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Higgins SA, Igwe DO, Coradetti S, Ramsey JS, DeBlasio SL, Pitino M, Shatters RG, Niedz R, Fleites LA, Heck M. Plant-Derived, Nodule-Specific Cysteine-Rich Peptides as a Novel Source of Biopesticides for Controlling Citrus Greening Disease. Phytopathology 2024:PHYTO09230322KC. [PMID: 38376984 DOI: 10.1094/phyto-09-23-0322-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Nodule-specific cysteine-rich (NCR) peptides, encoded in the genome of the Mediterranean legume Medicago truncatula (barrelclover), are known to regulate plant-microbe interactions. A subset of computationally derived 20-mer peptide fragments from 182 NCR peptides was synthesized to identify those with activity against the unculturable vascular pathogen associated with citrus greening disease, 'Candidatus Liberibacter asiaticus' (CLas). Grounded in a design of experiments framework, we evaluated the peptides in a screening pipeline involving three distinct assays: a bacterial culture assay with Liberibacter crescens, a CLas-infected excised citrus leaf assay, and an assay to evaluate effects on bacterial acquisition by the nymphal stage of hemipteran vector Diaphorina citri. A subset of the 20-mer NCR peptide fragments inhibits both CLas growth in citrus leaves and CLas acquisition by D. citri. Two peptides induced higher levels of D. citri mortality. These findings reveal 20-mer NCR peptides as a new class of plant-derived biopesticide molecules to control citrus greening disease.
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Affiliation(s)
- Steven A Higgins
- Emerging Pests and Pathogens Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853
| | - David O Igwe
- Plant Pathology and Plant Microbe Interactions Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Samuel Coradetti
- Emerging Pests and Pathogens Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853
| | - John S Ramsey
- Emerging Pests and Pathogens Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853
| | - Stacy L DeBlasio
- Emerging Pests and Pathogens Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853
| | | | - Robert G Shatters
- U.S. Horticultural Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Fort Pierce, FL 34945
| | - Randall Niedz
- U.S. Horticultural Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Fort Pierce, FL 34945
| | - Laura A Fleites
- Emerging Pests and Pathogens Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853
| | - Michelle Heck
- Emerging Pests and Pathogens Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853
- Plant Pathology and Plant Microbe Interactions Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
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Liu D, Hwang HJ, Otoupal PB, Geiselman GM, Kim J, Pomraning KR, Kim YM, Munoz N, Nicora CD, Gao Y, Burnum-Johnson KE, Jacobson O, Coradetti S, Kim J, Deng S, Dai Z, Prahl JP, Tanjore D, Lee TS, Magnuson JK, Gladden JM. Engineering Rhodosporidium toruloides for production of 3-hydroxypropionic acid from lignocellulosic hydrolysate. Metab Eng 2023; 78:72-83. [PMID: 37201565 DOI: 10.1016/j.ymben.2023.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/28/2023] [Accepted: 05/10/2023] [Indexed: 05/20/2023]
Abstract
Microbial production of valuable bioproducts is a promising route towards green and sustainable manufacturing. The oleaginous yeast, Rhodosporidium toruloides, has emerged as an attractive host for the production of biofuels and bioproducts from lignocellulosic hydrolysates. 3-hydroxypropionic acid (3HP) is an attractive platform molecule that can be used to produce a wide range of commodity chemicals. This study focuses on establishing and optimizing the production of 3HP in R. toruloides. As R. toruloides naturally has a high metabolic flux towards malonyl-CoA, we exploited this pathway to produce 3HP. Upon finding the yeast capable of catabolizing 3HP, we then implemented functional genomics and metabolomic analysis to identify the catabolic pathways. Deletion of a putative malonate semialdehyde dehydrogenase gene encoding an oxidative 3HP pathway was found to significantly reduce 3HP degradation. We further explored monocarboxylate transporters to promote 3HP transport and identified a novel 3HP transporter in Aspergillus pseudoterreus by RNA-seq and proteomics. Combining these engineering efforts with media optimization in a fed-batch fermentation resulted in 45.4 g/L 3HP production. This represents one of the highest 3HP titers reported in yeast from lignocellulosic feedstocks. This work establishes R. toruloides as a host for 3HP production from lignocellulosic hydrolysate at high titers, and paves the way for further strain and process optimization towards enabling industrial production of 3HP in the future.
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Affiliation(s)
- Di Liu
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA.
| | - Hee Jin Hwang
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA
| | - Peter B Otoupal
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA; DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Gina M Geiselman
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA; DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Joonhoon Kim
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kyle R Pomraning
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Young-Mo Kim
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Nathalie Munoz
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carrie D Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kristin E Burnum-Johnson
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Oslo Jacobson
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Samuel Coradetti
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA
| | - Jinho Kim
- DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shuang Deng
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ziyu Dai
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jan-Philip Prahl
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Deepti Tanjore
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Taek Soon Lee
- DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jon K Magnuson
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - John M Gladden
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA; DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
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Liu D, Geiselman GM, Coradetti S, Cheng YF, Kirby J, Prahl JP, Jacobson O, Sundstrom ER, Tanjore D, Skerker JM, Gladden J. Exploiting nonionic surfactants to enhance fatty alcohol production in Rhodosporidium toruloides. Biotechnol Bioeng 2020; 117:1418-1425. [PMID: 31981215 PMCID: PMC7187362 DOI: 10.1002/bit.27285] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/23/2019] [Accepted: 01/22/2020] [Indexed: 01/13/2023]
Abstract
Fatty alcohols (FOHs) are important feedstocks in the chemical industry to produce detergents, cosmetics, and lubricants. Microbial production of FOHs has become an attractive alternative to production in plants and animals due to growing energy demands and environmental concerns. However, inhibition of cell growth caused by intracellular FOH accumulation is one major issue that limits FOH titers in microbial hosts. In addition, identification of FOH‐specific exporters remains a challenge and previous studies towards this end are limited. To alleviate the toxicity issue, we exploited nonionic surfactants to promote the export of FOHs in Rhodosporidium toruloides, an oleaginous yeast that is considered an attractive next‐generation host for the production of fatty acid‐derived chemicals. Our results showed FOH export efficiency was dramatically improved and the growth inhibition was alleviated in the presence of small amounts of tergitol and other surfactants. As a result, FOH titers increase by 4.3‐fold at bench scale to 352.6 mg/L. With further process optimization in a 2‐L bioreactor, the titer was further increased to 1.6 g/L. The method we show here can potentially be applied to other microbial hosts and may facilitate the commercialization of microbial FOH production.
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Affiliation(s)
- Di Liu
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California.,Department of Energy, Agile BioFoundry, Emeryville, California
| | - Gina M Geiselman
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California.,Department of Energy, Agile BioFoundry, Emeryville, California
| | - Samuel Coradetti
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California.,Department of Energy, Agile BioFoundry, Emeryville, California
| | - Ya-Fang Cheng
- QB3-Berkeley, University of California, Berkeley, California
| | - James Kirby
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California.,Department of Energy, Agile BioFoundry, Emeryville, California
| | - Jan-Philip Prahl
- Department of Energy, Agile BioFoundry, Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, California
| | - Oslo Jacobson
- Department of Energy, Agile BioFoundry, Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, California
| | - Eric R Sundstrom
- Department of Energy, Agile BioFoundry, Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, California
| | - Deepti Tanjore
- Department of Energy, Agile BioFoundry, Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, California
| | | | - John Gladden
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California.,Department of Energy, Agile BioFoundry, Emeryville, California.,Joint BioEnergy Institute, Emeryville, California
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