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Beritza K, Watts EC, van der Hoorn RAL. Improving transient protein expression in agroinfiltrated Nicotiana benthamiana. THE NEW PHYTOLOGIST 2024; 243:846-850. [PMID: 38849321 DOI: 10.1111/nph.19894] [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: 03/22/2024] [Accepted: 05/02/2024] [Indexed: 06/09/2024]
Abstract
Agroinfiltration of Nicotiana benthamiana is routinely used in plant science and molecular pharming to transiently express proteins of interest. Here, we discuss four phenomena that should be avoided to improve transient expression. Immune responses can be avoided by depleting immune receptors and employing pathogen-derived effectors; transcript degradation by using silencing inhibitors or RNA interference machinery mutants; endoplasmic reticulum stress by co-expressing chaperones; and protein degradation can be avoided with subcellular targeting, protease mutants and co-expressing protease inhibitors. We summarise the reported increased yields for various recombinant proteins achieved with these approaches and highlight remaining challenges to further improve the efficiency of this versatile protein expression platform.
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Affiliation(s)
- Konstantina Beritza
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, OX1 3RB, Oxford, UK
| | - Emma C Watts
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, OX1 3RB, Oxford, UK
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, OX1 3RB, Oxford, UK
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2
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Ko SR, Lee S, Koo H, Seo H, Yu J, Kim YM, Kwon SY, Shin AY. High-quality chromosome-level genome assembly of Nicotiana benthamiana. Sci Data 2024; 11:386. [PMID: 38627408 PMCID: PMC11021556 DOI: 10.1038/s41597-024-03232-0] [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: 12/18/2023] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
Nicotiana benthamiana is a fundamental model organism in plant research. Recent advancements in genomic sequencing have revealed significant intraspecific genetic variations. This study addresses the pressing need for a precise genome sequence specific to its geographic origin by presenting a comprehensive genome assembly of the N. benthamiana LAB strain from the Republic of Korea (NbKLAB). We compare this assembly with the widely used NbLAB360 strain, shedding light on essential genomic differences between them. The outcome is a high-quality, chromosome-level genome assembly comprising 19 chromosomes, spanning 2,762 Mb, with an N50 of 142.6 Mb. Comparative analyses revealed notable variations, including 46,215 protein-coding genes, with an impressive 99.5% BUSCO completeness score. Furthermore, the NbKLAB assembly substantially improved the QV from 33% for NbLAB360 to 49%. This refined chromosomal genome assembly for N. benthamiana, in conjunction with comparative insights, provides a valuable resource for genomics research and molecular biology. This accomplishment forms a strong foundation for in-depth exploration into the intricacies of plant genetics and genomics, improved precision, and a comparative framework.
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Affiliation(s)
- Seo-Rin Ko
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Sanghee Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Biosystems and Bioengineering Program, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Hyunjin Koo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | | | | | - Yong-Min Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
- Digital Biotech Innovation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Biosystems and Bioengineering Program, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Korea.
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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3
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Shi W, Li J, Xie S, Wang X, Zhang Y, Yao H, Chen M, Li J, Deng Z. Selection of the Dominant Endophytes Based on Illumina Sequencing Analysis for Controlling Bacterial Wilt of Patchouli Caused by Ralstonia solanacearum. PLANT DISEASE 2024; 108:996-1004. [PMID: 38613135 DOI: 10.1094/pdis-09-23-1722-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Bacterial wilt caused by Ralstonia solanacearum (RS) is one of the most devastating diseases in patchouli (Pogostemon cablin [Blanco] Benth.), which results in low yield and quality of patchouli. However, no stable and effective control methods have been developed yet. To evaluate the potential of dominant bacterial endophytes in biocontrol, the endophytic bacterial diversity of patchouli was investigated based on Illumina sequencing analysis, and the ability of isolates belonging to the dominant bacterial genera to control RS wilt of patchouli was explored in pot experiments. A total of 245 bacterial genera were detected in patchouli plants, with the highest relative abundance of operational taxonomic units belonging to the genus Pseudomonas detected in roots, leaves, and stems. The Pseudomonas isolates S02, S09, and S26 showed antagonistic activity against RS in vitro and displayed many plant growth-promoting characteristics, including production of indole-3-acetic acid, siderophores, and 1-aminocyclopropane-1-carboxylic acid deaminase and phosphate- and potassium-solubilizing capability. Inoculation of patchouli plants with the isolates S02, S09, and S26 significantly improved shoot growth and decreased the incidence of bacterial wilt caused by RS. The results suggest that screening of dominant bacterial endophytes for effective biocontrol agents based on Illumina sequencing analysis is more efficient than random isolation and screening procedures.
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Affiliation(s)
- Wenguang Shi
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, Guangdong 518107, China
| | - Junyan Li
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Siyun Xie
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Xing Wang
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Yuxin Zhang
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Huaxiong Yao
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Meiqi Chen
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Jianbin Li
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Zujun Deng
- School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
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4
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Prudhomme N, Pastora R, Thomson S, Zheng E, Sproule A, Krieger JR, Murphy JP, Overy DP, Cossar D, McLean MD, Geddes-McAlister J. Bacterial growth-mediated systems remodelling of Nicotiana benthamiana defines unique signatures of target protein production in molecular pharming. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38516995 DOI: 10.1111/pbi.14342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024]
Abstract
The need for therapeutics to treat a plethora of medical conditions and diseases is on the rise and the demand for alternative approaches to mammalian-based production systems is increasing. Plant-based strategies provide a safe and effective alternative to produce biological drugs but have yet to enter mainstream manufacturing at a competitive level. Limitations associated with batch consistency and target protein production levels are present; however, strategies to overcome these challenges are underway. In this study, we apply state-of-the-art mass spectrometry-based proteomics to define proteome remodelling of the plant following agroinfiltration with bacteria grown under shake flask or bioreactor conditions. We observed distinct signatures of bacterial protein production corresponding to the different growth conditions that directly influence the plant defence responses and target protein production on a temporal axis. Our integration of proteomic profiling with small molecule detection and quantification reveals the fluctuation of secondary metabolite production over time to provide new insight into the complexities of dual system modulation in molecular pharming. Our findings suggest that bioreactor bacterial growth may promote evasion of early plant defence responses towards Agrobacterium tumefaciens (updated nomenclature to Rhizobium radiobacter). Furthermore, we uncover and explore specific targets for genetic manipulation to suppress host defences and increase recombinant protein production in molecular pharming.
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Affiliation(s)
- Nicholas Prudhomme
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | | | - Sarah Thomson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Edison Zheng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Amanda Sproule
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | | | - J Patrick Murphy
- Department of Biology, University of Prince Edward Island, Charlottetown, PE, Canada
| | - David P Overy
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Doug Cossar
- PlantForm Corporation Canada, Toronto, ON, Canada
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Vollheyde K, Dudley QM, Yang T, Oz MT, Mancinotti D, Fedi MO, Heavens D, Linsmith G, Chhetry M, Smedley MA, Harwood WA, Swarbreck D, Geu‐Flores F, Patron NJ. An improved Nicotiana benthamiana bioproduction chassis provides novel insights into nicotine biosynthesis. THE NEW PHYTOLOGIST 2023; 240:302-317. [PMID: 37488711 PMCID: PMC10952274 DOI: 10.1111/nph.19141] [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: 03/14/2023] [Accepted: 06/28/2023] [Indexed: 07/26/2023]
Abstract
The model plant Nicotiana benthamiana is an increasingly attractive organism for the production of high-value, biologically active molecules. However, N. benthamiana accumulates high levels of pyridine alkaloids, in particular nicotine, which complicates the downstream purification processes. Here, we report a new assembly of the N. benthamiana genome as well as the generation of low-nicotine lines by CRISPR/Cas9-based inactivation of berberine bridge enzyme-like proteins (BBLs). Triple as well as quintuple mutants accumulated three to four times less nicotine than the respective control lines. The availability of lines without functional BBLs allowed us to probe their catalytic role in nicotine biosynthesis, which has remained obscure. Notably, chiral analysis revealed that the enantiomeric purity of nicotine was fully lost in the quintuple mutants. In addition, precursor feeding experiments showed that these mutants cannot facilitate the specific loss of C6 hydrogen that characterizes natural nicotine biosynthesis. Our work delivers an improved N. benthamiana chassis for bioproduction and uncovers the crucial role of BBLs in the stereoselectivity of nicotine biosynthesis.
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Affiliation(s)
- Katharina Vollheyde
- Department of Plant and Environmental SciencesUniversity of Copenhagen1871 FrederiksbergCopenhagenDenmark
| | | | - Ting Yang
- Department of Plant and Environmental SciencesUniversity of Copenhagen1871 FrederiksbergCopenhagenDenmark
| | - Mehmet T. Oz
- Earlham Institute, Norwich Research ParkNorwichNorfolkNR4 7UZUK
| | - Davide Mancinotti
- Department of Plant and Environmental SciencesUniversity of Copenhagen1871 FrederiksbergCopenhagenDenmark
| | | | - Darren Heavens
- Earlham Institute, Norwich Research ParkNorwichNorfolkNR4 7UZUK
| | - Gareth Linsmith
- Earlham Institute, Norwich Research ParkNorwichNorfolkNR4 7UZUK
| | - Monika Chhetry
- John Innes Centre, Norwich Research ParkNorwichNorfolkNR4 7UHUK
| | - Mark A. Smedley
- John Innes Centre, Norwich Research ParkNorwichNorfolkNR4 7UHUK
| | | | - David Swarbreck
- Earlham Institute, Norwich Research ParkNorwichNorfolkNR4 7UZUK
| | - Fernando Geu‐Flores
- Department of Plant and Environmental SciencesUniversity of Copenhagen1871 FrederiksbergCopenhagenDenmark
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6
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Li R, Ma XY, Zhang YJ, Zhang YJ, Zhu H, Shao SN, Zhang DD, Klosterman SJ, Dai XF, Subbarao KV, Chen JY. Genome-wide identification and analysis of a cotton secretome reveals its role in resistance against Verticillium dahliae. BMC Biol 2023; 21:166. [PMID: 37542270 PMCID: PMC10403859 DOI: 10.1186/s12915-023-01650-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: 03/20/2023] [Accepted: 06/13/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND The extracellular space between the cell wall and plasma membrane is a battlefield in plant-pathogen interactions. Within this space, the pathogen employs its secretome to attack the host in a variety of ways, including immunity manipulation. However, the role of the plant secretome is rarely studied for its role in disease resistance. RESULTS Here, we examined the secretome of Verticillium wilt-resistant Gossypium hirsutum cultivar Zhongzhimian No.2 (ZZM2, encoding 95,327 predicted coding sequences) to determine its role in disease resistance against the wilt causal agent, Verticillium dahliae. Bioinformatics-driven analyses showed that the ZZM2 genome encodes 2085 secreted proteins and that these display disequilibrium in their distribution among the chromosomes. The cotton secretome displayed differences in the abundance of certain amino acid residues as compared to the remaining encoded proteins due to the localization of these putative proteins in the extracellular space. The secretome analysis revealed conservation for an allotetraploid genome, which nevertheless exhibited variation among orthologs and comparable unique genes between the two sub-genomes. Secretome annotation strongly suggested its involvement in extracellular stress responses (hydrolase activity, oxidoreductase activity, and extracellular region, etc.), thus contributing to resistance against the V. dahliae infection. Furthermore, the defense response genes (immunity marker NbHIN1, salicylic acid marker NbPR1, and jasmonic acid marker NbLOX4) were activated to varying degrees when Nicotina benthamiana leaves were agro-infiltrated with 28 randomly selected members, suggesting that the secretome plays an important role in the immunity response. Finally, gene silencing assays of 11 members from 13 selected candidates in ZZM2 displayed higher susceptibility to V. dahliae, suggesting that the secretome members confer the Verticillium wilt resistance in cotton. CONCLUSIONS Our data demonstrate that the cotton secretome plays an important role in Verticillium wilt resistance, facilitating the development of the resistance gene markers and increasing the understanding of the mechanisms regulating disease resistance.
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Affiliation(s)
- Ran Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Xi-Yue Ma
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ye-Jing Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yong-Jun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - He Zhu
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
- The Cotton Research Center of Liaoning Academy of Agricultural Sciences, National Cotton Industry Technology System Liaohe Comprehensive Experimental Station, Liaoning Provincial Institute of Economic Crops, Liaoyang, 111000, China
| | - Sheng-Nan Shao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dan-Dan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Steven J Klosterman
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA, USA
| | - Xiao-Feng Dai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis c/o United States Agricultural Research Station, Salinas, CA, USA.
| | - Jie-Yin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
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Stintzi A, Schaller A. Biogenesis of post-translationally modified peptide signals for plant reproductive development. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102274. [PMID: 35977439 DOI: 10.1016/j.pbi.2022.102274] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/23/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Post-translationally modified peptides (PMPs) are important regulators of plant growth and development. They are derived from larger inactive precursors by post-translational modification (PTM) and proteolytic processing to result in the bioactive peptide signals. We discuss how and why these modifications contribute to the bioactivity of inflorescence deficient in abscission (IDA), phytosulfokine (PSK), and peptides of the Casparian strip integrity factor (CIF) family, as signaling molecules during reproductive development. The emerging picture suggests that PTMs evolved to increase the specificity of interaction of PMPs with cognate receptors and of PMP precursors with processing proteases. Cleavage sites in PMP precursors are recognized by subtilases (SBTs) in a highly specific manner. SBT-mediated processing results in the activation of PMP signals regulating stress-induced flower drop, the formation of the embryonic cuticle, and pollen development.
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Affiliation(s)
- Annick Stintzi
- Department of Plant Physiology and Biochemistry, University of Hohenheim, 70593 Stuttgart, Germany
| | - Andreas Schaller
- Department of Plant Physiology and Biochemistry, University of Hohenheim, 70593 Stuttgart, Germany.
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8
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Lü P, Liu Y, Yu X, Shi CL, Liu X. The right microbe-associated molecular patterns for effective recognition by plants. Front Microbiol 2022; 13:1019069. [PMID: 36225366 PMCID: PMC9549324 DOI: 10.3389/fmicb.2022.1019069] [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: 08/14/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Plants are constantly exposed to diverse microbes and thus develop a sophisticated perceive system to distinguish non-self from self and identify non-self as friends or foes. Plants can detect microbes in apoplast via recognition of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) on the cell surface to activate appropriate signaling in response to microbes. MAMPs are highly conserved but essential molecules of microbes and often buried in microbes’ complex structure. Mature MAMPs are released from microbes by invasion-induced hydrolytic enzymes in apoplast and accumulate in proximity of plasma membrane-localized PRRs to be perceived as ligands to activate downstream signaling. In response, microbes developed strategies to counteract these processing. Here, we review how the form, the concentration, and the size of mature MAMPs affect the PRR-mediated immune signaling. In particular, we describe some potential applications and explore potential open questions in the fields.
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Affiliation(s)
- Pengpeng Lü
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
| | - Yi Liu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
| | - Xixi Yu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | | | - Xiaokun Liu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
- *Correspondence: Xiaokun Liu,
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9
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Reconstitution of monoterpene indole alkaloid biosynthesis in genome engineered Nicotiana benthamiana. Commun Biol 2022; 5:949. [PMID: 36088516 PMCID: PMC9464250 DOI: 10.1038/s42003-022-03904-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/25/2022] [Indexed: 12/17/2022] Open
Abstract
Monoterpene indole alkaloids (MIAs) are a diverse class of plant natural products that include a number of medicinally important compounds. We set out to reconstitute the pathway for strictosidine, a key intermediate of all MIAs, from central metabolism in Nicotiana benthamiana. A disadvantage of this host is that its rich background metabolism results in the derivatization of some heterologously produced molecules. Here we use transcriptomic analysis to identify glycosyltransferases that are upregulated in response to biosynthetic intermediates and produce plant lines with targeted mutations in the genes encoding them. Expression of the early MIA pathway in these lines produces a more favorable product profile. Strictosidine biosynthesis was successfully reconstituted, with the best yields obtained by the co-expression of 14 enzymes, of which a major latex protein-like enzyme (MLPL) from Nepeta (catmint) is critical for improving flux through the iridoid pathway. The removal of endogenous glycosyltransferases does not impact the yields of strictosidine, highlighting that the metabolic flux of the pathway enzymes to a stable biosynthetic intermediate minimizes the need to engineer the endogenous metabolism of the host. The production of strictosidine in planta expands the range of MIA products amenable to biological synthesis. The biosynthesis of strictosidine, a key intermediate of monoterpene indole alkaloids, was successfully reconstructed in Nicotiana benthamiana, demonstrating the potential of Nicotiana benthamiana as a bioproduction chassis for small molecules.
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Singh AA, Pillay P, Naicker P, Alexandre K, Malatji K, Mach L, Steinkellner H, Vorster J, Chikwamba R, Tsekoa TL. Transient proteolysis reduction of Nicotiana benthamiana-produced CAP256 broadly neutralizing antibodies using CRISPR/Cas9. FRONTIERS IN PLANT SCIENCE 2022; 13:953654. [PMID: 36061808 PMCID: PMC9433777 DOI: 10.3389/fpls.2022.953654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
The hypersensitive response is elicited by Agrobacterium infiltration of Nicotiana benthamiana, including the induction and accumulation of pathogenesis-related proteins, such as proteases. This includes the induction of the expression of several cysteine proteases from the C1 (papain-like cysteine protease) and C13 (legumain-like cysteine protease) families. This study demonstrates the role of cysteine proteases: NbVPE-1a, NbVPE-1b, and NbCysP6 in the proteolytic degradation of Nicotiana benthamiana (glycosylation mutant ΔXTFT)-produced anti-human immunodeficiency virus broadly neutralizing antibody, CAP256-VRC26.25. Three putative cysteine protease cleavage sites were identified in the fragment crystallizable region. We further demonstrate the transient coexpression of CAP256-VRC26.25 with CRISPR/Cas9-mediated genome editing vectors targeting the NbVPE-1a, NbVPE-1b, and NbCysP6 genes which resulted in a decrease in CAP256-VRC26.25 degradation. No differences in structural features were observed between the human embryonic kidney 293 (HEK293)-produced and ΔXTFT broadly neutralizing antibodies produced with and without the coexpression of genome-editing vectors. Furthermore, despite the presence of proteolytically degraded fragments of plant-produced CAP256-VRC26.25 without the coexpression of genome editing vectors, no influence on the in vitro functional activity was detected. Collectively, we demonstrate an innovative in planta strategy for improving the quality of the CAP256 antibodies through the transient expression of the CRISPR/Cas9 vectors.
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Affiliation(s)
- Advaita Acarya Singh
- Future Production: Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Priyen Pillay
- Future Production: Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Previn Naicker
- NextGen Health Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Kabamba Alexandre
- NextGen Health Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Kanyane Malatji
- NextGen Health Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Lukas Mach
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Herta Steinkellner
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Juan Vorster
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Rachel Chikwamba
- Future Production: Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Tsepo L. Tsekoa
- Future Production: Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
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11
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Backer R, Engelbrecht J, van den Berg N. Differing Responses to Phytophthora cinnamomi Infection in Susceptible and Partially Resistant Persea americana (Mill.) Rootstocks: A Case for the Role of Receptor-Like Kinases and Apoplastic Proteases. FRONTIERS IN PLANT SCIENCE 2022; 13:928176. [PMID: 35837458 PMCID: PMC9274290 DOI: 10.3389/fpls.2022.928176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
The hemibiotrophic plant pathogen Phytophthora cinnamomi Rands is the most devastating pathogen of avocado (Persea americana Mill.) and, as such, causes significant annual losses in the industry. Although the molecular basis of P. cinnamomi resistance in avocado and P. cinnamomi virulence determinants have been the subject of recent research, none have yet attempted to compare the transcriptomic responses of both pathogen and host during their interaction. In the current study, the transcriptomes of both avocado and P. cinnamomi were explored by dual RNA sequencing. The basis for partial resistance was sought by the inclusion of both susceptible (R0.12) and partially resistant (Dusa®) rootstocks sampled at early (6, 12 and 24 hours post-inoculation, hpi) and late time-points (120 hpi). Substantial differences were noted in the number of differentially expressed genes found in Dusa® and R0.12, specifically at 12 and 24 hpi. Here, the partially resistant rootstock perpetuated defense responses initiated at 6 hpi, while the susceptible rootstock abruptly reversed course. Instead, gene ontology enrichment confirmed that R0.12 activated pathways related to growth and development, essentially rendering its response at 12 and 24 hpi no different from that of the mock-inoculated controls. As expected, several classes of P. cinnamomi effector genes were differentially expressed in both Dusa® and R0.12. However, their expression differed between rootstocks, indicating that P. cinnamomi might alter the expression of its effector arsenal based on the rootstock. Based on some of the observed differences, several P. cinnamomi effectors were highlighted as potential candidates for further research. Similarly, the receptor-like kinase (RLK) and apoplastic protease coding genes in avocado were investigated, focusing on their potential role in differing rootstock responses. This study suggests that the basis of partial resistance in Dusa® is predicated on its ability to respond appropriately during the early stages following P. cinnamomi inoculation, and that important components of the first line of inducible defense, apoplastic proteases and RLKs, are likely to be important to the observed outcome.
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Affiliation(s)
- Robert Backer
- Hans Merensky Chair in Avocado Research, University of Pretoria, Pretoria, South Africa
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Juanita Engelbrecht
- Hans Merensky Chair in Avocado Research, University of Pretoria, Pretoria, South Africa
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Noëlani van den Berg
- Hans Merensky Chair in Avocado Research, University of Pretoria, Pretoria, South Africa
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
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12
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Park SH, Ji KY, Park SY, Kim HM, Ma SH, Do JH, Kang H, Kang HS, Oh DB, Shim JS, Joung YH. Immunotherapeutic effects of recombinant colorectal cancer antigen produced in tomato fruits. Sci Rep 2022; 12:9723. [PMID: 35697846 PMCID: PMC9192744 DOI: 10.1038/s41598-022-13839-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 05/30/2022] [Indexed: 11/09/2022] Open
Abstract
The production of pharmacological vaccines in plants has been an important goal in the field of plant biotechnology. GA733-2, the protein that is also known as colorectal carcinoma (CRC)-associated antigen, is a strong candidate to produce a colorectal cancer vaccine. Tomato is the one of the major targets for production of an edible vaccine, as tomato is a fruit consumed in fresh form. It also contains high content of vitamins that aid activation of immune response. In order to develop an edible colorectal cancer vaccine, the transgene rGA733-Fc that encodes a fusion protein of GA733-2, the fragment crystallizable (Fc) domain, and the ER retention motif (rGA733-Fc) was introduced into tomato plants (Solanumlycopersicum cv. Micro-Tom). The transgenic plants producing rGA733-Fc (rGA733-FcOX) protein were screened based on stable integration of transgene expression cassette and expression level of rGA733-Fc protein. Further glycosylation pattern analysis revealed that plant derived rGA733-Fc protein contains an oligomannose glycan structure, which is a typical glycosylation pattern found on ER-processing proteins. The red fruits of rGA733-FcOX transgenic tomato plants containing approximately 270 ng/g FW of rGA733-Fc protein were orally administered to C57BL/6 mice. Oral administration of tomato fruits of the rGA733-Fc expressing transgenic plants delayed colorectal cancer growth and stimulated immune responses compared to oral administration of tomato fruits of the h-Fc expressing transgenic plants in the C57BL/6J mice. This is the first study showing the possibility of producing an edible colorectal cancer vaccine using tomato plants. This research would be helpful for development of plant-derived cancer edible vaccines.
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Affiliation(s)
- Se Hee Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Korea
| | - Kon-Young Ji
- Herbal Medicine Research Division, Korea Institute of Oriental Medicine, Daejeon, 34054, Korea
| | - Seo Young Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Korea
| | - Hyun Min Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Korea
| | - Sang Hoon Ma
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Korea
| | - Ju Hui Do
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Korea
| | - Hyuno Kang
- Division of Analytical Science, Korea Basic Science Institute (KBSI), Daejeon, 34133, Republic of Korea
| | - Hyung Sik Kang
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Korea
| | - Doo-Byoung Oh
- Environmental Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Jae Sung Shim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Korea.
| | - Young Hee Joung
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Korea.
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13
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Geddes-McAlister J, Prudhomme N, Gutierrez Gongora D, Cossar D, McLean MD. The emerging role of mass spectrometry-based proteomics in molecular pharming practices. Curr Opin Chem Biol 2022; 68:102133. [DOI: 10.1016/j.cbpa.2022.102133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/02/2022] [Accepted: 02/23/2022] [Indexed: 12/11/2022]
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14
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Yingqi H, Lv Y, Zhang J, Ahmad N, Li Y, Wang N, Xiuming L, Na Y, Li X. Identification and functional characterization of safflower cysteine protease 1 as negative regulator in response to low-temperature stress in transgenic Arabidopsis. PLANTA 2022; 255:106. [PMID: 35445865 DOI: 10.1007/s00425-022-03875-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
We performed genome-wide and heterologous expression analysis of the safflower cysteine protease family and found that inhibition of CtCP1 expression enhanced plant cold resistance. Cysteine protease (CP) is mainly involved in plant senescence and stress responses. However, the molecular mechanism of endogenous cysteine protease inhibition in plant stress tolerance is yet unknown. Here, we report the discovery and functional characterization of a candidate CP1 gene from safflower. The conserved structural topology of CtCPs revealed important insights into their possible roles in plant growth and stress responses. The qRT-PCR results implied that most of CtCP genes were highly expressed at fading stage suggesting that they are most likely involved in senescence process. The CtCP1 expression was significantly induced at different time points under cold, NaCl, H2O2 and PEG stress, respectively. The in-vitro activity of heterologously expressed CtCP1 protein showed highest protease activity for casein and azocasein substrates. The expression and phenotypic data together with antioxidant activity and physiological indicators revealed that transgenic plants inhibited by CtCP1-anti showed higher tolerance to low temperature than WT and CtCP1-OE plants. Our findings demonstrated the discovery of a new Cysteine protease 1 gene that exerted a detrimental effect on transgenic Arabidopsis under low-temperature stress.
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Affiliation(s)
- Hong Yingqi
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Yanxi Lv
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Jianyi Zhang
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Naveed Ahmad
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Youbao Li
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Nan Wang
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Liu Xiuming
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China.
- Institute of Life Sciences, Wenzhou University, Wenzhou, 325035, Zhejiang, China.
- Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou, 325035, Zhejiang, China.
| | - Yao Na
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China.
| | - Xiaokun Li
- Institute of Life Sciences, Wenzhou University, Wenzhou, 325035, Zhejiang, China.
- Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou, 325035, Zhejiang, China.
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15
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Mandal MK, Kronenberger T, Zulka MI, Windshügel B, Schiermeyer A. Structure-based discovery of small molecules improving stability of human broadly-neutralizing anti-HIV antibody 2F5 in plant suspension cells. Biotechnol J 2022; 17:e2100266. [PMID: 35075794 DOI: 10.1002/biot.202100266] [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: 05/21/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 11/06/2022]
Abstract
The production of biopharmaceuticals in engineered plant-based systems is a promising technology that has proven its suitability for the production of various recombinant glyco-proteins that are currently undergoing clinical trials. However, compared to mammalian cell lines, the productivity of plant-based systems still requires further improvement. A major obstacle is the proteolytic degradation of recombinant target proteins by endogenous plant proteases mainly from the subtilisin family of serine proteases. In the present study, the authors screened for putative small molecule inhibitors for subtilases that are secreted from tobacco BY-2 suspension cells using an in silico approach. The effectiveness of the substances identified in this screen was subsequently tested in degradation assays using the human broadly-neutralizing anti-HIV monoclonal antibody 2F5 (mAb2F5) and spent BY-2 culture medium as a model system. Among 16 putative inhibitors identified by in silico studies, three naphthalene sulfonic acid derivatives showed inhibitory activity in in vitro degradation assays and are similar to or even more effective than phenylmethylsulfonyl fluoride (PMSF), a classical inhibitor of serine proteases, which served as positive control.
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Affiliation(s)
- Manoj K Mandal
- Fraunhofer Institute for Molecular Biotechnology and Applied Ecology IME, Aachen, Germany
| | - Thales Kronenberger
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Hamburg, Germany
| | - Marie I Zulka
- Fraunhofer Institute for Molecular Biotechnology and Applied Ecology IME, Aachen, Germany
| | - Björn Windshügel
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Hamburg, Germany
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Andreas Schiermeyer
- Fraunhofer Institute for Molecular Biotechnology and Applied Ecology IME, Aachen, Germany
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16
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Improving Protein Quantity and Quality—The Next Level of Plant Molecular Farming. Int J Mol Sci 2022; 23:ijms23031326. [PMID: 35163249 PMCID: PMC8836236 DOI: 10.3390/ijms23031326] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/15/2022] Open
Abstract
Plants offer several unique advantages in the production of recombinant pharmaceuticals for humans and animals. Although numerous recombinant proteins have been expressed in plants, only a small fraction have been successfully put into use. The hugely distinct expression systems between plant and animal cells frequently cause insufficient yield of the recombinant proteins with poor or undesired activity. To overcome the issues that greatly constrain the development of plant-produced pharmaceuticals, great efforts have been made to improve expression systems and develop alternative strategies to increase both the quantity and quality of the recombinant proteins. Recent technological revolutions, such as targeted genome editing, deconstructed vectors, virus-like particles, and humanized glycosylation, have led to great advances in plant molecular farming to meet the industrial manufacturing and clinical application standards. In this review, we discuss the technological advances made in various plant expression platforms, with special focus on the upstream designs and milestone achievements in improving the yield and glycosylation of the plant-produced pharmaceutical proteins.
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17
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Prudhomme N, Krieger JR, McLean MD, Cossar D, Geddes-McAlister J. Proteomic Profiling of Interplay Between Agrobacterium tumefaciens and Nicotiana benthamiana for Improved Molecular Pharming Outcomes. Methods Mol Biol 2022; 2456:275-286. [PMID: 35612749 DOI: 10.1007/978-1-0716-2124-0_19] [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: 11/29/2022]
Abstract
Transient expression of recombinant proteins in plants is being used as a platform for production of therapeutic proteins. Benefits of this system include a reduced cost of drug development, rapid delivery of new products to the market, and an ability to provide safe and efficacious medicines for diseases. Although plant-based production systems offer excellent potential for therapeutic protein production, barriers, such as plant host defense response, exist which negatively impact the yield of product. Here we provide a protocol using tandem mass tags and mass spectrometry-based proteomics to quickly and robustly quantify the change in abundance of host defense proteins produced during the production process. These proteins can then become candidates for genetic manipulation to create host plants with reduced plant defenses capable of producing higher therapeutic protein yields.
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Affiliation(s)
- Nicholas Prudhomme
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | | | | | - Doug Cossar
- PlantForm Corporation Canada, Toronto, ON, Canada
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18
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Singh AA, Pillay P, Tsekoa TL. Engineering Approaches in Plant Molecular Farming for Global Health. Vaccines (Basel) 2021; 9:vaccines9111270. [PMID: 34835201 PMCID: PMC8623924 DOI: 10.3390/vaccines9111270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 12/16/2022] Open
Abstract
Since the demonstration of the first plant-produced proteins of medical interest, there has been significant growth and interest in the field of plant molecular farming, with plants now being considered a viable production platform for vaccines. Despite this interest and development by a few biopharmaceutical companies, plant molecular farming is yet to be embraced by ‘big pharma’. The plant system offers a faster alternative, which is a potentially more cost-effective and scalable platform for the mass production of highly complex protein vaccines, owing to the high degree of similarity between the plant and mammalian secretory pathway. Here, we identify and address bottlenecks in the use of plants for vaccine manufacturing and discuss engineering approaches that demonstrate both the utility and versatility of the plant production system as a viable biomanufacturing platform for global health. Strategies for improving the yields and quality of plant-produced vaccines, as well as the incorporation of authentic posttranslational modifications that are essential to the functionality of these highly complex protein vaccines, will also be discussed. Case-by-case examples are considered for improving the production of functional protein-based vaccines. The combination of all these strategies provides a basis for the use of cutting-edge genome editing technology to create a general plant chassis with reduced host cell proteins, which is optimised for high-level protein production of vaccines with the correct posttranslational modifications.
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19
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Jutras PV, Soldan R, Dodds I, Schuster M, Preston GM, van der Hoorn RAL. AgroLux: bioluminescent Agrobacterium to improve molecular pharming and study plant immunity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:600-612. [PMID: 34369027 DOI: 10.1111/tpj.15454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 07/19/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Agroinfiltration in Nicotiana benthamiana is widely used to transiently express heterologous proteins in plants. However, the state of Agrobacterium itself is not well studied in agroinfiltrated tissues, despite frequent studies of immunity genes conducted through agroinfiltration. Here, we generated a bioluminescent strain of Agrobacterium tumefaciens GV3101 to monitor the luminescence of Agrobacterium during agroinfiltration. By integrating a single copy of the lux operon into the genome, we generated a stable 'AgroLux' strain, which is bioluminescent without affecting Agrobacterium growth in vitro and in planta. To illustrate its versatility, we used AgroLux to demonstrate that high light intensity post infiltration suppresses both Agrobacterium luminescence and protein expression. We also discovered that AgroLux can detect Avr/Cf-induced immune responses before tissue collapse, establishing a robust and rapid quantitative assay for the hypersensitive response (HR). Thus, AgroLux provides a non-destructive, versatile and easy-to-use imaging tool to monitor both Agrobacterium and plant responses.
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Affiliation(s)
- Philippe V Jutras
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Park Road, Oxford, OX1 3RB, UK
| | - Riccardo Soldan
- Department of Plant Sciences, University of Oxford, South Park Road, Oxford, OX1 3RB, UK
| | - Isobel Dodds
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Park Road, Oxford, OX1 3RB, UK
| | - Mariana Schuster
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Park Road, Oxford, OX1 3RB, UK
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, South Park Road, Oxford, OX1 3RB, UK
| | - Renier A L van der Hoorn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Park Road, Oxford, OX1 3RB, UK
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20
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Ma J, Ding X, Li Z, Wang S. Co-expression With Replicating Vector Overcoming Competitive Effects Derived by a Companion Protease Inhibitor in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:699442. [PMID: 34220920 PMCID: PMC8248793 DOI: 10.3389/fpls.2021.699442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/21/2021] [Indexed: 05/30/2023]
Abstract
Plant-based expression platforms are currently gaining acceptance as a viable alternative for the production of recombinant proteins (RPs), but the degradation of RPs by proteases in cells hinders their superb potentials. Co-expression of a protease inhibitor (PI) shows promise as a strategy to prevent RP from proteolytic degradation in plants. However, competitive effects behind the PI-RP co-expression system may mask or obfuscate the in situ protective effects of a companion PI. Here, we explored the competitive effects by co-expressing reteplase (rPA) with three unrelated PIs, namely NbPR4, HsTIMP, and SlCYS8, in Nicotiana benthamiana leaves. Remarkably, the accumulation of rPA was significantly repressed by each of the three PIs, suggesting that the competitive effects may be common among the PIs. The repression can be attenuated by reducing the PI inoculum dose in the co-inoculation mixtures, showing a negative correlation between the PI abundance of the PI-RP system and competitive effects. Interestingly, when a replicating vector was used to modulate the relative abundance of PI and RP in vivo, rPA was still boosted even at the maximal testing dose of PI, indicating that the competitive effects reduced to an ignorable level by this in vivo approach. Furthermore, a 7- to 12-fold increase of rPA was achieved, proving that it is a useful way for stimulating the potentials of a companion PI by overcoming competitive effects. And, this approach can be applied to molecular farming for improving the RP yields of plant expression systems.
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Affiliation(s)
- Jiexue Ma
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, Yinchuan, China
| | - Xiangzhen Ding
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, Yinchuan, China
- School of Life Science, Ningxia University, Yinchuan, China
| | - Zhiying Li
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, Yinchuan, China
- School of Life Science, Ningxia University, Yinchuan, China
| | - Sheng Wang
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, Yinchuan, China
- School of Life Science, Ningxia University, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, China
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21
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Drapal M, Enfissi EMA, Fraser PD. Metabolic effects of agro-infiltration on N. benthamiana accessions. Transgenic Res 2021; 30:303-315. [PMID: 33909228 PMCID: PMC8080481 DOI: 10.1007/s11248-021-00256-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/10/2021] [Indexed: 02/07/2023]
Abstract
Over the recent years, Nicotiana benthamiana has gained great importance as a chassis for the production of high value, low volume pharmaceuticals and/or active pharmaceutical ingredients (APIs). The process involving infiltration of the N. benthamiana leaves with Agrobacterium spp, harbouring vectors with the gene of interest, facilitates transient expression. To date, little information is available on the effect of the agro-infiltration process on the metabolome of N. benthamiana, which is necessary to improve the process for large-scale, renewable manufacturing of high value compounds and medical products. Hence, the objective of the present study was to assess metabolic adaptation of N. benthamiana as a response to the presence of Agrobacterium. The present study elucidated changes of the steady-state metabolism in the agroinfiltrated leaf area, the area around the infection and the rest of the plant. Furthermore, the study discusses the phenotypic advantages of the N. benthamiana lab strain, optimised for agro-infiltration, compared to three other wild accessions. Results showed that the lab strain has a different metabolic composition and showed less alterations of the phenylpropanoid pathway and cell wall remodelling in the agroinfiltrated leaf areas, for example chlorogenic acid, cadaverine and C18:0-2-glycerol ester. In conclusion, both of these alterations present potential candidates to improve the phenotype of the N. benthamiana lab strain for a more efficient transient expression process.
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Affiliation(s)
- Margit Drapal
- Biochemistry, Royal Holloway University of London, Egham, UK
| | | | - Paul D Fraser
- Biochemistry, Royal Holloway University of London, Egham, UK.
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22
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Stührwohldt N, Bühler E, Sauter M, Schaller A. Phytosulfokine (PSK) precursor processing by subtilase SBT3.8 and PSK signaling improve drought stress tolerance in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3427-3440. [PMID: 33471900 DOI: 10.1093/jxb/erab017] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/17/2021] [Indexed: 05/06/2023]
Abstract
Increasing drought stress poses a severe threat to agricultural productivity. Plants, however, have evolved numerous mechanisms to cope with such environmental stress. Here we report that the stress-induced production of a peptide signal contributes to stress tolerance. The expression of phytosulfokine (PSK) peptide precursor genes, and transcripts of three subtilisin-like serine proteases, SBT1.4, SBT3.7, and SBT3.8, were found to be up-regulated in response to osmotic stress. Stress symptoms were more pronounced in sbt3.8 loss-of-function mutants and could be alleviated by PSK treatment. Osmotic stress tolerance was improved in plants overexpressing the PSK1 precursor (proPSK1) or SBT3.8, resulting in higher fresh weight and improved lateral root development in transgenic plants compared with wild-type plants. We further showed that SBT3.8 is involved in the biogenesis of the bioactive PSK peptide. ProPSK1 was cleaved by SBT3.8 at the C-terminus of the PSK pentapeptide. Processing by SBT3.8 depended on the aspartic acid residue directly following the cleavage site. ProPSK1 processing was impaired in the sbt3.8 mutant. The data suggest that increased expression of proPSK1 in response to osmotic stress followed by the post-translational processing of proPSK1 by SBT3.8 leads to the production of PSK as a peptide signal for stress mitigation.
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Affiliation(s)
- Nils Stührwohldt
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Eric Bühler
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Margret Sauter
- Plant Developmental Biology and Physiology, University of Kiel, Kiel, Germany
| | - Andreas Schaller
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany
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23
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Godson A, van der Hoorn RAL. The front line of defence: a meta-analysis of apoplastic proteases in plant immunity. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3381-3394. [PMID: 33462613 PMCID: PMC8042752 DOI: 10.1093/jxb/eraa602] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/23/2020] [Indexed: 05/13/2023]
Abstract
Secreted proteases act at the front line of defence and play pivotal roles in disease resistance. However, the criteria for apoplastic immune proteases are not always defined and followed. Here, we critically reviewed 46 apoplastic proteases that function in plant defence. We found that most apoplastic immune proteases are induced upon infection, and 17 proteases are genetically required for the immune response. Proteolytic activity has been confirmed for most of the proteases but is rarely shown to be required for biological function, and the apoplastic location of proteases can be subjective and dynamic. Pathogen-derived inhibitors have only been described for cysteine and serine proteases, and the selection pressure acting on immune proteases is rarely investigated. We discuss six different mechanisms by which these proteases mediate plant immunity and summarize the challenges for future research.
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Affiliation(s)
- Alice Godson
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford, UK
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24
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Wang S, Xing R, Wang Y, Shu H, Fu S, Huang J, Paulus JK, Schuster M, Saunders DGO, Win J, Vleeshouwers V, Wang Y, Zheng X, van der Hoorn RAL, Dong S. Cleavage of a pathogen apoplastic protein by plant subtilases activates host immunity. THE NEW PHYTOLOGIST 2021; 229:3424-3439. [PMID: 33251609 DOI: 10.1111/nph.17120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
The plant apoplast is a harsh environment in which hydrolytic enzymes, especially proteases, accumulate during pathogen infection. However, the defense functions of most apoplastic proteases remain largely elusive. We show here that a newly identified small cysteine-rich secreted protein PC2 from the potato late blight pathogen Phytophthora infestans induces immunity in Solanum plants only after cleavage by plant apoplastic subtilisin-like proteases, such as tomato P69B. A minimal 61 amino acid core peptide carrying two key cysteines, conserved widely in most oomycete species, is sufficient for PC2-induced cell death. Furthermore, we showed that Kazal-like protease inhibitors, such as EPI1, produced by P. infestans prevent PC2 cleavage and dampen PC2 elicited host immunity. This study reveals that cleavage of pathogen proteins to release immunogenic peptides is an important function of plant apoplastic proteases.
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Affiliation(s)
- Shuaishuai Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rongkang Xing
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haidong Shu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shenggui Fu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jie Huang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Judith K Paulus
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Mariana Schuster
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Diane G O Saunders
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Vivianne Vleeshouwers
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaobo Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
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25
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Buyel JF, Stöger E, Bortesi L. Targeted genome editing of plants and plant cells for biomanufacturing. Transgenic Res 2021; 30:401-426. [PMID: 33646510 PMCID: PMC8316201 DOI: 10.1007/s11248-021-00236-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/03/2021] [Indexed: 02/07/2023]
Abstract
Plants have provided humans with useful products since antiquity, but in the last 30 years they have also been developed as production platforms for small molecules and recombinant proteins. This initially niche area has blossomed with the growth of the global bioeconomy, and now includes chemical building blocks, polymers and renewable energy. All these applications can be described as “plant molecular farming” (PMF). Despite its potential to increase the sustainability of biologics manufacturing, PMF has yet to be embraced broadly by industry. This reflects a combination of regulatory uncertainty, limited information on process cost structures, and the absence of trained staff and suitable manufacturing capacity. However, the limited adaptation of plants and plant cells to the requirements of industry-scale manufacturing is an equally important hurdle. For example, the targeted genetic manipulation of yeast has been common practice since the 1980s, whereas reliable site-directed mutagenesis in most plants has only become available with the advent of CRISPR/Cas9 and similar genome editing technologies since around 2010. Here we summarize the applications of new genetic engineering technologies to improve plants as biomanufacturing platforms. We start by identifying current bottlenecks in manufacturing, then illustrate the progress that has already been made and discuss the potential for improvement at the molecular, cellular and organism levels. We discuss the effects of metabolic optimization, adaptation of the endomembrane system, modified glycosylation profiles, programmable growth and senescence, protease inactivation, and the expression of enzymes that promote biodegradation. We outline strategies to achieve these modifications by targeted gene modification, considering case-by-case examples of individual improvements and the combined modifications needed to generate a new general-purpose “chassis” for PMF.
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Affiliation(s)
- J F Buyel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074, Aachen, Germany. .,Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
| | - E Stöger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - L Bortesi
- Aachen-Maastricht Institute for Biobased Materials (AMIBM), Maastricht University, Brightlands Chemelot Campus, Urmonderbaan 22, 6167 RD, Geleen, The Netherlands
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26
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Puchol Tarazona AA, Maresch D, Grill A, Bakalarz J, Torres Acosta JA, Castilho A, Steinkellner H, Mach L. Identification of two subtilisin-like serine proteases engaged in the degradation of recombinant proteins in Nicotiana benthamiana. FEBS Lett 2021; 595:379-388. [PMID: 33263189 PMCID: PMC8221030 DOI: 10.1002/1873-3468.14014] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/13/2020] [Accepted: 11/18/2020] [Indexed: 12/22/2022]
Abstract
The tobacco variant Nicotiana benthamiana has recently emerged as a versatile host for the manufacturing of protein therapeutics, but the fidelity of many recombinant proteins generated in this system is compromised by inadvertent proteolysis. Previous studies have revealed that the anti-HIV-1 antibodies 2F5 and PG9 as well as the protease inhibitor α1 -antitrypsin (A1AT) are particularly susceptible to N. benthamiana proteases. Here, we identify two subtilisin-like serine proteases (NbSBT1 and NbSBT2) whose combined action is sufficient to account for all major cleavage events observed upon expression of 2F5, PG9 and A1AT in N. benthamiana. We propose that downregulation of NbSBT1 and NbSBT2 activities could constitute a powerful means to optimize the performance of this promising platform for the production of biopharmaceuticals. DATABASES: NbSBT sequence data are available in the DDBJ/EMBL/GenBank databases under the accession numbers MN534996 to MN535005.
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Affiliation(s)
| | - Daniel Maresch
- Department of ChemistryUniversity of Natural Resources and Life SciencesViennaAustria
| | - Annette Grill
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Janet Bakalarz
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Juan A. Torres Acosta
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Alexandra Castilho
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Herta Steinkellner
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Lukas Mach
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life SciencesViennaAustria
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27
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Park SH, Ji KY, Kim HM, Ma SH, Park SY, Do JH, Oh DB, Kang HS, Shim JS, Joung YH. Optimization of the human colorectal carcinoma antigen GA733-2 production in tobacco plants. PLANT BIOTECHNOLOGY REPORTS 2021; 15:55-67. [PMID: 33520002 PMCID: PMC7825390 DOI: 10.1007/s11816-020-00657-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 05/02/2023]
Abstract
The colorectal carcinoma-associated protein GA733-2 is one of the representative candidate protein for the development of plant-derived colorectal cancer vaccine. Despite of its significant importance for colorectal vaccine development, low efficiency of GA733-2 production limits its wide applications. To improve productivity of GA733-2 in plants, we here tested multiple factors that affect expression of recombinant GA733-2 (rGA733-2) and rGA733 fused to fragment crystallizable (Fc) domain (rGA733-Fc) protein. The rGA733-2 and rGA733-Fc proteins were highly expressed when the pBINPLUS vector system was used for transient expression in tobacco plants. In addition, the length of interval between rGA733-2 and left border of T-DNA affected the expression of rGA733 protein. Transient expression analysis using various combinations of Agrobacterium tumefaciens strains (C58C1, LBA4404, and GV3101) and tobacco species (Nicotiana tabacum cv. Xanthi nc and Nicotiana benthamiana) revealed that higher accumulation of rGA733-2 and rGA733-Fc proteins were obtained by combination of A. tumefaciens LBA4404 and Nicotiana benthamiana. Transgenic plants generated by introduction of the rGA733-2 and rGA733-Fc expression cassettes also significantly accumulated corresponding recombinant proteins. Bioactivity and stability of the plant-derived rGA733 and rGA733-Fc were evaluated by further in vitro assay, western blot and N-glycosylation analysis. Collectively, we here suggest the optimal condition for efficient production of functional rGA733-2 protein in tobacco system.
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Affiliation(s)
- Se Hee Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186 Korea
| | - Kon-Young Ji
- Herbal Medicine Research Division, Korea Institute of Oriental Medicine, Daejeon, 34054 Korea
| | - Hyun Min Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186 Korea
| | - Sang Hoon Ma
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186 Korea
| | - Seo Young Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186 Korea
| | - Ju Hui Do
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186 Korea
| | - Doo-Byoung Oh
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Korea
- Department of Biosystems and Bioengineering, University of Science and Technology (UST), Daejeon, 34113 Korea
| | - Hyung Sik Kang
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186 Korea
| | - Jae Sung Shim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186 Korea
| | - Young Hee Joung
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186 Korea
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28
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Ghosh S, Kant R, Pradhan A, Jha G. RS_CRZ1, a C2H2-Type Transcription Factor Is Required for Pathogenesis of Rhizoctonia solani AG1-IA in Tomato. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:26-38. [PMID: 33030394 DOI: 10.1094/mpmi-05-20-0121-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Rhizoctonia solani is a necrotrophic fungal pathogen that causes disease in diverse plant species. In recent years, the genomic and transcriptomic studies have identified several candidate pathogenicity determinants of R. solani; however, most of them remain to be validated. In this study, we report a viral vector-based host-induced gene silencing (HIGS) as well as a dsRNA (double-stranded RNA)-based approach to effectively downregulate genes of R. solani AG1-IA (BRS1 strain) during pathogenesis in tomato. We tested a few of the in-planta upregulated R. solani genes and observed that silencing of one of them, i.e., RS_CRZ1 (a C2H2 type zinc finger transcription factor) significantly compromises the pathogenesis of R. solani in tomato. The RS_CRZ1-silenced plants not only exhibited significant reduction in disease symptoms, but the depth of pathogen colonization was also compromised. Furthermore, we identified the R. solani genes that were coregulated with RS_CRZ1 during the pathogenicity process. The HIGS-mediated silencing of a few of them [CL1756Contig1; subtilisin-like protease and CL1817Contig2; 2OG-Fe(II) oxygenase] compromised the pathogenesis of R. solani in tomato. The ectopic expression of RS_CRZ1 complemented the crz1 mutant of yeast and restored tolerance against various metal ion stress. Overall, our study reveals the importance of RS_CRZ1 in managing the hostile environment encountered during host colonization. Also, it emphasizes the relevance of the HIGS and dsRNA-based gene silencing approach toward functional characterization of pathogenicity determinants of R. solani.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Srayan Ghosh
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Ravi Kant
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Amrita Pradhan
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Gopaljee Jha
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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29
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Stührwohldt N, Ehinger A, Thellmann K, Schaller A. Processing and Formation of Bioactive CLE40 Peptide Are Controlled by Posttranslational Proline Hydroxylation. PLANT PHYSIOLOGY 2020; 184:1573-1584. [PMID: 32907884 PMCID: PMC7608152 DOI: 10.1104/pp.20.00528] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/27/2020] [Indexed: 06/01/2023]
Abstract
Small posttranslationally modified signaling peptides are proteolytically derived from larger precursor proteins and subject to several additional steps of modification, including Pro hydroxylation, Hyp glycosylation, and/or Tyr sulfation. The processing proteases and the relevance of posttranslational modifications for peptide biogenesis and activity are largely unknown. In this study these questions were addressed for the Clavata3/Endosperm Surrounding Region (CLE) peptide CLE40, a peptide regulator of stem cell differentiation in the Arabidopsis (Arabidopsis thaliana) root meristem. We identify three subtilases (SBT1.4, SBT1.7, and SBT4.13) that cleave the CLE40 precursor redundantly at two sites. C-terminal processing releases the mature peptide from its precursor and is thus required for signal biogenesis. SBT-mediated cleavage at a second site within the mature peptide attenuates the signal. The second cleavage is prevented by Pro hydroxylation, resulting in the formation of mature and bioactive CLE40 in planta. Our data reveal a role for posttranslational modification by Pro hydroxylation in the regulation of CLE40 formation and activity.
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Affiliation(s)
- Nils Stührwohldt
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Alexandra Ehinger
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Kerstin Thellmann
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Andreas Schaller
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, 70593 Stuttgart, Germany
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30
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Kourelis J, Malik S, Mattinson O, Krauter S, Kahlon PS, Paulus JK, van der Hoorn RAL. Evolution of a guarded decoy protease and its receptor in solanaceous plants. Nat Commun 2020; 11:4393. [PMID: 32879321 PMCID: PMC7468133 DOI: 10.1038/s41467-020-18069-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/03/2020] [Indexed: 12/26/2022] Open
Abstract
Rcr3 is a secreted protease of tomato that is targeted by fungal effector Avr2, a secreted protease inhibitor of the fungal pathogen Cladosporium fulvum. The Avr2-Rcr3 complex is recognized by receptor-like protein Cf-2, triggering hypersensitive cell death (HR) and disease resistance. Avr2 also targets Rcr3 paralog Pip1, which is not required for Avr2 recognition but contributes to basal resistance. Thus, Rcr3 acts as a guarded decoy in this interaction, trapping the fungus into a recognition event. Here we show that Rcr3 evolved > 50 million years ago (Mya), whereas Cf-2 evolved <6Mya by co-opting the pre-existing Rcr3 in the Solanum genus. Ancient Rcr3 homologs present in tomato, potato, eggplants, pepper, petunia and tobacco can be inhibited by Avr2 with the exception of tobacco Rcr3. Four variant residues in Rcr3 promote Avr2 inhibition, but the Rcr3 that co-evolved with Cf-2 lacks three of these residues, indicating that the Rcr3 co-receptor is suboptimal for Avr2 binding. Pepper Rcr3 triggers HR with Cf-2 and Avr2 when engineered for enhanced inhibition by Avr2. Nicotiana benthamiana (Nb) is a natural null mutant carrying Rcr3 and Pip1 alleles with deleterious frame-shift mutations. Resurrected NbRcr3 and NbPip1 alleles were active proteases and further NbRcr3 engineering facilitated Avr2 inhibition, uncoupled from HR signalling. The evolution of a receptor co-opting a conserved pathogen target contrasts with other indirect pathogen recognition mechanisms.
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Affiliation(s)
- Jiorgos Kourelis
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK
| | - Shivani Malik
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK
| | - Oliver Mattinson
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK
| | - Sonja Krauter
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK
| | - Parvinderdeep S Kahlon
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK
| | - Judith K Paulus
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK
| | - Renier A L van der Hoorn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK.
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31
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Margolin EA, Strasser R, Chapman R, Williamson AL, Rybicki EP, Meyers AE. Engineering the Plant Secretory Pathway for the Production of Next-Generation Pharmaceuticals. Trends Biotechnol 2020; 38:1034-1044. [PMID: 32818443 DOI: 10.1016/j.tibtech.2020.03.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/06/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023]
Abstract
Production of biologics in plants, or plant molecular pharming, is a promising protein expression technology that is receiving increasing attention from the pharmaceutical industry. Previously, low expression yields of recombinant proteins and the realization that certain post-translational modifications (PTMs) may not occur optimally limited the widespread acceptance of the technology. However, molecular engineering of the plant secretory pathway is now enabling the production of increasingly complex biomolecules using tailored protein-specific approaches to ensure their maturation. These involve the elimination of undesired processing events, and the introduction of heterologous biosynthetic machinery to support the production of specific target proteins. Here, we discuss recent advances in the production of pharmaceutical proteins in plants, which leverage the unique advantages of the technology.
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Affiliation(s)
- Emmanuel A Margolin
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Wellcome Trust Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa.
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Ros Chapman
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Anna-Lise Williamson
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Wellcome Trust Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Edward P Rybicki
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Ann E Meyers
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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32
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Guo Y, Dupont P, Mesarich CH, Yang B, McDougal RL, Panda P, Dijkwel P, Studholme DJ, Sambles C, Win J, Wang Y, Williams NM, Bradshaw RE. Functional analysis of RXLR effectors from the New Zealand kauri dieback pathogen Phytophthora agathidicida. MOLECULAR PLANT PATHOLOGY 2020; 21:1131-1148. [PMID: 32638523 PMCID: PMC7411639 DOI: 10.1111/mpp.12967] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 05/08/2023]
Abstract
New Zealand kauri is an ancient, iconic, gymnosperm tree species that is under threat from a lethal dieback disease caused by the oomycete Phytophthora agathidicida. To gain insight into this pathogen, we determined whether proteinaceous effectors of P. agathidicida interact with the immune system of a model angiosperm, Nicotiana, as previously shown for Phytophthora pathogens of angiosperms. From the P. agathidicida genome, we defined and analysed a set of RXLR effectors, a class of proteins that typically have important roles in suppressing or activating the plant immune system. RXLRs were screened for their ability to activate or suppress the Nicotiana plant immune system using Agrobacterium tumefaciens transient transformation assays. Nine P. agathidicida RXLRs triggered cell death or suppressed plant immunity in Nicotiana, of which three were expressed in kauri. For the most highly expressed, P. agathidicida (Pa) RXLR24, candidate cognate immune receptors associated with cell death were identified in Nicotiana benthamiana using RNA silencing-based approaches. Our results show that RXLRs of a pathogen of gymnosperms can interact with the immune system of an angiosperm species. This study provides an important foundation for studying the molecular basis of plant-pathogen interactions in gymnosperm forest trees, including kauri.
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Affiliation(s)
- Yanan Guo
- Bio‐Protection Research CentreSchool of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | | | - Carl H. Mesarich
- Bio‐Protection Research CentreSchool of Agriculture and EnvironmentMassey UniversityPalmerston NorthNew Zealand
| | - Bo Yang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | | | - Preeti Panda
- Scion (New Zealand Forest Research Institute Ltd.)RotoruaNew Zealand
- The New Zealand Institute for Plant and Food ResearchAucklandNew Zealand
| | - Paul Dijkwel
- Bio‐Protection Research CentreSchool of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | | | | | - Joe Win
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | - Yuanchao Wang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Nari M. Williams
- Scion (New Zealand Forest Research Institute Ltd.)RotoruaNew Zealand
- The New Zealand Institute for Plant and Food ResearchAucklandNew Zealand
| | - Rosie E. Bradshaw
- Bio‐Protection Research CentreSchool of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
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33
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Amobonye A, Bhagwat P, Pandey A, Singh S, Pillai S. Biotechnological potential of Beauveria bassiana as a source of novel biocatalysts and metabolites. Crit Rev Biotechnol 2020; 40:1019-1034. [DOI: 10.1080/07388551.2020.1805403] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ayodeji Amobonye
- Department of Biotechnology and Food Technology, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Prashant Bhagwat
- Department of Biotechnology and Food Technology, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Suren Singh
- Department of Biotechnology and Food Technology, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Santhosh Pillai
- Department of Biotechnology and Food Technology, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
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34
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Prudhomme N, Pastora R, Muselius B, McLean MD, Cossar D, Geddes-McAlister J. Exposure of Agrobacterium tumefaciens to agroinfiltration medium demonstrates cellular remodelling and may promote enhanced adaptability for molecular pharming. Can J Microbiol 2020; 67:85-97. [PMID: 32721220 DOI: 10.1139/cjm-2020-0239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Agroinfiltration is used to treat plants with modified strains of Agrobacterium tumefaciens for the purpose of transient in planta expression of genes transferred from the bacterium. These genes encode valuable recombinant proteins for therapeutic or industrial applications. Treatment of large quantities of plants for industrial-scale protein production exposes bacteria (harboring genes of interest) to agroinfiltration medium that is devoid of nutrients and carbon sources for prolonged periods of time (possibly upwards of 24 h). Such conditions may negatively influence bacterial viability, infectivity of plant cells, and target protein production. Here, we explored the role of timing in bacterial culture preparation for agroinfiltration using mass spectrometry-based proteomics to define changes in cellular processes. We observed distinct profiles associated with bacterial treatment conditions and exposure timing, including significant changes in proteins involved in pathogenesis, motility, and nutrient acquisition systems as the bacteria adapt to the new environment. These data suggest a progression towards increased cellular remodelling over time. In addition, we described changes in growth- and environment-specific processes over time, underscoring the interconnectivity of pathogenesis and chemotaxis-associated proteins with transport and metabolism. Overall, our results have important implications for the production of transiently expressed target protein products, as prolonged exposure to agroinfiltration medium suggests remodelling of the bacterial proteins towards enhanced infection of plant cells.
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Affiliation(s)
- N Prudhomme
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - R Pastora
- PlantForm Corporation Canada, Toronto, ON M4S 3E2, Canada
| | - B Muselius
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - M D McLean
- PlantForm Corporation Canada, Toronto, ON M4S 3E2, Canada
| | - D Cossar
- PlantForm Corporation Canada, Toronto, ON M4S 3E2, Canada
| | - J Geddes-McAlister
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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35
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Paulus JK, Kourelis J, Ramasubramanian S, Homma F, Godson A, Hörger AC, Hong TN, Krahn D, Ossorio Carballo L, Wang S, Win J, Smoker M, Kamoun S, Dong S, van der Hoorn RAL. Extracellular proteolytic cascade in tomato activates immune protease Rcr3. Proc Natl Acad Sci U S A 2020; 117:17409-17417. [PMID: 32616567 PMCID: PMC7382257 DOI: 10.1073/pnas.1921101117] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Proteolytic cascades regulate immunity and development in animals, but these cascades in plants have not yet been reported. Here we report that the extracellular immune protease Rcr3 of tomato is activated by P69B and other subtilases (SBTs), revealing a proteolytic cascade regulating extracellular immunity in solanaceous plants. Rcr3 is a secreted papain-like Cys protease (PLCP) of tomato that acts both in basal resistance against late blight disease (Phytophthora infestans) and in gene-for-gene resistance against the fungal pathogen Cladosporium fulvum (syn. Passalora fulva) Despite the prevalent model that Rcr3-like proteases can activate themselves at low pH, we found that catalytically inactive proRcr3 mutant precursors are still processed into mature mRcr3 isoforms. ProRcr3 is processed by secreted P69B and other Asp-selective SBTs in solanaceous plants, providing robust immunity through SBT redundancy. The apoplastic effector EPI1 of P. infestans can block Rcr3 activation by inhibiting SBTs, suggesting that this effector promotes virulence indirectly by preventing the activation of Rcr3(-like) immune proteases. Rcr3 activation in Nicotiana benthamiana requires a SBT from a different subfamily, indicating that extracellular proteolytic cascades have evolved convergently in solanaceous plants or are very ancient in the plant kingdom. The frequent incidence of Asp residues in the cleavage region of Rcr3-like proteases in solanaceous plants indicates that activation of immune proteases by SBTs is a general mechanism, illuminating a proteolytic cascade that provides robust apoplastic immunity.
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Affiliation(s)
- Judith K Paulus
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 2JD, United Kingdom
| | - Jiorgos Kourelis
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 2JD, United Kingdom
| | - Selva Ramasubramanian
- The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Felix Homma
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 2JD, United Kingdom
| | - Alice Godson
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 2JD, United Kingdom
| | - Anja C Hörger
- The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Tram Ngoc Hong
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 2JD, United Kingdom
- The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Daniel Krahn
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 2JD, United Kingdom
| | - Laura Ossorio Carballo
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 2JD, United Kingdom
| | - Shuaishuai Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Matthew Smoker
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 2JD, United Kingdom;
- The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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36
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Wang Y, Wang Y, Wang Y. Apoplastic Proteases: Powerful Weapons against Pathogen Infection in Plants. PLANT COMMUNICATIONS 2020; 1:100085. [PMID: 33367249 PMCID: PMC7748006 DOI: 10.1016/j.xplc.2020.100085] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 05/23/2023]
Abstract
Plants associate with diverse microbes that exert beneficial, neutral, or pathogenic effects inside the host. During the initial stages of invasion, the plant apoplast constitutes a hospitable environment for invading microbes, providing both water and nutrients. In response to microbial infection, a number of secreted proteins from host cells accumulate in the apoplastic space, which is related to microbial association or colonization processes. However, the molecular mechanisms underlying plant modulation of the apoplast environment and how plant-secreted proteases are involved in pathogen resistance are still poorly understood. Recently, several studies have reported the roles of apoplastic proteases in plant resistance against bacteria, fungi, and oomycetes. On the other hand, microbe-secreted proteins directly and/or indirectly inhibit host-derived apoplastic proteases to promote infection. These findings illustrate the importance of apoplastic proteases in plant-microbe interactions. Therefore, understanding the protease-mediated apoplastic battle between hosts and pathogens is of fundamental importance for understanding plant-pathogen interactions. Here, we provide an overview of plant-microbe interactions in the apoplastic space. We define the apoplast, summarize the physical and chemical properties of these structures, and discuss the roles of plant apoplastic proteases and pathogen protease inhibitors in host-microbe interactions. Challenges and future perspectives for research into protease-mediated apoplastic interactions are discussed, which may facilitate the engineering of resistant crops.
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Affiliation(s)
- Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiming Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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37
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Puchol Tarazona AA, Lobner E, Taubenschmid Y, Paireder M, Torres Acosta JA, Göritzer K, Steinkellner H, Mach L. Steric Accessibility of the Cleavage Sites Dictates the Proteolytic Vulnerability of the Anti-HIV-1 Antibodies 2F5, 2G12, and PG9 in Plants. Biotechnol J 2020; 15:e1900308. [PMID: 31657528 DOI: 10.1002/biot.201900308] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/20/2019] [Indexed: 12/26/2022]
Abstract
Broadly neutralizing antibodies (bNAbs) to human immunodeficiency virus type 1 (HIV-1) hold great promise for immunoprophylaxis and the suppression of viremia in HIV-positive individuals. Several studies have demonstrated that plants as Nicotiana benthamiana are suitable hosts for the generation of protective anti-HIV-1 antibodies. However, the production of the anti-HIV-1 bNAbs 2F5 and PG9 in N. benthamiana is associated with their processing by apoplastic proteases in the complementarity-determining-region (CDR) H3 loops of the heavy chains. Here, it is shown that apoplastic proteases can also cleave the CDR H3 loop of the bNAb 2G12 when the unusual domain exchange between its heavy chains is prevented by the replacement of Ile19 with Arg. It is demonstrated that CDR H3 proteolysis leads to a strong reduction of the antigen-binding potencies of 2F5, PG9, and 2G12-I19R. Inhibitor profiling experiments indicate that different subtilisin-like serine proteases account for bNAb fragmentation in the apoplast. Differential scanning calorimetry experiments corroborate that the antigen-binding domains of wild-type 2G12 and 4E10 are more compact than those of proteolysis-sensitive antibodies, thus shielding their CDR H3 regions from proteolytic attack. This suggests that the extent of proteolytic inactivation of bNAbs in plants is primarily dictated by the steric accessibility of their CDR H3 loops.
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Affiliation(s)
- Alejandro A Puchol Tarazona
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190, Vienna, Austria
| | - Elisabeth Lobner
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, A-1190, Vienna, Austria
| | - Yvonne Taubenschmid
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190, Vienna, Austria
| | - Melanie Paireder
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190, Vienna, Austria
| | - Juan A Torres Acosta
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190, Vienna, Austria
| | - Kathrin Göritzer
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190, Vienna, Austria
| | - Herta Steinkellner
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190, Vienna, Austria
| | - Lukas Mach
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190, Vienna, Austria
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38
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Jutras PV, Dodds I, van der Hoorn RA. Proteases of Nicotiana benthamiana: an emerging battle for molecular farming. Curr Opin Biotechnol 2020; 61:60-65. [PMID: 31765962 DOI: 10.1016/j.copbio.2019.10.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/19/2022]
Abstract
Molecular farming increasingly uses the tobacco relative Nicotiana benthamiana for production of recombinant proteins through transient expression. Several proteins are produced efficiently with this expression platform, but yields for other proteins are often very low. These low yields are frequently due to endogenous proteases. The latest genome annotations indicate that N. benthamiana encodes for at least 1243 putative proteases that probably act redundantly and consecutively on substrates in different subcellular compartments. Here, we discuss the N. benthamiana protease repertoire that may affect recombinant protein production and recent advances in protease depletion strategies to increase recombinant protein production in N. benthamiana.
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Affiliation(s)
- Philippe V Jutras
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, UK
| | - Isobel Dodds
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, UK
| | - Renier Al van der Hoorn
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, UK.
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Jutras PV, Sainsbury F, Goulet MC, Lavoie PO, Tardif R, Hamel LP, D'Aoust MA, Michaud D. pH Gradient Mitigation in the Leaf Cell Secretory Pathway Attenuates the Defense Response of Nicotiana benthamiana to Agroinfiltration. J Proteome Res 2020; 19:106-118. [PMID: 31789035 DOI: 10.1021/acs.jproteome.9b00409] [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: 11/30/2022]
Abstract
Partial neutralization of the Golgi lumen pH by the ectopic expression of influenza virus M2 proton channel is useful to stabilize acid-labile recombinant proteins in plant cells, but the impact of pH gradient mitigation on host cellular functions has not been investigated. Here, we assessed the unintended effects of M2 expression on the leaf proteome of Nicotiana benthamiana infiltrated with the bacterial gene vector Agrobacterium tumefaciens. An isobaric tags for relative and absolute quantification quantitative proteomics procedure was followed to compare the leaf proteomes of plants agroinfiltrated with either an "empty" vector or an M2-encoding vector. Leaves infiltrated with the empty vector had a low soluble protein content compared to noninfiltrated control leaves, associated with increased levels of stress-related proteins but decreased levels of photosynthesis-associated proteins. M2 expression partly compromised these effects of agroinfiltration to restore soluble protein content in the leaf tissue, associated with restored levels of photosynthesis-associated proteins and reduced levels of stress-related proteins in the apoplast. These data illustrate the cell-wide influence of the Golgi lumen pH homeostasis on the leaf proteome of N. benthamiana responding to microbial challenge. They also underline the relevance of assessing the eventual unintended effects of accessory proteins used to modulate specific cellular or metabolic functions in plant protein biofactories.
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Affiliation(s)
- Philippe V Jutras
- Centre de Recherche et d'Innovation sur les Végétaux , Université Laval , Québec G1V 0A6 , Canada
| | - Frank Sainsbury
- Griffith Institute for Drug Discovery , Griffith University , Nathan , QLD 4111 , Australia
| | - Marie-Claire Goulet
- Centre de Recherche et d'Innovation sur les Végétaux , Université Laval , Québec G1V 0A6 , Canada
| | | | | | | | | | - Dominique Michaud
- Centre de Recherche et d'Innovation sur les Végétaux , Université Laval , Québec G1V 0A6 , Canada
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40
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Schiermeyer A. Optimizing product quality in molecular farming. Curr Opin Biotechnol 2019; 61:15-20. [PMID: 31593785 DOI: 10.1016/j.copbio.2019.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/23/2019] [Accepted: 08/26/2019] [Indexed: 12/28/2022]
Abstract
The production of biopharmaceuticals in plant-based systems had faced several challenges that hampered broader adoption of this technology. In recent years, various plant production hosts have been improved by genetic engineering approaches to overcome obstacles with regard to post-translational modifications and integrity of target proteins. Together with optimized extraction and purification processes, those advances have put plant molecular farming in a more competitive position compared to established production systems. Certain biopharmaceuticals can be derived from plant systems with unique desired properties, qualifying them as biobetters.
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Affiliation(s)
- Andreas Schiermeyer
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Forckenbeckstrasse 6, 52074, Aachen, Germany.
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41
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Kourelis J, Kaschani F, Grosse-Holz FM, Homma F, Kaiser M, van der Hoorn RAL. A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana. BMC Genomics 2019; 20:722. [PMID: 31585525 PMCID: PMC6778390 DOI: 10.1186/s12864-019-6058-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/22/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect. RESULTS Here we present an improved proteome based on the Niben1.0.1 draft genome assembly guided by gene models from other Nicotiana species. Due to the fragmented nature of the Niben1.0.1 draft genome, many protein-encoding genes are missing or partial. We complement these missing proteins by similarly annotating other draft genome assemblies. This approach overcomes problems caused by mis-annotated exon-intron boundaries and mis-assigned short read transcripts to homeologs in polyploid genomes. With an estimated 98.1% completeness; only 53,411 protein-encoding genes; and improved protein lengths and functional annotations, this new predicted proteome is better in assigning spectra than the preceding proteome annotations. This dataset is more sensitive and accurate in proteomics applications, clarifying the detection by activity-based proteomics of proteins that were previously predicted to be inactive. Phylogenetic analysis of the subtilase family of hydrolases reveal inactivation of likely homeologs, associated with a contraction of the functional genome in this alloploid plant species. Finally, we use this new proteome annotation to characterize the extracellular proteome as compared to a total leaf proteome, which highlights the enrichment of hydrolases in the apoplast. CONCLUSIONS This proteome annotation provides the community working with Nicotiana benthamiana with an important new resource for functional proteomics.
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Affiliation(s)
- Jiorgos Kourelis
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Farnusch Kaschani
- Chemische Biologie, Zentrum fur Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Essen, Germany
| | - Friederike M Grosse-Holz
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Felix Homma
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Markus Kaiser
- Chemische Biologie, Zentrum fur Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Essen, Germany
| | - Renier A L van der Hoorn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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42
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Proteomics of PTI and Two ETI Immune Reactions in Potato Leaves. Int J Mol Sci 2019; 20:ijms20194726. [PMID: 31554174 PMCID: PMC6802228 DOI: 10.3390/ijms20194726] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/16/2019] [Accepted: 09/22/2019] [Indexed: 12/29/2022] Open
Abstract
Plants have a variety of ways to defend themselves against pathogens. A commonly used model of the plant immune system is divided into a general response triggered by pathogen-associated molecular patterns (PAMPs), and a specific response triggered by effectors. The first type of response is known as PAMP triggered immunity (PTI), and the second is known as effector-triggered immunity (ETI). To obtain better insight into changes of protein abundance in immunity reactions, we performed a comparative proteomic analysis of a PTI and two different ETI models (relating to Phytophthora infestans) in potato. Several proteins showed higher abundance in all immune reactions, such as a protein annotated as sterol carrier protein 2 that could be interesting since Phytophthora species are sterol auxotrophs. RNA binding proteins also showed altered abundance in the different immune reactions. Furthermore, we identified some PTI-specific changes of protein abundance, such as for example, a glyoxysomal fatty acid beta-oxidation multifunctional protein and a MAR-binding protein. Interestingly, a lysine histone demethylase was decreased in PTI, and that prompted us to also analyze protein methylation in our datasets. The proteins upregulated explicitly in ETI included several catalases. Few proteins were regulated in only one of the ETI interactions. For example, histones were only downregulated in the ETI-Avr2 interaction, and a putative multiprotein bridging factor was only upregulated in the ETI-IpiO interaction. One example of a methylated protein that increased in the ETI interactions was a serine hydroxymethyltransferase.
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43
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Jutras PV, Grosse‐Holz F, Kaschani F, Kaiser M, Michaud D, van der Hoorn RA. Activity-based proteomics reveals nine target proteases for the recombinant protein-stabilizing inhibitor SlCYS8 in Nicotiana benthamiana. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1670-1678. [PMID: 30742730 PMCID: PMC6662110 DOI: 10.1111/pbi.13092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 05/23/2023]
Abstract
Co-expression of protease inhibitors like the tomato cystatin SlCYS8 is useful to increase recombinant protein production in plants, but key proteases involved in protein proteolysis are still unknown. Here, we performed activity-based protein profiling to identify proteases that are inhibited by SlCYS8 in agroinfiltrated Nicotiana benthamiana. We discovered that SlCYS8 selectively suppresses papain-like cysteine protease (PLCP) activity in both apoplastic fluids and total leaf extracts, while not affecting vacuolar-processing enzyme and serine hydrolase activity. A robust concentration-dependent inhibition of PLCPs occurred in vitro when purified SlCYS8 was added to leaf extracts, indicating direct cystatin-PLCP interactions. Activity-based proteomics revealed that nine different Cathepsin-L/-F-like PLCPs are strongly inhibited by SlCYS8 in leaves. By contrast, the activity of five other Cathepsin-B/-H-like PLCPs, as well as 87 Ser hydrolases, was unaffected by SlCYS8. SlCYS8 expression prevented protein degradation by inhibiting intermediate and mature isoforms of granulin-containing proteases from the Resistant-to-Desiccation-21 (RD21) PLCP subfamily. Our data underline the key role of endogenous PLCPs on recombinant protein degradation and reveal candidate proteases for depletion strategies.
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Affiliation(s)
- Philippe V. Jutras
- Department of Plant SciencesPlant Chemetics LaboratoryUniversity of OxfordOxfordUK
| | | | - Farnusch Kaschani
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenEssenGermany
| | - Markus Kaiser
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenEssenGermany
| | - Dominique Michaud
- Centre de recherche et d'innovation sur les végétauxUniversité LavalQuébecCanada
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44
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Buscaill P, Chandrasekar B, Sanguankiattichai N, Kourelis J, Kaschani F, Thomas EL, Morimoto K, Kaiser M, Preston GM, Ichinose Y, van der Hoorn RAL. Glycosidase and glycan polymorphism control hydrolytic release of immunogenic flagellin peptides. Science 2019; 364:eaav0748. [PMID: 30975858 DOI: 10.1126/science.aav0748] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/12/2019] [Indexed: 11/02/2022]
Abstract
Plants and animals recognize conserved flagellin fragments as a signature of bacterial invasion. These immunogenic elicitor peptides are embedded in the flagellin polymer and require hydrolytic release before they can activate cell surface receptors. Although much of flagellin signaling is understood, little is known about the release of immunogenic fragments. We discovered that plant-secreted β-galactosidase 1 (BGAL1) of Nicotiana benthamiana promotes hydrolytic elicitor release and acts in immunity against pathogenic Pseudomonas syringae strains only when they carry a terminal modified viosamine (mVio) in the flagellin O-glycan. In counter defense, P. syringae pathovars evade host immunity by using BGAL1-resistant O-glycans or by producing a BGAL1 inhibitor. Polymorphic glycans on flagella are common to plant and animal pathogenic bacteria and represent an important determinant of host immunity to bacterial pathogens.
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Affiliation(s)
- Pierre Buscaill
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | | | | | - Farnusch Kaschani
- ZMB Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Emma L Thomas
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Kyoko Morimoto
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Markus Kaiser
- ZMB Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Yuki Ichinose
- The Graduate School of Environmental and Life Science, Okayama University, Japan
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Gomes M, Alvarez MA, Quellis LR, Becher ML, Castro JMDA, Gameiro J, Caporrino MC, Moura-da-Silva AM, de Oliveira Santos M. Expression of an scFv antibody fragment in Nicotiana benthamiana and in vitro assessment of its neutralizing potential against the snake venom metalloproteinase BaP1 from Bothrops asper. Toxicon 2019; 160:38-46. [PMID: 30802471 DOI: 10.1016/j.toxicon.2019.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/24/2019] [Accepted: 02/13/2019] [Indexed: 11/29/2022]
Abstract
Human accidents with venomous snakes represent an overwhelming public health problem, mainly in rural populations of underdeveloped countries. Their high incidence and the severity of the accidents result in 81,000 to 138,000 deaths per year. The treatment is based on the administration of purified antibodies, produced by hyper immunization of animals to generate immunoglobulins (Igs), and then obtained by fractionating hyper immune plasma. The use of recombinant antibodies is an alternative to conventional treatment of snakebite envenoming, particularly the Fv fragment, named the single-chain variable fragment (scFv). We have produced recombinant single chain variable fragment scFv against the venom of the pit viper Bothrops asper at high levels expressed transiently and stably in transgenic plants and in vitro cultures that is reactive to BaP1 (a metalloproteinase from B. asper venom). The yield from stably transformed plants was significantly (p > 0.05) higher than the results in from transient expression. In addition, scFvBaP1 yields from systems derived from stable transformation were: transgenic callus 62 μg/g (±2); biomass from cell suspension cultures 83 μg/g (±0.2); culture medium from suspensions 71.75 mg/L (±6.18). The activity of scFvBaP1 was confirmed by binding and neutralization of the fibrin degradation induced by BnP1 toxins from B. neuwiedi and by Atroxlysin Ia from B. atrox venoms. In the present work, we demonstrated the potential use of plant cells to produce scFvBaP1 to be used in the future as a biotechnological alternative to horse immunization protocols to produce anti-venoms to be used in human therapy against snakebites.
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Affiliation(s)
- Marinna Gomes
- Laboratorio de Genética, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, S/n - Martelos, Juiz de Fora, MG, 36036-330, Brazil
| | | | - Leonardo Ramos Quellis
- Laboratorio de Genética, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, S/n - Martelos, Juiz de Fora, MG, 36036-330, Brazil
| | - Melina Laguia Becher
- CONICET-Universidade Maimónides (CEBBAD), Hidalgo 775, Lab 603, Buenos Aires, Argentina
| | - Juciane Maria de Andrade Castro
- Laboratorio de Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, S/n - Martelos, Juiz de Fora, MG, 36036-330, Brazil
| | - Jacy Gameiro
- Laboratorio de Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, S/n - Martelos, Juiz de Fora, MG, 36036-330, Brazil
| | - Maria Cristina Caporrino
- Laboratorio de Imunopatologia, Instituto Butantan, Av. Vital Brazil, 1500, Butantã, CEP 05503-900 São Paulo, SP, Brazil
| | - Ana Maria Moura-da-Silva
- Laboratorio de Imunopatologia, Instituto Butantan, Av. Vital Brazil, 1500, Butantã, CEP 05503-900 São Paulo, SP, Brazil
| | - Marcelo de Oliveira Santos
- Laboratorio de Genética, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, S/n - Martelos, Juiz de Fora, MG, 36036-330, Brazil.
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Balakireva AV, Deviatkin AA, Zgoda VG, Kartashov MI, Zhemchuzhina NS, Dzhavakhiya VG, Golovin AV, Zamyatnin AA. Proteomics Analysis Reveals That Caspase-Like and Metacaspase-Like Activities Are Dispensable for Activation of Proteases Involved in Early Response to Biotic Stress in Triticum aestivum L. Int J Mol Sci 2018; 19:ijms19123991. [PMID: 30544979 PMCID: PMC6320887 DOI: 10.3390/ijms19123991] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/04/2018] [Accepted: 12/08/2018] [Indexed: 12/15/2022] Open
Abstract
Plants, including Triticum aestivum L., are constantly attacked by various pathogens which induce immune responses. Immune processes in plants are tightly regulated by proteases from different families within their degradome. In this study, a wheat degradome was characterized. Using profile hidden Markov model (HMMer) algorithm and Pfam database, comprehensive analysis of the T. aestivum genome revealed a large number of proteases (1544 in total) belonging to the five major protease families: serine, cysteine, threonine, aspartic, and metallo-proteases. Mass-spectrometry analysis revealed a 30% difference between degradomes of distinct wheat cultivars (Khakasskaya and Darya), and infection by biotrophic (Puccinia recondita Rob. ex Desm f. sp. tritici) or necrotrophic (Stagonospora nodorum) pathogens induced drastic changes in the presence of proteolytic enzymes. This study shows that an early immune response to biotic stress is associated with the same core of proteases from the C1, C48, C65, M24, M41, S10, S9, S8, and A1 families. Further liquid chromatography-mass spectrometry (LC-MS) analysis of the detected protease-derived peptides revealed that infection by both pathogens enhances overall proteolytic activity in wheat cells and leads to activation of proteolytic cascades. Moreover, sites of proteolysis were identified within the proteases, which probably represent targets of autocatalytic activation, or hydrolysis by another protease within the proteolytic cascades. Although predicted substrates of metacaspase-like and caspase-like proteases were similar in biotrophic and necrotrophic infections, proteolytic activation of proteases was not found to be associated with metacaspase-like and caspase-like activities. These findings indicate that the response of T. aestivum to biotic stress is regulated by unique mechanisms.
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Affiliation(s)
- Anastasia V Balakireva
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str., 8, bld. 2, Moscow 119991, Russia.
| | - Andrei A Deviatkin
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str., 8, bld. 2, Moscow 119991, Russia.
| | - Victor G Zgoda
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, bld. 8, Moscow 119121, Russia.
| | - Maxim I Kartashov
- All Russian Research Institute of Phytopathology, VNIIF, Bolshie Vyazemi, Odintsovsky distr., Moscow region 143050, Russia.
| | - Natalia S Zhemchuzhina
- All Russian Research Institute of Phytopathology, VNIIF, Bolshie Vyazemi, Odintsovsky distr., Moscow region 143050, Russia.
| | - Vitaly G Dzhavakhiya
- All Russian Research Institute of Phytopathology, VNIIF, Bolshie Vyazemi, Odintsovsky distr., Moscow region 143050, Russia.
| | - Andrey V Golovin
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str., 8, bld. 2, Moscow 119991, Russia.
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow 119992, Russia.
| | - Andrey A Zamyatnin
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str., 8, bld. 2, Moscow 119991, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
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47
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Hoernstein SNW, Fode B, Wiedemann G, Lang D, Niederkrüger H, Berg B, Schaaf A, Frischmuth T, Schlosser A, Decker EL, Reski R. Host Cell Proteome of Physcomitrella patens Harbors Proteases and Protease Inhibitors under Bioproduction Conditions. J Proteome Res 2018; 17:3749-3760. [PMID: 30226384 DOI: 10.1021/acs.jproteome.8b00423] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Host cell proteins are inevitable contaminants of biopharmaceuticals. Here, we performed detailed analyses of the host cell proteome of moss ( Physcomitrella patens) bioreactor supernatants using mass spectrometry and subsequent bioinformatics analysis. Distinguishing between the apparent secretome and intracellular contaminants, a complex extracellular proteolytic network including subtilisin-like proteases, metallo-proteases, and aspartic proteases was identified. Knockout of a subtilisin-like protease affected the overall extracellular proteolytic activity. Besides proteases, also secreted protease-inhibiting proteins such as serpins were identified. Further, we confirmed predicted cleavage sites of 40 endogenous signal peptides employing an N-terminomics approach. The present data provide novel aspects to optimize both product stability of recombinant biopharmaceuticals as well as their maturation along the secretory pathway. Data are available via ProteomeXchange with identifier PXD009517.
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Affiliation(s)
- Sebastian N W Hoernstein
- Plant Biotechnology, Faculty of Biology , University of Freiburg , Schaenzlestrasse 1 , D-79104 Freiburg , Germany
| | - Benjamin Fode
- Greenovation Biotech GmbH , Hans-Bunte-Strasse 19 , D-79108 Freiburg , Germany
| | - Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology , University of Freiburg , Schaenzlestrasse 1 , D-79104 Freiburg , Germany
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology , University of Freiburg , Schaenzlestrasse 1 , D-79104 Freiburg , Germany.,Plant Genome and System Biology , Helmholtz Center Munich , D-85764 Neuherberg , Germany
| | - Holger Niederkrüger
- Greenovation Biotech GmbH , Hans-Bunte-Strasse 19 , D-79108 Freiburg , Germany
| | - Birgit Berg
- Greenovation Biotech GmbH , Hans-Bunte-Strasse 19 , D-79108 Freiburg , Germany
| | - Andreas Schaaf
- Greenovation Biotech GmbH , Hans-Bunte-Strasse 19 , D-79108 Freiburg , Germany
| | - Thomas Frischmuth
- Greenovation Biotech GmbH , Hans-Bunte-Strasse 19 , D-79108 Freiburg , Germany
| | - Andreas Schlosser
- Rudolf-Virchow-Center for Experimental Biomedicine , University of Wuerzburg , D-97080 Wuerzburg , Germany
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology , University of Freiburg , Schaenzlestrasse 1 , D-79104 Freiburg , Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology , University of Freiburg , Schaenzlestrasse 1 , D-79104 Freiburg , Germany.,BIOSS - Centre for Biological Signalling Studies , University of Freiburg , D-79104 Freiburg , Germany
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48
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Grosse‐Holz F, Madeira L, Zahid MA, Songer M, Kourelis J, Fesenko M, Ninck S, Kaschani F, Kaiser M, van der Hoorn RA. Three unrelated protease inhibitors enhance accumulation of pharmaceutical recombinant proteins in Nicotiana benthamiana. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1797-1810. [PMID: 29509983 PMCID: PMC6131417 DOI: 10.1111/pbi.12916] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/25/2018] [Accepted: 02/28/2018] [Indexed: 05/21/2023]
Abstract
Agroinfiltrated Nicotiana benthamiana is a flexible and scalable platform for recombinant protein (RP) production, but its great potential is hampered by plant proteases that degrade RPs. Here, we tested 29 candidate protease inhibitors (PIs) in agroinfiltrated N. benthamiana leaves for enhancing accumulation of three unrelated RPs: glycoenzyme α-Galactosidase; glycohormone erythropoietin (EPO); and IgG antibody VRC01. Of the previously described PIs enhancing RP accumulation, we found only cystatin SlCYS8 to be effective. We identified three additional new, unrelated PIs that enhance RP accumulation: N. benthamiana NbPR4, NbPot1 and human HsTIMP, which have been reported to inhibit cysteine, serine and metalloproteases, respectively. Remarkably, accumulation of all three RPs is enhanced by each PI similarly, suggesting that the mechanism of degradation of unrelated RPs follows a common pathway. Inhibitory functions HsTIMP and SlCYS8 are required to enhance RP accumulation, suggesting that their target proteases may degrade RPs. Different PIs additively enhance RP accumulation, but the effect of each PI is dose-dependent. Activity-based protein profiling (ABPP) revealed that the activities of papain-like Cys proteases (PLCPs), Ser hydrolases (SHs) or vacuolar processing enzymes (VPEs) in leaves are unaffected upon expression of the new PIs, whereas SlCYS8 expression specifically suppresses PLCP activity only. Quantitative proteomics indicates that the three new PIs affect agroinfiltrated tissues similarly and that they all increase immune responses. NbPR4, NbPot1 and HsTIMP can be used to study plant proteases and improve RP accumulation in molecular farming.
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Affiliation(s)
| | - Luisa Madeira
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordOxfordUK
| | - Muhammad Awais Zahid
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordOxfordUK
| | - Molly Songer
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordOxfordUK
| | - Jiorgos Kourelis
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordOxfordUK
| | - Mary Fesenko
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordOxfordUK
| | - Sabrina Ninck
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstrEssenGermany
| | - Farnusch Kaschani
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstrEssenGermany
| | - Markus Kaiser
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstrEssenGermany
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49
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Bhardwaj N, Verma VK, Chaturvedi V, Verma P. GH10 XynF1 and Xyn11A: the predominant xylanase identified in the profiling of extracellular proteome of Aspergillus oryzae LC1. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1378-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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50
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Kovalyova Y, Hatzios SK. Activity-Based Protein Profiling at the Host-Pathogen Interface. Curr Top Microbiol Immunol 2018; 420:73-91. [PMID: 30203396 DOI: 10.1007/82_2018_129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Activity-based protein profiling (ABPP) is a technique for selectively detecting reactive amino acids in complex proteomes with the aid of chemical probes. Using probes that target catalytically active enzymes, ABPP can rapidly define the functional proteome of a biological system. In recent years, this approach has been increasingly applied to globally profile enzymes active at the host-pathogen interface of microbial infections. From in vitro co-culture systems to animal models of infection, these studies have revealed enzyme-mediated mechanisms of microbial pathogenicity, host immunity, and metabolic adaptation that dynamically shape pathogen interactions with the host.
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Affiliation(s)
- Yekaterina Kovalyova
- Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA.,Department of Chemistry, Yale University, New Haven, CT, 06511, USA
| | - Stavroula K Hatzios
- Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA. .,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06511, USA. .,Department of Chemistry, Yale University, New Haven, CT, 06511, USA.
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