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Lim-Hing S, Gandhi KJK, Villari C. The role of Manganese in tree defenses against pests and pathogens. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108641. [PMID: 38663267 DOI: 10.1016/j.plaphy.2024.108641] [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: 11/15/2023] [Revised: 03/25/2024] [Accepted: 04/17/2024] [Indexed: 05/12/2024]
Abstract
Manganese (Mn) deficiency is a widespread occurrence across different landscapes, including agricultural systems and managed forests, and causes interruptions in the normal metabolic functioning of plants. The microelement is well-characterized for its role in the oxygen-evolving complex in photosystem II and maintenance of photosynthetic structures. Mn is also required for a variety of enzymatic reactions in secondary metabolism, which play a crucial role in defense strategies for trees. Despite the strong relationship between Mn availability and the biosynthesis of defense-related compounds, there are few studies addressing how Mn deficiency can impact tree defense mechanisms and the ensuing ecological patterns and processes. Understanding this relationship and highlighting the potentially deleterious effects of Mn deficiency in trees can also inform silvicultural and management decisions to build more robust forests. In this review, we address this relationship, focusing on forest trees. We describe Mn availability in forest soils, characterize the known impacts of Mn deficiency in plant susceptibility, and discuss the relationship between Mn and defense-related compounds by secondary metabolite class. In our review, we find several lines of evidence that low Mn availability is linked with lowered or altered secondary metabolite activity. Additionally, we compile documented instances where Mn limitation has altered the defense capabilities of the host plant and propose potential ecological repercussions when studies are not available. Ultimately, this review aims to highlight the importance of untangling the effects of Mn limitation on the ecophysiology of plants, with a focus on forest trees in both managed and natural stands.
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Affiliation(s)
- Simone Lim-Hing
- D.B. Warnell School of Forestry and Natural Resources, University of Georgia, 180 East Green Street, Athens, 30602, Georgia, USA; Department of Plant Biology, University of Georgia, 120 Carlton Street, Athens, 30602, Georgia, USA.
| | - Kamal J K Gandhi
- D.B. Warnell School of Forestry and Natural Resources, University of Georgia, 180 East Green Street, Athens, 30602, Georgia, USA
| | - Caterina Villari
- D.B. Warnell School of Forestry and Natural Resources, University of Georgia, 180 East Green Street, Athens, 30602, Georgia, USA.
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Virklund A, Jendresen CB, Nielsen AT, Woodley JM. Characterization of tyrosine ammonia lyases from Flavobacterium johnsonian and Herpetosiphon aurantiacus. Biotechnol J 2023; 18:e2300111. [PMID: 37486789 DOI: 10.1002/biot.202300111] [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: 03/09/2023] [Revised: 06/12/2023] [Accepted: 07/12/2023] [Indexed: 07/26/2023]
Abstract
p-Coumaric acid (pCA) can be produced via bioprocessing and is a promising chemical precursor to making organic thin film transistors. However, the required tyrosine ammonia lyase (TAL) enzyme generally has a low specific activity and suffers from competitive product inhibition. Here we characterized the purified TAL variants from Flavobacterium johnsoniae and Herpetosiphon aurantiacus in terms of their susceptibility to product inhibition and their activity and stability across pH and temperature via initial rate experiments. FjTAL was found to be more active than previously described and to have a relatively weak affinity for pCA, but modeling revealed that product inhibition would still be problematic at industrially relevant product concentrations, due to the low solubility of the substrate tyrosine. The activity of both variants increased with temperature when tested up to 45°C, but HaTAL1 was more stable at elevated temperature. FjTAL is a promising biocatalyst for pCA production, but enzyme or bioprocess engineering are required to stabilize FjTAL and reduce product inhibition.
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Affiliation(s)
- Alexander Virklund
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Alex Toftgaard Nielsen
- Cysbio, Hørsholm, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
| | - John M Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
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Li Z, Li C, Cheng P, Yu G. Rhodotorula mucilaginosa—alternative sources of natural carotenoids, lipids, and enzymes for industrial use. Heliyon 2022; 8:e11505. [DOI: 10.1016/j.heliyon.2022.e11505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/19/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
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Oliveira KS, de Mello Prado R, Checchio MV, Gratão PL. Interaction of silicon and manganese in nutritional and physiological aspects of energy cane with high fiber content. BMC PLANT BIOLOGY 2022; 22:374. [PMID: 35902800 PMCID: PMC9335997 DOI: 10.1186/s12870-022-03766-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/20/2022] [Indexed: 05/17/2023]
Abstract
BACKGROUND Silicon (Si) is a multiple stress attenuator element in plants, however more research is needed to elucidate the actions in the plants defense system with low nutrition of manganese (Mn) for a prolonged period, and the attenuation mechanisms involved in the effects of Mn deficiency on energy cane with high fiber content. Thus, the objective of this study was to evaluate whether Si reduces the oxidative stress of the energy cane grown in low Mn in nutrient solution, to mitigate the effects of Mn deficiency, improving enzymatic and non-enzymatic defense, uptake of Mn the plant growth. METHODS An experiment was carried out with pre-sprouted seedlings of Saccharum spontaneum L. in a 2 × 2 factorial scheme in five replications in which the plants were grown under sufficiency (20.5 μmol L-1) and deficiency (0.1 μmol L-1) of Mn combined with the absence and presence of Si (2.0 mmol L-1) for 160 days from the application of the treatments. The following parameters were evaluated: accumulation of Mn and Si, H2O2, MDA, activity of SOD and GPOX, total phenol content, pigments, and quantum efficiency of PSII. RESULTS Mn deficiency induced the oxidative stress for increase the H2O2 and MDA content in leaves of plants and reduce the activity of antioxidant enzymes and total phenols causing damage to quantum efficiency of photosystem II and pigment content. Si attenuated the effects of Mn deficiency even for a longer period of stress by reducing H2O2 (18%) and MDA (32%) content, and increased the Mn uptake efficiency (53%), SOD activity (23%), GPOX (76%), phenol contents, thus improving growth. CONCLUSIONS The supply of Si promoted great nutritional and physiological improvements in energy cane with high fiber content in Mn deficiency. The results of this study propose the supply of Si via fertirrigation as a new sustainable strategy for energy cane cultivation in low Mn environments.
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Affiliation(s)
- Kamilla Silva Oliveira
- Department of Agricultural Production Sciences, Sector of Soils and Fertilizers, Laboratory of Plant Nutrition, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, São Paulo, 14884-900, Brazil.
| | - Renato de Mello Prado
- Department of Agricultural Production Sciences, Sector of Soils and Fertilizers, Laboratory of Plant Nutrition, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, São Paulo, 14884-900, Brazil
| | - Mirela Vantini Checchio
- Department of Biology Applied to Agriculture, Laboratory of Plant Physiology, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, São Paulo, 14884900, Brazil
| | - Priscila Lupino Gratão
- Department of Biology Applied to Agriculture, Laboratory of Plant Physiology, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, São Paulo, 14884900, Brazil
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Besada C, Hakami A, Pillai G, Yetsko K, Truong N, Little T, Pantano S, Dmello A. Preformulation studies with phenylalanine ammonia lyase: essential prelude to a microcapsule formulation for the management of phenylketonuria. J Pharm Sci 2022; 111:1857-1867. [DOI: 10.1016/j.xphs.2022.03.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 01/10/2023]
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Rahmatabadi SS, Sadeghian I, Ghasemi Y, Sakhteman A, Hemmati S. Identification and characterization of a sterically robust phenylalanine ammonia-lyase among 481 natural isoforms through association of in silico and in vitro studies. Enzyme Microb Technol 2018; 122:36-54. [PMID: 30638507 DOI: 10.1016/j.enzmictec.2018.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 11/14/2018] [Accepted: 12/09/2018] [Indexed: 10/27/2022]
Abstract
The enzyme phenylalanine ammonia lyase (PAL) is of special importance for the treatment of phenylketonuria patients. The aim of this study was to find a stable recombinant PAL with suitable kinetic properties among all natural PAL producing species using in silico and experimental approaches. To find such a stable PAL among 481 natural isoforms, 48,000 of 3-D models were predicted using the Modeller 9.10 program and evaluated by Ramachandran plot. Correlation analysis between Ramachandran plot and the energy of different thermodynamic components indicated that this plot could be an appropriate tool to predict protein stability. Hence, PAL6 from Lotus japonicus (LjPAL6) was selected as a stable isoform. Molecular dynamic (MD) simulation for 50 ns and docking has been conducted for LjPAL6-phenylalanine complex. The best PAL-phenylalanine frame was selected by re-docking with l-phenylalanine (L-Phe) and root-mean-square deviation (RMSD) value. MD simulation showed that the complex has a good stability, depicted by the low RMSD value, binding free energy and hydrogen bindings. Docking results showed that LjPAL6 has a high affinity toward l-Phe according to the low level of binding free energy. By overexpressing Ljpal6 in E. coli BL21, a total of 33.5 mg/l of protein was obtained, which has been increased to 83.7 mg/l via the optimization of LjPAL6 production using response surface methodology. The optimal pH and temperature were 8.5 and 50 °C, respectively. LjPAL6 showed a specific activity of 42 nkat/mg protein, with Km, Kcat and Kcat/Km values of 0.483 mM, 7 S-1 and 14.5 S-1 mM-1 for l-phe, respectively. In conclusion, finding models with the most reasonable stereo-chemical quality and lowest numbers of steric clashes would result in easier folding. Hence, in silico analyses of bulk data from natural origin will lead one to find an optimal model for in vitro studies and drug design.
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Affiliation(s)
- Seyyed Soheil Rahmatabadi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Issa Sadeghian
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amirhossein Sakhteman
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Shiva Hemmati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Zhu L, Zhou L, Cui W, Liu Z, Zhou Z. Mechanism-based site-directed mutagenesis to shift the optimum pH of the phenylalanine ammonia-lyase from Rhodotorula glutinis JN-1. ACTA ACUST UNITED AC 2014. [PMID: 28626644 PMCID: PMC5466100 DOI: 10.1016/j.btre.2014.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phenylalanine ammonia-lyase (RgPAL) from Rhodotorula glutinis JN-1 stereoselectively catalyzes the conversion of the l-phenylalanine into trans-cinnamic acid and ammonia, and was used in chiral resolution of dl-phenylalanine to produce the d-phenylalanine under acidic condition. However, the optimum pH of RgPAL is 9 and the RgPAL exhibits low catalytic efficiency at acidic side. Therefore, a mutant RgPAL with a lower optimum pH is expected. Based on catalytic mechanism and structure analysis, we constructed a mutant RgPAL-Q137E by site-directed mutagenesis, and found that this mutant had an extended optimum pH 7-9 with activity of 1.8-fold higher than that of the wild type at pH 7. As revealed by Friedel-Crafts-type mechanism of RgPAL, the improvement of the RgPAL-Q137E might be due to the negative charge of Glu137 which could stabilize the intermediate transition states through electrostatic interaction. The RgPAL-Q137E mutant was used to resolve the racemic dl-phenylalanine, and the conversion rate and the eeD value of d-phenylalanine using RgPAL-Q137E at pH 7 were increased by 29% and 48%, and achieved 93% and 86%, respectively. This work provides an effective strategy to shift the optimum pH which is favorable to further applications of RgPAL.
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Affiliation(s)
- Longbao Zhu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Li Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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Cui JD, Qiu JQ, Fan XW, Jia SR, Tan ZL. Biotechnological production and applications of microbial phenylalanine ammonia lyase: a recent review. Crit Rev Biotechnol 2013; 34:258-68. [PMID: 23688066 DOI: 10.3109/07388551.2013.791660] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Phenylalanine ammonia lyase (PAL) catalyzes the nonoxidative deamination of l-phenylalanine to form trans-cinnamic acid and a free ammonium ion. It plays a major role in the catabolism of l-phenylalanine. The presence of PAL has been reported in diverse plants, some fungi, Streptomyces and few Cyanobacteria. In the past two decades, PAL has gained considerable significance in several clinical, industrial and biotechnological applications. Since its discovery, much knowledge has been gathered with reference to the enzyme's importance in phenyl propanoid pathway of plants. In contrast, there is little knowledge about microbial PAL. Furthermore, the commercial source of the enzyme has been mainly obtained from the fungi. This study focuses on the recent advances on the physiological role of microbial PAL and the improvements of PAL biotechnological production both from our laboratory and many others as well as the latest advances on the new applications of microbial PAL.
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Affiliation(s)
- Jian Dong Cui
- Research Center for Fermentation Engineering of Hebei, College of Bioscience and Bioengineering, Hebei University of Science and Technology , Shijiazhang , P R China
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Gubica T, Pełka A, Pałka K, Temeriusz A, Kańska M. The influence of cyclomaltooligosaccharides (cyclodextrins) on the enzymatic decomposition of l-phenylalanine catalyzed by phenylalanine ammonia-lyase. Carbohydr Res 2011; 346:1855-9. [DOI: 10.1016/j.carres.2011.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 05/23/2011] [Accepted: 06/07/2011] [Indexed: 01/06/2023]
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Quinn AJ, Pickup MJ, D'Cunha GB. Enzyme activity evaluation of organic solvent-treated phenylalanine ammonia lyase. Biotechnol Prog 2011; 27:1554-60. [DOI: 10.1002/btpr.687] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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