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Mechanistic insights into dietary (poly)phenols and vascular dysfunction-related diseases using multi-omics and integrative approaches: Machine learning as a next challenge in nutrition research. Mol Aspects Med 2023; 89:101101. [PMID: 35728999 DOI: 10.1016/j.mam.2022.101101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/09/2022] [Accepted: 06/11/2022] [Indexed: 02/04/2023]
Abstract
Dietary (poly)phenols have been extensively studied for their vasculoprotective effects and consequently their role in preventing or delaying onsets of cardiovascular and metabolic diseases. Even though early studies have ascribed the vasculoprotective properties of (poly)phenols primarily on their putative free radical scavenging properties, recent data indicate that in biological systems, (poly)phenols act primarily through genomic and epigenomic mechanisms. The molecular mechanisms underlying their health properties are still not well identified, mainly due to the use of physiologically non-relevant conditions (native molecules or extracts at high concentrations, rather than circulating metabolites), but also due to the use of targeted genomic approaches aiming to evaluate the effect only on few specific genes, thus preventing to decipher detailed molecular mechanisms involved. The use of state-of-the-art untargeted analytical methods represents a significant breakthrough in nutrigenomics, as these methods enable detailed insights into the effects at each specific omics level. Moreover, the implementation of multi-omics approaches allows integration of different levels of regulation of cellular functions, to obtain a comprehensive picture of the molecular mechanisms of action of (poly)phenols. In combination with bioinformatics and the methods of machine learning, multi-omics has potential to make a huge contribution to the nutrition science. The aim of this review is to provide an overview of the use of the omics, multi-omics, and integrative approaches in studying the vasculoprotective properties of dietary (poly)phenols and address the potentials for use of the machine learning in nutrigenomics.
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Detailed Method for Performing the ExSTA Approach in Quantitative Bottom-Up Plasma Proteomics. Methods Mol Biol 2021; 2228:353-384. [PMID: 33950503 DOI: 10.1007/978-1-0716-1024-4_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The use of stable isotope-labeled standards (SIS) is an analytically valid means of quantifying proteins in biological samples. The nature of the labeled standards and their point of insertion in a bottom-up proteomic workflow can vary, with quantification methods utilizing curves in analytically sound practices. A promising quantification strategy for low sample amounts is external standard addition (ExSTA). In ExSTA, multipoint calibration curves are generated in buffer using serially diluted natural (NAT) peptides and a fixed concentration of SIS peptides. Equal concentrations of SIS peptides are spiked into experimental sample digests, with all digests (control and experimental) subjected to solid-phase extraction prior to liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis. Endogenous peptide concentrations are then determined using the regression equation of the standard curves. Given the benefits of ExSTA in large-scale analysis, a detailed protocol is provided herein for quantifying a multiplexed panel of 125 high-to-moderate abundance proteins in undepleted and non-enriched human plasma samples. The procedural details and recommendations for successfully executing all phases of this quantification approach are described. As the proteins have been putatively correlated with various noncommunicable diseases, quantifying these by ExSTA in large-scale studies should help rapidly and precisely assess their true biomarker efficacy.
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Liu H, Shiver AL, Price MN, Carlson HK, Trotter VV, Chen Y, Escalante V, Ray J, Hern KE, Petzold CJ, Turnbaugh PJ, Huang KC, Arkin AP, Deutschbauer AM. Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments. Cell Rep 2021; 34:108789. [PMID: 33657378 PMCID: PMC8121099 DOI: 10.1016/j.celrep.2021.108789] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 11/30/2020] [Accepted: 02/03/2021] [Indexed: 12/12/2022] Open
Abstract
Harnessing the microbiota for beneficial outcomes is limited by our poor understanding of the constituent bacteria, as the functions of most of their genes are unknown. Here, we measure the growth of a barcoded transposon mutant library of the gut commensal Bacteroides thetaiotaomicron on 48 carbon sources, in the presence of 56 stress-inducing compounds, and during mono-colonization of gnotobiotic mice. We identify 516 genes with a specific phenotype under only one or a few conditions, enabling informed predictions of gene function. For example, we identify a glycoside hydrolase important for growth on type I rhamnogalacturonan, a DUF4861 protein for glycosaminoglycan utilization, a 3-keto-glucoside hydrolase for disaccharide utilization, and a tripartite multidrug resistance system specifically for bile salt tolerance. Furthermore, we show that B. thetaiotaomicron uses alternative enzymes for synthesizing nitrogen-containing metabolic precursors based on ammonium availability and that these enzymes are used differentially in vivo in a diet-dependent manner.
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Affiliation(s)
- Hualan Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Morgan N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Valentine V Trotter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Veronica Escalante
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jayashree Ray
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kelsey E Hern
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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Efficient Confirmation of Plant Viral Proteins and Identification of Specific Viral Strains by nanoLC-ESI-Q-TOF Using Single-Leaf-Tissue Samples. Pathogens 2020; 9:pathogens9110966. [PMID: 33228257 PMCID: PMC7699591 DOI: 10.3390/pathogens9110966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/11/2020] [Accepted: 11/17/2020] [Indexed: 12/03/2022] Open
Abstract
Plant viruses are important pathogens that cause significant crop losses. A plant protein extraction protocol that combines crushing the tissue by a pestle in liquid nitrogen with subsequent crushing by a roller-ball crusher in urea solution, followed by RuBisCO depletion, reduction, alkylation, protein digestion, and ZipTip purification allowed us to substantially simplify the sample preparation by removing any other precipitation steps and to detect viral proteins from samples, even with less than 0.2 g of leaf tissue, by a medium resolution nanoLC-ESI-Q-TOF. The presence of capsid proteins or polyproteins of fourteen important viruses from seven different families (Geminiviridae, Luteoviridae, Bromoviridae, Caulimoviridae, Virgaviridae, Potyviridae, and Secoviridae) isolated from ten different economically important plant hosts was confirmed through many identified pathogen-specific peptides from a protein database of host proteins and potential pathogen proteins assembled separately for each host and based on existing online plant virus pathogen databases. The presented extraction protocol, combined with a medium resolution LC-MS/MS, represents a cost-efficient virus protein confirmation method that proved to be effective at identifying virus strains (as demonstrated for PPV, WDV) and distinct disease species of BYDV, as well as putative new viral protein sequences from single-plant-leaf tissue samples. Data are available via ProteomeXchange with identifier PXD022456.
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Schwartz TS. The Promises and the Challenges of Integrating Multi-Omics and Systems Biology in Comparative Stress Biology. Integr Comp Biol 2020; 60:89-97. [PMID: 32386307 DOI: 10.1093/icb/icaa026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Comparative stress biology is inherently a systems biology approach with the goal of integrating the molecular, cellular, and physiological responses with fitness outcomes. In this way, the systems biology approach is expected to provide a holistic understanding of how different stressors result in different fitness outcomes, and how different individuals (or populations or species) respond to stressors differently. In this perceptive article, I focus on the use of multiple types of -omics data in stress biology. Targeting students and those researchers who are considering integrating -omics approaches in their comparative stress biology studies, I discuss the promise of the integration of these measures for furthering our holistic understanding of how organisms respond to different stressors. I also discuss the logistical and conceptual challenges encountered when working with -omics data and the current hurdles to fully utilize these data in studies of stress biology in non-model organisms.
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Affiliation(s)
- Tonia S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
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6
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Leprêtre M, Palos-Ladeiro M, Faugere J, Almunia C, Lemoine J, Armengaud J, Geffard A, Salvador A. From shotgun to targeted proteomics: rapid Scout-MRM assay development for monitoring potential immunomarkers in Dreissena polymorpha. Anal Bioanal Chem 2020; 412:7333-7347. [DOI: 10.1007/s00216-020-02868-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/27/2020] [Accepted: 08/06/2020] [Indexed: 12/17/2022]
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7
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Incha MR, Thompson MG, Blake-Hedges JM, Liu Y, Pearson AN, Schmidt M, Gin JW, Petzold CJ, Deutschbauer AM, Keasling JD. Leveraging host metabolism for bisdemethoxycurcumin production in Pseudomonas putida. Metab Eng Commun 2020; 10:e00119. [PMID: 32280587 PMCID: PMC7136493 DOI: 10.1016/j.mec.2019.e00119] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/09/2019] [Accepted: 12/12/2019] [Indexed: 02/06/2023] Open
Abstract
Pseudomonas putida is a saprophytic bacterium with robust metabolisms and strong solvent tolerance making it an attractive host for metabolic engineering and bioremediation. Due to its diverse carbon metabolisms, its genome encodes an array of proteins and enzymes that can be readily applied to produce valuable products. In this work we sought to identify design principles and bottlenecks in the production of type III polyketide synthase (T3PKS)-derived compounds in P. putida. T3PKS products are widely used as nutraceuticals and medicines and often require aromatic starter units, such as coumaroyl-CoA, which is also an intermediate in the native coumarate catabolic pathway of P. putida. Using a randomly barcoded transposon mutant (RB-TnSeq) library, we assayed gene functions for a large portion of aromatic catabolism, confirmed known pathways, and proposed new annotations for two aromatic transporters. The 1,3,6,8-tetrahydroxynapthalene synthase of Streptomyces coelicolor (RppA), a microbial T3PKS, was then used to rapidly assay growth conditions for increased T3PKS product accumulation. The feruloyl/coumaroyl CoA synthetase (Fcs) of P. putida was used to supply coumaroyl-CoA for the curcuminoid synthase (CUS) of Oryza sativa, a plant T3PKS. We identified that accumulation of coumaroyl-CoA in this pathway results in extended growth lag times in P. putida. Deletion of the second step in coumarate catabolism, the enoyl-CoA hydratase-lyase (Ech), resulted in increased production of the type III polyketide bisdemethoxycurcumin.
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Affiliation(s)
- Matthew R. Incha
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Mitchell G. Thompson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Jacquelyn M. Blake-Hedges
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Allison N. Pearson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Matthias Schmidt
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jennifer W. Gin
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher J. Petzold
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Adam M. Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jay D. Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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8
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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] [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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9
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Chen Y, Guenther JM, Gin JW, Chan LJG, Costello Z, Ogorzalek TL, Tran HM, Blake-Hedges JM, Keasling JD, Adams PD, García Martín H, Hillson NJ, Petzold CJ. Automated “Cells-To-Peptides” Sample Preparation Workflow for High-Throughput, Quantitative Proteomic Assays of Microbes. J Proteome Res 2019; 18:3752-3761. [DOI: 10.1021/acs.jproteome.9b00455] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
| | - Joel M. Guenther
- Sandia National Laboratories (NTESS), Livermore, California 94551, United States
| | | | | | | | | | - Huu M. Tran
- Sandia National Laboratories (NTESS), Livermore, California 94551, United States
| | | | - Jay D. Keasling
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720-1460, United States
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Center for Synthetic Biochemistry, Synthetic Biology Institute, Shenzhen Institutes for Advanced Technologies, Shenzhen 518000, China
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10
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Thompson MG, Valencia LE, Blake-Hedges JM, Cruz-Morales P, Velasquez AE, Pearson AN, Sermeno LN, Sharpless WA, Benites VT, Chen Y, Baidoo EEK, Petzold CJ, Deutschbauer AM, Keasling JD. Omics-driven identification and elimination of valerolactam catabolism in Pseudomonas putida KT2440 for increased product titer. Metab Eng Commun 2019; 9:e00098. [PMID: 31720214 PMCID: PMC6838509 DOI: 10.1016/j.mec.2019.e00098] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/13/2019] [Accepted: 08/08/2019] [Indexed: 12/25/2022] Open
Abstract
Pseudomonas putida is a promising bacterial chassis for metabolic engineering given its ability to metabolize a wide array of carbon sources, especially aromatic compounds derived from lignin. However, this omnivorous metabolism can also be a hindrance when it can naturally metabolize products produced from engineered pathways. Herein we show that P. putida is able to use valerolactam as a sole carbon source, as well as degrade caprolactam. Lactams represent important nylon precursors, and are produced in quantities exceeding one million tons per year (Zhang et al., 2017). To better understand this metabolism we use a combination of Random Barcode Transposon Sequencing (RB-TnSeq) and shotgun proteomics to identify the oplBA locus as the likely responsible amide hydrolase that initiates valerolactam catabolism. Deletion of the oplBA genes prevented P. putida from growing on valerolactam, prevented the degradation of valerolactam in rich media, and dramatically reduced caprolactam degradation under the same conditions. Deletion of oplBA, as well as pathways that compete for precursors L-lysine or 5-aminovalerate, increased the titer of valerolactam from undetectable after 48 h of production to ~90 mg/L. This work may serve as a template to rapidly eliminate undesirable metabolism in non-model hosts in future metabolic engineering efforts. P. putida utilizes valerolactam as a sole carbon source and degrades caprolactam. With RB-TnSeq and proteomics we identify the lactam hydrolytic enzyme OplBA. Deleting oplBA prevents P. putida from growing on valerolactam. We increased titers of valerolactam in P. putida from 0 mg/L to ~90 mg/L.
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Affiliation(s)
- Mitchell G Thompson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Luis E Valencia
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint Program in Bioengineering, University of California, Berkeley/San Francisco, CA, 94720, USA
| | - Jacquelyn M Blake-Hedges
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Pablo Cruz-Morales
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Centro de Biotecnologia FEMSA, Instituto Tecnologico y de Estudios Superiores de Monterrey, Mexico
| | - Alexandria E Velasquez
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Allison N Pearson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Lauren N Sermeno
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - William A Sharpless
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Veronica T Benites
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint Program in Bioengineering, University of California, Berkeley/San Francisco, CA, 94720, USA.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark.,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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