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Wang H, Zhang R, Hu J, Fu R, Li J. In vitro and in silico analyses reveal the interaction between LysM receptor-like kinase3 of Solanum tuberosum and the carbohydrate elicitor Riclin octaose. Biotechnol J 2024; 19:e2300385. [PMID: 37903287 DOI: 10.1002/biot.202300385] [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: 08/02/2023] [Revised: 09/27/2023] [Accepted: 10/25/2023] [Indexed: 11/01/2023]
Abstract
As a carbohydrate elicitor, Riclin octaose (Rioc) activates the pattern-triggered immunity of Solanum tuberosum L., while how the plant perceives Rioc is unknown. Here, a pattern recognition receptor StLYK3 (LysM receptor-like kinase3) whose transcription level was significantly up-regulated after Rioc elicitation was investigated in vitro and in silico. The nucleotide that encoded the ectodomain of StLYK3 (StLYK3-ECD) was heterologously expressed in the Pichia pastoris strain GS115. The purified StLYK3-ECD had the molecular weight of 25.08 kDa and pI of 5.69. Afterwards interaction between StLYK3-ECD and Rioc was analyzed by isothermal titration calorimetry. The molar ratio of ligand to receptor, dissociation constant, and enthalpy were 1.28 ± 0.04, 26.7 ± 3.1 μM, and -45.0 ± 1.8 kJ mol-1 , respectively. Besides, molecular dynamics results indicated that StLYK3-ECD contained three carbohydrate-binding motifs and the first two motifs probably contributed to the interaction with Rioc via hydrogen bond and van de Waals' forces. Amino acids containing hydroxyl, amidic, and sulfhydryl groups took the main portion in the docking site. Moreover, replacing the 92nd threonyl (T) of StLYK3-ECD with valyl (V) resulted in the alteration of the preferred docking site. The dissociation constant drastically increased to 841.6 ± 232.4 μM. In conclusion, StLYK3 was a potential receptor of Rioc.
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Affiliation(s)
- Hongyang Wang
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
| | - Ruixin Zhang
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
| | - Junpeng Hu
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
| | - Renjie Fu
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
| | - Jing Li
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
- Center for Molecular Metabolism, Nanjing University of Science and Technology, Nanjing, China
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Attenuating the triacylglycerol catabolism enhanced lipid production of Rhodotorula strain U13N3. Appl Microbiol Biotechnol 2023; 107:1491-1501. [PMID: 36633623 DOI: 10.1007/s00253-023-12368-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/29/2022] [Accepted: 01/03/2023] [Indexed: 01/13/2023]
Abstract
Enhancing the lipid production of oleaginous yeasts is conducive to cutting the cost of feedstock for biodiesel. To increase the lipid productivity of Rhodotorula sp. U13N3, genes involving lipid degradation were knocked out and fermentation conditions were investigated. Results of transcription analysis demonstrated that genes encoding the ATG15-like lipase (ATG15) and peroxisomal acyl-CoA oxidase (ACOX2) were upregulated significantly at the lipogenesis stage. When ATG15 and ACOX2 were knocked out separately from the genome by the CRISPR/Cas9 method, both ΔATG15 and ΔACOX2 mutants showed better lipid production ability than the parent strain. Flow cytometry and confocal microscopic analyses indicated that simultaneous the knockout of ATG15 and ACOX2 did not impact the cell viability, whereas the lipid production was enhanced markedly as the lipid yield increased by 67.03% in shake flasks. Afterward, the ΔATG15ΔACOX2 transformant (TO2) was cultivated in shake flasks in the fed-batch mode; the highest biomass and lipid yield reached 45.76 g/L and 27.14 g/L at 216 h, respectively. Better performance was achieved when TO2 was cultivated in the 1-L bioreactor. At the end of fermentation (180 h), lipid content, yield, yield coefficient, and productivity reached 65.53%, 27.35 g/L, 0.277 g/g glycerol, and 0.152 g/L/h, respectively. These values were at the high level in comparison with Rhodotorula strains cultivated in glycerol media. Besides, fermentation modes did not affect the fatty acid composition of TO2 significantly. In conclusion, blocking the lipid degradation was an applicable strategy to increase the lipid production of Rhodotorula strains without compromising their cell viability. KEY POINTS: • ATG15-like lipase and acyl-CoA oxidase (ACOX2) participated in lipid degradation. • Knockout of ATG15 and ACOX2 increased lipid productivity, and lipid yield coefficient. • Cell viability maintained at high level in the knockout mutants during fermentation.
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Shao M, Chen Y, Gong Q, Miao S, Li C, Sun Y, Qin D, Guo X, Yan X, Cheng P, Yu G. Biocontrol endophytes Bacillus subtilis R31 influence the quality, transcriptome and metabolome of sweet corn. PeerJ 2023; 11:e14967. [PMID: 36883062 PMCID: PMC9985898 DOI: 10.7717/peerj.14967] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/07/2023] [Indexed: 03/06/2023] Open
Abstract
During colonization of soil and plants, biocontrol bacteria can effectively regulate the physiological metabolism of plants and induce disease resistance. To illustrate the influence of Bacillus subtilis R31 on the quality, transcriptome and metabolome of sweet corn, field studies were conducted at a corn experimental base in Zhuhai City. The results show that, after application of B. subtilis R31, sweet corn was more fruitful, with a 18.3 cm ear length, 5.0 cm ear diameter, 0.4 bald head, 403.9 g fresh weight of single bud, 272.0 g net weight of single ear, and 16.5 kernels sweetness. Combined transcriptomic and metabolomic analyses indicate that differentially expressed genes related to plant-pathogen interactions, MAPK signaling pathway-plant, phenylpropanoid biosynthesis, and flavonoid biosynthesis were significantly enriched. Moreover, the 110 upregulated DAMs were mainly involved in the flavonoid biosynthesis and flavone and flavonol biosynthesis pathways. Our study provides a foundation for investigating the molecular mechanisms by which biocontrol bacteria enhance crop nutrition and taste through biological means or genetic engineering at the molecular level.
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Affiliation(s)
- Mingwei Shao
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
| | - Yanhong Chen
- Zhuhai Modern Agriculture Development Center, Zhuhai, China
| | - Qingyou Gong
- Zhuhai Modern Agriculture Development Center, Zhuhai, China
| | - Shuang Miao
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
| | - Chunji Li
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
| | - Yunhao Sun
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
| | - Di Qin
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
| | - Xiaojian Guo
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
| | - Xun Yan
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
| | - Ping Cheng
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
| | - Guohui Yu
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
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Fu R, Meng D, Song B, Wang H, Zhang J, Li J. The carbohydrate elicitor Riclinoctaose facilitates defense and growth of potato roots by inducing changes in transcriptional and metabolic profiles. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 322:111349. [PMID: 35709981 DOI: 10.1016/j.plantsci.2022.111349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/05/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Promoting both root growth and defense is conducive to the production of potatoes (Solanum tuberosum L.), while the role of elicitors in this topic hasn't been fully understood. To investigate the effect of Riclinoctaose (RiOc) on root growth and defense, potato tissue cuttings were cultivated with different concentration of RiOc (0, 50, 200 mg/L) for 5 weeks and changes in root morphology, transcription, enzymatic and metabolomic profiles were monitored over time. The results indicated that RiOc triggered the salicylic acid (SA)-mediated defense response and facilitated the growth of adventitious and lateral roots in a dose- and time-dependent manner. MPK3/MPK6, SA- and auxin-signaling pathways and transcription factors such as WUS, SCR and GRAS4/GRAS9 participated in this process. Moreover, the 1H NMR based metabolome profiling demonstrated that potato roots altered the primary metabolism to respond to the RiOc elicitation and efficiency in production and allocation of defense and growth-related metabolites was improved. After 5-week treatment, the level of glucose, N-acetylglucosamine, glutamine, asparagine, isoleucine, valine, 3-hydroxyisovalerate and ferulate increased, while acetate, acetoacetate, fucose, and 2-hydroxyphenylacetate declined. In conclusion, RiOc played dual roles in activating the SA-mediated defense response and in promoting growth of potato roots by inducing changes in root transcription and metabolism.
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Affiliation(s)
- Renjie Fu
- Center for Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China
| | - Deyao Meng
- Center for Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China; School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China
| | - Baocai Song
- Center for Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China
| | - Hongyang Wang
- Center for Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China
| | - Jianfa Zhang
- Center for Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China; School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China
| | - Jing Li
- Center for Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China; School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China.
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