1
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Nava A, Fear AL, Lee N, Mellinger P, Lan G, McCauley J, Tan S, Kaplan N, Goyal G, Coates RC, Roberts J, Johnson Z, Hu R, Wu B, Ahn J, Kim WE, Wan Y, Yin K, Hillson N, Haushalter RW, Keasling JD. Automated Platform for the Plasmid Construction Process. ACS Synth Biol 2023; 12:3506-3513. [PMID: 37948662 PMCID: PMC10729297 DOI: 10.1021/acssynbio.3c00292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Indexed: 11/12/2023]
Abstract
There is a growing need for applications capable of handling large synthesis biology experiments. At the core of synthetic biology is the process of cloning and manipulating DNA as plasmids. Here, we report the development of an application named DNAda capable of writing automation instructions for any given DNA construct design generated by the J5 DNA assembly program. We also describe the automation pipeline and several useful features. The pipeline is particularly useful for the construction of combinatorial DNA assemblies. Furthermore, we demonstrate the platform by constructing a library of polyketide synthase parts, which includes 120 plasmids ranging in size from 7 to 14 kb from 4 to 7 DNA fragments.
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Affiliation(s)
- Alberto
A. Nava
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Anna Lisa Fear
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Namil Lee
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Peter Mellinger
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Guangxu Lan
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Joshua McCauley
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - Stephen Tan
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - Nurgul Kaplan
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - Garima Goyal
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - R. Cameron Coates
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - Jacob Roberts
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Zahmiria Johnson
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Romina Hu
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Bryan Wu
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Jared Ahn
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Woojoo E. Kim
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yao Wan
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Kevin Yin
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Plant and Microbial Biology, University
of California, Berkeley, Berkeley, California 94720, United States
| | - Nathan Hillson
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE
Agile BioFoundry, Emeryville, California 94608, United States
| | - Robert W. Haushalter
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
- Center
for Synthetic Biochemistry, Shenzhen Institutes
for Advanced Technologies, Shenzhen 518055, P.R. China
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, Kemitorvet, Building 220, Kongens Lyngby 2800, Denmark
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2
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Nava A, Roberts J, Haushalter RW, Wang Z, Keasling JD. Module-Based Polyketide Synthase Engineering for de Novo Polyketide Biosynthesis. ACS Synth Biol 2023; 12:3148-3155. [PMID: 37871264 PMCID: PMC10661043 DOI: 10.1021/acssynbio.3c00282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Indexed: 10/25/2023]
Abstract
Polyketide retrobiosynthesis, where the biosynthetic pathway of a given polyketide can be reversibly engineered due to the colinearity of the polyketide synthase (PKS) structure and function, has the potential to produce millions of organic molecules. Mixing and matching modules from natural PKSs is one of the routes to produce many of these molecules. Evolutionary analysis of PKSs suggests that traditionally used module boundaries may not lead to the most productive hybrid PKSs and that new boundaries around and within the ketosynthase domain may be more active when constructing hybrid PKSs. As this is still a nascent area of research, the generality of these design principles based on existing engineering efforts remains inconclusive. Recent advances in structural modeling and synthetic biology present an opportunity to accelerate PKS engineering by re-evaluating insights gained from previous engineering efforts with cutting edge tools.
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Affiliation(s)
- Alberto
A. Nava
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jacob Roberts
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Robert W. Haushalter
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Zilong Wang
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
- Center
for Synthetic Biochemistry, Shenzhen Institutes
for Advanced Technologies, Shenzhen 518055, P.R. China
- The
Novo
Nordisk Foundation Center for Biosustainability, Technical University Denmark, Kemitorvet, Building 220, Kongens Lyngby 2800, Denmark
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3
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Schmidt M, Lee N, Zhan C, Roberts JB, Nava AA, Keiser LS, Vilchez AA, Chen Y, Petzold CJ, Haushalter RW, Blank LM, Keasling JD. Maximizing Heterologous Expression of Engineered Type I Polyketide Synthases: Investigating Codon Optimization Strategies. ACS Synth Biol 2023; 12:3366-3380. [PMID: 37851920 PMCID: PMC10661030 DOI: 10.1021/acssynbio.3c00367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Indexed: 10/20/2023]
Abstract
Type I polyketide synthases (T1PKSs) hold enormous potential as a rational production platform for the biosynthesis of specialty chemicals. However, despite great progress in this field, the heterologous expression of PKSs remains a major challenge. One of the first measures to improve heterologous gene expression can be codon optimization. Although controversial, choosing the wrong codon optimization strategy can have detrimental effects on the protein and product levels. In this study, we analyzed 11 different codon variants of an engineered T1PKS and investigated in a systematic approach their influence on heterologous expression in Corynebacterium glutamicum, Escherichia coli, and Pseudomonas putida. Our best performing codon variants exhibited a minimum 50-fold increase in PKS protein levels, which also enabled the production of an unnatural polyketide in each of these hosts. Furthermore, we developed a free online tool (https://basebuddy.lbl.gov) that offers transparent and highly customizable codon optimization with up-to-date codon usage tables. In this work, we not only highlight the significance of codon optimization but also establish the groundwork for the high-throughput assembly and characterization of PKS pathways in alternative hosts.
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Affiliation(s)
- Matthias Schmidt
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Institute
of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, 52062 Aachen, Germany
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Namil Lee
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Chunjun Zhan
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jacob B. Roberts
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint
Program in Bioengineering, University of
California, Berkeley, California 94720, United States
| | - Alberto A. Nava
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Leah S. Keiser
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Aaron A. Vilchez
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Yan Chen
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Christopher J. Petzold
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Robert W. Haushalter
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Lars M. Blank
- Institute
of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, 52062 Aachen, Germany
| | - Jay D. Keasling
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint
Program in Bioengineering, University of
California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Environmental
Genomics and Systems Biology Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Center
for Synthetic Biochemistry, Institute for
Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen 518071, China
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4
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Zhan C, Lee N, Lan G, Dan Q, Cowan A, Wang Z, Baidoo EEK, Kakumanu R, Luckie B, Kuo RC, McCauley J, Liu Y, Valencia L, Haushalter RW, Keasling JD. Improved polyketide production in C. glutamicum by preventing propionate-induced growth inhibition. Nat Metab 2023; 5:1127-1140. [PMID: 37443355 DOI: 10.1038/s42255-023-00830-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/25/2023] [Indexed: 07/15/2023]
Abstract
Corynebacterium glutamicum is a promising host for production of valuable polyketides. Propionate addition, a strategy known to increase polyketide production by increasing intracellular methylmalonyl-CoA availability, causes growth inhibition in C. glutamicum. The mechanism of this inhibition was unclear before our work. Here we provide evidence that accumulation of propionyl-CoA and methylmalonyl-CoA induces growth inhibition in C. glutamicum. We then show that growth inhibition can be relieved by introducing methylmalonyl-CoA-dependent polyketide synthases. With germicidin as an example, we used adaptive laboratory evolution to leverage the fitness advantage of polyketide production in the presence of propionate to evolve improved germicidin production. Whole-genome sequencing revealed mutations in germicidin synthase, which improved germicidin titer, as well as mutations in citrate synthase, which effectively evolved the native glyoxylate pathway to a new methylcitrate pathway. Together, our results show that C. glutamicum is a capable host for polyketide production and we can take advantage of propionate growth inhibition to drive titers higher using laboratory evolution or to screen for production of polyketides.
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Affiliation(s)
- Chunjun Zhan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA
| | - Namil Lee
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA
| | - Guangxu Lan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Qingyun Dan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Aidan Cowan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Zilong Wang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ramu Kakumanu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bridget Luckie
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Rita C Kuo
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Joshua McCauley
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Luis Valencia
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Robert W Haushalter
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA.
- Center for Biosustainability, Danish Technical University, Lyngby, Denmark.
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
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5
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Otoupal PB, Geiselman GM, Oka AM, Barcelos CA, Choudhary H, Dinh D, Zhong W, Hwang H, Keasling JD, Mukhopadhyay A, Sundstrom E, Haushalter RW, Sun N, Simmons BA, Gladden JM. Advanced one-pot deconstruction and valorization of lignocellulosic biomass into triacetic acid lactone using Rhodosporidium toruloides. Microb Cell Fact 2022; 21:254. [PMID: 36482295 PMCID: PMC9733078 DOI: 10.1186/s12934-022-01977-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/19/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Rhodosporidium toruloides is capable of co-utilization of complex carbon sources and robust growth from lignocellulosic hydrolysates. This oleaginous yeast is therefore an attractive host for heterologous production of valuable bioproducts at high titers from low-cost, deconstructed biomass in an economically and environmentally sustainable manner. Here we demonstrate this by engineering R. toruloides to produce the polyketide triacetic acid lactone (TAL) directly from unfiltered hydrolysate deconstructed from biomass with minimal unit process operations. RESULTS Introduction of the 2-pyrone synthase gene into R. toruloides enabled the organism to produce 2.4 g/L TAL from simple media or 2.0 g/L from hydrolysate produced from sorghum biomass. Both of these titers are on par with titers from other better-studied microbial hosts after they had been heavily engineered. We next demonstrate that filtered hydrolysates produced from ensiled sorghum are superior to those derived from dried sorghum for TAL production, likely due to the substantial organic acids produced during ensiling. We also demonstrate that the organic acids found in ensiled biomass can be used for direct synthesis of ionic liquids within the biomass pretreatment process, enabling consolidation of unit operations of in-situ ionic liquid synthesis, pretreatment, saccharification, and fermentation into a one-pot, separations-free process. Finally, we demonstrate this consolidation in a 2 L bioreactor using unfiltered hydrolysate, producing 3.9 g/L TAL. CONCLUSION Many steps involved in deconstructing biomass into fermentable substrate can be combined into a distinct operation, and directly fed to cultures of engineered R. toruloides cultures for subsequent valorization into gram per liter titers of TAL in a cost-effective manner.
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Affiliation(s)
- Peter B. Otoupal
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,Agile BioFoundry, Department of Energy, Emeryville, CA USA
| | - Gina M. Geiselman
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,Agile BioFoundry, Department of Energy, Emeryville, CA USA
| | - Asun M. Oka
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Carolina A. Barcelos
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Hemant Choudhary
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA
| | - Duy Dinh
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Wenqing Zhong
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - HeeJin Hwang
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,Agile BioFoundry, Department of Energy, Emeryville, CA USA
| | - Jay D. Keasling
- grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA ,grid.47840.3f0000 0001 2181 7878Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA USA ,grid.47840.3f0000 0001 2181 7878Department of Bioengineering, University of California, Berkeley, Berkeley, CA USA ,grid.5170.30000 0001 2181 8870Center for Biosustainability, Danish Technical University, Lyngby, Denmark ,grid.458489.c0000 0001 0483 7922Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China
| | - Aindrila Mukhopadhyay
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA ,grid.184769.50000 0001 2231 4551Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Eric Sundstrom
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Robert W. Haushalter
- grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Ning Sun
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Blake A. Simmons
- grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,Agile BioFoundry, Department of Energy, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - John M. Gladden
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,Agile BioFoundry, Department of Energy, Emeryville, CA USA
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6
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Thompson MG, Incha MR, Pearson AN, Schmidt M, Sharpless WA, Eiben CB, Cruz-Morales P, Blake-Hedges JM, Liu Y, Adams CA, Haushalter RW, Krishna RN, Lichtner P, Blank LM, Mukhopadhyay A, Deutschbauer AM, Shih PM, Keasling JD. Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing. Appl Environ Microbiol 2020; 86:e01665-20. [PMID: 32826213 PMCID: PMC7580535 DOI: 10.1128/aem.01665-20] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/12/2020] [Indexed: 12/13/2022] Open
Abstract
With its ability to catabolize a wide variety of carbon sources and a growing engineering toolkit, Pseudomonas putida KT2440 is emerging as an important chassis organism for metabolic engineering. Despite advances in our understanding of the organism, many gaps remain in our knowledge of the genetic basis of its metabolic capabilities. The gaps are particularly noticeable in our understanding of both fatty acid and alcohol catabolism, where many paralogs putatively coding for similar enzymes coexist, making biochemical assignment via sequence homology difficult. To rapidly assign function to the enzymes responsible for these metabolisms, we leveraged random barcode transposon sequencing (RB-Tn-Seq). Global fitness analyses of transposon libraries grown on 13 fatty acids and 10 alcohols produced strong phenotypes for hundreds of genes. Fitness data from mutant pools grown on fatty acids of varying chain lengths indicated specific enzyme substrate preferences and enabled us to hypothesize that DUF1302/DUF1329 family proteins potentially function as esterases. From the data, we also postulate catabolic routes for the two biogasoline molecules isoprenol and isopentanol, which are catabolized via leucine metabolism after initial oxidation and activation with coenzyme A (CoA). Because fatty acids and alcohols may serve as both feedstocks and final products of metabolic-engineering efforts, the fitness data presented here will help guide future genomic modifications toward higher titers, rates, and yields.IMPORTANCE To engineer novel metabolic pathways into P. putida, a comprehensive understanding of the genetic basis of its versatile metabolism is essential. Here, we provide functional evidence for the putative roles of hundreds of genes involved in the fatty acid and alcohol metabolism of the bacterium. These data provide a framework facilitating precise genetic changes to prevent product degradation and to channel the flux of specific pathway intermediates as desired.
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Affiliation(s)
- Mitchell G Thompson
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant Biology, University of California, Davis, California, USA
| | - Matthew R Incha
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Allison N Pearson
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Matthias Schmidt
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - William A Sharpless
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher B Eiben
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Joint Program in Bioengineering, University of California, Berkeley, California, USA
| | - Pablo Cruz-Morales
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Centro de Biotecnología FEMSA, Instituto Tecnológico y de Estudios Superiores de Monterrey, Monterrey, México
| | - Jacquelyn M Blake-Hedges
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Catharine A Adams
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Robert W Haushalter
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rohith N Krishna
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Patrick Lichtner
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Lars M Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Patrick M Shih
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant Biology, University of California, Davis, California, USA
- Environmental and Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Joint Program in Bioengineering, University of California, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
- Institute for Quantitative Biosciences, University of California, Berkeley, California, USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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7
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Zargar A, Bailey CB, Haushalter RW, Eiben CB, Katz L, Keasling JD. Leveraging microbial biosynthetic pathways for the generation of 'drop-in' biofuels. Curr Opin Biotechnol 2017; 45:156-163. [PMID: 28427010 DOI: 10.1016/j.copbio.2017.03.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/24/2017] [Accepted: 03/03/2017] [Indexed: 01/21/2023]
Abstract
Advances in retooling microorganisms have enabled bioproduction of 'drop-in' biofuels, fuels that are compatible with existing spark-ignition, compression-ignition, and gas-turbine engines. As the majority of petroleum consumption in the United States consists of gasoline (47%), diesel fuel and heating oil (21%), and jet fuel (8%), 'drop-in' biofuels that replace these petrochemical sources are particularly attractive. In this review, we discuss the application of aldehyde decarbonylases to produce gasoline substitutes from fatty acid products, a recently crystallized reductase that could hydrogenate jet fuel precursors from terpene synthases, and the exquisite control of polyketide synthases to produce biofuels with desired physical properties (e.g., lower freezing points). With our increased understanding of biosynthetic logic of metabolic pathways, we discuss the unique advantages of fatty acid, terpene, and polyketide synthases for the production of bio-based gasoline, diesel and jet fuel.
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Affiliation(s)
- Amin Zargar
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, United States; QB3 Institute, University of California-Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, United States
| | - Constance B Bailey
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Robert W Haushalter
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Christopher B Eiben
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Leonard Katz
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, United States; QB3 Institute, University of California-Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, United States; Synthetic Biology Engineering Research Center, University of California, Berkeley, CA 94720, United States
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; QB3 Institute, University of California-Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, United States; Synthetic Biology Engineering Research Center, University of California, Berkeley, CA 94720, United States; Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, CA 94720, United States; Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, DK2970 Horsholm, Denmark.
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8
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Haushalter RW, Phelan RM, Hoh KM, Su C, Wang G, Baidoo EEK, Keasling JD. Production of Odd-Carbon Dicarboxylic Acids in Escherichia coli Using an Engineered Biotin-Fatty Acid Biosynthetic Pathway. J Am Chem Soc 2017; 139:4615-4618. [PMID: 28291347 DOI: 10.1021/jacs.6b11895] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dicarboxylic acids are commodity chemicals used in the production of plastics, polyesters, nylons, fragrances, and medications. Bio-based routes to dicarboxylic acids are gaining attention due to environmental concerns about petroleum-based production of these compounds. Some industrial applications require dicarboxylic acids with specific carbon chain lengths, including odd-carbon species. Biosynthetic pathways involving cytochrome P450-catalyzed oxidation of fatty acids in yeast and bacteria have been reported, but these systems produce almost exclusively even-carbon species. Here we report a novel pathway to odd-carbon dicarboxylic acids directly from glucose in Escherichia coli by employing an engineered pathway combining enzymes from biotin and fatty acid synthesis. Optimization of the pathway will lead to industrial strains for the production of valuable odd-carbon diacids.
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Affiliation(s)
- Robert W Haushalter
- Joint BioEnergy Institute, U.S. Department of Energy , 5885 Hollis Street, Emeryville, California 94608, United States.,Physical Bioscience Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Ryan M Phelan
- Joint BioEnergy Institute, U.S. Department of Energy , 5885 Hollis Street, Emeryville, California 94608, United States.,Physical Bioscience Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Kristina M Hoh
- Joint BioEnergy Institute, U.S. Department of Energy , 5885 Hollis Street, Emeryville, California 94608, United States.,Physical Bioscience Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Cindy Su
- Joint BioEnergy Institute, U.S. Department of Energy , 5885 Hollis Street, Emeryville, California 94608, United States.,Physical Bioscience Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - George Wang
- Joint BioEnergy Institute, U.S. Department of Energy , 5885 Hollis Street, Emeryville, California 94608, United States.,Physical Bioscience Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Edward E K Baidoo
- Joint BioEnergy Institute, U.S. Department of Energy , 5885 Hollis Street, Emeryville, California 94608, United States.,Physical Bioscience Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Jay D Keasling
- Joint BioEnergy Institute, U.S. Department of Energy , 5885 Hollis Street, Emeryville, California 94608, United States.,Physical Bioscience Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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9
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Haushalter RW, Groff D, Deutsch S, The L, Chavkin TA, Brunner SF, Katz L, Keasling JD. Development of an orthogonal fatty acid biosynthesis system in E. coli for oleochemical production. Metab Eng 2015; 30:1-6. [DOI: 10.1016/j.ymben.2015.04.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 04/03/2015] [Accepted: 04/06/2015] [Indexed: 01/02/2023]
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10
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Shakya G, Rivera H, Lee DJ, Jaremko MJ, La Clair JJ, Fox DT, Haushalter RW, Schaub AJ, Bruegger J, Barajas JF, White AR, Kaur P, Gwozdziowski ER, Wong F, Tsai SC, Burkart MD. Modeling linear and cyclic PKS intermediates through atom replacement. J Am Chem Soc 2014; 136:16792-9. [PMID: 25406716 PMCID: PMC4277753 DOI: 10.1021/ja5064857] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The
mechanistic details of many polyketide synthases (PKSs) remain
elusive due to the instability of transient intermediates that are
not accessible via conventional methods. Here we report an atom replacement
strategy that enables the rapid preparation of polyketone surrogates
by selective atom replacement, thereby providing key substrate mimetics
for detailed mechanistic evaluations. Polyketone mimetics are positioned
on the actinorhodin acyl carrier protein (actACP) to probe the underpinnings
of substrate association upon nascent chain elongation and processivity.
Protein NMR is used to visualize substrate interaction with the actACP,
where a tetraketide substrate is shown not to bind within the protein,
while heptaketide and octaketide substrates show strong association
between helix II and IV. To examine the later cyclization stages,
we extended this strategy to prepare stabilized cyclic intermediates
and evaluate their binding by the actACP. Elongated monocyclic mimics
show much longer residence time within actACP than shortened analogs.
Taken together, these observations suggest ACP-substrate association
occurs both before and after ketoreductase action upon the fully elongated
polyketone, indicating a key role played by the ACP within PKS timing
and processivity. These atom replacement mimetics offer new tools
to study protein and substrate interactions and are applicable to
a wide variety of PKSs.
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Affiliation(s)
- Gaurav Shakya
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California , Irvine, California 92697, United States
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11
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Haushalter RW, Kim W, Chavkin TA, The L, Garber ME, Nhan M, Adams PD, Petzold CJ, Katz L, Keasling JD. Production of anteiso-branched fatty acids in Escherichia coli; next generation biofuels with improved cold-flow properties. Metab Eng 2014; 26:111-118. [PMID: 25250846 DOI: 10.1016/j.ymben.2014.09.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/09/2014] [Accepted: 09/08/2014] [Indexed: 01/28/2023]
Abstract
Microbial fermentation is emerging as an increasingly important resource for the production of fatty acids to serve as precursors for renewable diesel as well as detergents, lubricants and other industrial chemicals, as an alternative to traditional sources of reduced carbon such as petroleum. A major disadvantage of fuels derived from biological sources is their undesirable physical properties such as high cloud and pour points, and high viscosity. Here we report the development of an Escherichia coli strain that efficiently produces anteiso-branched fatty acids, which can be converted into downstream products with lower cloud and pour points than the mixtures of compounds produced via the native metabolism of the cell. This work addresses a serious limitation that must be overcome in order to produce renewable biodiesel and oleochemicals that perform as well as their petroleum-based counterparts.
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Affiliation(s)
- Robert W Haushalter
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Woncheol Kim
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Ted A Chavkin
- QB3 Institute, University of California-Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, United States
| | - Lionadi The
- QB3 Institute, University of California-Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, United States
| | - Megan E Garber
- QB3 Institute, University of California-Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, United States
| | - Melissa Nhan
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Paul D Adams
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, CA 94720, United States
| | - Christopher J Petzold
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Leonard Katz
- QB3 Institute, University of California-Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, United States; Synthetic Biology Engineering Research Center, University of California, Berkeley, CA 94720, United States
| | - Jay D Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; QB3 Institute, University of California-Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, United States; Synthetic Biology Engineering Research Center, University of California, Berkeley, CA 94720, United States; Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, CA 94720, United States.
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12
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Ishikawa F, Haushalter RW, Lee DJ, Finzel K, Burkart MD. Sulfonyl 3-alkynyl pantetheinamides as mechanism-based cross-linkers of acyl carrier protein dehydratase. J Am Chem Soc 2013; 135:8846-9. [PMID: 23718183 DOI: 10.1021/ja4042059] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Acyl carrier proteins (ACPs) play a central role in acetate biosynthetic pathways, serving as tethers for substrates and growing intermediates. Activity and structural studies have highlighted the complexities of this role, and the protein-protein interactions of ACPs have recently come under scrutiny as a regulator of catalysis. As existing methods to interrogate these interactions have fallen short, we have sought to develop new tools to aid their study. Here we describe the design, synthesis, and application of pantetheinamides that can cross-link ACPs with catalytic β-hydroxy-ACP dehydratase (DH) domains by means of a 3-alkynyl sulfone warhead. We demonstrate this process by application to the Escherichia coli fatty acid synthase and apply it to probe protein-protein interactions with noncognate carrier proteins. Finally, we use solution-phase protein NMR spectroscopy to demonstrate that sulfonyl 3-alkynyl pantetheinamide is fully sequestered by the ACP, indicating that the crypto-ACP closely mimics the natural DH substrate. This cross-linking technology offers immediate potential to lock these biosynthetic enzymes in their native binding states by providing access to mechanistically cross-linked enzyme complexes, presenting a solution to ongoing structural challenges.
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Affiliation(s)
- Fumihiro Ishikawa
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, USA
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13
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Abstract
The reversible covalent attachment of chemical probes to proteins has long been sought as a means to visualize and manipulate proteins. Here we demonstrate the full reversibility of post-translational custom pantetheine modification of Escherichia coli acyl carrier protein for visualization and functional studies. We use this iterative enzymatic methodology in vitro to reversibly label acyl carrier protein variants and apply these tools to NMR structural studies of protein-substrate interactions.
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Affiliation(s)
- Nicolas M Kosa
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
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14
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Abstract
We targeted the development of a dehydratase (DH)-specific reactive probe that can facilitate detection, enrichment, and identification of DH enzymes in fatty acid synthases (FASs) and polyketide synthases (PKSs). The first reported mechanism-based inactivator, 3-decynoyl-N-acetylcysteamine (3-decynoyl-NAC), while active against the Escherichia coli β-hydroxydecanoyl thiol ester DH FabA, translates poorly to an activity-based probe because of nonspecific reactivity of the thioester moiety. Here we describe the design, synthesis, and utility of a DH-specific probe that contains a sulfonyl 3-alkyne reactive warhead engineered to avoid hydrolysis or nonenzymatic inactivation. When coupled with a fluorescent tag, this probe targets DH enzymes from recombinant type I and type II FAS and PKS enzyme systems and in whole proteomes. Activity studies, including FabA inactivation and antibiotic susceptibility, suggest that this sulfonyl 3-alkyne scaffold selectively targets a common DH mechanism. These studies indicate that the DH-specific mechanism-based probe can greatly accelerate both the functional characterization and molecular identification of virtually any type of FAS and PKS in complex proteomes.
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Affiliation(s)
- Fumihiro Ishikawa
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, USA
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15
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Rothmann M, Niessen S, Haushalter RW, Cravatt BF, Burkart MD. Resin-based investigation of acyl carrier protein interaction networks in Escherichia coli. Bioorg Med Chem 2011; 20:667-71. [PMID: 22104437 DOI: 10.1016/j.bmc.2011.10.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 10/06/2011] [Accepted: 10/17/2011] [Indexed: 11/25/2022]
Abstract
Protein-protein interactions play an integral role in metabolic regulation. Elucidation of these networks is complicated by the changing identity of the proteins themselves. Here we demonstrate a resin-based technique that leverages the unique tools for acyl carrier protein (ACP) modification with non-hydrolyzable linkages. ACPs from Escherichia coli and Shewanella oneidensis MR-1 are bound to Affigel-15 with varying acyl groups attached and introduced to proteomic samples. Isolation of these binding partners is followed by MudPIT analysis to identify each interactome with the variable of ACP-tethered substrates. These techniques allow for investigation of protein interaction networks with the changing identity of a given protein target.
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Affiliation(s)
- Michael Rothmann
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
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16
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Zhang F, Haushalter RC, Haushalter RW, Shi Y, Zhang Y, Ding K, Zhao D, Stucky GD. Rare-earth upconverting nanobarcodes for multiplexed biological detection. Small 2011; 7:1972-6. [PMID: 21726042 PMCID: PMC3516929 DOI: 10.1002/smll.201100629] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Indexed: 05/17/2023]
Affiliation(s)
- Fan Zhang
- Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, P. R. China
| | | | | | - Yifeng Shi
- Department of Chemistry and Biochemistry, University of California Santa Barbara, CA 93106-9510
| | - Yichi Zhang
- Department of Chemistry and Biochemistry, University of California Santa Barbara, CA 93106-9510
| | - Kunlun Ding
- Department of Chemistry and Biochemistry, University of California Santa Barbara, CA 93106-9510
| | - Dongyuan Zhao
- Department of Chemistry, and Laboratory of Advanced Materials, Fudan University, Shanghai 200433, P. R. China
| | - Galen D. Stucky
- Department of Chemistry and Biochemistry, University of California Santa Barbara, CA 93106-9510
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17
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Haushalter RW, Filipp FV, Ko KS, Yu R, Opella SJ, Burkart MD. Binding and "pKa" modulation of a polycyclic substrate analogue in a type II polyketide acyl carrier protein. ACS Chem Biol 2011; 6:413-8. [PMID: 21268653 DOI: 10.1021/cb200004k] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Type II polyketide synthases are biosynthetic enzymatic pathways responsible for the production of complex aromatic natural products with important biological activities. In these systems, biosynthetic intermediates are covalently bound to a small acyl carrier protein that associates with the synthase enzymes and delivers the bound intermediate to each active site. In the closely related fatty acid synthases of bacteria and plants, the acyl carrier protein acts to sequester and protect attached intermediates within its helices. Here we investigate the type II polyketide synthase acyl carrier protein from the actinorhodin biosynthetic pathway and demonstrate its ability to internalize the tricyclic, polar molecule emodic acid. Elucidating the interaction of acyl carrier proteins with bound analogues resembling late-stage intermediates in the actinorhodin pathway could prove valuable in efforts to engineer these systems toward rational design and biosynthesis of novel compounds.
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Affiliation(s)
- Robert W. Haushalter
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358, United States
| | - Fabian V. Filipp
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358, United States
| | - Kwang-seuk Ko
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358, United States
| | - Ricky Yu
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358, United States
| | - Stanley J. Opella
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358, United States
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358, United States
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18
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Meier JL, Haushalter RW, Burkart MD. A mechanism based protein crosslinker for acyl carrier protein dehydratases. Bioorg Med Chem Lett 2010; 20:4936-9. [PMID: 20620055 DOI: 10.1016/j.bmcl.2010.06.028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 06/04/2010] [Indexed: 12/01/2022]
Abstract
Recent advances in the structural study of fatty acid synthase (FAS) and polyketide synthase (PKS) biosynthetic enzymes have illuminated our understanding of modular enzymes of the acetate pathway. However, one significant and persistent challenge in such analyses is resolution of the acyl carrier protein (ACP), a small (approximately 9 kDa) protein to which biosynthetic intermediates are tethered throughout the biosynthetic cycle. Here we report a chemoenzymatic crosslinking strategy in which the installation of a historical suicide substrate scaffold upon the 4'-phosphopantetheine (PPant) arm of the ACP is used to capture the active site of acyl carrier protein dehydratase (DH) domains in FAS. Through the synthesis of a small panel of related probes we identify structural features essential for ACP-DH crosslinking, and apply gel-based assays to demonstrate the stability as well as purification strategies for isolation of the chemoenzymatically modified ACP. Applying these carrier protein crosslinking techniques to the structural analysis of FAS and PKS complexes has the potential to provide snapshots of these biosynthetic assembly lines at work.
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Affiliation(s)
- Jordan L Meier
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, United States
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Haushalter RW, Worthington AS, Hur GH, Burkart MD. An orthogonal purification strategy for isolating crosslinked domains of modular synthases. Bioorg Med Chem Lett 2008; 18:3039-42. [PMID: 18249538 DOI: 10.1016/j.bmcl.2008.01.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 01/07/2008] [Accepted: 01/08/2008] [Indexed: 10/22/2022]
Abstract
Chemo-enzymatic methods for covalently crosslinking carrier proteins with partner enzymes within modular synthases hold promise for elucidating and engineering metabolic pathways. Our efforts to crystallize the ACP-KS complexes of fatty acid synthases have been complicated by difficulties in the purification of the crosslinked complex from the other proteins in the reaction. Here we present a solution that employs an orthogonal purification strategy to achieve the quantity and level of purity necessary for further studies of this complex.
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Affiliation(s)
- Robert W Haushalter
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
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