1
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Zargar A, Lal R, Valencia L, Wang J, Backman TWH, Cruz-Morales P, Kothari A, Werts M, Wong AR, Bailey CB, Loubat A, Liu Y, Chen Y, Chang S, Benites VT, Hernández AC, Barajas JF, Thompson MG, Barcelos C, Anayah R, Martin HG, Mukhopadhyay A, Petzold CJ, Baidoo EEK, Katz L, Keasling JD. Chemoinformatic-Guided Engineering of Polyketide Synthases. J Am Chem Soc 2020; 142:9896-9901. [DOI: 10.1021/jacs.0c02549] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amin Zargar
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
- QB3 Institute, University of California−Berkeley, 5885 Hollis Street, Fourth Floor, Emeryville, California 94608, United States
| | - Ravi Lal
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Luis Valencia
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Jessica Wang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Tyler William H. Backman
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Pablo Cruz-Morales
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Ankita Kothari
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Miranda Werts
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Andrew R. Wong
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Constance B. Bailey
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
- QB3 Institute, University of California−Berkeley, 5885 Hollis Street, Fourth Floor, Emeryville, California 94608, United States
| | - Arthur Loubat
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Yuzhong Liu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Yan Chen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Samantha Chang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Veronica T. Benites
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
- Department of Energy, Agile BioFoundry, Emeryville, California 94608, United States
| | - Amanda C. Hernández
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Jesus F. Barajas
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
- Department of Energy, Agile BioFoundry, Emeryville, California 94608, United States
| | - Mitchell G. Thompson
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Carolina Barcelos
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Rasha Anayah
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Hector Garcia Martin
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
- Department of Energy, Agile BioFoundry, Emeryville, California 94608, United States
- BCAM, Basque Center for Applied Mathematics, 48009 Bilbao, Spain
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Christopher J. Petzold
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
- Department of Energy, Agile BioFoundry, Emeryville, California 94608, United States
| | - Edward E. K. Baidoo
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
- Department of Energy, Agile BioFoundry, Emeryville, California 94608, United States
| | - Leonard Katz
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- QB3 Institute, University of California−Berkeley, 5885 Hollis Street, Fourth Floor, Emeryville, California 94608, United States
| | - Jay D. Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
- QB3 Institute, University of California−Berkeley, 5885 Hollis Street, Fourth Floor, Emeryville, California 94608, United States
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
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2
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Snoek T, Chaberski EK, Ambri F, Kol S, Bjørn SP, Pang B, Barajas JF, Welner DH, Jensen MK, Keasling JD. Evolution-guided engineering of small-molecule biosensors. Nucleic Acids Res 2020; 48:e3. [PMID: 31777933 PMCID: PMC6943132 DOI: 10.1093/nar/gkz954] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [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] [Received: 08/20/2019] [Revised: 10/06/2019] [Accepted: 10/24/2019] [Indexed: 11/14/2022] Open
Abstract
Allosteric transcription factors (aTFs) have proven widely applicable for biotechnology and synthetic biology as ligand-specific biosensors enabling real-time monitoring, selection and regulation of cellular metabolism. However, both the biosensor specificity and the correlation between ligand concentration and biosensor output signal, also known as the transfer function, often needs to be optimized before meeting application needs. Here, we present a versatile and high-throughput method to evolve prokaryotic aTF specificity and transfer functions in a eukaryote chassis, namely baker's yeast Saccharomyces cerevisiae. From a single round of mutagenesis of the effector-binding domain (EBD) coupled with various toggled selection regimes, we robustly select aTF variants of the cis,cis-muconic acid-inducible transcription factor BenM evolved for change in ligand specificity, increased dynamic output range, shifts in operational range, and a complete inversion-of-function from activation to repression. Importantly, by targeting only the EBD, the evolved biosensors display DNA-binding affinities similar to BenM, and are functional when ported back into a prokaryotic chassis. The developed platform technology thus leverages aTF evolvability for the development of new host-agnostic biosensors with user-defined small-molecule specificities and transfer functions.
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Affiliation(s)
- Tim Snoek
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Evan K Chaberski
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Francesca Ambri
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Stefan Kol
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Sara P Bjørn
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Bo Pang
- Joint BioEnergy Institute, Emeryville, CA, USA
| | | | - Ditte H Welner
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.,Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, CA, USA.,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
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3
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Thompson MG, Pearson AN, Barajas JF, Cruz-Morales P, Sedaghatian N, Costello Z, Garber ME, Incha MR, Valencia LE, Baidoo EEK, Martin HG, Mukhopadhyay A, Keasling JD. Identification, Characterization, and Application of a Highly Sensitive Lactam Biosensor from Pseudomonas putida. ACS Synth Biol 2020; 9:53-62. [PMID: 31841635 DOI: 10.1021/acssynbio.9b00292] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Caprolactam is an important polymer precursor to nylon traditionally derived from petroleum and produced on a scale of 5 million tons per year. Current biological pathways for the production of caprolactam are inefficient with titers not exceeding 2 mg/L, necessitating novel pathways for its production. As development of novel metabolic routes often require thousands of designs and result in low product titers, a highly sensitive biosensor for the final product has the potential to rapidly speed up development times. Here we report a highly sensitive biosensor for valerolactam and caprolactam from Pseudomonas putida KT2440 which is >1000× more sensitive to an exogenous ligand than previously reported sensors. Manipulating the expression of the sensor oplR (PP_3516) substantially altered the sensing parameters, with various vectors showing Kd values ranging from 700 nM (79.1 μg/L) to 1.2 mM (135.6 mg/L). Our most sensitive construct was able to detect in vivo production of caprolactam above background at ∼6 μg/L. The high sensitivity and range of OplR is a powerful tool toward the development of novel routes to the biological synthesis of caprolactam.
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Affiliation(s)
- Mitchell G. Thompson
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Allison N. Pearson
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jesus F. Barajas
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Energy Agile BioFoundry, Emeryville, California 94608, United States
| | - Pablo Cruz-Morales
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Centro de Biotecnologia FEMSA, Instituto Tecnologico y de Estudios superiores de Monterrey, Monterrey, 64849, Mexico
| | - Nima Sedaghatian
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Zak Costello
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Energy Agile BioFoundry, Emeryville, California 94608, United States
| | - Megan E. Garber
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Comparative Biochemistry Graduate Group, University of California, Berkeley, California United States
| | - Matthew R. Incha
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Luis E. Valencia
- Joint BioEnergy Institute, 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/San Francisco, California 94720, United States
| | - Edward E. K. Baidoo
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Hector Garcia Martin
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Energy Agile BioFoundry, Emeryville, California 94608, United States
- BCAM, Basque Center for Applied Mathematics, Bilbao, Spain
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Comparative Biochemistry Graduate Group, University of California, Berkeley, California United States
| | - Jay D. Keasling
- Joint BioEnergy Institute, 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/San Francisco, 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, Lyngby, Denmark
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4
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Blake-Hedges JM, Pereira JH, Cruz-Morales P, Thompson MG, Barajas JF, Chen J, Krishna RN, Chan LJG, Nimlos D, Alonso-Martinez C, Baidoo EEK, Chen Y, Gin JW, Katz L, Petzold CJ, Adams PD, Keasling JD. Structural Mechanism of Regioselectivity in an Unusual Bacterial Acyl-CoA Dehydrogenase. J Am Chem Soc 2020; 142:835-846. [PMID: 31793780 DOI: 10.1021/jacs.9b09187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Terminal alkenes are easily derivatized, making them desirable functional group targets for polyketide synthase (PKS) engineering. However, they are rarely encountered in natural PKS systems. One mechanism for terminal alkene formation in PKSs is through the activity of an acyl-CoA dehydrogenase (ACAD). Herein, we use biochemical and structural analysis to understand the mechanism of terminal alkene formation catalyzed by an γ,δ-ACAD from the biosynthesis of the polyketide natural product FK506, TcsD. While TcsD is homologous to canonical α,β-ACADs, it acts regioselectively at the γ,δ-position and only on α,β-unsaturated substrates. Furthermore, this regioselectivity is controlled by a combination of bulky residues in the active site and a lateral shift in the positioning of the FAD cofactor within the enzyme. Substrate modeling suggests that TcsD utilizes a novel set of hydrogen bond donors for substrate activation and positioning, preventing dehydrogenation at the α,β position of substrates. From the structural and biochemical characterization of TcsD, key residues that contribute to regioselectivity and are unique to the protein family were determined and used to identify other putative γ,δ-ACADs that belong to diverse natural product biosynthetic gene clusters. These predictions are supported by the demonstration that a phylogenetically distant homologue of TcsD also regioselectively oxidizes α,β-unsaturated substrates. This work exemplifies a powerful approach to understand unique enzymatic reactions and will facilitate future enzyme discovery, inform enzyme engineering, and aid natural product characterization efforts.
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Affiliation(s)
- Jacquelyn M Blake-Hedges
- Department of Chemistry , University of California , Berkeley , California 94720 , United States.,Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Jose Henrique Pereira
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Pablo Cruz-Morales
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Mitchell G Thompson
- Joint BioEnergy Institute , 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
| | - Jesus F Barajas
- Joint BioEnergy Institute , 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
| | - Jeffrey Chen
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Rohith N Krishna
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Leanne Jade G Chan
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Danika Nimlos
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Catalina Alonso-Martinez
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Edward E K Baidoo
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Yan Chen
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Department of Energy Agile BioFoundry , Emeryville , California 94608 , United States
| | - Jennifer W Gin
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Department of Energy Agile BioFoundry , Emeryville , California 94608 , United States
| | - Leonard Katz
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,QB3 Institute , University of California-Berkeley , Emeryville , California 94608 , United States
| | - Christopher J Petzold
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Department of Energy Agile BioFoundry , Emeryville , California 94608 , United States
| | - Paul D Adams
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Jay D Keasling
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,QB3 Institute , University of California-Berkeley , Emeryville , California 94608 , United States.,Department of Chemical & Biomolecular Engineering, Department of Bioengineering , University of California-Berkeley , Berkeley , California 94720 , United States.,Novo Nordisk Foundation Center for Biosustainability , Technical University Denmark , DK2970 Horsholm , Denmark.,Center for Synthetic Biochemistry , Shenzhen Institutes for Advanced Technologies , Shenzhen 518055 , P. R. China
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5
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Barajas JF, Wehrs M, To M, Cruickshanks L, Urban R, McKee A, Gladden J, Goh EB, Brown ME, Pierotti D, Carothers JM, Mukhopadhyay A, Keasling JD, Fortman JL, Singer SW, Bailey CB. Isolation and Characterization of Bacterial Cellulase Producers for Biomass Deconstruction: A Microbiology Laboratory Course. J Microbiol Biol Educ 2019; 20:jmbe-20-34. [PMID: 31388393 PMCID: PMC6656525 DOI: 10.1128/jmbe.v20i2.1723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/22/2019] [Indexed: 06/10/2023]
Abstract
The conversion of biomass to biofuels presents a solution to one of the largest global challenges of our era, climate change. A critical part of this pipeline is the process of breaking down cellulosic sugars from plant matter to be used by microbes containing biosynthetic pathways that produce biofuels or bioproducts. In this inquiry-based course, students complete a research project that isolates cellulase-producing bacteria from samples collected from the environment. After obtaining isolates, the students characterize the production of cellulases. Students then amplify and sequence the 16S rRNA genes of confirmed cellulase producers and use bioinformatic methods to identify the bacterial isolates. Throughout the course, students learn about the process of generating biofuels and bioproducts through the deconstruction of cellulosic biomass to form monosaccharides from the biopolymers in plant matter. The program relies heavily on active learning and enables students to connect microbiology with issues of sustainability. In addition, it provides exposure to basic microbiology, molecular biology, and biotechnology laboratory techniques and concepts. The described activity was initially developed for the Introductory College Level Experience in Microbiology (iCLEM) program, a research-based immersive laboratory course at the US Department of Energy Joint BioEnergy Institute. Originally designed as an accelerated program for high-potential, low-income, high school students (11th-12th grade), this curriculum could also be implemented for undergraduate coursework in a research-intensive laboratory course at a two- or four-year college or university.
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Affiliation(s)
- Jesus F. Barajas
- Agile BioFoundry, Emeryville, CA 94608
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Maren Wehrs
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
| | - Milton To
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
| | | | - Rochelle Urban
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
- University of Southern California Viterbi School of Engineering, Los Angeles, CA 90089
| | - Adrienne McKee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
- Helix OpCo, San Carlos, CA 94070
| | - John Gladden
- Sandia National Laboratories, Livermore CA 94551
| | - Ee-Been Goh
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
- Lygos Inc., Berkeley, CA 94710
| | - Margaret E. Brown
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
- MicroByre, Berkeley, CA 94720
| | - Diane Pierotti
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
| | - James M. Carothers
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
| | - Jay D. Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195
- QB3 Institute, University of California-Berkeley, Emeryville, CA 94608
- University of California, Berkeley, Department of Chemical & Biomolecular Engineering, Berkeley, CA 94720
- University of California, Berkeley, Department of Bioengineering, Berkeley, CA 94720
- Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, DK2970-Horsholm, Denmark
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Jeffrey L. Fortman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Steven W. Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
| | - Constance B. Bailey
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
- QB3 Institute, University of California-Berkeley, Emeryville, CA 94608
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6
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Milligan JC, Lee DJ, Jackson DR, Schaub AJ, Beld J, Barajas JF, Hale JJ, Luo R, Burkart MD, Tsai SC. Molecular basis for interactions between an acyl carrier protein and a ketosynthase. Nat Chem Biol 2019; 15:669-671. [PMID: 31209348 DOI: 10.1038/s41589-019-0301-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/01/2019] [Indexed: 12/30/2022]
Abstract
Fatty acid synthases are dynamic ensembles of enzymes that can biosynthesize long hydrocarbon chains efficiently. Here we visualize the interaction between the Escherichia coli acyl carrier protein (AcpP) and β-ketoacyl-ACP-synthase I (FabB) using X-ray crystallography, NMR, and molecular dynamics simulations. We leveraged this structural information to alter lipid profiles in vivo and provide a molecular basis for how protein-protein interactions can regulate the fatty acid profile in E. coli.
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Affiliation(s)
- Jacob C Milligan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - D John Lee
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - David R Jackson
- Department of Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Andrew J Schaub
- Department of Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Joris Beld
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Jesus F Barajas
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Joseph J Hale
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
| | - Shiou-Chuan Tsai
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA. .,Department of Chemistry, University of California, Irvine, Irvine, CA, USA. .,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA.
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7
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Barajas JF, Finzel K, Valentic TR, Shakya G, Gamarra N, Martinez D, Meier JL, Vagstad AL, Newman AG, Townsend CA, Burkart MD, Tsai SC. Structural and Biochemical Analysis of Protein-Protein Interactions Between the Acyl-Carrier Protein and Product Template Domain. Angew Chem Int Ed Engl 2018; 55:13005-13009. [PMID: 27653519 DOI: 10.1002/anie.201605401] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/18/2016] [Indexed: 11/08/2022]
Abstract
In fungal non-reducing polyketide synthases (NR-PKS) the acyl-carrier protein (ACP) carries the growing polyketide intermediate through iterative rounds of elongation, cyclization and product release. This process occurs through a controlled, yet enigmatic coordination of the ACP with its partner enzymes. The transient nature of ACP interactions with these catalytic domains imposes a major obstacle for investigation of the influence of protein-protein interactions on polyketide product outcome. To further our understanding about how the ACP interacts with the product template (PT) domain that catalyzes polyketide cyclization, we developed the first mechanism-based crosslinkers for NR-PKSs. Through in vitro assays, in silico docking and bioinformatics, ACP residues involved in ACP-PT recognition were identified. We used this information to improve ACP compatibility with non-cognate PT domains, which resulted in the first gain-of-function ACP with improved interactions with its partner enzymes. This advance will aid in future combinatorial biosynthesis of new polyketides.
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Affiliation(s)
- Jesus F Barajas
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Kara Finzel
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Timothy R Valentic
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Gaurav Shakya
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Nathan Gamarra
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Delsy Martinez
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Jordan L Meier
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anna L Vagstad
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Adam G Newman
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Shiou-Chuan Tsai
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA.
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8
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Affiliation(s)
- Amin Zargar
- Lawrence Berkeley National LaboratoryJoint BioEnergy InstituteEmeryvilleCA94608
- Physical Biosciences Div.Lawrence Berkeley National LaboratoryBerkeleyCA94720
| | - Jesus F. Barajas
- Physical Biosciences Div.Lawrence Berkeley National LaboratoryBerkeleyCA94720
- Dept. of Energy Agile BioFoundryEmeryvilleCA94608
| | - Ravi Lal
- Lawrence Berkeley National LaboratoryJoint BioEnergy InstituteEmeryvilleCA94608
| | - Jay D. Keasling
- Lawrence Berkeley National LaboratoryJoint BioEnergy InstituteEmeryvilleCA94608
- Physical Biosciences Div.Lawrence Berkeley National LaboratoryBerkeleyCA94720
- QB3 Institute, University of California‐BerkeleyEmeryvilleCA94608
- Dept. of Chemical and Biomolecular EngineeringUniversity of CaliforniaBerkeleyCA94720
- Dept. of BioengineeringUniversity of CaliforniaBerkeleyCA94720
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9
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Barajas JF, Zargar A, Pang B, Benites VT, Gin J, Baidoo EEK, Petzold CJ, Hillson NJ, Keasling JD. Cover Feature: Biochemical Characterization of β-Amino Acid Incorporation in Fluvirucin B 2
Biosynthesis (ChemBioChem 13/2018). Chembiochem 2018. [DOI: 10.1002/cbic.201800299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jesus F. Barajas
- Department of Energy Agile BioFoundry; 5885 Hollis Street 4th floor Emeryville CA 94608 USA
- Biological Systems and Engineering Division; Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley CA 94720 USA
| | - Amin Zargar
- Biological Systems and Engineering Division; Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley CA 94720 USA
- Joint BioEnergy Institute; 5885 Hollis Street 4th floor Emeryville CA 94608 USA
| | - Bo Pang
- Biological Systems and Engineering Division; Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley CA 94720 USA
- Joint BioEnergy Institute; 5885 Hollis Street 4th floor Emeryville CA 94608 USA
| | - Veronica T. Benites
- Department of Energy Agile BioFoundry; 5885 Hollis Street 4th floor Emeryville CA 94608 USA
- Biological Systems and Engineering Division; Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley CA 94720 USA
- Joint BioEnergy Institute; 5885 Hollis Street 4th floor Emeryville CA 94608 USA
| | - Jennifer Gin
- Biological Systems and Engineering Division; Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley CA 94720 USA
- Joint BioEnergy Institute; 5885 Hollis Street 4th floor Emeryville CA 94608 USA
| | - Edward E. K. Baidoo
- Department of Energy Agile BioFoundry; 5885 Hollis Street 4th floor Emeryville CA 94608 USA
- Biological Systems and Engineering Division; Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley CA 94720 USA
- Joint BioEnergy Institute; 5885 Hollis Street 4th floor Emeryville CA 94608 USA
| | - Christopher J. Petzold
- Department of Energy Agile BioFoundry; 5885 Hollis Street 4th floor Emeryville CA 94608 USA
- Biological Systems and Engineering Division; Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley CA 94720 USA
- Joint BioEnergy Institute; 5885 Hollis Street 4th floor Emeryville CA 94608 USA
| | - Nathan J. Hillson
- Department of Energy Agile BioFoundry; 5885 Hollis Street 4th floor Emeryville CA 94608 USA
- Biological Systems and Engineering Division; Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley CA 94720 USA
- Joint BioEnergy Institute; 5885 Hollis Street 4th floor Emeryville CA 94608 USA
| | - Jay D. Keasling
- Biological Systems and Engineering Division; Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley CA 94720 USA
- Joint BioEnergy Institute; 5885 Hollis Street 4th floor Emeryville CA 94608 USA
- QB3 Institute; University of California-Berkeley; 174 Stanley Hall Berkeley CA 94720 USA
- Department of Chemical and Biomolecular Engineering; Department of Bioengineering; University of California-Berkeley; 201 Gilman Hall Berkeley CA 94720 USA
- Novo Nordisk Foundation Center for Biosustainability; Technical University Denmark; 2800 kgs. Lingby Denmark
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10
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Barajas JF, Zargar A, Pang B, Benites VT, Gin J, Baidoo EEK, Petzold CJ, Hillson NJ, Keasling JD. Biochemical Characterization of β-Amino Acid Incorporation in Fluvirucin B 2 Biosynthesis. Chembiochem 2018; 19:1391-1395. [PMID: 29603548 DOI: 10.1002/cbic.201800169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Indexed: 11/10/2022]
Abstract
Naturally occurring lactams, such as the polyketide-derived macrolactams, provide a diverse class of natural products that could enhance existing chemically produced lactams. Although β-amino acid loading in the fluvirucin B2 polyketide pathway was proposed by a previously identified putative biosynthetic gene cluster, biochemical characterization of the complete loading enzymes has not been described. Here we elucidate the complete biosynthetic pathway of the β-amino acid loading pathway in fluvirucin B2 biosynthesis. We demonstrate the promiscuity of the loading pathway to utilize a range of amino acids and further illustrate the ability to introduce non-native acyl transferases to selectively transfer β-amino acids onto a polyketide synthase (PKS) loading platform. The results presented here provide a detailed biochemical description of β-amino acid selection and will further aid in future efforts to develop engineered lactam-producing PKS platforms.
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Affiliation(s)
- Jesus F Barajas
- Department of Energy Agile BioFoundry, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Amin Zargar
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA
| | - Bo Pang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA
| | - Veronica T Benites
- Department of Energy Agile BioFoundry, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA
| | - Jennifer Gin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA
| | - Edward E K Baidoo
- Department of Energy Agile BioFoundry, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA
| | - Christopher J Petzold
- Department of Energy Agile BioFoundry, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA
| | - Nathan J Hillson
- Department of Energy Agile BioFoundry, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, 5885 Hollis Street, 4th floor, Emeryville, CA, 94608, USA.,QB3 Institute, University of California-Berkeley, 174 Stanley Hall, Berkeley, CA, 94720, USA.,Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of California-Berkeley, 201 Gilman Hall, Berkeley, CA, 94720, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, 2800 kgs., Lingby, Denmark
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11
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Yuzawa S, Bailey CB, Fujii T, Jocic R, Barajas JF, Benites VT, Baidoo EEK, Chen Y, Petzold CJ, Katz L, Keasling JD. Heterologous Gene Expression of N-Terminally Truncated Variants of LipPks1 Suggests a Functionally Critical Structural Motif in the N-terminus of Modular Polyketide Synthase. ACS Chem Biol 2017; 12:2725-2729. [PMID: 29028314 DOI: 10.1021/acschembio.7b00714] [Citation(s) in RCA: 8] [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] [Indexed: 11/29/2022]
Abstract
Streptomyces genomes have a high G + C content and typically use an ATG or GTG codon to initiate protein synthesis. Although gene-finding tools perform well in low GC genomes, it is known that the accuracy in predicting a translational start site (TSS) is much less for high GC genomes. LipPks1 is a Streptomyces-derived, well-characterized modular polyketide synthase (PKS). Using this enzyme as a model, we experimentally investigated the effects of alternative TSSs using a heterologous host, Streptomyces venezuelae. One of the TSSs employed boosted the protein level by 59-fold and the product yield by 23-fold compared to the originally annotated start codon. Interestingly, a structural model of the PKS indicated the presence of a structural motif in the N-terminus, which may explain the observed different protein levels together with a proline and arginine-rich sequence that may inhibit translational initiation. This structure was also found in six other modular PKSs that utilize noncarboxylated starter substrates, which may guide the selection of optimal TSSs in conjunction with start-codon prediction software.
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Affiliation(s)
- Satoshi Yuzawa
- Biogical
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint BioEnegy Institute, Emeryville, California 94608, United States
- Agile BioFoundary, Emeryville, California 94608, United States
| | - Constance B. Bailey
- Biogical
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tatsuya Fujii
- Research
Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology, Higashi-hiroshima, Hiroshima, 739-0046, Japan
| | - Renee Jocic
- Biogical
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Agile BioFoundary, Emeryville, California 94608, United States
| | | | - Veronica T. Benites
- Biogical
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint BioEnegy Institute, Emeryville, California 94608, United States
- Agile BioFoundary, Emeryville, California 94608, United States
| | - Edward E. K. Baidoo
- Biogical
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint BioEnegy Institute, Emeryville, California 94608, United States
- Agile BioFoundary, Emeryville, California 94608, United States
| | - Yan Chen
- Biogical
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint BioEnegy Institute, Emeryville, California 94608, United States
| | - Christopher J. Petzold
- Biogical
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint BioEnegy Institute, Emeryville, California 94608, United States
- Agile BioFoundary, Emeryville, California 94608, United States
| | - Leonard Katz
- QB3
Institute, University of California, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Biogical
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint BioEnegy Institute, Emeryville, California 94608, United States
- QB3
Institute, University of California, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
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12
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Barajas JF, Blake-Hedges JM, Bailey CB, Curran S, Keasling JD. Engineered polyketides: Synergy between protein and host level engineering. Synth Syst Biotechnol 2017; 2:147-166. [PMID: 29318196 PMCID: PMC5655351 DOI: 10.1016/j.synbio.2017.08.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/26/2017] [Accepted: 08/26/2017] [Indexed: 01/01/2023] Open
Abstract
Metabolic engineering efforts toward rewiring metabolism of cells to produce new compounds often require the utilization of non-native enzymatic machinery that is capable of producing a broad range of chemical functionalities. Polyketides encompass one of the largest classes of chemically diverse natural products. With thousands of known polyketides, modular polyketide synthases (PKSs) share a particularly attractive biosynthetic logic for generating chemical diversity. The engineering of modular PKSs could open access to the deliberate production of both existing and novel compounds. In this review, we discuss PKS engineering efforts applied at both the protein and cellular level for the generation of a diverse range of chemical structures, and we examine future applications of PKSs in the production of medicines, fuels and other industrially relevant chemicals.
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Key Words
- ACP, Acyl carrier protein
- AT, Acyltransferase
- CoL, CoA-Ligase
- Commodity chemical
- DE, Dimerization element
- DEBS, 6-deoxyerythronolide B synthase
- DH, Dehydratase
- ER, Enoylreductase
- FAS, Fatty acid synthases
- KR, Ketoreductase
- KS, Ketosynthase
- LM, Loading module
- LTTR, LysR-type transcriptional regulator
- Metabolic engineering
- Natural products
- PCC, Propionyl-CoA carboxylase
- PDB, Precursor directed biosynthesis
- PK, Polyketide
- PKS, Polyketide synthase
- Polyketide
- Polyketide synthase
- R, Reductase domain
- SARP, Streptomyces antibiotic regulatory protein
- SNAC, N-acetylcysteamine
- Synthetic biology
- TE, Thioesterase
- TKL, Triketide lactone
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Affiliation(s)
| | | | - Constance B. Bailey
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Samuel Curran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jay. D. Keasling
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- QB3 Institute, University of California, Berkeley, Emeryville, CA 94608, USA
- Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, DK2970 Horsholm, Denmark
- Corresponding author. Joint BioEnergy Institute, Emeryville, CA 94608, USA.Joint BioEnergy InstituteEmeryvilleCA94608USA
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13
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Zhang J, Barajas JF, Burdu M, Wang G, Baidoo EE, Keasling JD. Application of an Acyl-CoA Ligase from Streptomyces aizunensis for Lactam Biosynthesis. ACS Synth Biol 2017; 6:884-890. [PMID: 28414905 DOI: 10.1021/acssynbio.6b00372] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
ε-Caprolactam and δ-valerolactam are important commodity chemicals used in the manufacture of nylons, with millions of tons produced annually. Biological production of these highly valued chemicals has been limited due to a lack of enzymes that cyclize ω-amino fatty acid precursors to corresponding lactams under ambient conditions. In this study, we demonstrated production of these chemicals using ORF26, an acyl-CoA ligase involved in the biosynthesis of ECO-02301 in Streptomyces aizunensis. This enzyme has a broad substrate spectrum and can cyclize 4-aminobutyric acid into γ-butyrolactam, 5-aminovaleric acid into δ-valerolactam and 6-aminocaproic acid into ε-caprolactam. Recombinant E. coli expressing ORF26 produced valerolactam and caprolactam when 5-aminovaleric acid and 6-aminocaproic acid were added to the culture medium. Upon coexpressing ORF26 with a metabolic pathway that produced 5-aminovaleric acid from lysine, we were able to demonstrate production of δ-valerolactam from lysine.
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Affiliation(s)
- Jingwei Zhang
- UCSF-UCB
Joint Graduate Group in Bioengineering, University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Synthetic
Biology Engineering Research Center, University of California, Berkeley, California 94720, United States
| | - Jesus F. Barajas
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Mehmet Burdu
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - George Wang
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Edward E. Baidoo
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Jay D. Keasling
- UCSF-UCB
Joint Graduate Group in Bioengineering, University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Synthetic
Biology Engineering Research Center, University of California, Berkeley, California 94720, United States
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
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14
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Abstract
Lactams are an important class of commodity chemicals used in the manufacture of nylons, with millions of tons produced every year. Biological production of lactams could be greatly improved by high-throughput sensors for lactam biosynthesis. To identify biosensors of lactams, we applied a chemoinformatic approach inspired by small molecule drug discovery. We define this approach as analogue generation toward catabolizable chemicals or AGTC. We discovered a lactam biosensor based on the ChnR/Pb transcription factor-promoter pair. The microbial biosensor is capable of sensing ε-caprolactam, δ-valerolactam, and butyrolactam in a dose-dependent manner. The biosensor has sufficient specificity to discriminate against lactam biosynthetic intermediates and therefore could potentially be applied for high-throughput metabolic engineering for industrially important high titer lactam biosynthesis.
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Affiliation(s)
- Jingwei Zhang
- Joint BioEnergy Institute, Emeryville, California United States
| | | | - Mehmet Burdu
- Joint BioEnergy Institute, Emeryville, California United States
| | - Thomas L. Ruegg
- Joint BioEnergy Institute, Emeryville, California United States
| | - Bryton Dias
- Joint BioEnergy Institute, Emeryville, California United States
| | - Jay D. Keasling
- Joint BioEnergy Institute, Emeryville, California United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California United States
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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15
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Phelan RM, Sachs D, Petkiewicz SJ, Barajas JF, Blake-Hedges JM, Thompson MG, Reider Apel A, Rasor BJ, Katz L, Keasling JD. Development of Next Generation Synthetic Biology Tools for Use in Streptomyces venezuelae. ACS Synth Biol 2017; 6:159-166. [PMID: 27605473 DOI: 10.1021/acssynbio.6b00202] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Streptomyces have a rich history as producers of important natural products and this genus of bacteria has recently garnered attention for its potential applications in the broader context of synthetic biology. However, the dearth of genetic tools available to control and monitor protein production precludes rapid and predictable metabolic engineering that is possible in hosts such as Escherichia coli or Saccharomyces cerevisiae. In an effort to improve genetic tools for Streptomyces venezuelae, we developed a suite of standardized, orthogonal integration vectors and an improved method to monitor protein production in this host. These tools were applied to characterize heterologous promoters and various attB chromosomal integration sites. A final study leveraged the characterized toolset to demonstrate its use in producing the biofuel precursor bisabolene using a chromosomally integrated expression system. These tools advance S. venezuelae to be a practical host for future metabolic engineering efforts.
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Affiliation(s)
- Ryan M. Phelan
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Daniel Sachs
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Shayne J. Petkiewicz
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Jesus F. Barajas
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | | | | | - Amanda Reider Apel
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Blake J. Rasor
- Department
of Biology, Miami University, 212 Pearson Hall, Oxford, Ohio 45046, United States
| | | | - Jay D. Keasling
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé, DK2970-Hørsholm, Denmark
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16
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Barajas JF, Finzel K, Valentic TR, Shakya G, Gamarra N, Martinez D, Meier JL, Vagstad AL, Newman AG, Townsend CA, Burkart MD, Tsai SC. Structural and Biochemical Analysis of Protein-Protein Interactions Between the Acyl-Carrier Protein and Product Template Domain. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jesus F. Barajas
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
| | - Kara Finzel
- Department of Chemistry and Biochemistry; University of California, San Diego; La Jolla CA 92093 USA
| | - Timothy R. Valentic
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
| | - Gaurav Shakya
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
| | - Nathan Gamarra
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
| | - Delsy Martinez
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
| | - Jordan L. Meier
- Department of Chemistry and Biochemistry; University of California, San Diego; La Jolla CA 92093 USA
| | - Anna L. Vagstad
- Department of Chemistry; The Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
| | - Adam G. Newman
- Department of Chemistry; The Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
| | - Craig A. Townsend
- Department of Chemistry; The Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry; University of California, San Diego; La Jolla CA 92093 USA
| | - Shiou-Chuan Tsai
- Department of Molecular Biology and Biochemistry; Chemistry, and Pharmaceutical Sciences; University of California, Irvine; Irvine CA 92697 USA
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17
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Jackson DR, Yu X, Wang G, Patel AB, Calveras J, Barajas JF, Sasaki E, Metsä-Ketelä M, Liu HW, Rohr J, Tsai SC. Insights into Complex Oxidation during BE-7585A Biosynthesis: Structural Determination and Analysis of the Polyketide Monooxygenase BexE. ACS Chem Biol 2016; 11:1137-47. [PMID: 26813028 DOI: 10.1021/acschembio.5b00913] [Citation(s) in RCA: 9] [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] [Indexed: 12/22/2022]
Abstract
Cores of aromatic polyketides are essential for their biological activities. Most type II polyketide synthases (PKSs) biosynthesize these core structures involving the minimal PKS, a PKS-associated ketoreductase (KR) and aromatases/cyclases (ARO/CYCs). Oxygenases (OXYs) are rarely involved. BE-7585A is an anticancer polyketide with an angucyclic core. (13)C isotope labeling experiments suggest that its angucyclic core may arise from an oxidative rearrangement of a linear anthracyclinone. Here, we present the crystal structure and functional analysis of BexE, the oxygenase proposed to catalyze this key oxidative rearrangement step that generates the angucyclinone framework. Biochemical assays using various linear anthracyclinone model compounds combined with docking simulations narrowed down the substrate of BexE to be an immediate precursor of aklaviketone, possibly 12-deoxy-aklaviketone. The structural analysis, docking simulations, and biochemical assays provide insights into the role of BexE in BE-7585A biosynthesis and lay the groundwork for engineering such framework-modifying enzymes in type II PKSs.
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Affiliation(s)
- David R. Jackson
- Department
of Molecular Biology and Biochemistry, Department of Chemistry, and
Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Xia Yu
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Guojung Wang
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Avinash B. Patel
- Department
of Molecular Biology and Biochemistry, Department of Chemistry, and
Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Jordi Calveras
- Division
of Medicinal Chemistry, College of Pharmacy and Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jesus F. Barajas
- Department
of Molecular Biology and Biochemistry, Department of Chemistry, and
Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Eita Sasaki
- Division
of Medicinal Chemistry, College of Pharmacy and Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | | | - Hung-wen Liu
- Division
of Medicinal Chemistry, College of Pharmacy and Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jürgen Rohr
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Shiou-Chuan Tsai
- Department
of Molecular Biology and Biochemistry, Department of Chemistry, and
Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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18
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Jackson DR, Tu SS, Nguyen M, Barajas JF, Schaub AJ, Krug D, Pistorius D, Luo R, Müller R, Tsai SC. Structural Insights into Anthranilate Priming during Type II Polyketide Biosynthesis. ACS Chem Biol 2016; 11:95-103. [PMID: 26473393 DOI: 10.1021/acschembio.5b00500] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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
The incorporation of nonacetate starter units during type II polyketide biosynthesis helps diversify natural products. Currently, there are few enzymatic strategies for the incorporation of nonacetate starter units in type II polyketide synthase (PKS) pathways. Here we report the crystal structure of AuaEII, the anthranilate:CoA ligase responsible for the generation of anthraniloyl-CoA, which is used as a starter unit by a type II PKS in aurachin biosynthesis. We present structural and protein sequence comparisons to other aryl:CoA ligases. We also compare the AuaEII crystal structure to a model of a CoA ligase homologue, AuaE, which is present in the same gene cluster. AuaE is predicted to have the same fold as AuaEII, but instead of CoA ligation, AuaE catalyzes acyl transfer of anthranilate from anthraniloyl-CoA to the acyl carrier protein (ACP). Together, this work provides insight into the molecular basis for starter unit selection of anthranilate in type II PKS biosynthesis.
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Affiliation(s)
| | | | | | | | | | - Daniel Krug
- Department
of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical
Research Saarland (HIPS), Helmholtz Centre for Infection Research
(HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Dominik Pistorius
- Department
of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical
Research Saarland (HIPS), Helmholtz Centre for Infection Research
(HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | | | - Rolf Müller
- Department
of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical
Research Saarland (HIPS), Helmholtz Centre for Infection Research
(HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
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19
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Barajas JF, Phelan RM, Schaub AJ, Kliewer JT, Kelly PJ, Jackson DR, Luo R, Keasling JD, Tsai SC. Comprehensive Structural and Biochemical Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols. ACTA ACUST UNITED AC 2015; 22:1018-29. [PMID: 26235055 DOI: 10.1016/j.chembiol.2015.06.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/05/2015] [Accepted: 06/22/2015] [Indexed: 01/22/2023]
Abstract
The terminal reductase (R) domain from the non-ribosomal peptide synthetase (NRPS) module MxaA in Stigmatella aurantiaca Sga15 catalyzes a non-processive four-electron reduction to produce the myxalamide family of secondary metabolites. Despite widespread use in nature, a lack of structural and mechanistic information concerning reductive release from polyketide synthase (PKS) and NRPS assembly lines principally limits our ability to redesign R domains with altered or improved activity. Here we report crystal structures for MxaA R, both in the absence and, for the first time, in the presence of the NADPH cofactor. Molecular dynamics simulations were employed to provide a deeper understanding of this domain and further identify residues critical for structural integrity, substrate binding, and catalysis. Aggregate computational and structural findings provided a basis for mechanistic investigations and, in the process, delivered a rationally altered variant with improved activity toward highly reduced substrates.
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Affiliation(s)
- Jesus F Barajas
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Ryan M Phelan
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; QB3 Institute, University of California, Berkeley, Berkeley, CA 94270, USA
| | - Andrew J Schaub
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Jaclyn T Kliewer
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Peter J Kelly
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - David R Jackson
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Jay D Keasling
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; QB3 Institute, University of California, Berkeley, Berkeley, CA 94270, USA; Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Shiou-Chuan Tsai
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA.
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20
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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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21
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Nezames CD, Sjogren CA, Barajas JF, Larsen PB. The Arabidopsis cell cycle checkpoint regulators TANMEI/ALT2 and ATR mediate the active process of aluminum-dependent root growth inhibition. Plant Cell 2012; 24:608-21. [PMID: 22345493 PMCID: PMC3315236 DOI: 10.1105/tpc.112.095596] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 01/06/2012] [Accepted: 02/02/2012] [Indexed: 05/17/2023]
Abstract
Aluminum (Al) toxicity is a global issue that severely limits root growth in acidic soils. Isolation of suppressors of the Arabidopsis thaliana Al-hypersensitive mutant, als3-1, resulted in identification of a cell cycle checkpoint factor, ALUMINUM TOLERANT2 (ALT2), which monitors and responds to DNA damage. ALT2 is required for active stoppage of root growth after Al exposure, because alt2 loss-of-function mutants fail to halt root growth after Al exposure, do not accumulate CyclinB1;1 in the root tip, and fail to force differentiation of the quiescent center. Thus, alt2-1 mutants are highly tolerant of Al levels that are severely inhibitory to the wild type. The alt2-1 allele is a loss-of-function mutation in a protein containing a putative DDB1-binding WD40 motif, previously identified as TANMEI, which is required for assessment of DNA integrity, including monitoring of DNA crosslinks. alt2-1 and atr loss-of-function mutants, the latter of which affects the cell cycle checkpoint ATAXIA TELANGIECTASIA-MUTATED AND RAD3-RELATED, are severely sensitive to DNA crosslinking agents and have increased Al tolerance. These results suggest that Al likely acts as a DNA-damaging agent in vivo and that Al-dependent root growth inhibition, in part, arises from detection of and response to this damage by TANMEI/ALT2 and ATR, both of which actively halt cell cycle progression and force differentiation of the quiescent center.
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Affiliation(s)
| | | | | | - Paul B. Larsen
- Department of Biochemistry, University of California, Riverside, California 92521
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