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Sword TT, Dinglasan JLN, Abbas GSK, Barker JW, Spradley ME, Greene ER, Gooden DS, Emrich SJ, Gilchrist MA, Doktycz MJ, Bailey CB. Profiling expression strategies for a type III polyketide synthase in a lysate-based, cell-free system. Sci Rep 2024; 14:12983. [PMID: 38839808 PMCID: PMC11153635 DOI: 10.1038/s41598-024-61376-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 05/06/2024] [Indexed: 06/07/2024] Open
Abstract
Some of the most metabolically diverse species of bacteria (e.g., Actinobacteria) have higher GC content in their DNA, differ substantially in codon usage, and have distinct protein folding environments compared to tractable expression hosts like Escherichia coli. Consequentially, expressing biosynthetic gene clusters (BGCs) from these bacteria in E. coli often results in a myriad of unpredictable issues with regard to protein expression and folding, delaying the biochemical characterization of new natural products. Current strategies to achieve soluble, active expression of these enzymes in tractable hosts can be a lengthy trial-and-error process. Cell-free expression (CFE) has emerged as a valuable expression platform as a testbed for rapid prototyping expression parameters. Here, we use a type III polyketide synthase from Streptomyces griseus, RppA, which catalyzes the formation of the red pigment flaviolin, as a reporter to investigate BGC refactoring techniques. We applied a library of constructs with different combinations of promoters and rppA coding sequences to investigate the synergies between promoter and codon usage. Subsequently, we assess the utility of cell-free systems for prototyping these refactoring tactics prior to their implementation in cells. Overall, codon harmonization improves natural product synthesis more than traditional codon optimization across cell-free and cellular environments. More importantly, the choice of coding sequences and promoters impact protein expression synergistically, which should be considered for future efforts to use CFE for high-yield protein expression. The promoter strategy when applied to RppA was not completely correlated with that observed with GFP, indicating that different promoter strategies should be applied for different proteins. In vivo experiments suggest that there is correlation, but not complete alignment between expressing in cell free and in vivo. Refactoring promoters and/or coding sequences via CFE can be a valuable strategy to rapidly screen for catalytically functional production of enzymes from BCGs, which advances CFE as a tool for natural product research.
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Affiliation(s)
- Tien T Sword
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Jaime Lorenzo N Dinglasan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Ghaeath S K Abbas
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
- School of Chemistry, University of Sydney, Sydney, NSW, Australia
| | - J William Barker
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Madeline E Spradley
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Elijah R Greene
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Damian S Gooden
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Scott J Emrich
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA
- Department of Electrical Engineering and Computer Science, University of Tennessee-Knoxville, Knoxville, TN, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Michael A Gilchrist
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA.
| | - Constance B Bailey
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA.
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA.
- School of Chemistry, University of Sydney, Sydney, NSW, Australia.
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2
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Jang Y, Lee YJ, Gong G, Lee SM, Um Y, Kim KH, Ko JK. Carbon dioxide valorization into resveratrol via lithoautotrophic fermentation using engineered Cupriavidus necator H16. Microb Cell Fact 2024; 23:122. [PMID: 38678199 PMCID: PMC11055273 DOI: 10.1186/s12934-024-02398-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Industrial biomanufacturing of value-added products using CO2 as a carbon source is considered more sustainable, cost-effective and resource-efficient than using common carbohydrate feedstocks. Cupriavidus necator H16 is a representative H2-oxidizing lithoautotrophic bacterium that can be utilized to valorize CO2 into valuable chemicals and has recently gained much attention as a promising platform host for versatile C1-based biomanufacturing. Since this microbial platform is genetically tractable and has a high-flux carbon storage pathway, it has been engineered to produce a variety of valuable compounds from renewable carbon sources. In this study, the bacterium was engineered to produce resveratrol autotrophically using an artificial phenylpropanoid pathway. RESULTS The heterologous genes involved in the resveratrol biosynthetic pathway-tyrosine ammonia lyase (TAL), 4-coumaroyl CoA ligase (4CL), and stilbene synthase (STS) -were implemented in C. necator H16. The overexpression of acetyl-CoA carboxylase (ACC), disruption of the PHB synthetic pathway, and an increase in the copy number of STS genes enhanced resveratrol production. In particular, the increased copies of VvSTS derived from Vitis vinifera resulted a 2-fold improvement in resveratrol synthesis from fructose. The final engineered CR-5 strain produced 1.9 mg/L of resveratrol from CO2 and tyrosine via lithoautotrophic fermentation. CONCLUSIONS To the best of our knowledge, this study is the first to describe the valorization of CO2 into polyphenolic compounds by engineering a phenylpropanoid pathway using the lithoautotrophic bacterium C. necator H16, demonstrating the potential of this strain a platform for sustainable chemical production.
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Affiliation(s)
- Yongjae Jang
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Yeon Ji Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Gyeongtaek Gong
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792, Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792, Republic of Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea.
- Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792, Republic of Korea.
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3
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Borchert AJ, Bleem AC, Lim HG, Rychel K, Dooley KD, Kellermyer ZA, Hodges TL, Palsson BO, Beckham GT. Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440. mSystems 2024; 9:e0094223. [PMID: 38323821 PMCID: PMC10949508 DOI: 10.1128/msystems.00942-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/07/2024] [Indexed: 02/08/2024] Open
Abstract
There is growing interest in engineering Pseudomonas putida KT2440 as a microbial chassis for the conversion of renewable and waste-based feedstocks, and metabolic engineering of P. putida relies on the understanding of the functional relationships between genes. In this work, independent component analysis (ICA) was applied to a compendium of existing fitness data from randomly barcoded transposon insertion sequencing (RB-TnSeq) of P. putida KT2440 grown in 179 unique experimental conditions. ICA identified 84 independent groups of genes, which we call fModules ("functional modules"), where gene members displayed shared functional influence in a specific cellular process. This machine learning-based approach both successfully recapitulated previously characterized functional relationships and established hitherto unknown associations between genes. Selected gene members from fModules for hydroxycinnamate metabolism and stress resistance, acetyl coenzyme A assimilation, and nitrogen metabolism were validated with engineered mutants of P. putida. Additionally, functional gene clusters from ICA of RB-TnSeq data sets were compared with regulatory gene clusters from prior ICA of RNAseq data sets to draw connections between gene regulation and function. Because ICA profiles the functional role of several distinct gene networks simultaneously, it can reduce the time required to annotate gene function relative to manual curation of RB-TnSeq data sets. IMPORTANCE This study demonstrates a rapid, automated approach for elucidating functional modules within complex genetic networks. While Pseudomonas putida randomly barcoded transposon insertion sequencing data were used as a proof of concept, this approach is applicable to any organism with existing functional genomics data sets and may serve as a useful tool for many valuable applications, such as guiding metabolic engineering efforts in other microbes or understanding functional relationships between virulence-associated genes in pathogenic microbes. Furthermore, this work demonstrates that comparison of data obtained from independent component analysis of transcriptomics and gene fitness datasets can elucidate regulatory-functional relationships between genes, which may have utility in a variety of applications, such as metabolic modeling, strain engineering, or identification of antimicrobial drug targets.
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Affiliation(s)
- Andrew J. Borchert
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Alissa C. Bleem
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Agile BioFoundry, Emeryville, California, USA
| | - Hyun Gyu Lim
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Joint BioEnergy Institute, Emeryville, California, USA
- Department of Biological Engineering, Inha University, Incheon, Korea
| | - Kevin Rychel
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Keven D. Dooley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Agile BioFoundry, Emeryville, California, USA
| | - Zoe A. Kellermyer
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Tracy L. Hodges
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Agile BioFoundry, Emeryville, California, USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Joint BioEnergy Institute, Emeryville, California, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Department of Pediatrics, University of California, San Diego, California, USA
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Agile BioFoundry, Emeryville, California, USA
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Utomo JC, Barrell HB, Kumar R, Smith J, Brant MS, De la Hoz Siegler H, Ro DK. Reconstructing curcumin biosynthesis in yeast reveals the implication of caffeoyl-shikimate esterase in phenylpropanoid metabolic flux. Metab Eng 2024; 82:286-296. [PMID: 38387678 DOI: 10.1016/j.ymben.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/31/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Curcumin is a polyphenolic natural product from the roots of turmeric (Curcuma longa). It has been a popular coloring and flavoring agent in food industries with known health benefits. The conventional phenylpropanoid pathway is known to proceed from phenylalanine via p-coumaroyl-CoA intermediate. Although hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) plays a key catalysis in the biosynthesis of phenylpropanoid products at the downstream of p-coumaric acid, a recent discovery of caffeoyl-shikimate esterase (CSE) showed that an alternative pathway exists. Here, the biosynthetic efficiency of the conventional and the alternative pathway in producing feruloyl-CoA was examined using curcumin production in yeast. A novel modular multiplex genome-edit (MMG)-CRISPR platform was developed to facilitate rapid integrations of up to eight genes into the yeast genome in two steps. Using this MMG-CRISPR platform and metabolic engineering strategies, the alternative CSE phenylpropanoid pathway consistently showed higher titers (2-19 folds) of curcumin production than the conventional pathway in engineered yeast strains. In shake flask cultures using a synthetic minimal medium without phenylalanine, the curcumin production titer reached up to 1.5 mg/L, which is three orders of magnitude (∼4800-fold) improvement over non-engineered base strain. This is the first demonstration of de novo curcumin biosynthesis in yeast. Our work shows the critical role of CSE in improving the metabolic flux in yeast towards the phenylpropanoid biosynthetic pathway. In addition, we showcased the convenience and reliability of modular multiplex CRISPR/Cas9 genome editing in constructing complex synthetic pathways in yeast.
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Affiliation(s)
- Joseph Christian Utomo
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Hailey Brynn Barrell
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Rahul Kumar
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Jessica Smith
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Maximilian Simon Brant
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Hector De la Hoz Siegler
- Department of Chemical and Petroleum Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Dae-Kyun Ro
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada.
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5
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Kruse LH, Sunstrum FG, Garcia D, López Pérez G, Jancsik S, Bohlmann J, Irmisch S. Improved production of the antidiabetic metabolite montbretin A in Nicotiana benthamiana: discovery, characterization, and use of Crocosmia shikimate shunt genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:766-785. [PMID: 37960967 DOI: 10.1111/tpj.16528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
The plant-specialized metabolite montbretin A (MbA) is being developed as a new treatment option for type-2 diabetes, which is among the ten leading causes of premature death and disability worldwide. MbA is a complex acylated flavonoid glycoside produced in small amounts in below-ground organs of the perennial plant Montbretia (Crocosmia × crocosmiiflora). The lack of a scalable production system limits the development and potential application of MbA as a pharmaceutical or nutraceutical. Previous efforts to reconstruct montbretin biosynthesis in Nicotiana benthamiana (Nb) resulted in low yields of MbA and higher levels of montbretin B (MbB) and montbretin C (MbC). MbA, MbB, and MbC are nearly identical metabolites differing only in their acyl moieties, derived from caffeoyl-CoA, coumaroyl-CoA, and feruloyl-CoA, respectively. In contrast to MbA, MbB and MbC are not pharmaceutically active. To utilize the montbretia caffeoyl-CoA biosynthesis for improved MbA engineering in Nb, we cloned and characterized enzymes of the shikimate shunt of the general phenylpropanoid pathway, specifically hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (CcHCT), p-coumaroylshikimate 3'-hydroxylase (CcC3'H), and caffeoylshikimate esterase (CcCSE). Gene expression patterns suggest that CcCSE enables the predominant formation of MbA, relative to MbB and MbC, in montbretia. This observation is supported by results from in vitro characterization of CcCSE and reconstruction of the shikimate shunt in yeast. Using CcHCT together with montbretin biosynthetic genes in multigene constructs resulted in a 30-fold increase of MbA in Nb. This work advances our understanding of the phenylpropanoid pathway and features a critical step towards improved MbA production in bioengineered Nb.
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Affiliation(s)
- Lars H Kruse
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Frederick G Sunstrum
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Daniela Garcia
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Guillermo López Pérez
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Sharon Jancsik
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Forest and Conservation Science, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Sandra Irmisch
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Plant Sciences, Institute of Biology, Leiden University, Leiden, 2333 BE, Netherlands
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6
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Pearson AN, Incha MR, Ho CN, Schmidt M, Roberts JB, Nava AA, Keasling JD. Characterization and Diversification of AraC/XylS Family Regulators Guided by Transposon Sequencing. ACS Synth Biol 2024; 13:206-219. [PMID: 38113125 DOI: 10.1021/acssynbio.3c00441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
In this study, we explored the development of engineered inducible systems. Publicly available data from previous transposon sequencing assays were used to identify regulators of metabolism in Pseudomonas putida KT2440. For AraC family regulators (AFRs) represented in these data, we posited AFR/promoter/inducer groupings. Twelve promoters were characterized for a response to their proposed inducers in P. putida, and the resultant data were used to create and test nine two-plasmid sensor systems in Escherichia coli. Several of these were further developed into a palette of single-plasmid inducible systems. From these experiments, we observed an unreported inducer response from a previously characterized AFR, demonstrated that the addition of a P. putida transporter improved the sensor dynamics of an AFR in E. coli, and identified an uncharacterized AFR with a novel potential inducer specificity. Finally, targeted mutations in an AFR, informed by structural predictions, enabled the further diversification of these inducible plasmids.
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Affiliation(s)
- Allison N Pearson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Matthew R Incha
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Cindy N Ho
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Matthias Schmidt
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Aachen 52062, Germany
| | - Jacob B Roberts
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint Program in Bioengineering, University of California, Berkeley/San Francisco, California 94720, United States
| | - Alberto A Nava
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Jay D Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint Program in Bioengineering, University of California, Berkeley/San Francisco, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen 518055, China
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7
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Espín-Sánchez D, Preisegger L, Mazzolenis R, Santana M, Saparrat MCN, Pedrini N, Huarte-Bonnet C. Dark Pigments in Entomopathogenic Fungal Microsclerotia: Preliminary Evidence of a 1,8-Dihydroxynaphthalene-melanin-like Compound in Metarhizium robertsii. J Fungi (Basel) 2023; 9:1162. [PMID: 38132763 PMCID: PMC10744409 DOI: 10.3390/jof9121162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
Metarhizium robertsii microsclerotia are fungal aggregates composed of compacted, pigmented hyphae. As they are highly tolerant to desiccation and produce infective conidia, they are promising candidates to be formulated as bioinsecticides. Despite this potential, the nature of the pigments within these structures remains unclear. In this study, routine culture media used for the differentiation of M. robertsii microsclerotia were supplemented with four melanin inhibitors, and the resulting propagules were characterized. Inhibitors of the 1,8-dihydroxynaphthalene (DHN)-melanin biosynthetic pathway such as tricyclazole and guaiacol induced significant phenotypic and molecular modifications in the obtained M. robertsii propagules, which exhibited a more spherical shape, reduced size, and increased susceptibility to desiccation, heat, and oxidative stress than microsclerotia obtained without inhibitors. Additionally, genes encoding for a polyketide synthase (Mrpks2) and a putative 1,3,6,8-tetrahydroxynaphthalene reductase (Mrthnr), potentially involved in the DHN-melanin biosynthetic pathway, were upregulated in fungi grown in the inhibitor-added media. In conclusion, M. robertsii microsclerotia contain melanins of type DHN that might play a role in both microsclerotia differentiation and environmental stress tolerance.
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Affiliation(s)
- Daysi Espín-Sánchez
- Instituto de Investigaciones Bioquímicas de La Plata “Profesor Doctor Rodolfo R. Brenner” (INIBIOLP), Universidad Nacional de La Plata (UNLP)-CCT-La Plata-CONICET, La Plata 1900, Argentina; (D.E.-S.); (L.P.); (R.M.); (M.S.)
| | - Lautaro Preisegger
- Instituto de Investigaciones Bioquímicas de La Plata “Profesor Doctor Rodolfo R. Brenner” (INIBIOLP), Universidad Nacional de La Plata (UNLP)-CCT-La Plata-CONICET, La Plata 1900, Argentina; (D.E.-S.); (L.P.); (R.M.); (M.S.)
| | - Romina Mazzolenis
- Instituto de Investigaciones Bioquímicas de La Plata “Profesor Doctor Rodolfo R. Brenner” (INIBIOLP), Universidad Nacional de La Plata (UNLP)-CCT-La Plata-CONICET, La Plata 1900, Argentina; (D.E.-S.); (L.P.); (R.M.); (M.S.)
| | - Marianela Santana
- Instituto de Investigaciones Bioquímicas de La Plata “Profesor Doctor Rodolfo R. Brenner” (INIBIOLP), Universidad Nacional de La Plata (UNLP)-CCT-La Plata-CONICET, La Plata 1900, Argentina; (D.E.-S.); (L.P.); (R.M.); (M.S.)
| | - Mario C. N. Saparrat
- Instituto de Fisiología Vegetal (INFIVE), Universidad Nacional de La Plata (UNLP)-CCT-La Plata-CONICET, La Plata 1900, Argentina;
| | - Nicolás Pedrini
- Instituto de Investigaciones Bioquímicas de La Plata “Profesor Doctor Rodolfo R. Brenner” (INIBIOLP), Universidad Nacional de La Plata (UNLP)-CCT-La Plata-CONICET, La Plata 1900, Argentina; (D.E.-S.); (L.P.); (R.M.); (M.S.)
| | - Carla Huarte-Bonnet
- Instituto de Investigaciones Bioquímicas de La Plata “Profesor Doctor Rodolfo R. Brenner” (INIBIOLP), Universidad Nacional de La Plata (UNLP)-CCT-La Plata-CONICET, La Plata 1900, Argentina; (D.E.-S.); (L.P.); (R.M.); (M.S.)
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8
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Garber ME, Frank V, Kazakov AE, Incha MR, Nava AA, Zhang H, Valencia LE, Keasling JD, Rajeev L, Mukhopadhyay A. REC protein family expansion by the emergence of a new signaling pathway. mBio 2023; 14:e0262223. [PMID: 37991384 PMCID: PMC10746176 DOI: 10.1128/mbio.02622-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 10/20/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE We explore when and why large classes of proteins expand into new sequence space. We used an unsupervised machine learning approach to observe the sequence landscape of REC domains of bacterial response regulator proteins. We find that within-gene recombination can switch effector domains and, consequently, change the regulatory context of the duplicated protein.
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Affiliation(s)
- Megan E. Garber
- Department of Comparative Biochemistry, University of California, Berkeley, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Vered Frank
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Alexey E. Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matthew R. Incha
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Alberto A. Nava
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Hanqiao Zhang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Luis E. Valencia
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Jay D. Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
- Center for Biosustainability, Danish Technical University, Lyngby, Denmark
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Lara Rajeev
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aindrila Mukhopadhyay
- Department of Comparative Biochemistry, University of California, Berkeley, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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9
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Yue YY, Ye YQ, Zhou ZY, Zhang MD, Jia YW, Du ZJ. Winogradskyella vincentii sp. nov. and Winogradskyella alexanderae sp. nov., two novel bacteria isolated from intertidal sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37750765 DOI: 10.1099/ijsem.0.006039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023] Open
Abstract
Two novel Gram-stain-negative, facultative anaerobic, chemoheterotrophic, non-motile and rod-shaped strains were isolated from intertidal sediment sampled at Xiaoshi Island, Weihai, PR China. Full sequence analysis of the 16S rRNA genes showed that the two strains were closely related to members of the genus Winogradskyella and the phylogenetic similarities to their closest relative, Winogradskyella aquimaris, were 96.7 and 95.8 %, respectively. The DNA G+C contents of strains 2Y89T and D23T were 33.3 and 35.1 mol%, respectively. The respiratory quinone detected in both strains was MK-6. The major fatty acids detected in strain 2Y89T were iso-C15 : 0 and iso-C15 : 1G, and in strain D23T they were iso-C15 : 1G, iso-C15 : 0 and iso-C17 : 03-OH. The principal polar lipids of strain 2Y89T mainly included phosphatidylethanolamine, aminoglycolipids, unidentified aminolipids, unidentified glycolipids and unidentified lipids; strain D23T was the same as strain 2Y89T except that it did not contain aminoglycolipids. Based on the phenotypic, chemical taxonomic, genotypic and phylogenetic features established in this study, we suggest that the new strains represent two novel species of the genus Winogradskyella, for which the names Winogradskyella vincentii sp. nov. (type strain 2Y89T=MCCC 1H00477T=KCTC 92034T) and Winogradskyella alexanderae sp. nov. (type strain D23T=MCCC 1H00462T=KCTC 92023T) are proposed.
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Affiliation(s)
- Yu-Yan Yue
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Yu-Qi Ye
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zi-Yang Zhou
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Meng-Di Zhang
- Joint Science College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Ya-Wei Jia
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, PR China
- Weihai Research Institute of Industrial Technology of Shandong University, 264209, PR China
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10
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Li J, Fu J, Yue C, Shang Y, Ye BC. Highly Efficient Biosynthesis of Protocatechuic Acid via Recombinant Pseudomonas putida KT2440. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37365996 DOI: 10.1021/acs.jafc.3c01511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Owing to their physiological activities, plant-derived phenolic acids, such as protocatechuic acid (PCA), have extensive applications and market prospects. However, traditional production processes present numerous challenges and cannot meet increasing market demands. Hence, we aimed to biosynthesize PCA by constructing an efficient microbial factory via metabolic engineering of Pseudomonas putida KT2440. Glucose metabolism was engineered by deleting the genes for gluconate 2-dehydrogenase to enhance PCA biosynthesis. To increase the biosynthetic metabolic flux, one extra copy of the genes aroGopt, aroQ, and aroB was inserted into the genome. The resultant strain, KGVA04, produced 7.2 g/L PCA. By inserting the degradation tags GSD and DAS to decrease the amount of shikimate dehydrogenase, PCA biosynthesis was increased to 13.2 g/L in shake-flask fermentation and 38.8 g/L in fed-batch fermentation. To the best of our knowledge, this was the first use of degradation tags to adjust the amount of a key enzyme at the protein level in P. putida KT2440, evidencing the remarkable potential of this method for naturally producing phenolic acids.
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Affiliation(s)
- Jin Li
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jianli Fu
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Cheng Yue
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yanzhe Shang
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
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11
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Lin P, Fu Z, Liu X, Liu C, Bai Z, Yang Y, Li Y. Direct Utilization of Peroxisomal Acetyl-CoA for the Synthesis of Polyketide Compounds in Saccharomyces cerevisiae. ACS Synth Biol 2023; 12:1599-1607. [PMID: 37172280 DOI: 10.1021/acssynbio.2c00678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Polyketides are a class of natural products with many applications but are mainly appealing as pharmaceuticals. Heterologous production of polyketides in the yeast Saccharomyces cerevisiae has been widely explored because of the many merits of this model eukaryotic microorganism. Although acetyl-CoA and malonyl-CoA, the precursors for polyketide synthesis, are distributed in several yeast subcellular organelles, only cytosolic synthesis of polyketides has been pursued in previous studies. In this study, we investigate polyketide synthesis by directly using acetyl-CoA in the peroxisomes of yeast strain CEN.PK2-1D. We first demonstrate that the polyketide flaviolin can be synthesized in this organelle upon peroxisomal colocalization of native acetyl-CoA carboxylase and 1,3,6,8-tetrahydroxynaphthalene synthase (a type III polyketide synthase). Next, using the synthesis of the polyketide triacetic acid lactone as an example, we show that (1) a new peroxisome targeting sequence, pPTS1, is more effective than the previously reported ePTS1 for peroxisomal polyketide synthesis; (2) engineering peroxisome proliferation is effective to boost polyketide production; and (3) peroxisomes provide an additional acetyl-CoA reservoir and extra space to accommodate enzymes so that utilizing the peroxisomal pathway plus the cytosolic pathway produces more polyketide than the cytosolic pathway alone. This research lays the groundwork for more efficient heterologous polyketide biosynthesis using acetyl-CoA pools in subcellular organelles.
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Affiliation(s)
- Pingxin Lin
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
| | - Zhenhao Fu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
| | - Xiuxia Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
| | - Chunli Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
| | - Zhonghu Bai
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yankun Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Ye Li
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
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12
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Fu J, Wang Z, Miao H, Yu C, Zheng Z, Ouyang J. Rapid adaptive evolution of Bacillus coagulans to undetoxified corncob hydrolysates for lactic acid production and new insights into its high phenolic degradation. BIORESOURCE TECHNOLOGY 2023; 383:129246. [PMID: 37247791 DOI: 10.1016/j.biortech.2023.129246] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
Here, an adapted Bacillus coagulans (Weizmannia coagulans) strain CC17B-1 was developed for lignocellulosic lactic acid production through a short and rapid adaptive laboratory evolution technique. Without any detoxification, two actual corn cob hydrolysates from the factory were effectively fermented to lactic acid within 60 h. Strain CC17B-1 is capable of degrading all nine determined phenolic compounds in the hydrolysate, with the only exception being vanillic acid. Notably, its tolerances for ferulic acid and p-coumaric acid are the highest doses reported in anaerobic microbes. A proposed degradation pathway showed that strain CC17B-1 could convert phenolic aldehydes to phenolic alcohol and then further degrade them completely. This work provides new ideas for the microbe phenolic degradation pathway and paves the way for industrial lactic acid production from lignocellulosic biomass.
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Affiliation(s)
- Jiaming Fu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Zijie Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Hongcheng Miao
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Chang Yu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Zhaojuan Zheng
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Jia Ouyang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
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13
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Borchert AJ, Bleem A, Beckham GT. RB-TnSeq identifies genetic targets for improved tolerance of Pseudomonas putida towards compounds relevant to lignin conversion. Metab Eng 2023; 77:208-218. [PMID: 37059293 DOI: 10.1016/j.ymben.2023.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/21/2023] [Accepted: 04/12/2023] [Indexed: 04/16/2023]
Abstract
Lignin-derived mixtures intended for bioconversion commonly contain high concentrations of aromatic acids, aliphatic acids, and salts. The inherent toxicity of these chemicals places a significant bottleneck upon the effective use of microbial systems for the valorization of these mixtures. Pseudomonas putida KT2440 can tolerate stressful quantities of several lignin-related compounds, making this bacterium a promising host for converting these chemicals to valuable bioproducts. Nonetheless, further increasing P. putida tolerance to chemicals in lignin-rich substrates has the potential to improve bioprocess performance. Accordingly, we employed random barcoded transposon insertion sequencing (RB-TnSeq) to reveal genetic determinants in P. putida KT2440 that influence stress outcomes during exposure to representative constituents found in lignin-rich process streams. The fitness information obtained from the RB-TnSeq experiments informed engineering of strains via deletion or constitutive expression of several genes. Namely, ΔgacAS, ΔfleQ, ΔlapAB, ΔttgR::Ptac:ttgABC, Ptac:PP_1150:PP_1152, ΔrelA, and ΔPP_1430 mutants showed growth improvement in the presence of single compounds, and some also exhibited greater tolerance when grown using a complex chemical mixture representative of a lignin-rich chemical stream. Overall, this work demonstrates the successful implementation of a genome-scale screening tool for the identification of genes influencing stress tolerance against notable compounds within lignin-enriched chemical streams, and the genetic targets identified herein offer promising engineering targets for improving feedstock tolerance in lignin valorization strains of P. putida KT2440.
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Affiliation(s)
- Andrew J Borchert
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Alissa Bleem
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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14
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Gauttam R, Eng T, Zhao Z, Ul Ain Rana Q, Simmons BA, Yoshikuni Y, Mukhopadhyay A, Singer SW. Development of genetic tools for heterologous protein expression in a pentose-utilizing environmental isolate of Pseudomonas putida. Microb Biotechnol 2023; 16:645-661. [PMID: 36691869 PMCID: PMC9948227 DOI: 10.1111/1751-7915.14205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/17/2022] [Indexed: 01/25/2023] Open
Abstract
Pseudomonas putida has emerged as a promising host for the conversion of biomass-derived sugars and aromatic intermediates into commercially relevant biofuels and bioproducts. Most of the strain development studies previously published have focused on P. putida KT2440, which has been engineered to produce a variety of non-native bioproducts. However, P. putida is not capable of metabolizing pentose sugars, which can constitute up to 25% of biomass hydrolysates. Related P. putida isolates that metabolize a larger fraction of biomass-derived carbon may be attractive as complementary hosts to P. putida KT2440. Here we describe genetic tool development for P. putida M2, a soil isolate that can metabolize pentose sugars. The functionality of five inducible promoter systems and 12 ribosome binding sites was assessed to regulate gene expression. The utility of these expression systems was confirmed by the production of indigoidine from C6 and C5 sugars. Chromosomal integration and expression of non-native genes was achieved by using chassis-independent recombinase-assisted genome engineering (CRAGE) for single-step gene integration of biosynthetic pathways directly into the genome of P. putida M2. These genetic tools provide a foundation to develop hosts complementary to P. putida KT2440 and expand the ability of this versatile microbial group to convert biomass to bioproducts.
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Affiliation(s)
- Rahul Gauttam
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Thomas Eng
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Zhiying Zhao
- Joint Genome Institute, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Qurrat Ul Ain Rana
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Blake A Simmons
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yasuo Yoshikuni
- Joint Genome Institute, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aindrila Mukhopadhyay
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Steven W Singer
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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15
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Fenster JA, Werner AZ, Tay JW, Gillen M, Schirokauer L, Hill NC, Watson A, Ramirez KJ, Johnson CW, Beckham GT, Cameron JC, Eckert CA. Dynamic and single cell characterization of a CRISPR-interference toolset in Pseudomonas putida KT2440 for β-ketoadipate production from p-coumarate. Metab Eng Commun 2022; 15:e00204. [PMID: 36093381 PMCID: PMC9460563 DOI: 10.1016/j.mec.2022.e00204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/22/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Pseudomonas putida KT2440 is a well-studied bacterium for the conversion of lignin-derived aromatic compounds to bioproducts. The development of advanced genetic tools in P. putida has reduced the turnaround time for hypothesis testing and enabled the construction of strains capable of producing various products of interest. Here, we evaluate an inducible CRISPR-interference (CRISPRi) toolset on fluorescent, essential, and metabolic targets. Nuclease-deficient Cas9 (dCas9) expressed with the arabinose (8K)-inducible promoter was shown to be tightly regulated across various media conditions and when targeting essential genes. In addition to bulk growth data, single cell time lapse microscopy was conducted, which revealed intrinsic heterogeneity in knockdown rate within an isoclonal population. The dynamics of knockdown were studied across genomic targets in exponentially-growing cells, revealing a universal 1.75 ± 0.38 h quiescent phase after induction where 1.5 ± 0.35 doublings occur before a phenotypic response is observed. To demonstrate application of this CRISPRi toolset, β-ketoadipate, a monomer for performance-advantaged nylon, was produced at a 4.39 ± 0.5 g/L and yield of 0.76 ± 0.10 mol/mol from p-coumarate, a hydroxycinnamic acid that can be derived from grasses. These cultivation metrics were achieved by using the higher strength IPTG (1K)-inducible promoter to knockdown the pcaIJ operon in the βKA pathway during early exponential phase. This allowed the majority of the carbon to be shunted into the desired product while eliminating the need for a supplemental carbon and energy source to support growth and maintenance. Developed an inducible dCas9-based CRISPR interference toolset in Pseudomonas putida KT2440. Characterized single-cell dynamics of fluorescent and essential gene knockdown. Applied the toolset for glucose-free production of β-ketoadipate from p-coumarate. Produced β-ketoadipate at titer of 4.39 ± 0.5 g/L and 0.76 ± 0.10 mol/mol yield.
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Affiliation(s)
- Jacob A. Fenster
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80309, USA
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Allison Z. Werner
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Jian Wei Tay
- BioFrontiers Institute, 3415 Colorado Avenue, Boulder, CO, 80309, USA
| | - Matthew Gillen
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Leo Schirokauer
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Nicholas C. Hill
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Audrey Watson
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
- BioFrontiers Institute, 3415 Colorado Avenue, Boulder, CO, 80309, USA
| | - Kelsey J. Ramirez
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Christopher W. Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Jeffrey C. Cameron
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- Corresponding author. Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO 80309, USA.
| | - Carrie A. Eckert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Corresponding author. PO Box 2008, MS6060 Oak Ridge, TN 37831-6060.
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16
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Liu D, Sica MS, Mao J, Chao LFI, Siewers V. A p-Coumaroyl-CoA Biosensor for Dynamic Regulation of Naringenin Biosynthesis in Saccharomyces cerevisiae. ACS Synth Biol 2022; 11:3228-3238. [PMID: 36137537 PMCID: PMC9594313 DOI: 10.1021/acssynbio.2c00111] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In vivo biosensors that can convert metabolite concentrations into measurable output signals are valuable tools for high-throughput screening and dynamic pathway control in the field of metabolic engineering. Here, we present a novel biosensor in Saccharomyces cerevisiae that is responsive to p-coumaroyl-CoA, a central precursor of many flavonoids. The sensor is based on the transcriptional repressor CouR from Rhodopseudomonas palustris and was applied in combination with a previously developed malonyl-CoA biosensor for dual regulation of p-coumaroyl-CoA synthesis within the naringenin production pathway. Using this approach, we obtained a naringenin titer of 47.3 mg/L upon external precursor feeding, representing a 15-fold increase over the nonregulated system.
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17
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Borchert AJ, Bleem A, Beckham GT. Experimental and Analytical Approaches for Improving the Resolution of Randomly Barcoded Transposon Insertion Sequencing (RB-TnSeq) Studies. ACS Synth Biol 2022; 11:2015-2021. [PMID: 35657709 PMCID: PMC9208016 DOI: 10.1021/acssynbio.2c00119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Randomly barcoded transposon insertion sequencing (RB-TnSeq) is an efficient, multiplexed method to determine microbial gene function during growth under a selection condition of interest. This technique applies to growth, tolerance, and persistence studies in a variety of hosts, but the wealth of data generated can complicate the identification of the most critical gene targets. Experimental and analytical methods for improving the resolution of RB-TnSeq are proposed, using Pseudomonas putida KT2440 as an example organism. Several key parameters, such as baseline media selection, substantially influence the determination of gene fitness. We also present options to increase statistical confidence in gene fitness, including increasing the number of biological replicates and passaging the baseline culture in parallel with selection conditions. These considerations provide practitioners with several options to identify genes of importance in TnSeq data sets, thereby streamlining metabolic characterization.
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Affiliation(s)
- Andrew J. Borchert
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Alissa Bleem
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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18
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Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing. Appl Environ Microbiol 2022; 88:e0243021. [PMID: 35285712 DOI: 10.1128/aem.02430-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas putida KT2440 has long been studied for its diverse and robust metabolisms, yet many genes and proteins imparting these growth capacities remain uncharacterized. Using pooled mutant fitness assays, we identified genes and proteins involved in the assimilation of 52 different nitrogen containing compounds. To assay amino acid biosynthesis, 19 amino acid drop-out conditions were also tested. From these 71 conditions, significant fitness phenotypes were elicited in 672 different genes including 100 transcriptional regulators and 112 transport-related proteins. We divide these conditions into 6 classes, and propose assimilatory pathways for the compounds based on this wealth of genetic data. To complement these data, we characterize the substrate range of three promiscuous aminotransferases relevant to metabolic engineering efforts in vitro. Furthermore, we examine the specificity of five transcriptional regulators, explaining some fitness data results and exploring their potential to be developed into useful synthetic biology tools. In addition, we use manifold learning to create an interactive visualization tool for interpreting our BarSeq data, which will improve the accessibility and utility of this work to other researchers. IMPORTANCE Understanding the genetic basis of P. putida's diverse metabolism is imperative for us to reach its full potential as a host for metabolic engineering. Many target molecules of the bioeconomy and their precursors contain nitrogen. This study provides functional evidence linking hundreds of genes to their roles in the metabolism of nitrogenous compounds, and provides an interactive tool for visualizing these data. We further characterize several aminotransferases, lactamases, and regulators, which are of particular interest for metabolic engineering.
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19
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Rainha J, Rodrigues JL, Faria C, Rodrigues LR. Curcumin biosynthesis from ferulic acid by engineered Saccharomyces cerevisiae. Biotechnol J 2021; 17:e2100400. [PMID: 34882970 DOI: 10.1002/biot.202100400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND GOAL Curcumin is a polyphenolic compound found in Curcuma longa. This bioactive molecule has several reported health-benefit effects, being the anticarcinogenic activity among the most promising ones. However, curcumin extraction from natural sources is hampered by impure products obtained from harsh chemicals and limited by plant seasonality and high prices. Therefore, curcumin heterologous production emerged as an interesting alternative. Escherichia coli has been explored as chassis but the implementation of the pathway in Saccharomyces cerevisiae can have several advantages, including its generally regarded as safe status. Hence, S. cerevisiae was engineered for the first time to produce curcumin from its precursor ferulic acid. METHODS AND RESULTS The enzymes 4-coumarate-CoA ligase (4CL1) from Arabidopsis thaliana or feruloyl-CoA synthetase (FerA) from Pseudomonas paucimobilis and type III polyketide synthases (PKSs) from Oryza sativa or C. longa were expressed in BY4741 strain. To avoid ferulic acid deviation, the gene FDC1 coding a ferulic acid decarboxylase was deleted. The maximum curcumin titer was obtained with FerA combined with C. longa PKSs (2.7 mg L-1 ). CONCLUSIONS AND IMPLICATIONS Up to our knowledge, this is the first work reporting the expression of a feruloyl-CoA synthase and also curcuminoid biosynthetic enzymes in S. cerevisiae, and consequently, curcumin production.
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Affiliation(s)
- João Rainha
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Joana L Rodrigues
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Cristiana Faria
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal.,SilicoLife Lda., Braga, Portugal
| | - Lígia R Rodrigues
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
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20
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Towards robust Pseudomonas cell factories to harbour novel biosynthetic pathways. Essays Biochem 2021; 65:319-336. [PMID: 34223620 PMCID: PMC8314020 DOI: 10.1042/ebc20200173] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/01/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023]
Abstract
Biotechnological production in bacteria enables access to numerous valuable chemical compounds. Nowadays, advanced molecular genetic toolsets, enzyme engineering as well as the combinatorial use of biocatalysts, pathways, and circuits even bring new-to-nature compounds within reach. However, the associated substrates and biosynthetic products often cause severe chemical stress to the bacterial hosts. Species of the Pseudomonas clade thus represent especially valuable chassis as they are endowed with multiple stress response mechanisms, which allow them to cope with a variety of harmful chemicals. A built-in cell envelope stress response enables fast adaptations that sustain membrane integrity under adverse conditions. Further, effective export machineries can prevent intracellular accumulation of diverse harmful compounds. Finally, toxic chemicals such as reactive aldehydes can be eliminated by oxidation and stress-induced damage can be recovered. Exploiting and engineering these features will be essential to support an effective production of natural compounds and new chemicals. In this article, we therefore discuss major resistance strategies of Pseudomonads along with approaches pursued for their targeted exploitation and engineering in a biotechnological context. We further highlight strategies for the identification of yet unknown tolerance-associated genes and their utilisation for engineering next-generation chassis and finally discuss effective measures for pathway fine-tuning to establish stable cell factories for the effective production of natural compounds and novel biochemicals.
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21
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Cook TB, Jacobson TB, Venkataraman MV, Hofstetter H, Amador-Noguez D, Thomas MG, Pfleger BF. Stepwise genetic engineering of Pseudomonas putida enables robust heterologous production of prodigiosin and glidobactin A. Metab Eng 2021; 67:112-124. [PMID: 34175462 DOI: 10.1016/j.ymben.2021.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/14/2021] [Accepted: 06/19/2021] [Indexed: 12/21/2022]
Abstract
Polyketide synthases (PKS) and nonribosomal peptide synthetases (NRPS) comprise biosynthetic pathways that provide access to diverse, often bioactive natural products. Metabolic engineering can improve production metrics to support characterization and drug-development studies, but often native hosts are difficult to genetically manipulate and/or culture. For this reason, heterologous expression is a common strategy for natural product discovery and characterization. Many bacteria have been developed to express heterologous biosynthetic gene clusters (BGCs) for producing polyketides and nonribosomal peptides. In this article, we describe tools for using Pseudomonas putida, a Gram-negative soil bacterium, as a heterologous host for producing natural products. Pseudomonads are known to produce many natural products, but P. putida production titers have been inconsistent in the literature and often low compared to other hosts. In recent years, synthetic biology tools for engineering P. putida have greatly improved, but their application towards production of natural products is limited. To demonstrate the potential of P. putida as a heterologous host, we introduced BGCs encoding the synthesis of prodigiosin and glidobactin A, two bioactive natural products synthesized from a combination of PKS and NRPS enzymology. Engineered strains exhibited robust production of both compounds after a single chromosomal integration of the corresponding BGC. Next, we took advantage of a set of genome-editing tools to increase titers by modifying transcription and translation of the BGCs and increasing the availability of auxiliary proteins required for PKS and NRPS activity. Lastly, we discovered genetic modifications to P. putida that affect natural product synthesis, including a strategy for removing a carbon sink that improves product titers. These efforts resulted in production strains capable of producing 1.1 g/L prodigiosin and 470 mg/L glidobactin A.
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Affiliation(s)
- Taylor B Cook
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Tyler B Jacobson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Maya V Venkataraman
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Heike Hofstetter
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael G Thomas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.
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22
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Eng T, Banerjee D, Lau AK, Bowden E, Herbert RA, Trinh J, Prahl JP, Deutschbauer A, Tanjore D, Mukhopadhyay A. Engineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bioreactor. Metab Eng 2021; 66:229-238. [PMID: 33964456 DOI: 10.1016/j.ymben.2021.04.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/30/2021] [Accepted: 04/30/2021] [Indexed: 12/18/2022]
Abstract
Pseudomonas putida KT2440 is an emerging biomanufacturing host amenable for use with renewable carbon streams including aromatics such as para-coumarate. We used a pooled transposon library disrupting nearly all (4,778) non-essential genes to characterize this microbe under common stirred-tank bioreactor parameters with quantitative fitness assays. Assessing differential fitness values by monitoring changes in mutant strain abundance identified 33 gene mutants with improved fitness across multiple stirred-tank bioreactor formats. Twenty-one deletion strains from this subset were reconstructed, including GacA, a regulator, TtgB, an ABC transporter, and PP_0063, a lipid A acyltransferase. Thirteen deletion strains with roles in varying cellular functions were evaluated for conversion of para-coumarate, to a heterologous bioproduct, indigoidine. Several mutants, such as the ΔgacA strain improved fitness in a bioreactor by 35 fold and showed an 8-fold improvement in indigoidine production (4.5 g/L, 0.29 g/g, 23% of maximum theoretical yield) from para-coumarate as the carbon source.
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Affiliation(s)
- Thomas Eng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885, Hollis Street, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885, Hollis Street, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA
| | - Andrew K Lau
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885, Hollis Street, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA
| | - Emily Bowden
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885, Hollis Street, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA
| | - Robin A Herbert
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885, Hollis Street, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA
| | - Jessica Trinh
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885, Hollis Street, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Hollis Street, Emeryville, CA, 5885, USA
| | - Adam Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Hollis Street, Emeryville, CA, 5885, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885, Hollis Street, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA.
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23
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Martin-Pascual M, Batianis C, Bruinsma L, Asin-Garcia E, Garcia-Morales L, Weusthuis RA, van Kranenburg R, Martins Dos Santos VAP. A navigation guide of synthetic biology tools for Pseudomonas putida. Biotechnol Adv 2021; 49:107732. [PMID: 33785373 DOI: 10.1016/j.biotechadv.2021.107732] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022]
Abstract
Pseudomonas putida is a microbial chassis of huge potential for industrial and environmental biotechnology, owing to its remarkable metabolic versatility and ability to sustain difficult redox reactions and operational stresses, among other attractive characteristics. A wealth of genetic and in silico tools have been developed to enable the unravelling of its physiology and improvement of its performance. However, the rise of this microbe as a promising platform for biotechnological applications has resulted in diversification of tools and methods rather than standardization and convergence. As a consequence, multiple tools for the same purpose have been generated, whilst most of them have not been embraced by the scientific community, which has led to compartmentalization and inefficient use of resources. Inspired by this and by the substantial increase in popularity of P. putida, we aim herein to bring together and assess all currently available (wet and dry) synthetic biology tools specific for this microbe, focusing on the last 5 years. We provide information on the principles, functionality, advantages and limitations, with special focus on their use in metabolic engineering. Additionally, we compare the tool portfolio for P. putida with those for other bacterial chassis and discuss potential future directions for tool development. Therefore, this review is intended as a reference guide for experts and new 'users' of this promising chassis.
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Affiliation(s)
- Maria Martin-Pascual
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Christos Batianis
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Lyon Bruinsma
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Enrique Asin-Garcia
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Luis Garcia-Morales
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Richard van Kranenburg
- Corbion, Gorinchem 4206 AC, The Netherlands; Laboratory of Microbiology, Wageningen University & Research, Wageningen 6708 WE, the Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands; LifeGlimmer GmbH, Berlin 12163, Germany.
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24
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Liu Y, Cruz-Morales P, Zargar A, Belcher MS, Pang B, Englund E, Dan Q, Yin K, Keasling JD. Biofuels for a sustainable future. Cell 2021; 184:1636-1647. [PMID: 33639085 DOI: 10.1016/j.cell.2021.01.052] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/16/2021] [Accepted: 01/27/2021] [Indexed: 12/26/2022]
Abstract
Rapid increases of energy consumption and human dependency on fossil fuels have led to the accumulation of greenhouse gases and consequently, climate change. As such, major efforts have been taken to develop, test, and adopt clean renewable fuel alternatives. Production of bioethanol and biodiesel from crops is well developed, while other feedstock resources and processes have also shown high potential to provide efficient and cost-effective alternatives, such as landfill and plastic waste conversion, algal photosynthesis, as well as electrochemical carbon fixation. In addition, the downstream microbial fermentation can be further engineered to not only increase the product yield but also expand the chemical space of biofuels through the rational design and fine-tuning of biosynthetic pathways toward the realization of "designer fuels" and diverse future applications.
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Affiliation(s)
- Yuzhong Liu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Pablo Cruz-Morales
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Amin Zargar
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Michael S Belcher
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Bo Pang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Elias Englund
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Qingyun Dan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Kevin Yin
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA; Departments of Chemical and Biomolecular Engineering and of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, Horsholm, Denmark; Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
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25
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Recent Advances in the Heterologous Biosynthesis of Natural Products from Streptomyces. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11041851] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Streptomyces is a significant source of natural products that are used as therapeutic antibiotics, anticancer and antitumor agents, pesticides, and dyes. Recently, with the advances in metabolite analysis, many new secondary metabolites have been characterized. Moreover, genome mining approaches demonstrate that many silent and cryptic biosynthetic gene clusters (BGCs) and many secondary metabolites are produced in very low amounts under laboratory conditions. One strain many compounds (OSMAC), overexpression/deletion of regulatory genes, ribosome engineering, and promoter replacement have been utilized to activate or enhance the production titer of target compounds. Hence, the heterologous expression of BGCs by transferring to a suitable production platform has been successfully employed for the detection, characterization, and yield quantity production of many secondary metabolites. In this review, we introduce the systematic approach for the heterologous production of secondary metabolites from Streptomyces in Streptomyces and other hosts, the genome analysis tools, the host selection, and the development of genetic control elements for heterologous expression and the production of secondary metabolites.
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26
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Wada A, Prates ÉT, Hirano R, Werner AZ, Kamimura N, Jacobson DA, Beckham GT, Masai E. Characterization of aromatic acid/proton symporters in Pseudomonas putida KT2440 toward efficient microbial conversion of lignin-related aromatics. Metab Eng 2021; 64:167-179. [PMID: 33549838 DOI: 10.1016/j.ymben.2021.01.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/10/2020] [Accepted: 01/30/2021] [Indexed: 11/18/2022]
Abstract
Pseudomonas putida KT2440 (hereafter KT2440) is a well-studied platform bacterium for the production of industrially valuable chemicals from heterogeneous mixtures of aromatic compounds obtained from lignin depolymerization. KT2440 can grow on lignin-related monomers, such as ferulate (FA), 4-coumarate (4CA), vanillate (VA), 4-hydroxybenzoate (4HBA), and protocatechuate (PCA). Genes associated with their catabolism are known, but knowledge about the uptake systems remains limited. In this work, we studied the KT2440 transporters of lignin-related monomers and their substrate selectivity. Based on the inhibition by protonophores, we focused on five genes encoding aromatic acid/H+ symporter family transporters categorized into major facilitator superfamily that uses the proton motive force. The mutants of PP_1376 (pcaK) and PP_3349 (hcnK) exhibited significantly reduced growth on PCA/4HBA and FA/4CA, respectively, while no change was observed on VA for any of the five gene mutants. At pH 9.0, the conversion of these compounds by hcnK mutant (FA/4CA) and vanK mutant (VA) was dramatically reduced, revealing that these transporters are crucial for the uptake of the anionic substrates at high pH. Uptake assays using 14C-labeled substrates in Escherichia coli and biosensor-based assays confirmed that PcaK, HcnK, and VanK have ability to take up PCA, FA/4CA, and VA/PCA, respectively. Additionally, analyses of the predicted protein structures suggest that the size and hydropathic properties of the substrate-binding sites of these transporters determine their substrate preferences. Overall, this study reveals that at physiological pH, PcaK and HcnK have a major role in the uptake of PCA/4HBA and FA/4CA, respectively, and VanK is a VA/PCA transporter. This information can contribute to the engineering of strains for the efficient conversion of lignin-related monomers to value-added chemicals.
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Affiliation(s)
- Ayumu Wada
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Érica T Prates
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Ryo Hirano
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Allison Z Werner
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Naofumi Kamimura
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Daniel A Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan.
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27
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Kumar M, You S, Beiyuan J, Luo G, Gupta J, Kumar S, Singh L, Zhang S, Tsang DCW. Lignin valorization by bacterial genus Pseudomonas: State-of-the-art review and prospects. BIORESOURCE TECHNOLOGY 2021; 320:124412. [PMID: 33249259 DOI: 10.1016/j.biortech.2020.124412] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 06/12/2023]
Abstract
The most prominent aromatic feedstock on Earth is lignin, however, lignin valorization is still an underrated subject. The principal preparatory strategies for lignin valorization are fragmentation and depolymerization which help in the production of fuels and chemicals. Owing to lignin's structural heterogeneity, these strategies result in product generation which requires tedious separation and purification to extract target products. The bacterial genus Pseudomonas has been dominant for its lignin valorization potency, owing to a robust enzymatic machinery that is used to funnel variable lignin derivatives into certain target products such as polyhydroxyalkanotes (PHAs) and cis, cis-muconic acid (MA). In this review, the potential of genus Pseudomonas in lignin valorization is critically reviewed along with the advanced genetic techniques and tools to ease the use of lignin/lignin-model compounds for the synthesis of bioproducts. This review also highlights the research gaps in lignin biovalorization and discuss the challenges and possibilities for future research.
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Affiliation(s)
- Manish Kumar
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; CSIR - National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440 020, India
| | - Siming You
- University of Glasgow, James Watt School of Engineering, Glasgow G12 8 QQ, United Kingdom
| | - Jingzi Beiyuan
- Biochar Engineering Technology Research Center of Guangdong Province, School of Environment and Chemical Engineering, Foshan University, Foshan 528000, China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Juhi Gupta
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sunil Kumar
- CSIR - National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440 020, India
| | - Lal Singh
- CSIR - National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440 020, India
| | - Shicheng Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Daniel C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
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28
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Sun L, Xin F, Alper HS. Bio-synthesis of food additives and colorants-a growing trend in future food. Biotechnol Adv 2021; 47:107694. [PMID: 33388370 DOI: 10.1016/j.biotechadv.2020.107694] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/24/2020] [Accepted: 12/27/2020] [Indexed: 02/07/2023]
Abstract
Food additives and colorants are extensively used in the food industry to improve food quality and safety during processing, storage and packing. Sourcing of these molecules is predominately through three means: extraction from natural sources, chemical synthesis, and bio-production, with the first two being the most utilized. However, growing demands for sustainability, safety and "natural" products have renewed interest in using bio-based production methods. Likewise, the move to more cultured foods and meat alternatives requires the production of new additives and colorants. The production of bio-based food additives and colorants is an interdisciplinary research endeavor and represents a growing trend in future food. To highlight the potential of microbial hosts for food additive and colorant production, we focus on current advances for example molecules based on their utilization stage and bio-production yield as follows: (I) approved and industrially produced with high titers; (II) approved and produced with decent titers (in the g/L range), but requiring further engineering to reduce production costs; (III) approved and produced with very early stage titers (in the mg/L range); and (IV) new/potential candidates that have not been approved but can be sourced through microbes. Promising approaches, as well as current challenges and future directions will also be thoroughly discussed for the bioproduction of these food additives and colorants.
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Affiliation(s)
- Lichao Sun
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China.
| | - Fengjiao Xin
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China.
| | - Hal S Alper
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, United States; McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, United States.
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29
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Fenster JA, Eckert CA. High-Throughput Functional Genomics for Energy Production. Curr Opin Biotechnol 2020; 67:7-14. [PMID: 33152605 DOI: 10.1016/j.copbio.2020.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
Functional genomics remains a foundational field for establishing genotype-phenotype relationships that enable strain engineering. High-throughput (HTP) methods accelerate the Design-Build-Test-Learn cycle that currently drives synthetic biology towards a forward engineering future. Trackable mutagenesis techniques including transposon insertion sequencing and CRISPR-Cas-mediated genome editing allow for rapid fitness profiling of a collection, or library, of mutants to discover beneficial mutations. Due to the relative speed of these experiments compared to adaptive evolution experiments, iterative rounds of mutagenesis can be implemented for next-generation metabolic engineering efforts to design complex production and tolerance phenotypes. Additionally, the expansion of these mutagenesis techniques to novel bacteria are opening up industrial microbes that show promise for establishing a bio-based economy.
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Affiliation(s)
- Jacob A Fenster
- Chemical and Biological Engineering, University of Colorado, Boulder CO, United States; Renewable and Sustainable Energy Institute, University of Colorado, Boulder CO, United States
| | - Carrie A Eckert
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder CO, United States; National Renewable Energy Laboratory, Golden CO, United States.
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30
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Hogenkamp F, Hilgers F, Knapp A, Klaus O, Bier C, Binder D, Jaeger KE, Drepper T, Pietruszka J. Effect of Photocaged Isopropyl β-d-1-thiogalactopyranoside Solubility on the Light Responsiveness of LacI-controlled Expression Systems in Different Bacteria. Chembiochem 2020; 22:539-547. [PMID: 32914927 PMCID: PMC7894499 DOI: 10.1002/cbic.202000377] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/31/2020] [Indexed: 01/02/2023]
Abstract
Photolabile protecting groups play a significant role in controlling biological functions and cellular processes in living cells and tissues, as light offers high spatiotemporal control, is non‐invasive as well as easily tuneable. In the recent past, photo‐responsive inducer molecules such as 6‐nitropiperonyl‐caged IPTG (NP‐cIPTG) have been used as optochemical tools for Lac repressor‐controlled microbial expression systems. To further expand the applicability of the versatile optochemical on‐switch, we have investigated whether the modulation of cIPTG water solubility can improve the light responsiveness of appropriate expression systems in bacteria. To this end, we developed two new cIPTG derivatives with different hydrophobicity and demonstrated both an easy applicability for the light‐mediated control of gene expression and a simple transferability of this optochemical toolbox to the biotechnologically relevant bacteria Pseudomonas putida and Bacillus subtilis. Notably, the more water‐soluble cIPTG derivative proved to be particularly suitable for light‐mediated gene expression in these alternative expression hosts.
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Affiliation(s)
- Fabian Hogenkamp
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
| | - Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
| | - Andreas Knapp
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
| | - Oliver Klaus
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
| | - Claus Bier
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
| | - Dennis Binder
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany.,Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany.,Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich, Stetternicher Forst, 52426, Jülich, Germany
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31
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Schwanemann T, Otto M, Wierckx N, Wynands B. Pseudomonasas Versatile Aromatics Cell Factory. Biotechnol J 2020; 15:e1900569. [DOI: 10.1002/biot.201900569] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/08/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Tobias Schwanemann
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology Forschungszentrum Jülich, GmbH 52425 Jülich Germany
| | - Maike Otto
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology Forschungszentrum Jülich, GmbH 52425 Jülich Germany
| | - Nick Wierckx
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology Forschungszentrum Jülich, GmbH 52425 Jülich Germany
| | - Benedikt Wynands
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology Forschungszentrum Jülich, GmbH 52425 Jülich Germany
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32
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Thompson MG, Incha MR, Pearson AN, Schmidt M, Sharpless WA, Eiben CB, Cruz-Morales P, Blake-Hedges JM, Liu Y, Adams CA, Haushalter RW, Krishna RN, Lichtner P, Blank LM, Mukhopadhyay A, Deutschbauer AM, Shih PM, Keasling JD. Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing. Appl Environ Microbiol 2020; 86:e01665-20. [PMID: 32826213 PMCID: PMC7580535 DOI: 10.1128/aem.01665-20] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/12/2020] [Indexed: 12/13/2022] Open
Abstract
With its ability to catabolize a wide variety of carbon sources and a growing engineering toolkit, Pseudomonas putida KT2440 is emerging as an important chassis organism for metabolic engineering. Despite advances in our understanding of the organism, many gaps remain in our knowledge of the genetic basis of its metabolic capabilities. The gaps are particularly noticeable in our understanding of both fatty acid and alcohol catabolism, where many paralogs putatively coding for similar enzymes coexist, making biochemical assignment via sequence homology difficult. To rapidly assign function to the enzymes responsible for these metabolisms, we leveraged random barcode transposon sequencing (RB-Tn-Seq). Global fitness analyses of transposon libraries grown on 13 fatty acids and 10 alcohols produced strong phenotypes for hundreds of genes. Fitness data from mutant pools grown on fatty acids of varying chain lengths indicated specific enzyme substrate preferences and enabled us to hypothesize that DUF1302/DUF1329 family proteins potentially function as esterases. From the data, we also postulate catabolic routes for the two biogasoline molecules isoprenol and isopentanol, which are catabolized via leucine metabolism after initial oxidation and activation with coenzyme A (CoA). Because fatty acids and alcohols may serve as both feedstocks and final products of metabolic-engineering efforts, the fitness data presented here will help guide future genomic modifications toward higher titers, rates, and yields.IMPORTANCE To engineer novel metabolic pathways into P. putida, a comprehensive understanding of the genetic basis of its versatile metabolism is essential. Here, we provide functional evidence for the putative roles of hundreds of genes involved in the fatty acid and alcohol metabolism of the bacterium. These data provide a framework facilitating precise genetic changes to prevent product degradation and to channel the flux of specific pathway intermediates as desired.
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Affiliation(s)
- Mitchell G Thompson
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant Biology, University of California, Davis, California, USA
| | - Matthew R Incha
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Allison N Pearson
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Matthias Schmidt
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - William A Sharpless
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher B Eiben
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Joint Program in Bioengineering, University of California, Berkeley, California, USA
| | - Pablo Cruz-Morales
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Centro de Biotecnología FEMSA, Instituto Tecnológico y de Estudios Superiores de Monterrey, Monterrey, México
| | - Jacquelyn M Blake-Hedges
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Catharine A Adams
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Robert W Haushalter
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rohith N Krishna
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Patrick Lichtner
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Lars M Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Patrick M Shih
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant Biology, University of California, Davis, California, USA
- Environmental and Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Joint Program in Bioengineering, University of California, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
- Institute for Quantitative Biosciences, University of California, Berkeley, California, USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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