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Tomoiaga RB, Ágoston G, Boros K, Nagy LC, Toşa MI, Paizs C, Bencze LC. The Biocatalytic Potential of Aromatic Ammonia-Lyase from Loktanella atrilutea. Chembiochem 2024; 25:e202400011. [PMID: 38415939 DOI: 10.1002/cbic.202400011] [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: 01/04/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 02/29/2024]
Abstract
Characterization of the aromatic ammonia-lyase from Loktanella atrilutea (LaAAL) revealed reduced activity towards canonical AAL substrates: l-Phe, l-Tyr, and l-His, contrasted by its pronounced efficiency towards 3,4-dimethoxy-l-phenylalanine. Assessing the optimal conditions, LaAAL exhibited maximal activity at pH 9.5 in the ammonia elimination reaction route, distinct from the typical pH ranges of most PALs and TALs. Within the exploration of the ammonia source for the opposite, synthetically valuable ammonia addition reaction, the stability of LaAAL exhibited a positive correlation with the ammonia concentration, with the highest stability in 4 M ammonium carbamate of unadjusted pH of ~9.5. While the enzyme activity increased with rising temperatures yet, the highest operational stability and highest stationary conversions of LaAAL were observed at 30 °C. The substrate scope analysis highlighted the catalytic adaptability of LaAAL in the hydroamination of diverse cinnamic acids, especially of meta-substituted and di-/multi-substituted analogues, with structural modelling exposing steric clashes between the substrates' ortho-substituents and catalytic site residues. LaAAL showed a predilection for ammonia elimination, while classifying as a tyrosine ammonia-lyase (TAL) among the natural AAL classes. However, its distinctive attributes, such as genomic context, unique substrate specificity and catalytic fingerprint, suggest a potential natural role beyond those of known AAL classes.
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Affiliation(s)
- R B Tomoiaga
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeş Bolyai University, Arany János Str. 11, RO-400028, Cluj-Napoca, Romania
| | - G Ágoston
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeş Bolyai University, Arany János Str. 11, RO-400028, Cluj-Napoca, Romania
| | - K Boros
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeş Bolyai University, Arany János Str. 11, RO-400028, Cluj-Napoca, Romania
| | - L C Nagy
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeş Bolyai University, Arany János Str. 11, RO-400028, Cluj-Napoca, Romania
| | - M I Toşa
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeş Bolyai University, Arany János Str. 11, RO-400028, Cluj-Napoca, Romania
| | - C Paizs
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeş Bolyai University, Arany János Str. 11, RO-400028, Cluj-Napoca, Romania
| | - L C Bencze
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeş Bolyai University, Arany János Str. 11, RO-400028, Cluj-Napoca, Romania
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2
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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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3
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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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4
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Tomoiagă RB, Tork SD, Filip A, Nagy LC, Bencze LC. Phenylalanine ammonia-lyases: combining protein engineering and natural diversity. Appl Microbiol Biotechnol 2023; 107:1243-1256. [PMID: 36662259 DOI: 10.1007/s00253-023-12374-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: 10/17/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/21/2023]
Abstract
In this study, rational design and saturation mutagenesis efforts for engineering phenylalanine ammonia-lyase from Petroselinum crispum (PcPAL) provided tailored PALs active towards challenging, highly valuable di-substituted substrates, such as the L-DOPA precursor 3,4-dimethoxy-L-phenylalanine or the 3-bromo-4-methoxy-phenylalanine. The rational design approach and saturation mutagenesis strategy unveiled identical PcPAL variants of improved activity, highlighting the limited mutational variety of the substrate specificity-modulator residues, L134, F137, I460 of PcPAL. Due to the restricted catalytic efficiency of the best performing L134A/I460V and F137V/I460V PcPAL variants, we imprinted these beneficial mutations to PALs of different origins. The variants of PALs from Arabidopsis thaliana (AtPAL) and Anabaena variabilis (AvPAL) showed higher catalytic efficiency than their PcPAL homologues. Further, the engineered PALs were also compared in terms of catalytic efficiency with a novel aromatic ammonia-lyase from Loktanella atrilutea (LaAAL), close relative of the metagenome-derived aromatic ammonia-lyase AL-11, reported recently to possess atypically high activity towards substrates with electron-donor aromatic substituents. Indeed, LaAAL outperformed the engineered Pc/At/AvPALs in the production of 3,4-dimethoxy-L-phenylalanine; however, in case of 3-bromo-4-methoxy derivatives it showed no activity, with computational results supporting the occurrence of steric hindrance. Transferring the unique array of selectivity modulator residues from LaAAL to the well-characterized PALs did not enhance their activity towards the targeted substrates. Moreover, applying the rational design strategy valid for these well-characterized PALs to LaAAL decreased its activity. These results suggest that distinct tailoring rationale is required for LaAAL/AL-11-like aromatic ammonia-lyases, which might represent a distinct PAL subclass, with natural reaction and substrate scope modified through evolutionary processes. KEY POINTS: • PAL-activity for challenging substrates generated by protein engineering • Rational/semi-rational protein engineering reveals constrained mutational variability • Engineered PALs are outperformed by novel ALs of distinct catalytic site signature.
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Affiliation(s)
- Raluca Bianca Tomoiagă
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Street 11, 400028, Cluj-Napoca, Romania
| | - Souad Diana Tork
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Street 11, 400028, Cluj-Napoca, Romania
| | - Alina Filip
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Street 11, 400028, Cluj-Napoca, Romania
| | - Levente Csaba Nagy
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Street 11, 400028, Cluj-Napoca, Romania
| | - László Csaba Bencze
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Street 11, 400028, Cluj-Napoca, Romania.
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5
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Tork SD, Nagy EZA, Tomoiagă RB, Bencze LC. Engineered, Scalable Production of Optically Pure l-Phenylalanines Using Phenylalanine Ammonia-Lyase from Arabidopsis thaliana. J Org Chem 2023; 88:852-862. [PMID: 36583610 DOI: 10.1021/acs.joc.2c02106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An efficient preparative-scale synthetic procedure of l-phenylalanine derivatives has been developed using mutant variants of phenylalanine ammonia-lyase from Arabidopsis thaliana (AtPAL). After rigorous reaction engineering, the AtPAL-catalyzed hydroamination reaction of cinnamic acids provided several unnatural amino acids of high synthetic value, such as (S)-m- and (S)-p-methoxyphenylalanine; (S)-o- and (S)-m-methylphenylalanine; and (S)-o- and (S)-p-bromophenylalanine at preparative scale, significantly surpassing the catalytic efficiency in terms of conversions and yields of the previously reported PcPAL-based biotransformations. The AtPAL variants tolerated high substrate and product concentrations, representing an important extension of the PAL-toolbox, while the engineered biocatalytic procedures of improved E-factor and space-time yields fulfill the requirements of sustainable and green chemistry, providing facile access to valuable amino acid building blocks.
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Affiliation(s)
- Souad Diana Tork
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babes̨-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
| | - Emma Zsófia Aletta Nagy
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babes̨-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
| | - Raluca Bianca Tomoiagă
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babes̨-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
| | - László Csaba Bencze
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babes̨-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
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6
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Cho S, Yang X, Won KJ, Leone VA, Chang EB, Guzman G, Ko Y, Bae ON, Lee H, Jeong H. Phenylpropionic acid produced by gut microbiota alleviates acetaminophen-induced hepatotoxicity. Gut Microbes 2023; 15:2231590. [PMID: 37431867 PMCID: PMC10337503 DOI: 10.1080/19490976.2023.2231590] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 06/13/2023] [Accepted: 06/27/2023] [Indexed: 07/12/2023] Open
Abstract
The gut microbiota affects hepatic drug metabolism. However, gut microbial factors modulating hepatic drug metabolism are largely unknown. In this study, using a mouse model of acetaminophen (APAP)-induced hepatotoxicity, we identified a gut bacterial metabolite that controls the hepatic expression of CYP2E1 that catalyzes the conversion of APAP to a reactive, toxic metabolite. By comparing C57BL/6 substrain mice from two different vendors, Jackson (6J) and Taconic (6N), which are genetically similar but harbor different gut microbiotas, we established that the differences in the gut microbiotas result in differential susceptibility to APAP-induced hepatotoxicity. 6J mice exhibited lower susceptibility to APAP-induced hepatotoxicity than 6N mice, and such phenotypic difference was recapitulated in germ-free mice by microbiota transplantation. Comparative untargeted metabolomic analysis of portal vein sera and liver tissues between conventional and conventionalized 6J and 6N mice led to the identification of phenylpropionic acid (PPA), the levels of which were higher in 6J mice. PPA supplementation alleviated APAP-induced hepatotoxicity in 6N mice by lowering hepatic CYP2E1 levels. Moreover, PPA supplementation also reduced carbon tetrachloride-induced liver injury mediated by CYP2E1. Our data showed that previously known PPA biosynthetic pathway is responsible for PPA production. Surprisingly, while PPA in 6N mouse cecum contents is almost undetectable, 6N cecal microbiota produces PPA as well as 6J cecal microbiota in vitro, suggesting that PPA production in the 6N gut microbiota is suppressed in vivo. However, previously known gut bacteria harboring the PPA biosynthetic pathway were not detected in either 6J or 6N microbiota, suggesting the presence of as-yet-unidentified PPA-producing gut microbes. Collectively, our study reveals a novel biological function of the gut bacterial metabolite PPA in the gut-liver axis and presents a critical basis for investigating PPA as a modulator of CYP2E1-mediated liver injury and metabolic diseases.
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Affiliation(s)
- Sungjoon Cho
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Xiaotong Yang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Kyoung-Jae Won
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Vanessa A Leone
- Department of Animal & Dairy Sciences, College of Agriculture & Life Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Eugene B Chang
- Section of Gastroenterology, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, IL, USA
| | - Grace Guzman
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Yeonju Ko
- College of Pharmacy, Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan, Republic of Korea
| | - Ok-Nam Bae
- College of Pharmacy, Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan, Republic of Korea
| | - Hyunwoo Lee
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, IN, USA
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
| | - Hyunyoung Jeong
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, IN, USA
- Department of Pharmacy Practice, College of Pharmacy, Purdue University, West Lafayette, IN, USA
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7
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Citric Acid Changes the Fingerprint of Flavonoids and Promotes Their Accumulation in Phellinus igniarius (L.) Quél. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010068. [PMID: 36676017 PMCID: PMC9861953 DOI: 10.3390/life13010068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022]
Abstract
Phellinus igniarius is a valuable medicinal fungus. P. igniarius is rich in a variety of chemical compounds with medicinal value, among which are flavonoids. Therefore, increasing the content of flavonoids in P. igniarius is beneficial for its potential use in medicinal applications. This study demonstrated that exogenous treatment with citric acid (CA) could significantly increase flavonoid accumulation in P. igniarius. Additionally, we found that CA induced the biosynthesis of flavonoids in a concentration- and time-dependent manner. The flavonoid content could be increased up to 60.96 mg/g when using the treatment with 2.77 mM citric acid for 69.74 h, which was determined by using the response surface method. The changes in the fingerprint profiles of P. igniarius flavonoids with the treatment of CA as an exogenous inducer were also analyzed. In this study, the effect of citric acid as the exogenous inducer on the flavonoid content of P. igniarius was studied, and the processing conditions were optimized through the surface response curve. This approach provides novel insights and a theoretical basis for the production of high-quality P. igniarius.
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8
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Towards a general approach for tailoring the hydrophobic binding site of phenylalanine ammonia-lyases. Sci Rep 2022; 12:10606. [PMID: 35739148 PMCID: PMC9226071 DOI: 10.1038/s41598-022-14585-0] [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: 03/24/2022] [Accepted: 06/09/2022] [Indexed: 11/23/2022] Open
Abstract
Unnatural substituted amino acids play an important role as chiral building blocks, especially for pharmaceutical industry, where the synthesis of chiral biologically active molecules still represents an open challenge. Recently, modification of the hydrophobic binding pocket of phenylalanine ammonia-lyase from Petroselinum crispum (PcPAL) resulted in specifically tailored PcPAL variants, contributing to a rational design template for PAL-activity enhancements towards the differently substituted substrate analogues. Within this study we tested the general applicability of this rational design model in case of PALs, of different sources, such as from Arabidopsis thaliana (AtPAL) and Rhodosporidium toruloides (RtPAL). With some exceptions, the results support that the positions of substrate specificity modulating residues are conserved among PALs, thus the mutation with beneficial effect for PAL-activity enhancement can be predicted using the established rational design model. Accordingly, the study supports that tailoring PALs of different origins and different substrate scope, can be performed through a general method. Moreover, the fact that AtPAL variants I461V, L133A and L257V, all outperformed in terms of catalytic efficiency the corresponding, previously reported, highly efficient PcPAL variants, of identical catalytic site, suggests that not only catalytic site differences influence the PAL-activity, thus for the selection of the optimal PAL-biocatalysts for a targeted process, screening of PALs from different origins, should be included.
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Trivedi VD, Chappell TC, Krishna NB, Shetty A, Sigamani GG, Mohan K, Ramesh A, R PK, Nair NU. In-Depth Sequence–Function Characterization Reveals Multiple Pathways to Enhance Enzymatic Activity. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05508] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Vikas D. Trivedi
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Todd C. Chappell
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | | | - Anuj Shetty
- Kcat Enzymatic Private Limited, Bengaluru, Karnataka, India 560005
| | | | - Karishma Mohan
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Athreya Ramesh
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Pravin Kumar R
- Kcat Enzymatic Private Limited, Bengaluru, Karnataka, India 560005
| | - Nikhil U. Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
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10
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Menon N, Richmond D, Rahman MR, Menon BRK. Versatile and Facile One-Pot Biosynthesis for Amides and Carboxylic Acids in E. coli by Engineering Auxin Pathways of Plant Microbiomes. ACS Catal 2022. [DOI: 10.1021/acscatal.1c04901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Navya Menon
- The Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry CV4 7AL, U.K
- Collaborative Teaching Laboratory, The University of Birmingham, Birmingham B15 2TT, U.K
| | - Daniel Richmond
- The Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry CV4 7AL, U.K
| | - Mohammad Rejaur Rahman
- The Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry CV4 7AL, U.K
| | - Binuraj R. K. Menon
- The Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry CV4 7AL, U.K
- School of Biological Sciences, The University of Portsmouth, Portsmouth PO1 2DY, U.K
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11
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Boros K, Moisă ME, Nagy CL, Paizs C, Toşa MI, Bencze LC. Robust, site-specifically immobilized phenylalanine ammonia-lyases for the enantioselective ammonia addition of cinnamic acids. Catal Sci Technol 2021; 11:5553-5563. [PMID: 34745555 PMCID: PMC8504149 DOI: 10.1039/d1cy00195g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/28/2021] [Indexed: 01/16/2023]
Abstract
Phenylalanine ammonia-lyases (PALs) catalyse the non-oxidative deamination of l-phenylalanine to trans-cinnamic acid, while in the presence of high ammonia concentration, the synthetically attractive reverse reaction occurs. Although they have been intensively studied, the wider application of PALs for the large scale synthesis of non-natural amino acids is still rather limited, mainly due to the decreased operational stability of PALs under the high ammonia concentration conditions of ammonia addition. Herein, we describe the development of a highly stable and active immobilized PAL-biocatalyst obtained through site-specific covalent immobilization onto single-walled carbon nanotubes (SWCNTs), employing maleimide/thiol coupling of engineered enzymes containing surficial Cys residues. The immobilization method afforded robust biocatalysts (by strong covalent attachment to the support) and allowed modulation of enzymatic activity (by proper selection of binding site, controlling the orientation of the enzyme attached to the support). The novel biocatalysts were investigated in PAL-catalyzed reactions, focusing on the synthetically challenging ammonia addition reaction. The optimization of the immobilization (enzyme load) and reaction conditions (substrate : biocatalyst ratio, ammonia source, reaction temperature) involving the best performing biocatalyst SWCNTNH2 -SS-PcPAL was performed. The biocatalyst, under the optimal reaction conditions, showed high catalytic efficiency, providing excellent conversion (c ∼90% in 10 h) of cinnamic acid into l-Phe, and more importantly, possesses high operational stability, maintaining its high efficiency over >7 reaction cycles. Moreover, the site-specifically immobilized PcPAL L134A/S614C and PcPAL I460V/S614C variants were successfully applied in the synthesis of several l-phenylalanine analogues of high synthetic value, providing perspectives for the efficient replacement of classical synthetic methods for l-phenylalanines with a mild, selective and eco-friendly enzymatic alternative.
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Affiliation(s)
- Krisztina Boros
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University Arany János Str. 11 RO-400028 Cluj-Napoca Romania
| | - Mădălina Elena Moisă
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University Arany János Str. 11 RO-400028 Cluj-Napoca Romania
| | - Csaba Levente Nagy
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University Arany János Str. 11 RO-400028 Cluj-Napoca Romania
| | - Csaba Paizs
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University Arany János Str. 11 RO-400028 Cluj-Napoca Romania
| | - Monica Ioana Toşa
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University Arany János Str. 11 RO-400028 Cluj-Napoca Romania
| | - László Csaba Bencze
- Enzymology and Applied Biocatalysis Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University Arany János Str. 11 RO-400028 Cluj-Napoca Romania
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12
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Kempa EE, Galman JL, Parmeggiani F, Marshall JR, Malassis J, Fontenelle CQ, Vendeville JB, Linclau B, Charnock SJ, Flitsch SL, Turner NJ, Barran PE. Rapid Screening of Diverse Biotransformations for Enzyme Evolution. JACS AU 2021; 1:508-516. [PMID: 34056634 PMCID: PMC8154213 DOI: 10.1021/jacsau.1c00027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Indexed: 06/12/2023]
Abstract
The lack of label-free high-throughput screening technologies presents a major bottleneck in the identification of active and selective biocatalysts, with the number of variants often exceeding the capacity of traditional analytical platforms to assess their activity in a practical time scale. Here, we show the application of direct infusion of biotransformations to the mass spectrometer (DiBT-MS) screening to a variety of enzymes, in different formats, achieving sample throughputs equivalent to ∼40 s per sample. The heat map output allows rapid selection of active enzymes within 96-well plates facilitating identification of industrially relevant biocatalysts. This DiBT-MS screening workflow has been applied to the directed evolution of a phenylalanine ammonia lyase (PAL) as a case study, enhancing its activity toward electron-rich cinnamic acid derivatives which are relevant to lignocellulosic biomass degradation. Additional benefits of the screening platform include the discovery of biocatalysts (kinases, imine reductases) with novel activities and the incorporation of ion mobility technology for the identification of product hits with increased confidence.
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Affiliation(s)
- Emily E Kempa
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - James L Galman
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Fabio Parmeggiani
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Via Mancinelli 7, 20131 Milano, Italy
| | - James R Marshall
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Julien Malassis
- School of Chemistry, University of Southampton, Highfield, SO17 1BJ Southampton, United Kingdom
| | - Clement Q Fontenelle
- School of Chemistry, University of Southampton, Highfield, SO17 1BJ Southampton, United Kingdom
| | | | - Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, SO17 1BJ Southampton, United Kingdom
| | - Simon J Charnock
- Prozomix Ltd., Building 4, West End Ind. Estate, Haltwhistle, Northumberland NE49 9HA, United Kingdom
| | - Sabine L Flitsch
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nicholas J Turner
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita E Barran
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
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Bata Z, Molnár Z, Madaras E, Molnár B, Sánta-Bell E, Varga A, Leveles I, Qian R, Hammerschmidt F, Paizs C, Vértessy BG, Poppe L. Substrate Tunnel Engineering Aided by X-ray Crystallography and Functional Dynamics Swaps the Function of MIO-Enzymes. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00266] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zsófia Bata
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Zsófia Molnár
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Erzsébet Madaras
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Bence Molnár
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Evelin Sánta-Bell
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Andrea Varga
- Biocatalysis and Biotransformation Research Centre, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Str. 11, RO-400028 Cluj-Napoca, Romania
| | - Ibolya Leveles
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Renzhe Qian
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, A-1090 Vienna, Austria
| | - Friedrich Hammerschmidt
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, A-1090 Vienna, Austria
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research Centre, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Str. 11, RO-400028 Cluj-Napoca, Romania
| | - Beáta G. Vértessy
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - László Poppe
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Biocatalysis and Biotransformation Research Centre, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Str. 11, RO-400028 Cluj-Napoca, Romania
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Zhang F, Ren J, Zhan J. Identification and Characterization of an Efficient Phenylalanine Ammonia-Lyase from Photorhabdus luminescens. Appl Biochem Biotechnol 2021; 193:1099-1115. [PMID: 33411135 DOI: 10.1007/s12010-020-03477-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/30/2020] [Indexed: 01/06/2023]
Abstract
A putative aromatic amino acid ammonia-lyase gene (named Pl-pal) was discovered in Photorhabdus luminescens DSM 3368. BLAST and phylogenetic analyses predicted that this enzyme is a histidine ammonia-lyase, whereas sequence alignment suggested that it is more likely a phenylalanine ammonia-lyase (PAL). This gene was amplified from P. luminescens and expressed in Escherichia coli BL21(DE3). The function of Pl-PAL (58 kDa) was characterized by in vitro enzymatic reactions with L-phenylalanine (L-Phe), L-tyrosine (L-Tyr), L-histidine (L-His), and L-tryptophan (L-Trp). Pl-PAL can convert L-Phe and L-Tyr to trans-cinnamic acid and p-coumaric acid, respectively, but had no function on L-His and L-Trp. The optimum temperature and pH were determined to be 40 °C and 11.0, respectively. Under the optimal conditions, Pl-PAL had a kcat/Km value of 0.52 s-1 mM-1 with L-Phe as the substrate, while only 0.013 s-1 mM-1 for L-Tyr. Therefore, the primary function of Pl-PAL was determined to be PAL. The Pl-pal-harboring E. coli strain was used as a whole-cell biocatalyst to produce trans-cinnamic acid from L-Phe. The overall molar conversion rate and productivity were 65.98% and 228.10 mg L-1 h-1, respectively, after the cells were repeatedly utilized 7 times. This work thus provides a promising strain for industrial production of trans-cinnamic acid.
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Affiliation(s)
- Fang Zhang
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, 84322, USA.,College of Life Science and Chemistry, Faculty of Environment and Life, Beijing University of Technology, 100 Pingleyuan, Chaoyang District, Beijing, 100124, China
| | - Jie Ren
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, 84322, USA
| | - Jixun Zhan
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, 84322, USA.
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15
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Moisă ME, Amariei DA, Nagy EZA, Szarvas N, Toșa MI, Paizs C, Bencze LC. Fluorescent enzyme-coupled activity assay for phenylalanine ammonia-lyases. Sci Rep 2020; 10:18418. [PMID: 33116226 PMCID: PMC7595223 DOI: 10.1038/s41598-020-75474-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/07/2020] [Indexed: 11/30/2022] Open
Abstract
Phenylalanine ammonia-lyases (PALs) catalyse the non-oxidative deamination of l-phenylalanine to trans-cinnamic acid, while in the presence of high ammonia concentration the reverse reaction occurs. PALs have been intensively studied, however, their industrial applications for amino acids synthesis remained limited, mainly due to their decreased operational stability or limited substrate specificity. The application of extensive directed evolution procedures to improve their stability, activity or selectivity, is hindered by the lack of reliable activity assays allowing facile screening of PAL-activity within large-sized mutant libraries. Herein, we describe the development of an enzyme-coupled fluorescent assay applicable for PAL-activity screens at whole cell level, involving decarboxylation of trans-cinnamic acid (the product of the PAL reaction) by ferulic acid decarboxylase (FDC1) and a photochemical reaction of the produced styrene with a diaryltetrazole, that generates a detectable, fluorescent pyrazoline product. The general applicability of the fluorescent assay for PALs of different origin, as well as its versatility for the detection of tyrosine ammonia-lyase (TAL) activity have been also demonstrated. Accordingly, the developed procedure provides a facile tool for the efficient activity screens of large mutant libraries of PALs in presence of non-natural substrates of interest, being essential for the substrate-specificity modifications/tailoring of PALs through directed evolution-based protein engineering.
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Affiliation(s)
- Mădălina E Moisă
- Biocatalysis and Biotransformations Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Str. 11, 400028, Cluj-Napoca, Romania
| | - Diana A Amariei
- Biocatalysis and Biotransformations Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Str. 11, 400028, Cluj-Napoca, Romania
| | - Emma Z A Nagy
- Biocatalysis and Biotransformations Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Str. 11, 400028, Cluj-Napoca, Romania
| | - Nóra Szarvas
- Biocatalysis and Biotransformations Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Str. 11, 400028, Cluj-Napoca, Romania
| | - Monica I Toșa
- Biocatalysis and Biotransformations Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Str. 11, 400028, Cluj-Napoca, Romania
| | - Csaba Paizs
- Biocatalysis and Biotransformations Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Str. 11, 400028, Cluj-Napoca, Romania
| | - László C Bencze
- Biocatalysis and Biotransformations Research Center, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Arany János Str. 11, 400028, Cluj-Napoca, Romania.
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16
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Biomedical applications of microbial phenylalanine ammonia lyase: Current status and future prospects. Biochimie 2020; 177:142-152. [PMID: 32828824 DOI: 10.1016/j.biochi.2020.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/01/2020] [Accepted: 08/18/2020] [Indexed: 12/18/2022]
Abstract
Phenylalanine ammonia lyase (PAL) has recently emerged as an important therapeutic enzyme with several biomedical applications. The enzyme catabolizes l-phenylalanine to trans-cinnamate and ammonia. PAL is widely distributed in higher plants, some algae, ferns, and microorganisms, but absent in animals. Although microbial PAL has been extensively exploited in the past for producing industrially important metabolites, its high substrate specificity and catalytic efficacy lately spurred interest in its biomedical applications. PEG-PAL drug named Palynziq™, isolated from Anabaena variabilis has been recently approved for the treatment of adult phenylketonuria (PKU) patients. Further, it has exhibited high potency in regressing tumors and treating tyrosine related metabolic abnormalities like tyrosinemia. Several therapeutically valuable metabolites have been biosynthesized via its catalytic action including dietary supplements, antimicrobial peptides, aspartame, amino-acids, and their derivatives. This review focuses on all the prospective biomedical applications of PAL. It also provides an overview of the structure, production parameters, and various strategies to improve the therapeutic potential of this enzyme. Engineered PAL with improved pharmacodynamic and pharmacokinetic properties will further establish this enzyme as a highly efficient biological drug.
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Arafa AM, Abdel-Ghany AE, El-Dahmy SI, Abdelaziz S, El-Ayouty Y, El-Sayed ASA. Purification and Characterization of Anabaena flos-aquae Phenylalanine Ammonia-Lyase as a Novel Approach for Myristicin Biotransformation. J Microbiol Biotechnol 2020; 30:622-632. [PMID: 31581382 PMCID: PMC9728195 DOI: 10.4014/jmb.1908.08009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Phenylalanine ammonia-lyase (PAL) catalyzes the reversible deamination of phenylalanine to cinnamic acid and ammonia. Algae have been considered as biofactories for PAL production, however, biochemical characterization of PAL and its potency for myristicin biotransformation into MMDA (3-methoxy-4, 5-methylenedioxyamphetamine) has not been studied yet. Thus, PAL from Anabaena flos-aquae and Spirulina platensis has been purified, comparatively characterized and its affinity to transform myristicin was assessed. The specific activity of purified PAL from S. platensis (73.9 μmol/mg/min) and A. flos-aquae (30.5 μmol/mg/min) was increased by about 2.9 and 2.4 folds by gel-filtration comparing to their corresponding crude enzymes. Under denaturing-PAGE, a single proteineous band with a molecular mass of 64 kDa appeared for A. flos-aquae and S. platensis PAL. The biochemical properties of the purified PAL from both algal isolates were determined comparatively. The optimum temperature of S. platensis and A. flos-aquae PAL for forward or reverse activity was reported at 30°C, while the optimum pH for PAL enzyme isolated from A. flos-aquae was 8.9 for forward and reverse activities, and S. platensis PAL had maximum activities at pH 8.9 and 8 for forward and reverse reactions, respectively. Luckily, the purified PALs have the affinity to hydroaminate the myristicin to MMDA successfully in one step. Furthermore, a successful method for synthesis of MMDA from myristicin in two steps was also established. Gas chromatography-mass spectrometry (GC-MS) analysis was conducted to track the product formation.
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Affiliation(s)
- Asmaa M. Arafa
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Afaf E. Abdel-Ghany
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Samih I. El-Dahmy
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Sahar Abdelaziz
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Yassin El-Ayouty
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt
| | - Ashraf S. A. El-Sayed
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt,Corresponding author Phone: +2-01024686495 E-mail:
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18
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The production of L- and D-phenylalanines using engineered phenylalanine ammonia lyases from Petroselinum crispum. Sci Rep 2019; 9:20123. [PMID: 31882791 PMCID: PMC6934771 DOI: 10.1038/s41598-019-56554-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/12/2019] [Indexed: 12/17/2022] Open
Abstract
The biocatalytic synthesis of l- and d-phenylalanine analogues of high synthetic value have been developed using as biocatalysts mutant variants of phenylalanine ammonia lyase from Petroselinum crispum (PcPAL), specifically tailored towards mono-substituted phenylalanine and cinnamic acid substrates. The catalytic performance of the engineered PcPAL variants was optimized within the ammonia elimination and ammonia addition reactions, focusing on the effect of substrate concentration, biocatalyst:substrate ratio, reaction buffer and reaction time, on the conversion and enantiomeric excess values. The optimal conditions provided an efficient preparative scale biocatalytic procedure of valuable phenylalanines, such as (S)-m-methoxyphenylalanine (Y = 40%, ee > 99%), (S)-p-bromophenylalanine (Y = 82%, ee > 99%), (S)-m-(trifluoromethyl)phenylalanine (Y = 26%, ee > 99%), (R)-p-methylphenylalanine, (Y = 49%, ee = 95%) and (R)-m-(trifluoromethyl)phenylalanine (Y = 34%, ee = 93%).
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Khan MR, Adam V, Rizvi TF, Zhang B, Ahamad F, Jośko I, Zhu Y, Yang M, Mao C. Nanoparticle-Plant Interactions: Two-Way Traffic. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1901794. [PMID: 31318142 PMCID: PMC6800249 DOI: 10.1002/smll.201901794] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/24/2019] [Indexed: 05/03/2023]
Abstract
In this Review, an effort is made to discuss the most recent progress and future trend in the two-way traffic of the interactions between plants and nanoparticles (NPs). One way is the use of plants to synthesize NPs in an environmentally benign manner with a focus on the mechanism and optimization of the synthesis. Another way is the effects of synthetic NPs on plant fate with a focus on the transport mechanisms of NPs within plants as well as NP-mediated seed germination and plant development. When NPs are in soil, they can be adsorbed at the root surface, followed by their uptake and inter/intracellular movement in the plant tissues. NPs may also be taken up by foliage under aerial deposition, largely through stomata, trichomes, and cuticles, but the exact mode of NP entry into plants is not well documented. The NP-plant interactions may lead to inhibitory or stimulatory effects on seed germination and plant development, depending on NP compositions, concentrations, and plant species. In numerous cases, radiation-absorbing efficiency, CO2 assimilation capacity, and delay of chloroplast aging have been reported in the plant response to NP treatments, although the mechanisms involved in these processes remain to be studied.
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Affiliation(s)
- Mujeebur Rahman Khan
- Department of Plant Protection, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Tanveer Fatima Rizvi
- Department of Plant Protection, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, U.S.A
| | - Faheem Ahamad
- Department of Plant Protection, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Izabela Jośko
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences, Akademicka 12, 20-033 Lublin, Poland
| | - Ye Zhu
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, Institute for Biomedical Science, Engineering and Technology, University of Oklahoma, Norman, OK 73019, U.S.A
| | - Mingying Yang
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Chuanbin Mao
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, Institute for Biomedical Science, Engineering and Technology, University of Oklahoma, Norman, OK 73019, U.S.A
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20
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Nagy EZA, Tork SD, Lang PA, Filip A, Irimie FD, Poppe L, Toşa MI, Schofield CJ, Brem J, Paizs C, Bencze LC. Mapping the Hydrophobic Substrate Binding Site of Phenylalanine Ammonia-Lyase from Petroselinum crispum. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02108] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Emma Z. A. Nagy
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
| | - Souad D. Tork
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
| | - Pauline A. Lang
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Alina Filip
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
| | - Florin D. Irimie
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
| | - László Poppe
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Monica I. Toşa
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
| | - Christopher J. Schofield
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jürgen Brem
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
| | - László C. Bencze
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Street 11, RO-400028 Cluj-Napoca, Romania
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Maurer A, Leisinger F, Lim D, Seebeck FP. Structure and Mechanism of Ergothionase fromTreponema denticola. Chemistry 2019; 25:10298-10303. [DOI: 10.1002/chem.201901866] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/21/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Alice Maurer
- Department for ChemistryUniversity of Basel Mattenstrasse 24a Basel 4002 Switzerland
| | - Florian Leisinger
- Department for ChemistryUniversity of Basel Mattenstrasse 24a Basel 4002 Switzerland
| | - David Lim
- Department for ChemistryUniversity of Basel Mattenstrasse 24a Basel 4002 Switzerland
| | - Florian P. Seebeck
- Department for ChemistryUniversity of Basel Mattenstrasse 24a Basel 4002 Switzerland
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22
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Hernández-Chávez G, Martinez A, Gosset G. Metabolic engineering strategies for caffeic acid production in Escherichia coli. ELECTRON J BIOTECHN 2019. [DOI: 10.1016/j.ejbt.2018.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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23
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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: 20] [Impact Index Per Article: 3.3] [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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Devine PN, Howard RM, Kumar R, Thompson MP, Truppo MD, Turner NJ. Extending the application of biocatalysis to meet the challenges of drug development. Nat Rev Chem 2018. [DOI: 10.1038/s41570-018-0055-1] [Citation(s) in RCA: 191] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Filip A, Nagy EZA, Tork SD, Bánóczi G, Toşa MI, Irimie FD, Poppe L, Paizs C, Bencze LC. Tailored Mutants of Phenylalanine Ammonia-Lyase from Petroselinum crispum for the Synthesis of Bulky l- and d-Arylalanines. ChemCatChem 2018; 10:2627-2633. [PMID: 30069247 PMCID: PMC6055856 DOI: 10.1002/cctc.201800258] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/10/2018] [Indexed: 12/12/2022]
Abstract
Tailored mutants of phenylalanine ammonia-lyase from Petroselinum crispum (PcPAL) were created and tested in ammonia elimination from various sterically demanding, non-natural analogues of phenylalanine and in ammonia addition reactions into the corresponding (E)-arylacrylates. The wild-type PcPAL was inert or exhibited quite poor conversions in both reactions with all members of the substrate panel. Appropriate single mutations of residue F137 and the highly conserved residue I460 resulted in PcPAL variants that were active in ammonia elimination but still had a poor activity in ammonia addition onto bulky substrates. However, combined mutations that involve I460 besides the well-studied F137 led to mutants that exhibited activity in ammonia addition as well. The synergistic multiple mutations resulted in substantial substrate scope extension of PcPAL and opened up new biocatalytic routes for the synthesis of both enantiomers of valuable phenylalanine analogues, such as (4-methoxyphenyl)-, (napthalen-2-yl)-, ([1,1'-biphenyl]-4-yl)-, (4'-fluoro-[1,1'-biphenyl]-4-yl)-, and (5-phenylthiophene-2-yl)alanines.
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Affiliation(s)
- Alina Filip
- Biocatalysis and Biotransformation Research CentreFaculty of Chemistry and Chemical EngineeringBabeş-Bolyai University of Cluj-NapocaArany János Str. 11400028Cluj-NapocaRomania
| | - Emma Z. A. Nagy
- Biocatalysis and Biotransformation Research CentreFaculty of Chemistry and Chemical EngineeringBabeş-Bolyai University of Cluj-NapocaArany János Str. 11400028Cluj-NapocaRomania
| | - Souad D. Tork
- Biocatalysis and Biotransformation Research CentreFaculty of Chemistry and Chemical EngineeringBabeş-Bolyai University of Cluj-NapocaArany János Str. 11400028Cluj-NapocaRomania
| | - Gergely Bánóczi
- Biocatalysis and Biotransformation Research CentreFaculty of Chemistry and Chemical EngineeringBabeş-Bolyai University of Cluj-NapocaArany János Str. 11400028Cluj-NapocaRomania
| | - Monica I. Toşa
- Biocatalysis and Biotransformation Research CentreFaculty of Chemistry and Chemical EngineeringBabeş-Bolyai University of Cluj-NapocaArany János Str. 11400028Cluj-NapocaRomania
| | - Florin D. Irimie
- Biocatalysis and Biotransformation Research CentreFaculty of Chemistry and Chemical EngineeringBabeş-Bolyai University of Cluj-NapocaArany János Str. 11400028Cluj-NapocaRomania
| | - László Poppe
- Biocatalysis and Biotransformation Research CentreFaculty of Chemistry and Chemical EngineeringBabeş-Bolyai University of Cluj-NapocaArany János Str. 11400028Cluj-NapocaRomania
- Department of Organic Chemistry and TechnologyBudapest University of Technology and EconomicsMűegyetem rkp. 31111BudapestHungary
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research CentreFaculty of Chemistry and Chemical EngineeringBabeş-Bolyai University of Cluj-NapocaArany János Str. 11400028Cluj-NapocaRomania
| | - László C. Bencze
- Biocatalysis and Biotransformation Research CentreFaculty of Chemistry and Chemical EngineeringBabeş-Bolyai University of Cluj-NapocaArany János Str. 11400028Cluj-NapocaRomania
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Ahmed ST, Parmeggiani F, Weise NJ, Flitsch SL, Turner NJ. Engineered Ammonia Lyases for the Production of Challenging Electron-Rich l-Phenylalanines. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00496] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Syed T. Ahmed
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Fabio Parmeggiani
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Weise
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Sabine L. Flitsch
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Turner
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
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