed for stable multicopy chromosomal integration of heterologous genes. In this technique, flanking an antibiotic selection marker and a gene of interest with identical regions of homology permits gene duplication via recA mediated homologous recombination. A strong selective pressure for gene duplication can be applied by increasing antibiotic concentration, and in a week's time one can create a set of strains with a wide range of cassette copy numbers (upward of 20×), which can be made stable by deletion of recA. Herein, we describe a generalized workflow for this methodology.
MeSH term(s)	Chromosomes ; Chromosomes, Bacterial ; Escherichia coli/genetics ; Evolution, Molecular ; Gene Deletion ; Gene Duplication ; Metabolic Engineering ; Metabolic Networks and Pathways ; Plasmids/genetics ; Rec A Recombinases/genetics ; Rec A Recombinases/metabolism ; Reproducibility of Results ; Transformation, Genetic
Chemical Substances	Rec A Recombinases (EC 2.7.7.-)
Language	English
Publishing date	2019-02-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9142-6_4
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Article ; Online: Biotechnological production of natural zero-calorie sweeteners.

Philippe, Ryan N / De Mey, Marjan / Anderson, Jeff / Ajikumar, Parayil Kumaran

Current opinion in biotechnology

2014 Volume 26, Page(s) 155–161

Abstract: The increasing public awareness of adverse health impacts from excessive sugar consumption has created increasing interest in plant-derived, natural low-calorie or zero-calorie sweeteners. Two plant species which contain natural sweeteners, Stevia ... ...

Abstract	The increasing public awareness of adverse health impacts from excessive sugar consumption has created increasing interest in plant-derived, natural low-calorie or zero-calorie sweeteners. Two plant species which contain natural sweeteners, Stevia rebaudiana and Siraitia grosvenorii, have been extensively profiled to identify molecules with high intensity sweetening properties. However, sweetening ability does not necessarily make a product viable for commercial applications. Some criteria for product success are proposed to identify which targets are likely to be accepted by consumers. Limitations of plant-based production are discussed, and a case is put forward for the necessity of biotechnological production methods such as plant cell culture or microbial fermentation to meet needs for commercial-scale production of natural sweeteners.
MeSH term(s)	Biotechnology/economics ; Biotechnology/methods ; Calorimetry ; Cucurbitaceae/chemistry ; Food Industry/economics ; Food Industry/methods ; Humans ; Stevia/chemistry ; Sweetening Agents/chemistry ; Sweetening Agents/economics ; Sweetening Agents/isolation & purification ; Sweetening Agents/supply & distribution
Chemical Substances	Sweetening Agents
Language	English
Publishing date	2014-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	1052045-4
ISSN	1879-0429 ; 0958-1669
ISSN (online)	1879-0429
ISSN	0958-1669
DOI	10.1016/j.copbio.2014.01.004
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Article ; Online: Publisher Correction: Engineered bidirectional promoters enable rapid multi-gene co-expression optimization.

Vogl, Thomas / Kickenweiz, Thomas / Pitzer, Julia / Sturmberger, Lukas / Weninger, Astrid / Biggs, Bradley W / Köhler, Eva-Maria / Baumschlager, Armin / Fischer, Jasmin Elgin / Hyden, Patrick / Wagner, Marlies / Baumann, Martina / Borth, Nicole / Geier, Martina / Ajikumar, Parayil Kumaran / Glieder, Anton

Nature communications

2021 Volume 12, Issue 1, Page(s) 1287

Language	English
Publishing date	2021-02-18
Publishing country	England
Document type	Published Erratum
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-21369-z
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Article ; Online: Heterologous expression and characterization of plant Taxadiene-5α-Hydroxylase (CYP725A4) in Escherichia coli.

Rouck, John Edward / Biggs, Bradley Walters / Kambalyal, Amogh / Arnold, William R / De Mey, Marjan / Ajikumar, Parayil Kumaran / Das, Aditi

Protein expression and purification

2017 Volume 132, Page(s) 60–67

Abstract: Taxadiene-5α-Hydroxylase (CYP725A4) is a membrane-bound plant cytochrome P450 that catalyzes the oxidation of taxadiene to taxadiene-5α-ol. This oxidation is a key step in the production of the valuable cancer therapeutic and natural plant product, taxol. ...

Abstract	Taxadiene-5α-Hydroxylase (CYP725A4) is a membrane-bound plant cytochrome P450 that catalyzes the oxidation of taxadiene to taxadiene-5α-ol. This oxidation is a key step in the production of the valuable cancer therapeutic and natural plant product, taxol. In this work, we report the bacterial expression and purification of six different constructs of CYP725A4. All six of these constructs are N-terminally modified and three of them are fused to cytochrome P450 reductase to form a chimera construct. The construct with the highest yield of CYP725A4 protein was then selected for substrate binding and kinetic analysis. Taxadiene binding followed type-1 substrate patterns with an observed K
MeSH term(s)	Alkenes/chemistry ; Binding Sites ; Cytochrome P-450 Enzyme System/biosynthesis ; Cytochrome P-450 Enzyme System/chemistry ; Cytochrome P-450 Enzyme System/genetics ; Cytochrome P-450 Enzyme System/isolation & purification ; Diterpenes/chemistry ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Kinetics ; Plant Proteins/biosynthesis ; Plant Proteins/chemistry ; Plant Proteins/genetics ; Plant Proteins/isolation & purification ; Recombinant Proteins/biosynthesis ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/isolation & purification ; Taxus/enzymology ; Taxus/genetics
Chemical Substances	Alkenes ; Diterpenes ; Plant Proteins ; Recombinant Proteins ; taxa-4(5),11(12)diene ; Cytochrome P-450 Enzyme System (9035-51-2)
Language	English
Publishing date	2017-01-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1055455-5
ISSN	1096-0279 ; 1046-5928
ISSN (online)	1096-0279
ISSN	1046-5928
DOI	10.1016/j.pep.2017.01.008
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Article ; Online: Stabilized gene duplication enables long-term selection-free heterologous pathway expression.

Tyo, Keith E J / Ajikumar, Parayil Kumaran / Stephanopoulos, Gregory

Nature biotechnology

2009 Volume 27, Issue 8, Page(s) 760–765

Abstract: Engineering robust microbes for the biotech industry typically requires high-level, genetically stable expression of heterologous genes and pathways. Although plasmids have been used for this task, fundamental issues concerning their genetic stability ... ...

Abstract	Engineering robust microbes for the biotech industry typically requires high-level, genetically stable expression of heterologous genes and pathways. Although plasmids have been used for this task, fundamental issues concerning their genetic stability have not been adequately addressed. Here we describe chemically inducible chromosomal evolution (CIChE), a plasmid-free, high gene copy expression system for engineering Escherichia coli. CIChE uses E. coli recA homologous recombination to evolve a chromosome with approximately 40 consecutive copies of a recombinant pathway. Pathway copy number is stabilized by recA knockout, and the resulting engineered strain requires no selection markers and is unaffected by plasmid instabilities. Comparison of CIChE-engineered strains with equivalent plasmids revealed that CIChE improved genetic stability approximately tenfold and growth phase-specific productivity approximately fourfold for a strain producing the high metabolic burden-biopolymer poly-3-hydroxybutyrate. We also increased the yield of the nutraceutical lycopene by 60%. CIChE should be applicable in many organisms, as it only requires having targeted genomic integration methods and a recA homolog.
MeSH term(s)	3-Hydroxybutyric Acid/metabolism ; Alleles ; Anti-Bacterial Agents/pharmacology ; Carotenoids/metabolism ; Chromosomes, Bacterial/genetics ; DNA, Recombinant/genetics ; Directed Molecular Evolution ; Escherichia coli/genetics ; Gene Dosage/drug effects ; Gene Duplication/drug effects ; Gene Expression/drug effects ; Genomic Instability/drug effects ; Lycopene ; Mutation/genetics ; Plasmids/genetics ; Selection, Genetic ; Time Factors
Chemical Substances	Anti-Bacterial Agents ; DNA, Recombinant ; Carotenoids (36-88-4) ; Lycopene (SB0N2N0WV6) ; 3-Hydroxybutyric Acid (TZP1275679)
Language	English
Publishing date	2009-07-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/nbt.1555
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Article ; Online: DNA-directed assembly microarray for protein and small molecule inhibitor screening.

Kiat, Ng Jin / Simeon, Fritz / Phon, Too Heng / Ajikumar, Parayil Kumaran

Methods in molecular biology (Clifton, N.J.)

2011 Volume 716, Page(s) 127–140

Abstract: A robust high-throughput and high-fidelity screening platform for identifying and validating potential target molecules is the key for drug development. During the past decade, microarray platforms have demonstrated enormous potential for developing ... ...

Abstract	A robust high-throughput and high-fidelity screening platform for identifying and validating potential target molecules is the key for drug development. During the past decade, microarray platforms have demonstrated enormous potential for developing robust tools for small molecules as well as protein-based drug discovery and analysis. Recently, we developed a DNA-directed assembly microarray platform with improved screening and immobilization strategies. In contrast to conventional microarray platforms, our technique allows the solution phase interaction of the probes and analytes in a biological environment and further the detection through the directed assembly of specific DNA probes on a dendrimer-modified glass surface. Herein, we describe the detailed experimental protocols in performing the DNA-directed assembly platform for antibody microarray, a RNA polymerase-DNA binding microarray, and a drug-screening microarray.
MeSH term(s)	Animals ; Antibodies/chemistry ; Base Sequence ; DNA, Single-Stranded/chemistry ; DNA-Directed RNA Polymerases/antagonists & inhibitors ; DNA-Directed RNA Polymerases/metabolism ; Dendrimers/chemistry ; Drug Evaluation, Preclinical/instrumentation ; Drug Evaluation, Preclinical/methods ; Equipment Design ; Humans ; Molecular Sequence Data ; Protein Array Analysis/instrumentation ; Protein Array Analysis/methods ; Protein Binding ; Proteins/antagonists & inhibitors ; Proteins/metabolism
Chemical Substances	Antibodies ; DNA, Single-Stranded ; Dendrimers ; PAMAM Starburst ; Proteins ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
Language	English
Publishing date	2011
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-61779-012-6_7
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Article ; Online: Overcoming heterologous protein interdependency to optimize P450-mediated Taxol precursor synthesis in Escherichia coli.

Biggs, Bradley Walters / Lim, Chin Giaw / Sagliani, Kristen / Shankar, Smriti / Stephanopoulos, Gregory / De Mey, Marjan / Ajikumar, Parayil Kumaran

Proceedings of the National Academy of Sciences of the United States of America

2016 Volume 113, Issue 12, Page(s) 3209–3214

Abstract: Recent advances in metabolic engineering have demonstrated the potential to exploit biological chemistry for the synthesis of complex molecules. Much of the progress to date has leveraged increasingly precise genetic tools to control the transcription ... ...

Abstract	Recent advances in metabolic engineering have demonstrated the potential to exploit biological chemistry for the synthesis of complex molecules. Much of the progress to date has leveraged increasingly precise genetic tools to control the transcription and translation of enzymes for superior biosynthetic pathway performance. However, applying these approaches and principles to the synthesis of more complex natural products will require a new set of tools for enabling various classes of metabolic chemistries (i.e., cyclization, oxygenation, glycosylation, and halogenation) in vivo. Of these diverse chemistries, oxygenation is one of the most challenging and pivotal for the synthesis of complex natural products. Here, using Taxol as a model system, we use nature's favored oxygenase, the cytochrome P450, to perform high-level oxygenation chemistry in Escherichia coli. An unexpected coupling of P450 expression and the expression of upstream pathway enzymes was discovered and identified as a key obstacle for functional oxidative chemistry. By optimizing P450 expression, reductase partner interactions, and N-terminal modifications, we achieved the highest reported titer of oxygenated taxanes (∼570 ± 45 mg/L) in E. coli. Altogether, this study establishes E. coli as a tractable host for P450 chemistry, highlights the potential magnitude of protein interdependency in the context of synthetic biology and metabolic engineering, and points to a promising future for the microbial synthesis of complex chemical entities.
MeSH term(s)	Antineoplastic Agents, Phytogenic/metabolism ; Cytochrome P-450 Enzyme System/physiology ; Escherichia coli/metabolism ; Paclitaxel/metabolism
Chemical Substances	Antineoplastic Agents, Phytogenic ; Cytochrome P-450 Enzyme System (9035-51-2) ; Paclitaxel (P88XT4IS4D)
Language	English
Publishing date	2016-03-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1515826113
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Article ; Online: Integrating the protein and metabolic engineering toolkits for next-generation chemical biosynthesis.

Pirie, Christopher M / De Mey, Marjan / Jones Prather, Kristala L / Ajikumar, Parayil Kumaran

ACS chemical biology

2013 Volume 8, Issue 4, Page(s) 662–672

Abstract: Through microbial engineering, biosynthesis has the potential to produce thousands of chemicals used in everyday life. Metabolic engineering and synthetic biology are fields driven by the manipulation of genes, genetic regulatory systems, and enzymatic ... ...

Abstract	Through microbial engineering, biosynthesis has the potential to produce thousands of chemicals used in everyday life. Metabolic engineering and synthetic biology are fields driven by the manipulation of genes, genetic regulatory systems, and enzymatic pathways for developing highly productive microbial strains. Fundamentally, it is the biochemical characteristics of the enzymes themselves that dictate flux through a biosynthetic pathway toward the product of interest. As metabolic engineers target sophisticated secondary metabolites, there has been little recognition of the reduced catalytic activity and increased substrate/product promiscuity of the corresponding enzymes compared to those of central metabolism. Thus, fine-tuning these enzymatic characteristics through protein engineering is paramount for developing high-productivity microbial strains for secondary metabolites. Here, we describe the importance of protein engineering for advancing metabolic engineering of secondary metabolism pathways. This pathway integrated enzyme optimization can enhance the collective toolkit of microbial engineering to shape the future of chemical manufacturing.
MeSH term(s)	Biocatalysis ; Metabolism ; Protein Engineering
Language	English
Publishing date	2013-04-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/cb300634b
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