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Bharadwaj P, Barua A, Bisht M, Sarkar DK, Biswas S, Franklin G, Mondal D. Understanding the Effect of Ionic Liquid-Mediated Solvent Engineering on the Kinetics and Thermodynamic Stability of Phenylalanine Ammonia-Lyase. J Phys Chem B 2024; 128:9102-9110. [PMID: 39267442 PMCID: PMC11440588 DOI: 10.1021/acs.jpcb.4c04272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/29/2024] [Accepted: 09/03/2024] [Indexed: 09/17/2024]
Abstract
Phenylalanine ammonia-lyase (PAL) plays a central role in the phenylpropanoid pathway and in the treatment of phenylketonuria. However, the integration of PAL into sustainable industrial biocatalysis is hampered by its instability under harsh conditions. This study demonstrates that ionic liquid (IL)-assisted solvent (Tris-HCl buffer) engineering enables improvement of the reaction kinetics and thermodynamic stability of Rhodotorula glutinisPAL (RgPAL) under various stresses. Under optimized conditions, a 66.2% higher Kcat value, >60% remaining activity after 5 weeks of storage at room temperature, and >80% activity of RgPAL after incubation at 60 °C for 1 h were obtained in the [Ch][Ac]-blended Tris-HCl solvent compared to pristine Tris-HCl. The spectroscopic and molecular docking results suggest that the higher extent of hydration and the soft interactions complemented by the ILs with the D-chain residues of RgPAL jointly contributed to achieving more stable and active conformations of RgPAL. The enzyme showed a higher melting temperature (Tm) in ILs+Tris-HCl compared to that in pristine Tris-HCl, with less change in enthalpy (ΔHfu) and entropy (ΔSfu) of unfolding. Overall, IL-mediated solvent engineering alters the microenvironment of RgPAL and allows the development of a robust PAL-based biocatalytic system.
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Affiliation(s)
- Pranav Bharadwaj
- Institute
of Plant Genetics (IPG), Polish Academy of Sciences, Poznań 60-479, Poland
- Centre
for Nano and Material Sciences, Jain (Deemed-to-be
University), Jain Global Campus, Bangalore, Karnataka 562112, India
| | - Avishak Barua
- Institute
of Plant Genetics (IPG), Polish Academy of Sciences, Poznań 60-479, Poland
| | - Meena Bisht
- Institute
of Plant Genetics (IPG), Polish Academy of Sciences, Poznań 60-479, Poland
- Department
of Chemistry, Sri Venkateswara College,
University of Delhi, New Delhi, Dhaula Kuan 110021, India
| | | | - Sagar Biswas
- Institute
of Plant Genetics (IPG), Polish Academy of Sciences, Poznań 60-479, Poland
| | - Gregory Franklin
- Institute
of Plant Genetics (IPG), Polish Academy of Sciences, Poznań 60-479, Poland
| | - Dibyendu Mondal
- Institute
of Plant Genetics (IPG), Polish Academy of Sciences, Poznań 60-479, Poland
- Centre
for Nano and Material Sciences, Jain (Deemed-to-be
University), Jain Global Campus, Bangalore, Karnataka 562112, India
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2
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Schwarze CM, Petersen M. Phenylalanine ammonia-lyases and 4-coumaric acid coenzyme A ligases in Chara braunii, Marchantia polymorpha, and Physcomitrium patens as extant model organisms for plant terrestrialization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2797-2815. [PMID: 39052447 DOI: 10.1111/tpj.16950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 07/13/2024] [Indexed: 07/27/2024]
Abstract
The conquest of land posed severe problems to plants which they had to cope with by adapting biosynthetic capacities. Adaptations to respond to UV irradiation, water loss, pathogen and herbivore defense, and the earth's pull were essential. Chemical compounds alleviating these problems can be synthesized by the phenylpropanoid pathway, the core of which are three enzymes: phenylalanine ammonia-lyase (PAL), cinnamic acid 4-hydroxylase, and 4-coumaric acid coenzyme A-ligase (4CL). The genomes of model organisms, Chara braunii as aquatic alga and the two bryophytes Physcomitrium patens and Marchantia polymorpha, were searched for sequences encoding PAL and 4CL and selected sequences heterologously expressed in Escherichia coli for biochemical characterization. Several possible isoforms were identified for both enzymes in Marchantia polymorpha and Physcomitrium patens, while only one or two isoforms could be retrieved for Chara braunii. Active forms of both enzymes were found in all three organisms, although the catalytic efficiencies varied in a wide range. l-Phenylalanine was accepted as best substrate by all PAL-like enzymes, despite annotations in some cases suggesting different activities. The substrate spectrum of 4CLs was more diverse, but caffeic and/or 4-coumaric acids generally were the best-accepted substrates. Our investigations show that PAL and 4CL, important enzymes for the formation of phenolic compounds, are present and active in extant charophytes and bryophytes as model organisms for the conquest of land.
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Affiliation(s)
- Christoph Michael Schwarze
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Str. 4, Marburg, 35037, Germany
| | - Maike Petersen
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Str. 4, Marburg, 35037, Germany
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3
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Jangra N, Kawatra A, Datten B, Gupta S, Gulati P. Recent trends in targeted delivery of smart nanocarrier-based microbial enzymes for therapeutic applications. Drug Discov Today 2024; 29:103915. [PMID: 38340953 DOI: 10.1016/j.drudis.2024.103915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/19/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Smart carrier-based immobilization has widened the use of enzymes for the treatment of several disorders. Large surface areas, tunable morphology, and surface modification ability aid the targeted and controlled release of therapeutic enzymes from such formulations. Smart nanocarriers, such as polymeric carriers, liposomes, and silica have also increased the stability, half-life, and permeability of these enzymes. In this review, summarize recent advances in the smart immobilization of microbial enzymes and their development as precision nanomedicine for the treatment of cancer, thrombosis, phenylketonuria (PKU), and wound healing. We also discuss the challenges and measures to be adopted for the successful clinical translation of these formulations.
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Affiliation(s)
- Nikita Jangra
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Anubhuti Kawatra
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Bharti Datten
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Shefali Gupta
- Department of Industrial Microbiology, Sam Higginbottom University of Agriculture Technology and Sciences (SHUATS), Allahabad, Uttar Pradesh
| | - Pooja Gulati
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India.
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4
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Fan S, Wei X, Lü R, Feng C, Zhang Q, Lü X, Jin Y, Yan M, Yang Z. Roles of the N-terminal motif in improving the activity and soluble expression of phenylalanine ammonia lyases in Escherichia coli. Int J Biol Macromol 2024; 262:130248. [PMID: 38367782 DOI: 10.1016/j.ijbiomac.2024.130248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/19/2024]
Abstract
Phenylalanine ammonia-lyase (PAL) has various applications in fine chemical manufacturing and the pharmaceutical industry. In particular, PAL derived from Anabaena variabilis (AvPAL) is used as a therapeutic agent to the treat phenylketonuria in clinical settings. In this study, we aligned the amino acid sequences of AvPAL and PAL derived from Nostoc punctiforme (NpPAL) to obtain several mutants with enhanced activity, expression yield, and thermal stability via amino acid substitution and saturation mutagenesis at the N-terminal position. Enzyme kinetic experiments revealed that the kcat values of NpPAL-N2K, NpPAL-I3T, and NpPAL-T4L mutants were increased to 3.2-, 2.8-, and 3.3-fold that of the wild-type, respectively. Saturation mutagenesis of the fourth amino acid in AvPAL revealed that the kcat values of AvPAL-L4N, AvPAL-L4P, AvPAL-L4Q and AvPAL-L4S increased to 4.0-, 3.7-, 3.6-, and 3.2-fold, respectively. Additionally, the soluble protein yield of AvPAL-L4K increased to approximately 14 mg/L, which is approximately 3.5-fold that of AvPAL. Molecular dynamics studies further revealed that maintaining the attacking state of the reaction and N-terminal structure increased the rate of catalytic reaction and improved the solubility of proteins. These findings provide new insights for the rational design of PAL in the future.
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Affiliation(s)
- Shuai Fan
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xiyu Wei
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Ruijie Lü
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Cuiyue Feng
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Qian Zhang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xudong Lü
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yuanyuan Jin
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Maocai Yan
- School of Pharmacy, Jining Medical University, Rizhao 276800, Shandong, China.
| | - Zhaoyong Yang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
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Kaur A, Yadav VG, Pawar SV, Sembi JK. Insights to Phenylalanine Ammonia Lyase (PAL) and Secondary Metabolism in Orchids: An in silico Approach. Biochem Genet 2024; 62:413-435. [PMID: 37358673 DOI: 10.1007/s10528-023-10428-3] [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: 11/23/2022] [Accepted: 06/07/2023] [Indexed: 06/27/2023]
Abstract
The phenylalanine ammonia lyase (PAL) catalyses the first step of phenylpropanoid metabolic pathway which leads to the biosynthesis of a diverse group of secondary metabolites. Orchids serve as a rich source of metabolites and the availability of genome or transcriptome for selected orchid species provides an opportunity to analyse the PAL genes in orchids. In the present study, 21 PAL genes were characterized using bioinformatics tools in nine orchid species (Apostasia shenzhenica, Cypripedium formosanum, Dendrobium catenatum, Phalaenopsis aphrodite, Phalaenopsis bellina, Phalaenopsis equestris, Phalaenopsis lueddemanniana, Phalaenopsis modesta and Phalaenopsis schilleriana). Multiple sequence alignment confirmed the presence of PAL-specific conserved domains (N-terminal, MIO, core, shielding and C-terminal domain). All these proteins were predicted to be hydrophobic in nature and to have cytoplasmic localisation. Structural modelling depicted the presence of alpha helices, extended strands, beta turns and random coils in their structure. Ala-Ser-Gly triad known for substrate binding and catalysis of MIO-domain was found to be completely conserved in all the proteins. Phylogenetic study showed that the PALs of pteridophytes, gymnosperms and angiosperms clustered together in separate clades. Expression profiling showed tissue-specific expression for all the 21 PAL genes in the various reproductive and vegetative tissues which suggested their diverse role in growth and development. This study provides insights to the molecular characterization of PAL genes which may help in developing biotechnological strategies to enhance the synthesis of phenylpropanoids in orchids and other heterologous systems for pharmaceutical applications.
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Affiliation(s)
- Arshpreet Kaur
- Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Vikramaditya G Yadav
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, V6T1Z3, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, V6T1Z3, Canada
| | - Sandip V Pawar
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India
| | - Jaspreet K Sembi
- Department of Botany, Panjab University, Chandigarh, 160014, India.
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6
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Albogami A, Naguib DM. Agricultural wastes: a new promising source for phenylalanine ammonia-lyase as anticancer agent. 3 Biotech 2024; 14:22. [PMID: 38156037 PMCID: PMC10751285 DOI: 10.1007/s13205-023-03871-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 11/21/2023] [Indexed: 12/30/2023] Open
Abstract
The present study aims to investigate the physicochemical characteristics of phenylalanine ammonia-lyase (PAL) extracted from agricultural waste and its potential use as an anticancer agent in comparison to microbial PAL. We extracted and partially purified PAL from agricultural waste sources. We assessed the temperature and pH range of PAL and determined enzyme kinetics parameters including Michaelis constants (Km), maximum velocity (Vmax), and specificity constant values (Vmax/Km). Additionally, we examined the effects of different storage temperatures on PAL activity. In our analysis, we compared the efficacy of agricultural waste-derived PAL with PAL from Rhodotorula glutinis. The results demonstrated that PAL extracted from agricultural waste exhibited significantly higher specific activity (Vmax/Km) compared to its microbial counterpart. The agricultural waste-derived PAL displayed a stronger affinity for phenylalanine, as indicated by a lower Km value than the microbial PAL did. Furthermore, PAL from agricultural waste maintained activity across a broader temperature and pH range (15-75 °C, pH 5-11), in contrast to microbial PAL (20-60 °C, pH 5.5-10). Importantly, the PAL derived from agricultural waste exhibited superior stability, retaining over 90% of its activity after 6 months of storage at room temperature (25 °C), whereas microbial PAL lost more than 70% of its activity under similar storage conditions. In anticancer experiments against various cancer cell lines, agricultural waste-derived PAL demonstrated greater anticancer activity compared to microbial PAL. These findings suggest that PAL sourced from agricultural waste has the potential to be a safe and effective natural anticancer agent.
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Affiliation(s)
- Abdulaziz Albogami
- Biology Department, Faculty of Science, Al-Baha University (BU), Alaqiq, Saudi Arabia
| | - Deyala M. Naguib
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
- Biology Department, Faculty of Science and Arts in Al-Mikhwah, Al-Baha University (BU), Al-Mikhwah, Saudi Arabia
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7
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Pavale S, Dalei SK, Sokhal P, Biswas B, Meena K, Adlakha N. Engineering phenylalanine ammonia lyase to limit feedback inhibition by cinnamate and enhance biotransformation. Biotechnol J 2024; 19:e2300275. [PMID: 37861236 DOI: 10.1002/biot.202300275] [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: 06/08/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 10/21/2023]
Abstract
Phenylalanine ammonia-lyase (PAL) is a crucial enzyme for various biotechnology applications, such as producing phenols, antioxidants, and nutraceuticals. However, feedback inhibition from its product, cinnamic acid, limits its forward reaction rate. Therefore, this study aims to address the feedback inhibition in PAL using enzyme engineering strategies. Random and site-directed mutagenesis approaches were utilized to screen mutant enzymes with ameliorated tolerance against cinnamic acid. A thermotolerant and cinnamate-tolerant mutant was rationally identified using a high throughput screening method and subsequent biochemical characterization. We evaluated cinnamate affinity among the seven rationally selected mutations, and the T102E mutation was identified as the most promising mutant. This mutant showed a six-fold reduction in the affinity of PAL for cinnamic acid and a two-fold increase in operational stability compared with native PAL. Furthermore, the enzyme was immobilized on carbon nanotubes to increase its robustness and reusability. The immobilized mutant PAL showed greater efficiency in the deamination of phenylalanine present in protein hydrolysate than its free form. The rationale behind the enhancement of cinnamate tolerance was validated using molecular dynamic simulations. Overall, the knowledge of the sequence-function relationship of PAL was applied to drive enzyme engineering to develop highly tolerant PAL.
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Affiliation(s)
- Siddhi Pavale
- Synthetic Biology and Bioprocessing group, Regional Centre for Biotechnology, NCR-Biotech Cluster, Faridabad, India
| | - Sudipt Kumar Dalei
- Synthetic Biology and Bioprocessing group, Regional Centre for Biotechnology, NCR-Biotech Cluster, Faridabad, India
| | - Preeti Sokhal
- Synthetic Biology and Bioprocessing group, Regional Centre for Biotechnology, NCR-Biotech Cluster, Faridabad, India
| | - Biswambhar Biswas
- Synthetic Biology and Bioprocessing group, Regional Centre for Biotechnology, NCR-Biotech Cluster, Faridabad, India
| | - Kunal Meena
- Synthetic Biology and Bioprocessing group, Regional Centre for Biotechnology, NCR-Biotech Cluster, Faridabad, India
| | - Nidhi Adlakha
- Synthetic Biology and Bioprocessing group, Regional Centre for Biotechnology, NCR-Biotech Cluster, Faridabad, India
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8
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Kim JY, Kang HW. β-Aminobutyric Acid and Powdery Mildew Infection Enhanced the Activation of Defense-Related Genes and Salicylic Acid in Cucumber ( Cucumis sativus L.). Genes (Basel) 2023; 14:2087. [PMID: 38003030 PMCID: PMC10671336 DOI: 10.3390/genes14112087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/01/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Powdery mildew disease, caused by Sphaerotheca fusca, is a major disease affecting cucumbers cultivated in greenhouses. This study was conducted to find defense genes induced by β-aminobutyric acid (BABA) and powdery mildew in cucumber. Disease severities of 25% and 5% were exhibited by the 2000 and 5000 mg/L BABA-treated cucumber, respectively. BABA did not affect the spore germination of the powdery mildew pathogen, showing that BABA is not an antifungal agent against the pathogen. In quantitative real-time PCR analysis, BABA-treated cucumber upregulated the transcriptional levels of the defense genes CsPAL, CsPR3, CsPR1, CsLOX1, CsLOX23, Cs LecRK6.1, CsWRKY20, and Cupi4 in cucumber to maximum levels at 48 h, whereas CsLecRK6.1 reached maximum expression after 24 h, and further, salicylic acid (SA) levels were significantly increased in BABA-treated cucumber plants. In addition, the cucumber infected with powdery mildew underwent a 1.6- to 47.3-fold enhancement in the defense genes PAL, PR3, PR1, Lox1, Lox 23, LecRK6.1, WRKY20, and Cupi4 compared to heathy cucumber. These results suggest that the BABA-induced defense response is associated with SA signaling pathway-dependent systemic acquired resistance (SAR) in cucumber, which is involved in plant resistance mechanisms.
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Affiliation(s)
- Ja-Yoon Kim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea;
| | - Hee-Wan Kang
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea;
- Institute of Genetic Engineering, Hankyong National University, Anseong 17579, Republic of Korea
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Du Z, Qu F, Zhang C, Chen Z, Li Y, Wen L. Multi-Omics Analyses Unravel Metabolic and Transcriptional Differences in Tender Shoots from Two Sechium edule Varieties. Curr Issues Mol Biol 2023; 45:9060-9075. [PMID: 37998745 PMCID: PMC10670898 DOI: 10.3390/cimb45110568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023] Open
Abstract
Chaylte vine, the tender shoot of Sechium edule, is popular among vegetable consumers because of its high nutritional content, crisp texture, and unique flavor. Existing studies on the nutrient composition of chaylte vines are mostly simple chemical determinations, which have limited the breeding of specialized cultivars and the development of related industries. Using metabolomics combined with transcriptomics, this study analyzed the metabolic characteristics and related molecular mechanisms of two common varieties of chaylte vines: green-skinned (SG) and white-skinned (SW). Between the two varieties, a total of 277 differentially accumulated metabolites (DAMs) and 739 differentially expressed genes (DEGs) were identified. Furthermore, chemical assays demonstrated that the SW exhibited a higher total flavonoid content and antioxidant capacity. In conclusion, it was found that the SG samples exhibited a higher diversity of flavonoid subclasses compared to the SW samples, despite having a lower total flavonoid content. This inconsistent finding was likely due to the differential expression of the phenylalanine ammonia-lyase (PAL) and chalcone synthase (CHS) genes in the two varieties. These results laid the foundation for investigating the mechanisms involved in flavonoid regulation and the breeding of specialized S. edule cultivars for chaylte vine production.
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Affiliation(s)
| | | | | | | | - Yurong Li
- Guizhou Horticulture Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550009, China; (Z.D.); (F.Q.); (C.Z.); (Z.C.); (L.W.)
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10
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Zhu BF, Liu Y, Pei XQ, Wu ZL. Characterization of Phenylalanine Ammonia Lyases from Lettuce ( Lactuca sativa L.) as Robust Biocatalysts for the Production of d- and l-Amino Acids. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2935-2942. [PMID: 36734156 DOI: 10.1021/acs.jafc.2c07890] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Phenylalanine ammonia lyase (PAL) catalyzes the reversible conversion of l-phenylalanine into the corresponding trans-cinnamic acid, providing a route to optically pure α-amino acids. We explored the catalytic function of all five PALs encoded in the genome of lettuce (Lactuca sativa L.) that are previously known to be involved in wound browning. All LsPALs were active toward l-phenylalanine in the ammonia elimination reaction and displayed maximum activity at 55-60 °C and pH 9.0-9.5. However, four of them, LsPAL1-LsPAL4, showed significantly higher activity and thermal stability than LsPAL5, as well as a broader substrate spectrum including some challenging substrates with steric demanding or electron-donating substituents. The best one LsPAL3 was subjected to the kinetic resolution of a panel of 21 rac-phenylalanine derivatives, as well as the ammonia addition of 21 cinnamic acid derivatives. It showed excellent enantioselectivity in most cases and significantly better activity than previously described PALs for a number of challenging non-natural substrates, demonstrating its great potential in biocatalysis.
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Affiliation(s)
- Bo-Feng Zhu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu610041, China
- College of Life Sciences, Sichuan University, No. 29 Wangjiang Road, Chengdu610064, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Yan Liu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu610041, China
| | - Xiao-Qiong Pei
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu610041, China
| | - Zhong-Liu Wu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu610041, China
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11
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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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12
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Torab M, Jafari-Sabet M, Najafizadeh P, Sadegipour A, Rahimi-Moghaddam P, Ebrahimi SA. Oral administration of phenylalanine molecularly imprinted polymer (MIP) benefits PKU mouse model. J Inherit Metab Dis 2022; 45:696-709. [PMID: 35527480 DOI: 10.1002/jimd.12513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/11/2022]
Abstract
Phenylketonuria (PKU) is a rare genetic disorder caused by a defect in the metabolism of phenylalanine (Phe). Currently, the most commonly used treatment for PKU is dietary Phe restriction. Problems associated with Phe restricted diets include lack of universal availability, high treatment costs, and reduced adherence to continued treatment with age and finally the development of psychological and neurological problems in a significant proportion of patients despite early start of treatment. One possible approach to decreasing blood Phe level, is inhibition of GI tract absorption of this amino acid. We had previously shown that a Phe selective molecularly imprinted polymer was able to bind Phe in the GI tract and attenuate its plasma concentration. In this work, we used different orally administered Phe selective molecularly imprinted polymer doses in a PKU mouse model to further study the effects of this treatment on biochemical profile and cognitive function in test animals. Treatments started 21 days postnatally. After 3 weeks, brain and plasma amino acid profiles and brain monoaminergic neurotransmitter concentrations were measured. Behavioral profile was also evaluated. Treatment with 2% and 5% Phe selective molecularly imprinted polymer significantly reduced levels of blood Phe in PKU model animals (46% and 48% respectively) meanwhile levels of other amino acids remained unchanged. Brain dopamine concentrations in hippocampus was effectively restored by supplementation of Phe selective molecularly imprinted polymer. Finally, polymer treatment improved locomotor dysfunction in PKU model animals. Our data suggest that the Phe selective molecularly imprinted polymer can be a new candidate for treatment of PKU patients. Take home message: Orally administered Phenylalanine Selective Molecularly Imprinted Polymer is able to inhibit absorption of phenylalanine from the GI tract and may offer a new treatment, in conjunction with dietary restriction, for PKU patients.
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Affiliation(s)
- Mansour Torab
- Department of Pharmacology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Jafari-Sabet
- Department of Pharmacology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Parvaneh Najafizadeh
- Department of Pharmacology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Sadegipour
- Department of Pathology, Oncopathology Research Center, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Soltan A Ebrahimi
- Department of Pharmacology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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Bo S, Ni X, Guo J, Liu Z, Wang X, Sheng Y, Zhang G, Yang J. Carotenoid Biosynthesis: Genome-Wide Profiling, Pathway Identification in Rhodotorula glutinis X-20, and High-Level Production. Front Nutr 2022; 9:918240. [PMID: 35782944 PMCID: PMC9247606 DOI: 10.3389/fnut.2022.918240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/13/2022] [Indexed: 01/04/2023] Open
Abstract
Rhodotorula glutinis, as a member of the family Sporidiobolaceae, is of great value in the field of biotechnology. However, the evolutionary relationship of R. glutinis X-20 with Rhodosporidiobolus, Sporobolomyces, and Rhodotorula are not well understood, and its metabolic pathways such as carotenoid biosynthesis are not well resolved. Here, genome sequencing and comparative genome techniques were employed to improve the understanding of R. glutinis X-20. Phytoene desaturase (crtI) and 15-cis-phytoene synthase/lycopene beta-cyclase (crtYB), key enzymes in carotenoid pathway from R. glutinis X-20 were more efficiently expressed in S. cerevisiae INVSc1 than in S. cerevisiae CEN.PK2-1C. High yielding engineered strains were obtained by using synthetic biology technology constructing carotenoid pathway in S. cerevisiae and optimizing the precursor supply after fed-batch fermentation with palmitic acid supplementation. Genome sequencing analysis and metabolite identification has enhanced the understanding of evolutionary relationships and metabolic pathways in R. glutinis X-20, while heterologous construction of carotenoid pathway has facilitated its industrial application.
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Improved production of antioxidant-phenolic compounds and certain fungal phenolic-associated enzymes under solid-state fermentation of chia seeds with Trichoderma reesei: response surface methodology-based optimization. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2022. [DOI: 10.1007/s11694-022-01447-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
AbstractChia seeds (CS) are becoming increasingly consumed due to their great nutritional and therapeutic properties. In this study, solid-state fermentation (SSF) of CS by Trichoderma reesei was employed to maximize the production of the antioxidant-phenolic compounds and some fungal phenolic-associated enzymes (α-amylase, xylanase, β-glucosidase, polygalacturonase, and phenylalanine ammonia-lyase). The SSF-conditions were statistically optimized using response surface methodology (RSM). In the statistical model, four variables were analyzed at two levels. According to RSM, the adjusted R2 (< 0.9) is reasonably consistent with the predicted R2 (< 0.9), indicating that the statistical model is valid. The optimal conditions for maximum production of both phenolic compounds and fungal phenolic-associated enzymes were found to be 28 °C, pH 7.0, 20% moisture, and 7-day fermentation. The total phenolic content of fermented CS (FCS) increased 23 folds and total antioxidant activity was enhanced by 113- and 150-fold using DPPH and ABTS methods, respectively. Three new phenolics (kaempferol, apigenin, and p-coumaric) were recognized in FCS using HPLC analysis. The activities of all the extracted phenolic-associated enzymes showed strong correlations with the phenolic content of FCS. Against some human-pathogenic bacteria, FCS extract displayed considerably better antibacterial activity than UFCS extract. Finally, the phenolic-rich-FCS can be employed as a dietary supplement as well as an antibacterial agent. Furthermore, T. reesei has produced considerable quantities of industrially valuable enzymes.
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Wang S, Liu Z, Wang X, Liu R, Zou L. Mushrooms Do Produce Flavonoids: Metabolite Profiling and Transcriptome Analysis of Flavonoid Synthesis in the Medicinal Mushroom Sanghuangporus baumii. J Fungi (Basel) 2022; 8:jof8060582. [PMID: 35736065 PMCID: PMC9225156 DOI: 10.3390/jof8060582] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/22/2022] [Accepted: 05/26/2022] [Indexed: 02/04/2023] Open
Abstract
Mushrooms produce a large number of medicinal bioactive metabolites with antioxidant, anticancer, antiaging, and other biological activities. However, whether they produce flavonoids and, if so, how they synthesize them remains a matter of some debate. In the present study, we combined flavonoid-targeted metabolomics and transcriptome analysis to explore the flavonoid synthesis in the medicinal mushroom Sanghuangporus baumii. The S. baumii synthesized 81 flavonoids on a chemically defined medium. The multiple classes of flavonoids present were consistent with the biosynthetic routes in plants. However, paradoxically, most of the genes that encode enzymes involved in the flavonoid biosynthetic pathway are missing from S. baumii. Only four genes related to flavonoid synthesis were found in S. baumii, among which phenylalanine ammonia lyase gene (PAL) is a key gene regulating flavonoid synthesis, and overexpression of SbPAL increases the accumulation of flavonoids. These results suggest that the flavonoid synthesis pathway in S. baumii is different from that in known plants, and the missing genes may be replaced by genes from the same superfamilies but are only distantly related. Thus, this study provides a novel method to produce flavonoids by metabolic engineering using mushrooms.
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Affiliation(s)
| | | | | | | | - Li Zou
- Correspondence: ; Tel.: +86-451-82190384
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Sarı T, Dede S, Yusufoğlu B, Karakuş E. Determination of L-Phenylalanine in Human Plasma Samples with New Fluorometric Method. Appl Biochem Biotechnol 2022; 194:1259-1270. [PMID: 34661869 DOI: 10.1007/s12010-021-03694-7] [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: 05/25/2021] [Accepted: 10/04/2021] [Indexed: 10/20/2022]
Abstract
The measurement of phenylalanine in biological fluids for the diagnosis of phenylketonuria (PKU) in newborns and the monitoring/therapeutic drug monitoring of individuals with PKU are especially important. Owing to the importance of PKU monitoring in clinical medicine, a new fluorometric method was developed for the determination of L-phenylalanine in serum samples. This method is based on the relationship between phenylalanine ammonia-lyase (PAL) and o-phthalaldehyde (OPA). PAL catalyzes the conversion of phenylalanine to ammonia and trans-cinnamic acid. The formed ammonia reacts with OPA in the presence of sodium sulfite, giving a fluorescent product. The presence of sulfide in an alkaline environment prevents OPA from reacting with other amino acids while allowing it to react only with ammonia. Method characterization and optimization studies, such as the effects of pH, temperature, and interferents, were carried out. The amount of L-phenylalanine in a human serum sample was successfully determined by using the fluorescence emission intensity of the fluorescent product formed as a result of the reaction between OPA and ammonia. The linear range of the method is between 10 μM and 10 mM. The obtained result showed good agreement with the results of the biochemistry analysis laboratory. Recoveries of 95.41% and 73.39% were obtained for phenylalanine and ammonia, respectively. This PAL-OPA-based fluorometric method for phenylalanine is practical, easy to operate, low cost, highly sensitive, and selective and can also be used for the simultaneous determination of ammonia in human serum samples.
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Affiliation(s)
- Tolga Sarı
- Department of Chemistry, Faculty of Arts and Sciences, Yildiz Technical University, Davutpaşa Street, Esenler, 34290, Istanbul, Turkey
| | - Süreyya Dede
- Department of Chemistry, Faculty of Arts and Sciences, Yildiz Technical University, Davutpaşa Street, Esenler, 34290, Istanbul, Turkey
| | - Büşra Yusufoğlu
- Department of Chemistry, Faculty of Arts and Sciences, Yildiz Technical University, Davutpaşa Street, Esenler, 34290, Istanbul, Turkey
| | - Emine Karakuş
- Department of Chemistry, Faculty of Arts and Sciences, Yildiz Technical University, Davutpaşa Street, Esenler, 34290, Istanbul, Turkey.
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Phelan RM, Abrahamson MJ, Brown JTC, Zhang RK, Zwick CR. Development of Scalable Processes with Underutilized Biocatalyst Classes. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryan M. Phelan
- Process Research and Development, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Michael J. Abrahamson
- Operations Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Jesse T. C. Brown
- Process Research and Development, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Ruijie K. Zhang
- Discovery Chemistry and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Christian R. Zwick
- Process Research and Development, AbbVie Inc., North Chicago, Illinois 60064, United States
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Microbial arginine deiminase: A multifaceted green catalyst in biomedical sciences. Int J Biol Macromol 2022; 196:151-162. [PMID: 34920062 DOI: 10.1016/j.ijbiomac.2021.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/03/2021] [Accepted: 12/04/2021] [Indexed: 12/18/2022]
Abstract
Arginine deiminase is a well-recognized guanidino-modifying hydrolase that catalyzes the conversion of L-arginine to citrulline and ammonia. Their biopotential to regress tumors via amino acid deprivation therapy (AADT) has been well established. PEGylated formulation of recombinant Mycoplasma ADI is in the last-phase clinical trials against various arginine-auxotrophic cancers like hepatocellular carcinoma, melanoma, and mesothelioma. Recently, ADIs have attained immense importance in several other biomedical applications, namely treatment of Alzheimer's, as an antiviral drug, bioproduction of nutraceutical L-citrulline and bio-analytics involving L-arginine detection. Considering the wide applications of this biodrug, the demand for ADI is expected to escalate several-fold in the coming years. However, the sustainable production aspects of the enzyme with improved pharmacokinetics is still limited, creating bottlenecks for effective biopharmaceutical development. To circumvent the lacunae in enzyme production with appropriate paradigms of 'quality-by-design' an explicit overview of its properties with 'biobetter' formulations strategies are required. Present review provides an insight into all the potential biomedical applications of ADI along with the improvements required for its reach to clinics. Recent research advances with special emphasis on the development of ADI as a 'biobetter' enzyme have also been comprehensively elaborated.
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Genomics and lipidomics analysis of the biotechnologically important oleaginous red yeast Rhodotorula glutinis ZHK provides new insights into its lipid and carotenoid metabolism. BMC Genomics 2020; 21:834. [PMID: 33243144 PMCID: PMC7690147 DOI: 10.1186/s12864-020-07244-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 11/18/2020] [Indexed: 11/26/2022] Open
Abstract
Background Rhodotorula glutinis is recognized as a biotechnologically important oleaginous red yeast, which synthesizes numerous meritorious compounds with wide industrial usages. One of the most notable properties of R. glutinis is the formation of intracellular lipid droplets full of carotenoids. However, the basic genomic features that underlie the biosynthesis of these valuable compounds in R. glutinis have not been fully documented. To reveal the biotechnological potential of R. glutinis, the genomics and lipidomics analysis was performed through the Next-Generation Sequencing and HPLC-MS-based metabolomics technologies. Results Here, we firstly assemble the genome of R. glutinis ZHK into 21.8 Mb, containing 30 scaffolds and 6774 predicted genes with a N50 length of 14, 66,672 bp and GC content of 67.8%. Genome completeness assessment (BUSCO alignment: 95.3%) indicated the genome assembly with a high-quality features. According to the functional annotation of the genome, we predicted several key genes involved in lipids and carotenoids metabolism as well as certain industrial enzymes biosynthesis. Comparative genomics results suggested that most of orthologous genes have underwent the strong purifying selection within the five Rhodotorula species, especially genes responsible for carotenoids biosynthesis. Furthermore, a total of 982 lipids were identified using the lipidomics approaches, mainly including triacylglycerols, diacylglyceryltrimethylhomo-ser and phosphatidylethanolamine. Conclusion Using whole genome shotgun sequencing, we comprehensively analyzed the genome of R. glutinis and predicted several key genes involved in lipids and carotenoids metabolism. By performing comparative genomic analysis, we show that most of the ortholog genes have undergone strong purifying selection within the five Rhodotorula species. Furthermore, we identified 982 lipid species using lipidomic approaches. These results provided valuable resources to further advance biotechnological applications of R .glutinis. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07244-z.
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