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Shrestha S, Awasthi D, Chen Y, Gin J, Petzold CJ, Adams PD, Simmons BA, Singer SW. Simultaneous carbon catabolite repression governs sugar and aromatic co-utilization in Pseudomonas putida M2. Appl Environ Microbiol 2023; 89:e0085223. [PMID: 37724856 PMCID: PMC10617552 DOI: 10.1128/aem.00852-23] [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: 05/21/2023] [Accepted: 07/14/2023] [Indexed: 09/21/2023] Open
Abstract
Pseudomonas putida have emerged as promising biocatalysts for the conversion of sugars and aromatic compounds obtained from lignocellulosic biomass. Understanding the role of carbon catabolite repression (CCR) in these strains is critical to optimize biomass conversion to fuels and chemicals. The CCR functioning in P. putida M2, a strain capable of consuming both hexose and pentose sugars as well as aromatic compounds, was investigated by cultivation experiments, proteomics, and CRISPRi-based gene repression. Strain M2 co-utilized sugars and aromatic compounds simultaneously; however, during cultivation with glucose and aromatic compounds (p-coumarate and ferulate) mixture, intermediates (4-hydroxybenzoate and vanillate) accumulated, and substrate consumption was incomplete. In contrast, xylose-aromatic consumption resulted in transient intermediate accumulation and complete aromatic consumption, while xylose was incompletely consumed. Proteomics analysis revealed that glucose exerted stronger repression than xylose on the aromatic catabolic proteins. Key glucose (Eda) and xylose (XylX) catabolic proteins were also identified at lower abundance during cultivation with aromatic compounds implying simultaneous catabolite repression by sugars and aromatic compounds. Reduction of crc expression via CRISPRi led to faster growth and glucose and p-coumarate uptake in the CRISPRi strains compared to the control, while no difference was observed on xylose+p-coumarate. The increased abundances of Eda and amino acid biosynthesis proteins in the CRISPRi strain further supported these observations. Lastly, small RNAs (sRNAs) sequencing results showed that CrcY and CrcZ homologues levels in M2, previously identified in P. putida strains, were lower under strong CCR (glucose+p-coumarate) condition compared to when repression was absent (p-coumarate or glucose only).IMPORTANCEA newly isolated Pseudomonas putida strain, P. putida M2, can utilize both hexose and pentose sugars as well as aromatic compounds making it a promising host for the valorization of lignocellulosic biomass. Pseudomonads have developed a regulatory strategy, carbon catabolite repression, to control the assimilation of carbon sources in the environment. Carbon catabolite repression may impede the simultaneous and complete metabolism of sugars and aromatic compounds present in lignocellulosic biomass and hinder the development of an efficient industrial biocatalyst. This study provides insight into the cellular physiology and proteome during mixed-substrate utilization in P. putida M2. The phenotypic and proteomics results demonstrated simultaneous catabolite repression in the sugar-aromatic mixtures, while the CRISPRi and sRNA sequencing demonstrated the potential role of the crc gene and small RNAs in carbon catabolite repression.
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Affiliation(s)
- Shilva Shrestha
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Deepika Awasthi
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jennifer Gin
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher J. Petzold
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, California, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Blake A. Simmons
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Steven W. Singer
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Eng T, Banerjee D, Menasalvas J, Chen Y, Gin J, Choudhary H, Baidoo E, Chen JH, Ekman A, Kakumanu R, Diercks YL, Codik A, Larabell C, Gladden J, Simmons BA, Keasling JD, Petzold CJ, Mukhopadhyay A. Maximizing microbial bioproduction from sustainable carbon sources using iterative systems engineering. Cell Rep 2023; 42:113087. [PMID: 37665664 DOI: 10.1016/j.celrep.2023.113087] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/10/2023] [Accepted: 08/18/2023] [Indexed: 09/06/2023] Open
Abstract
Maximizing the production of heterologous biomolecules is a complex problem that can be addressed with a systems-level understanding of cellular metabolism and regulation. Specifically, growth-coupling approaches can increase product titers and yields and also enhance production rates. However, implementing these methods for non-canonical carbon streams is challenging due to gaps in metabolic models. Over four design-build-test-learn cycles, we rewire Pseudomonas putida KT2440 for growth-coupled production of indigoidine from para-coumarate. We explore 4,114 potential growth-coupling solutions and refine one design through laboratory evolution and ensemble data-driven methods. The final growth-coupled strain produces 7.3 g/L indigoidine at 77% maximum theoretical yield in para-coumarate minimal medium. The iterative use of growth-coupling designs and functional genomics with experimental validation was highly effective and agnostic to specific hosts, carbon streams, and final products and thus generalizable across many systems.
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Affiliation(s)
- Thomas Eng
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Deepanwita Banerjee
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Javier Menasalvas
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yan Chen
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer Gin
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hemant Choudhary
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA
| | - Edward Baidoo
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jian Hua Chen
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Axel Ekman
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ramu Kakumanu
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yuzhong Liu Diercks
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alex Codik
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Carolyn Larabell
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John Gladden
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA
| | - Blake A Simmons
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jay D Keasling
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; QB3 Institute, University of California, Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, USA; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, 2970 Horsholm, Denmark; Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Christopher J Petzold
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aindrila Mukhopadhyay
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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3
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Awasthi D, Tang YH, Amer B, Baidoo EEK, Gin J, Chen Y, Petzold CJ, Kalyuzhnaya M, Singer SW. OUP accepted manuscript. J Ind Microbiol Biotechnol 2022; 49:6521446. [PMID: 35134957 PMCID: PMC9118986 DOI: 10.1093/jimb/kuac002] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/19/2022] [Indexed: 11/15/2022]
Abstract
Rhamnolipids (RLs) are well-studied biosurfactants naturally produced by pathogenic strains of Pseudomonas aeruginosa. Current methods to produce RLs in native and heterologous hosts have focused on carbohydrates as production substrate; however, methane (CH4) provides an intriguing alternative as a substrate for RL production because it is low cost and may mitigate greenhouse gas emissions. Here, we demonstrate RL production from CH4 by Methylotuvimicrobium alcaliphilum DSM19304. RLs are inhibitory to M. alcaliphilum growth (<0.05 g/l). Adaptive laboratory evolution was performed by growing M. alcaliphilum in increasing concentrations of RLs, producing a strain that grew in the presence of 5 g/l of RLs. Metabolomics and proteomics of the adapted strain grown on CH4 in the absence of RLs revealed metabolic changes, increase in fatty acid production and secretion, alterations in gluconeogenesis, and increased secretion of lactate and osmolyte products compared with the parent strain. Expression of plasmid-borne RL production genes in the parent M. alcaliphilum strain resulted in cessation of growth and cell death. In contrast, the adapted strain transformed with the RL production genes showed no growth inhibition and produced up to 1 μM of RLs, a 600-fold increase compared with the parent strain, solely from CH4. This work has promise for developing technologies to produce fatty acid-derived bioproducts, including biosurfactants, from CH4.
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Affiliation(s)
- Deepika Awasthi
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yung-Hsu Tang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bashar Amer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Edward E K Baidoo
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer Gin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Marina Kalyuzhnaya
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Steven W Singer
- Correspondence should be addressed to: Steven W. Singer. Tel: 510-486-5556; Fax: 510-486-4252; E-mail:
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Gin J, Vlachadis-Castles A, Yudi M. Feasibility of Selective Coronary Angiogram and Percutaneous Coronary Intervention Following Self-Expanding Transcatheter Aortic Valve Implantation – A Systematic Review and Meta-Analysis. Heart Lung Circ 2022. [DOI: 10.1016/j.hlc.2022.06.587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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5
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Eiben CB, de Rond T, Bloszies C, Gin J, Chiniquy J, Baidoo EEK, Petzold CJ, Hillson NJ, Fiehn O, Keasling JD. Mevalonate Pathway Promiscuity Enables Noncanonical Terpene Production. ACS Synth Biol 2019; 8:2238-2247. [PMID: 31576747 DOI: 10.1021/acssynbio.9b00230] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 01/10/2023]
Abstract
Lepidoptera (butterflies and moths) make the six-carbon compounds homoisopentenyl pyrophosphate (HIPP) and homodimethylallyl pyrophosphate (HDMAPP) that are incorporated into 16, 17, and 18 carbon farnesyl pyrophosphate (FPP) analogues. In this work we heterologously expressed the lepidopteran modified mevalonate pathway, a propionyl-CoA ligase, and terpene cyclases in E. coli to produce several novel terpenes containing 16 carbons. Changing the terpene cyclase generated different novel terpene product profiles. To further validate the new compounds we confirmed 13C propionate was incorporated, and that the masses and fragmentation patterns were consistent with novel 16 carbon terpenes by GC-QTOF. On the basis of the available farnesyl pyrophosphate analogues lepidoptera produce, this approach should greatly expand the reachable biochemical space with applications in areas where terpenes have traditionally found uses.
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Affiliation(s)
- Christopher B. Eiben
- Department of Bioengineering, University of California, San Francisco, California 94143, United States
| | - Tristan de Rond
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Clayton Bloszies
- National Institute of Health West Coast Metabolomics Center, University of California Davis, Davis, California 95616, United States
| | - Jennifer Gin
- Department of Energy Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
- Department of Energy Agile BioFoundry, Emeryville, California 94608, United States
| | - Jennifer Chiniquy
- Department of Energy Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
- Department of Energy Agile BioFoundry, Emeryville, California 94608, United States
| | - Edward E. K. Baidoo
- Department of Energy Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
- Department of Energy Agile BioFoundry, Emeryville, California 94608, United States
| | - Christopher J. Petzold
- Department of Energy Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
- Department of Energy Agile BioFoundry, Emeryville, California 94608, United States
| | - Nathan J. Hillson
- Department of Energy Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
- Department of Energy Agile BioFoundry, Emeryville, California 94608, United States
| | - Oliver Fiehn
- National Institute of Health West Coast Metabolomics Center, University of California Davis, Davis, California 95616, United States
| | - Jay D. Keasling
- Department of Energy Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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6
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Opgenorth P, Costello Z, Okada T, Goyal G, Chen Y, Gin J, Benites V, de Raad M, Northen TR, Deng K, Deutsch S, Baidoo EEK, Petzold CJ, Hillson NJ, Garcia Martin H, Beller HR. Lessons from Two Design-Build-Test-Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning. ACS Synth Biol 2019; 8:1337-1351. [PMID: 31072100 DOI: 10.1021/acssynbio.9b00020] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [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: 12/26/2022]
Abstract
The Design-Build-Test-Learn (DBTL) cycle, facilitated by exponentially improving capabilities in synthetic biology, is an increasingly adopted metabolic engineering framework that represents a more systematic and efficient approach to strain development than historical efforts in biofuels and biobased products. Here, we report on implementation of two DBTL cycles to optimize 1-dodecanol production from glucose using 60 engineered Escherichia coli MG1655 strains. The first DBTL cycle employed a simple strategy to learn efficiently from a relatively small number of strains (36), wherein only the choice of ribosome-binding sites and an acyl-ACP/acyl-CoA reductase were modulated in a single pathway operon including genes encoding a thioesterase (UcFatB1), an acyl-ACP/acyl-CoA reductase (Maqu_2507, Maqu_2220, or Acr1), and an acyl-CoA synthetase (FadD). Measured variables included concentrations of dodecanol and all proteins in the engineered pathway. We used the data produced in the first DBTL cycle to train several machine-learning algorithms and to suggest protein profiles for the second DBTL cycle that would increase production. These strategies resulted in a 21% increase in dodecanol titer in Cycle 2 (up to 0.83 g/L, which is more than 6-fold greater than previously reported batch values for minimal medium). Beyond specific lessons learned about optimizing dodecanol titer in E. coli, this study had findings of broader relevance across synthetic biology applications, such as the importance of sequencing checks on plasmids in production strains as well as in cloning strains, and the critical need for more accurate protein expression predictive tools.
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Affiliation(s)
- Paul Opgenorth
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Zak Costello
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Takuya Okada
- Research Institute for Bioscience Product & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8680, Japan
| | - Garima Goyal
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Yan Chen
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Jennifer Gin
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Veronica Benites
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Markus de Raad
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Trent R. Northen
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Kai Deng
- Sandia National Laboratories, Livermore, California 94550, United States
| | - Samuel Deutsch
- DOE Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Edward E. K. Baidoo
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Christopher J. Petzold
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Nathan J. Hillson
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- DOE Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Hector Garcia Martin
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- BCAM, Basque Center for Applied Mathematics, 48009 Bilbao, Spain
| | - Harry R. Beller
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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7
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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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8
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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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9
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d'Espaux L, Ghosh A, Runguphan W, Wehrs M, Xu F, Konzock O, Dev I, Nhan M, Gin J, Reider Apel A, Petzold CJ, Singh S, Simmons BA, Mukhopadhyay A, García Martín H, Keasling JD. Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks. Metab Eng 2017; 42:115-125. [PMID: 28606738 DOI: 10.1016/j.ymben.2017.06.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/26/2017] [Accepted: 06/05/2017] [Indexed: 11/17/2022]
Abstract
Fatty alcohols in the C12-C18 range are used in personal care products, lubricants, and potentially biofuels. These compounds can be produced from the fatty acid pathway by a fatty acid reductase (FAR), yet yields from the preferred industrial host Saccharomyces cerevisiae remain under 2% of the theoretical maximum from glucose. Here we improved titer and yield of fatty alcohols using an approach involving quantitative analysis of protein levels and metabolic flux, engineering enzyme level and localization, pull-push-block engineering of carbon flux, and cofactor balancing. We compared four heterologous FARs, finding highest activity and endoplasmic reticulum localization from a Mus musculus FAR. After screening an additional twenty-one single-gene edits, we identified increasing FAR expression; deleting competing reactions encoded by DGA1, HFD1, and ADH6; overexpressing a mutant acetyl-CoA carboxylase; limiting NADPH and carbon usage by the glutamate dehydrogenase encoded by GDH1; and overexpressing the Δ9-desaturase encoded by OLE1 as successful strategies to improve titer. Our final strain produced 1.2g/L fatty alcohols in shake flasks, and 6.0g/L in fed-batch fermentation, corresponding to ~ 20% of the maximum theoretical yield from glucose, the highest titers and yields reported to date in S. cerevisiae. We further demonstrate high-level production from lignocellulosic feedstocks derived from ionic-liquid treated switchgrass and sorghum, reaching 0.7g/L in shake flasks. Altogether, our work represents progress towards efficient and renewable microbial production of fatty acid-derived products.
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Affiliation(s)
- Leo d'Espaux
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Amit Ghosh
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Weerawat Runguphan
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Maren Wehrs
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Feng Xu
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA 94551, United States; Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA 94551, United States
| | - Oliver Konzock
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Ishaan Dev
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, United States
| | - Melissa Nhan
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Jennifer Gin
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Amanda Reider Apel
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Christopher J Petzold
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Seema Singh
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA 94551, United States; Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA 94551, United States
| | - Blake A Simmons
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA 94551, United States; Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA 94551, United States
| | - Aindrila Mukhopadhyay
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Héctor García Martín
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Jay D Keasling
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, United States; Department of Bioengineering, University of California, Berkeley, CA 94720, United States; The Novo Nordisk Foundation Center for Sustainability, Technical University of Denmark, Denmark.
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10
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Shymansky CM, Wang G, Baidoo EEK, Gin J, Apel AR, Mukhopadhyay A, García Martín H, Keasling JD. Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism. Front Bioeng Biotechnol 2017; 5:31. [PMID: 28596955 PMCID: PMC5443151 DOI: 10.3389/fbioe.2017.00031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 01/11/2017] [Accepted: 04/25/2017] [Indexed: 11/13/2022] Open
Abstract
13C metabolic flux analysis (13C MFA) is an important systems biology technique that has been used to investigate microbial metabolism for decades. The heterotrimer Snf1 kinase complex plays a key role in the preference Saccharomyces cerevisiae exhibits for glucose over galactose, a phenomenon known as glucose repression or carbon catabolite repression. The SIP1 gene, encoding a part of this complex, has received little attention, presumably, because its knockout lacks a growth phenotype. We present a fluxomic investigation of the relative effects of the presence of galactose in classically glucose-repressing media and/or knockout of SIP1 using a multi-scale variant of 13C MFA known as 2-Scale 13C metabolic flux analysis (2S-13C MFA). In this study, all strains have the galactose metabolism deactivated (gal1Δ background) so as to be able to separate the metabolic effects purely related to glucose repression from those arising from galactose metabolism. The resulting flux profiles reveal that the presence of galactose in classically glucose-repressing conditions, for a CEN.PK113-7D gal1Δ background, results in a substantial decrease in pentose phosphate pathway (PPP) flux and increased flow from cytosolic pyruvate and malate through the mitochondria toward cytosolic branched-chain amino acid biosynthesis. These fluxomic redistributions are accompanied by a higher maximum specific growth rate, both seemingly in violation of glucose repression. Deletion of SIP1 in the CEN.PK113-7D gal1Δ cells grown in mixed glucose/galactose medium results in a further increase. Knockout of this gene in cells grown in glucose-only medium results in no change in growth rate and a corresponding decrease in glucose and ethanol exchange fluxes and flux through pathways involved in aspartate/threonine biosynthesis. Glucose repression appears to be violated at a 1/10 ratio of galactose-to-glucose. Based on the scientific literature, we may have conducted our experiments near a critical sugar ratio that is known to allow galactose to enter the cell. Additionally, we report a number of fluxomic changes associated with these growth rate increases and unexpected flux profile redistributions resulting from deletion of SIP1 in glucose-only medium.
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Affiliation(s)
- Christopher M Shymansky
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, USA.,Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - George Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, USA
| | - Edward E K Baidoo
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, USA
| | - Jennifer Gin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, USA
| | - Amanda Reider Apel
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, USA
| | - Héctor García Martín
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, USA.,DOE Agile Biofoundry, Emeryville, CA, USA.,BCAM, Basque Center for Applied Mathematics, Mazarredo, Bilbao, Basque Country, Spain
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, USA.,Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA.,Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
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11
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Nguyen A, Adams H, Gin J, Yap N, Wilson-O'Brien A, Garlick J, Wilson AM. Total serum bilirubin is an independent risk factor for coronary artery disease in men compared to women. Acta Cardiol 2016; 71:685-689. [PMID: 27920456 DOI: 10.2143/ac.71.6.3178187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Ghosh A, Ando D, Gin J, Runguphan W, Denby C, Wang G, Baidoo EEK, Shymansky C, Keasling JD, García Martín H. 13C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids. Front Bioeng Biotechnol 2016; 4:76. [PMID: 27761435 PMCID: PMC5050205 DOI: 10.3389/fbioe.2016.00076] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [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: 08/16/2016] [Accepted: 09/20/2016] [Indexed: 11/24/2022] Open
Abstract
Efficient redirection of microbial metabolism into the abundant production of desired bioproducts remains non-trivial. Here, we used flux-based modeling approaches to improve yields of fatty acids in Saccharomyces cerevisiae. We combined 13C labeling data with comprehensive genome-scale models to shed light onto microbial metabolism and improve metabolic engineering efforts. We concentrated on studying the balance of acetyl-CoA, a precursor metabolite for the biosynthesis of fatty acids. A genome-wide acetyl-CoA balance study showed ATP citrate lyase from Yarrowia lipolytica as a robust source of cytoplasmic acetyl-CoA and malate synthase as a desirable target for downregulation in terms of acetyl-CoA consumption. These genetic modifications were applied to S. cerevisiae WRY2, a strain that is capable of producing 460 mg/L of free fatty acids. With the addition of ATP citrate lyase and downregulation of malate synthase, the engineered strain produced 26% more free fatty acids. Further increases in free fatty acid production of 33% were obtained by knocking out the cytoplasmic glycerol-3-phosphate dehydrogenase, which flux analysis had shown was competing for carbon flux upstream with the carbon flux through the acetyl-CoA production pathway in the cytoplasm. In total, the genetic interventions applied in this work increased fatty acid production by ~70%.
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Affiliation(s)
- Amit Ghosh
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; Indian Institute of Technology (IIT), School of Energy Science and Engineering, Kharagpur, India
| | - David Ando
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| | - Jennifer Gin
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| | - Weerawat Runguphan
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani, Thailand
| | - Charles Denby
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| | - George Wang
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| | - Edward E K Baidoo
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
| | - Chris Shymansky
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Jay D Keasling
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA; Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, Horsholm, Denmark
| | - Héctor García Martín
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA
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13
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van Sorge NM, Cole JN, Kuipers K, Henningham A, Aziz RK, Kasirer-Friede A, Lin L, Berends ETM, Davies MR, Dougan G, Zhang F, Dahesh S, Shaw L, Gin J, Cunningham M, Merriman JA, Hütter J, Lepenies B, Rooijakkers SHM, Malley R, Walker MJ, Shattil SJ, Schlievert PM, Choudhury B, Nizet V. The classical lancefield antigen of group a Streptococcus is a virulence determinant with implications for vaccine design. Cell Host Microbe 2015; 15:729-740. [PMID: 24922575 DOI: 10.1016/j.chom.2014.05.009] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 04/15/2014] [Accepted: 04/29/2014] [Indexed: 12/19/2022]
Abstract
Group A Streptococcus (GAS) is a leading cause of infection-related mortality in humans. All GAS serotypes express the Lancefield group A carbohydrate (GAC), comprising a polyrhamnose backbone with an immunodominant N-acetylglucosamine (GlcNAc) side chain, which is the basis of rapid diagnostic tests. No biological function has been attributed to this conserved antigen. Here we identify and characterize the GAC biosynthesis genes, gacA through gacL. An isogenic mutant of the glycosyltransferase gacI, which is defective for GlcNAc side-chain addition, is attenuated for virulence in two infection models, in association with increased sensitivity to neutrophil killing, platelet-derived antimicrobials in serum, and the cathelicidin antimicrobial peptide LL-37. Antibodies to GAC lacking the GlcNAc side chain and containing only polyrhamnose promoted opsonophagocytic killing of multiple GAS serotypes and protected against systemic GAS challenge after passive immunization. Thus, the Lancefield antigen plays a functional role in GAS pathogenesis, and a deeper understanding of this unique polysaccharide has implications for vaccine development.
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Affiliation(s)
- Nina M van Sorge
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.,Medical Microbiology, University Medical Center Utrecht,3584 CX Utrecht, The Netherlands
| | - Jason N Cole
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.,Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland,QLD 4072, Australia
| | - Kirsten Kuipers
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Anna Henningham
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Ramy K Aziz
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.,Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University,11562 Cairo, Egypt
| | - Ana Kasirer-Friede
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Leo Lin
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Evelien T M Berends
- Medical Microbiology, University Medical Center Utrecht,3584 CX Utrecht, The Netherlands
| | - Mark R Davies
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland,QLD 4072, Australia.,The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, CB10 1SA,United Kingdom
| | - Gordon Dougan
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, CB10 1SA,United Kingdom
| | - Fan Zhang
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA 02115, USA
| | - Samira Dahesh
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Laura Shaw
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Jennifer Gin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Madeleine Cunningham
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Joseph A Merriman
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Julia Hütter
- Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, 14476 Potsdam, Germany.,Freie Universität Berlin, Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, 14195 Berlin, Germany
| | - Bernd Lepenies
- Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, 14476 Potsdam, Germany.,Freie Universität Berlin, Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, 14195 Berlin, Germany
| | - Suzan H M Rooijakkers
- Medical Microbiology, University Medical Center Utrecht,3584 CX Utrecht, The Netherlands
| | - Richard Malley
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA 02115, USA
| | - Mark J Walker
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland,QLD 4072, Australia
| | - Sanford J Shattil
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Patrick M Schlievert
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Biswa Choudhury
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Victor Nizet
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA.,Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA
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14
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Hann N, Yap N, Gin J, Nguyen A, Adams H, Wilson A. Candidates for novel lipid-lowering therapies: persistently high on-treatment LDL-C in STEMI and NSTEMI patients. Heart Lung Circ 2015. [DOI: 10.1016/j.hlc.2015.06.173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Nguyen A, Adams H, Gin J, Yap N, Wilson A. Less time since smoking cessation predicts acute coronary syndrome in high risk patients. Heart Lung Circ 2015. [DOI: 10.1016/j.hlc.2015.06.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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16
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Yap N, Gin J, Nguyen A, Adams H, Wilson A. Increasing renal impairment predicts lower low-density lipoprotein levels independent of statin use in high cardiovascular risk patients. Heart Lung Circ 2015. [DOI: 10.1016/j.hlc.2015.06.180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Cole J, Sorge N, Kuipers K, Henningham A, Aziz R, Kasirer‐Friede A, Lin L, Berends E, Davies M, Dougan G, Zhang F, Dahesh S, Shaw L, Gin J, Cunningham M, Merriman J, Rooijakkers S, Malley R, Walker M, Shattil S, Schlievert P, Choudhury B, Nizet V. Genetics and virulence role of the classical group A Streptococcus Lancefield antigen (790.2). FASEB J 2014. [DOI: 10.1096/fasebj.28.1_supplement.790.2] [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: 11/11/2022]
Affiliation(s)
- Jason Cole
- UC San DiegoLA JollaCAUnited States
- University of QueenslandSt LuciaAustralia
| | - Nina Sorge
- University Medical Center Utrecht UtrechtNetherlands
| | | | - Anna Henningham
- UC San DiegoLA JollaCAUnited States
- University of QueenslandSt LuciaAustralia
| | | | | | - Leo Lin
- UC San DiegoLA JollaCAUnited States
| | | | | | - Gordan Dougan
- The Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
| | - Fan Zhang
- Boston Children's HospitalBOSTONMAUnited States
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18
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Shaikh AS, Tang YJ, Mukhopadhyay A, Martín HG, Gin J, Benke PI, Keasling JD. Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein. Biotechnol Prog 2010; 26:52-6. [PMID: 19899123 DOI: 10.1002/btpr.325] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microbial production of many commercially important secondary metabolites occurs during stationary phase, and methods to measure metabolic flux during this growth phase would be valuable. Metabolic flux analysis is often based on isotopomer information from proteinogenic amino acids. As such, flux analysis primarily reflects the metabolism pertinent to the growth phase during which most proteins are synthesized. To investigate central metabolism and amino acids synthesis activity during stationary phase, addition of fully (13)C-labeled glucose followed by induction of green fluorescent protein (GFP) expression during stationary phase was used. Our results indicate that Escherichia coli was able to produce new proteins (i.e., GFP) in the stationary phase, and the amino acids in GFP were mostly from degraded proteins synthesized during the exponential growth phase. Among amino acid biosynthetic pathways, only those for serine, alanine, glutamate/glutamine, and aspartate/asparagine had significant activity during the stationary phase.
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Affiliation(s)
- Afshan S Shaikh
- Dept. of Chemical Engineering, University of California, Berkeley, CA 94720, USA
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