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Xie X, Lin M, Xiao G, Liu H, Wang F, Liu D, Ma L, Wang Q, Li Z. Phenolic amides (avenanthramides) in oats - an update review. Bioengineered 2024; 15:2305029. [PMID: 38258524 PMCID: PMC10807472 DOI: 10.1080/21655979.2024.2305029] [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: 10/28/2023] [Accepted: 01/07/2024] [Indexed: 01/24/2024] Open
Abstract
Oats (Avena sativa L.) are one of the worldwide cereal crops. Avenanthramides (AVNs), the unique plant alkaloids of secondary metabolites found in oats, are nutritionally important for humans and animals. Numerous bioactivities of AVNs have been investigated and demonstrated in vivo and in vitro. Despite all these, researchers from all over the world are taking efforts to learn more knowledge about AVNs. In this work, we highlighted the recent updated findings that have increased our understanding of AVNs bioactivity, distribution, and especially the AVNs biosynthesis. Since the limits content of AVNs in oats strictly hinders the demand, understanding the mechanisms underlying AVN biosynthesis is important not only for developing a renewable, sustainable, and environmentally friendly source in both plants and microorganisms but also for designing effective strategies for enhancing their production via induction and metabolic engineering. Future directions for improving AVN production in native producers and heterologous systems for food and feed use are also discussed. This summary will provide a broad view of these specific natural products from oats.
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Affiliation(s)
- Xi Xie
- College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Miaoyan Lin
- College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Gengsheng Xiao
- College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Huifan Liu
- College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Feng Wang
- College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Dongjie Liu
- College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Lukai Ma
- College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Qin Wang
- College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Zhiyong Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
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2
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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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3
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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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4
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Alahmadi A, Dmello A. Detrimental Effects of Elevated Temperatures on the Structure and Activity of Phenylalanine Ammonia Lyase-Bovine Serum Albumin Mixtures and the Stabilizing Potential of Surfactant and Sugars. AAPS PharmSciTech 2022; 23:297. [DOI: 10.1208/s12249-022-02446-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
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5
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Qin Y, Li Q, An Q, Li D, Huang S, Zhao Y, Chen W, Zhou J, Liao H. A phenylalanine ammonia lyase from Fritillaria unibracteata promotes drought tolerance by regulating lignin biosynthesis and SA signaling pathway. Int J Biol Macromol 2022; 213:574-588. [PMID: 35643154 DOI: 10.1016/j.ijbiomac.2022.05.161] [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: 03/21/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 11/05/2022]
Abstract
Drought is one of the key threatening environmental factors for plant and agriculture. Phenylalanine ammonia lyase (PAL) is a key enzyme involved in plant defense against abiotic stress, however, the role of PAL in drought tolerance remains elusive. Here, a PAL member (FuPAL1) containing noncanonical Ala-Ser-Gly triad was isolated from Fritillaria unibracteata, one important alpine pharmaceutical plant. FuPAL1, mainly distributed in cytosol, was more conserved than FuCOMT and FuCHI at both nucleotide and amino acid levels. FuPAL1 was overexpressed in Escherichia coli and the purified recombinant FuPAL1 protein showed catalytic preference on L-Phe than L-Tyr. Homology modeling and site-mutation of FuPAL1 exhibited FuPAL1 took part in the ammonization process by forming MIO-like group, and Phe141, Ser208, Ileu218 and Glu490 played key roles in substrate binding and (or) catalysis. HPLC analysis showed that lignin and salicylic acid levels increased but total flavonoid levels decreased in FuPAL1 transgenic Arabidopsis compared to wild-type plants. Moreover, FuPAL1 transgenic Arabidopsis significantly enhanced its drought tolerance, which suggested that FuPAL1 mediated tolerance to drought by inducing the biosynthesis and accumulation of salicylic acid and lignin. Taken together, our results confirmed that the FuPAL1 played an important role in drought tolerance, and FuPAL1 might be a valuable target for genetic improvement of drought resistance in future.
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Affiliation(s)
- Yu Qin
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Qiue Li
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Qiuju An
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Dexin Li
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Sipei Huang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Yongyang Zhao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Weijia Chen
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Jiayu Zhou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China.
| | - Hai Liao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China.
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6
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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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7
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Peng F, Engel U, Aliyu H, Rudat J. Origin and Evolution of Enzymes with MIO Prosthetic Group: Microbial Coevolution After the Mass Extinction Event. Front Genet 2022; 13:851738. [PMID: 35422843 PMCID: PMC9002059 DOI: 10.3389/fgene.2022.851738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/16/2022] [Indexed: 11/20/2022] Open
Abstract
After major mass extinction events, ancient plants and terrestrial vertebrates were faced with various challenges, especially ultraviolet (UV) light. These stresses probably resulted in changes in the biosynthetic pathways, which employed the MIO (3,5-dihydro-5-methylidene-4H-imidazole-4-one)-dependent enzymes (ammonia-lyase and aminomutase), leading to enhanced accumulation of metabolites for defense against UV radiation, pathogens, and microorganisms. Up to now, the origin and evolution of genes from this superfamily have not been extensively studied. In this report, we perform an analysis of the phylogenetic relations between the members of the aromatic amino acid MIO-dependent enzymes (AAM), which demonstrate that they most probably have a common evolutionary origin from ancient bacteria. In early soil environments, numerous bacterial species with tyrosine ammonia-lyase genes (TAL; EC 4.3.1.23) developed tyrosine aminomutase (TAM; EC 5.4.3.6) activity as a side reaction for competing with their neighbors in the community. These genes also evolved into other TAL-like enzymes, such as histidine ammonia-lyase (HAL, EC 4.3.1.3) and phenylalanine ammonia-lyase (PAL; EC 4.3.1.24), in different bacterial species for metabolite production and accumulation for adaptation to adverse terrestrial environmental conditions. On the other hand, the existence of phenylalanine aminomutase (PAM; EC 5.4.3.10) and phenylalanine/tyrosine ammonia-lyase (PTAL; EC 4.3.1.25) strongly indicates the horizontal gene transfer (HGT) between bacteria, fungi, and plants in symbiotic association after acquiring the PAL gene from their ancestor.
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Affiliation(s)
- Fei Peng
- Institute of Process Engineering in Life Sciences, II, Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ulrike Engel
- Institute of Process Engineering in Life Sciences, II, Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Habibu Aliyu
- Institute of Process Engineering in Life Sciences, II, Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jens Rudat
- Institute of Process Engineering in Life Sciences, II, Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
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8
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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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Martín JF, Liras P. Comparative Molecular Mechanisms of Biosynthesis of Naringenin and Related Chalcones in Actinobacteria and Plants: Relevance for the Obtention of Potent Bioactive Metabolites. Antibiotics (Basel) 2022; 11:antibiotics11010082. [PMID: 35052959 PMCID: PMC8773403 DOI: 10.3390/antibiotics11010082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/01/2022] [Accepted: 01/07/2022] [Indexed: 02/04/2023] Open
Abstract
Naringenin and its glycosylated derivative naringin are flavonoids that are synthesized by the phenylpropanoid pathway in plants. We found that naringenin is also formed by the actinobacterium Streptomyces clavuligerus, a well-known microorganism used to industrially produce clavulanic acid. The production of naringenin in S. clavuligerus involves a chalcone synthase that uses p-coumaric as a starter unit and a P450 monoxygenase, encoded by two adjacent genes (ncs-ncyP). The p-coumaric acid starter unit is formed by a tyrosine ammonia lyase encoded by an unlinked, tal, gene. Deletion and complementation studies demonstrate that these three genes are required for biosynthesis of naringenin in S. clavuligerus. Other actinobacteria chalcone synthases use caffeic acid, ferulic acid, sinapic acid or benzoic acid as starter units in the formation of different antibiotics and antitumor agents. The biosynthesis of naringenin is restricted to a few Streptomycess species and the encoding gene cluster is present also in some Saccharotrix and Kitasatospora species. Phylogenetic comparison of S. clavuligerus naringenin chalcone synthase with homologous proteins of other actinobacteria reveal that this protein is closely related to chalcone synthases that use malonyl-CoA as a starter unit for the formation of red-brown pigment. The function of the core enzymes in the pathway, such as the chalcone synthase and the tyrosine ammonia lyase, is conserved in plants and actinobacteria. However, S. clavuligerus use a P450 monooxygenase proposed to complete the cyclization step of the naringenin chalcone, whereas this reaction in plants is performed by a chalcone isomerase. Comparison of the plant and S. clavuligerus chalcone synthases indicates that they have not been transmitted between these organisms by a recent horizontal gene transfer phenomenon. We provide a comprehensive view of the molecular genetics and biochemistry of chalcone synthases and their impact on the development of antibacterial and antitumor compounds. These advances allow new bioactive compounds to be obtained using combinatorial strategies. In addition, processes of heterologous expression and bioconversion for the production of naringenin and naringenin-derived compounds in yeasts are described.
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Song S, Wang L, Su J, Xu Z, Hsu CH, Hua C, Lyu P, Li J, Peng X, Kojima T, Nobusue S, Telychko M, Zheng Y, Chuang FC, Sakaguchi H, Wong MW, Lu J. Manifold dynamic non-covalent interactions for steering molecular assembly and cyclization. Chem Sci 2021; 12:11659-11667. [PMID: 34667560 PMCID: PMC8442717 DOI: 10.1039/d1sc03733a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/04/2021] [Indexed: 12/14/2022] Open
Abstract
Deciphering rich non-covalent interactions that govern many chemical and biological processes is crucial for the design of drugs and controlling molecular assemblies and their chemical transformations. However, real-space characterization of these weak interactions in complex molecular architectures at the single bond level has been a longstanding challenge. Here, we employed bond-resolved scanning probe microscopy combined with an exhaustive structural search algorithm and quantum chemistry calculations to elucidate multiple non-covalent interactions that control the cohesive molecular clustering of well-designed precursor molecules and their chemical reactions. The presence of two flexible bromo-triphenyl moieties in the precursor leads to the assembly of distinct non-planar dimer and trimer clusters by manifold non-covalent interactions, including hydrogen bonding, halogen bonding, C-H⋯π and lone pair⋯π interactions. The dynamic nature of weak interactions allows for transforming dimers into energetically more favourable trimers as molecular density increases. The formation of trimers also facilitates thermally-triggered intermolecular Ullmann coupling reactions, while the disassembly of dimers favours intramolecular cyclization, as evidenced by bond-resolved imaging of metalorganic intermediates and final products. The richness of manifold non-covalent interactions offers unprecedented opportunities for controlling the assembly of complex molecular architectures and steering on-surface synthesis of quantum nanostructures.
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Affiliation(s)
- Shaotang Song
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Lulu Wang
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Jie Su
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Zhen Xu
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Chia-Hsiu Hsu
- Department of Physics, National Sun Yat-sen University Kaohsiung 80424 Taiwan
- Physics Division, National Center for Theoretical Sciences Taipei, 10617 Taiwan
| | - Chenqiang Hua
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University Hangzhou People's Republic of China
| | - Pin Lyu
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Jing Li
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Xinnan Peng
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Takahiro Kojima
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Shunpei Nobusue
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Mykola Telychko
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Yi Zheng
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University Hangzhou People's Republic of China
| | - Feng-Chuan Chuang
- Department of Physics, National Sun Yat-sen University Kaohsiung 80424 Taiwan
- Physics Division, National Center for Theoretical Sciences Taipei, 10617 Taiwan
| | - Hiroshi Sakaguchi
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Ming Wah Wong
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Jiong Lu
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
- Centre for Advanced 2D Materials (CA2DM), National University of Singapore 6 Science Drive 2 Singapore 117546 Singapore
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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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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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Jeandet P, Vannozzi A, Sobarzo-Sánchez E, Uddin MS, Bru R, Martínez-Márquez A, Clément C, Cordelier S, Manayi A, Nabavi SF, Rasekhian M, El-Saber Batiha G, Khan H, Morkunas I, Belwal T, Jiang J, Koffas M, Nabavi SM. Phytostilbenes as agrochemicals: biosynthesis, bioactivity, metabolic engineering and biotechnology. Nat Prod Rep 2021; 38:1282-1329. [PMID: 33351014 DOI: 10.1039/d0np00030b] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: 1976 to 2020. Although constituting a limited chemical family, phytostilbenes represent an emblematic group of molecules among natural compounds. Ever since their discovery as antifungal compounds in plants and their ascribed role in human health and disease, phytostilbenes have never ceased to arouse interest for researchers, leading to a huge development of the literature in this field. Owing to this, the number of references to this class of compounds has reached the tens of thousands. The objective of this article is thus to offer an overview of the different aspects of these compounds through a large bibliography analysis of more than 500 articles. All the aspects regarding phytostilbenes will be covered including their chemistry and biochemistry, regulation of their biosynthesis, biological activities in plants, molecular engineering of stilbene pathways in plants and microbes as well as their biotechnological production by plant cell systems.
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Affiliation(s)
- Philippe Jeandet
- Research Unit "Induced Resistance and Plant Bioprotection", EA 4707, SFR Condorcet FR CNRS 3417, Faculty of Sciences, University of Reims Champagne-Ardenne, PO Box 1039, 51687 Reims Cedex 2, France.
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment (DAFNAE), University of Padova, 35020 Legnaro, PD, Italy
| | - Eduardo Sobarzo-Sánchez
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Spain and Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Chile
| | - Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh and Neuroscience Research Network, Dhaka, Bangladesh
| | - Roque Bru
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, Alicante, Spain
| | - Ascension Martínez-Márquez
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, Alicante, Spain
| | - Christophe Clément
- Research Unit "Induced Resistance and Plant Bioprotection", EA 4707, SFR Condorcet FR CNRS 3417, Faculty of Sciences, University of Reims Champagne-Ardenne, PO Box 1039, 51687 Reims Cedex 2, France.
| | - Sylvain Cordelier
- Research Unit "Induced Resistance and Plant Bioprotection", EA 4707, SFR Condorcet FR CNRS 3417, Faculty of Sciences, University of Reims Champagne-Ardenne, PO Box 1039, 51687 Reims Cedex 2, France.
| | - Azadeh Manayi
- Medicinal Plants Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, 1417614411 Tehran, Iran
| | - Seyed Fazel Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran 14359-16471, Iran
| | - Mahsa Rasekhian
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, AlBeheira, Egypt
| | - Haroon Khan
- Department of Pharmacy, Faculty of Chemical and Life Sciences, Abdul Wali Khan University Mardan, 23200, Pakistan
| | - Iwona Morkunas
- Department of Plant Physiology, Poznań University of Life Sciences, Wołyńska 35, 60-637 Poznań, Poland
| | - Tarun Belwal
- Zhejiang University, College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, Hangzhou 310058, The People's Republic of China
| | - Jingjie Jiang
- Dorothy and Fred Chau '71 Constellation Professor, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Room 4005D, 110 8th Street, Troy, NY 12180, USA
| | - Mattheos Koffas
- Dorothy and Fred Chau '71 Constellation Professor, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Room 4005D, 110 8th Street, Troy, NY 12180, USA
| | - Seyed Mohammad Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran 14359-16471, Iran
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14
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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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15
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Microbial enzymes for deprivation of amino acid metabolism in malignant cells: biological strategy for cancer treatment. Appl Microbiol Biotechnol 2020; 104:2857-2869. [PMID: 32037468 DOI: 10.1007/s00253-020-10432-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/23/2020] [Accepted: 02/03/2020] [Indexed: 12/17/2022]
Abstract
Amino acid deprivation therapy (AADT) is emerging as a promising strategy for the development of novel therapeutics against cancer. This biological therapy relies upon the differences in the metabolism of cancer and normal cells. The rapid growth of tumors results in decreased expression of certain enzymes leading to auxotrophy for some specific amino acids. These auxotrophic tumors are targeted by amino acid-depleting enzymes. The depletion of amino acid selectively inhibits tumor growth as the normal cells can synthesize amino acids by their usual machinery. The enzymes used in AADT are mostly obtained from microbes for their easy availability. Microbial L-asparaginase is already approved by FDA for the treatment of acute lymphoblastic leukemia. Arginine deiminase and methionase are under clinical trials and the therapeutic potential of lysine oxidase, glutaminase and phenylalanine ammonia lyase is also being explored. The present review provides an overview of microbial amino acid depriving enzymes. Various attributes of these enzymes like structure, mode of action, production, formulations, and targeted cancers are discussed. The challenges faced and the combat strategies to establish AADT in standard cancer armamentarium are also reviewed.Key Points • Amino acid deprivation therapy is a potential therapy for auxotrophic tumors. • Microbial enzymes are used due to their ease of manipulation and high productivity. • Enzyme properties are improved by PEGylation, encapsulation, and genetic engineering. • AADT can be employed as combinational therapy for better containment of cancer.
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Barros J, Dixon RA. Plant Phenylalanine/Tyrosine Ammonia-lyases. TRENDS IN PLANT SCIENCE 2020; 25:66-79. [PMID: 31679994 DOI: 10.1016/j.tplants.2019.09.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 05/13/2023]
Abstract
Aromatic amino acid deaminases are key enzymes mediating carbon flux from primary to secondary metabolism in plants. Recent studies have uncovered a tyrosine ammonia-lyase that contributes to the typical characteristics of grass cell walls and contributes to about 50% of the total lignin synthesized by the plant. Grasses are currently preferred bioenergy feedstocks and lignin is the most important limiting factor in the conversion of plant biomass to liquid biofuels, as well as being an abundant renewable carbon source that can be industrially exploited. Further research on the structure, evolution, regulation, and biological function of functionally distinct ammonia-lyases has multiple implications for improving the economics of the agri-food and biofuel industries.
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Affiliation(s)
- Jaime Barros
- BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA; Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA; Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Richard A Dixon
- BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA; Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA; Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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17
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Souza GM, Van Sluys MA, Lembke CG, Lee H, Margarido GRA, Hotta CT, Gaiarsa JW, Diniz AL, Oliveira MDM, Ferreira SDS, Nishiyama MY, ten-Caten F, Ragagnin GT, Andrade PDM, de Souza RF, Nicastro GG, Pandya R, Kim C, Guo H, Durham AM, Carneiro MS, Zhang J, Zhang X, Zhang Q, Ming R, Schatz MC, Davidson B, Paterson AH, Heckerman D. Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. Gigascience 2019; 8:giz129. [PMID: 31782791 PMCID: PMC6884061 DOI: 10.1093/gigascience/giz129] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 05/23/2019] [Accepted: 10/08/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10-13 sets of chromosomes from 2 Saccharum species. The ploidy, hybridity, and size of the genome, estimated to have >10 Gb, pose a challenge for sequencing. RESULTS Here we present a gene space assembly of SP80-3280, including 373,869 putative genes and their potential regulatory regions. The alignment of single-copy genes in diploid grasses to the putative genes indicates that we could resolve 2-6 (up to 15) putative homo(eo)logs that are 99.1% identical within their coding sequences. Dissimilarities increase in their regulatory regions, and gene promoter analysis shows differences in regulatory elements within gene families that are expressed in a species-specific manner. We exemplify these differences for sucrose synthase (SuSy) and phenylalanine ammonia-lyase (PAL), 2 gene families central to carbon partitioning. SP80-3280 has particular regulatory elements involved in sucrose synthesis not found in the ancestor Saccharum spontaneum. PAL regulatory elements are found in co-expressed genes related to fiber synthesis within gene networks defined during plant growth and maturation. Comparison with sorghum reveals predominantly bi-allelic variations in sugarcane, consistent with the formation of 2 "subgenomes" after their divergence ∼3.8-4.6 million years ago and reveals single-nucleotide variants that may underlie their differences. CONCLUSIONS This assembly represents a large step towards a whole-genome assembly of a commercial sugarcane cultivar. It includes a rich diversity of genes and homo(eo)logous resolution for a representative fraction of the gene space, relevant to improve biomass and food production.
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Affiliation(s)
- Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
| | - Carolina Gimiliani Lembke
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Hayan Lee
- Cold Spring Harbor Laboratory, One Bungtown Road, Koch Building #1119, Cold Spring Harbor, NY11724, United States of America
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CACA94598, United States of America
| | - Gabriel Rodrigues Alves Margarido
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias, 11, Piracicaba, SP 13418-900, Brazil
| | - Carlos Takeshi Hotta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Jonas Weissmann Gaiarsa
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
| | - Augusto Lima Diniz
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Mauro de Medeiros Oliveira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Sávio de Siqueira Ferreira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
| | - Milton Yutaka Nishiyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, Av. Vital Brasil, 1500, São Paulo, SP05503-900, Brazil
| | - Felipe ten-Caten
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Geovani Tolfo Ragagnin
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
| | - Pablo de Morais Andrade
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Robson Francisco de Souza
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av.Professor Lineu Prestes, 1734, São Paulo, SP 05508-900, Brazil
| | - Gianlucca Gonçalves Nicastro
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av.Professor Lineu Prestes, 1734, São Paulo, SP 05508-900, Brazil
| | - Ravi Pandya
- Microsoft Research, One Microsoft Way, Redmond, WA 98052, United States of America
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, 120 Green Street, Athens, GA 30602-7223,United States of America
- Department of Crop Science, Chungnam National University, 99 Daehak Ro Yuseong Gu, Deajeon,34134, South Korea
| | - Hui Guo
- Plant Genome Mapping Laboratory, University of Georgia, 120 Green Street, Athens, GA 30602-7223,United States of America
| | - Alan Mitchell Durham
- Departamento de Ciências da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, Rua do Matão, 1010, São Paulo, SP 05508-090, Brazil
| | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Washington Luis km 235, Araras, SP 13.565-905, Brazil
| | - Jisen Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
| | - Xingtan Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
| | - Qing Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 201 W. Gregory Dr. Urbana, Urbana, Illinois 61801, United States of America
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, One Bungtown Road, Koch Building #1119, Cold Spring Harbor, NY11724, United States of America
- Departments of Computer Science and Biology, Johns Hopkins University, 3400 North Charles Street,Baltimore, MD 21218-2608, United States of America
| | - Bob Davidson
- Microsoft Research, One Microsoft Way, Redmond, WA 98052, United States of America
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, 120 Green Street, Athens, GA 30602-7223,United States of America
| | - David Heckerman
- Microsoft Research, One Microsoft Way, Redmond, WA 98052, United States of America
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Zhou XL, Chen ZD, Zhou YM, Shi RH, Li ZJ. The Effect of Tartary Buckwheat Flavonoids in Inhibiting the Proliferation of MGC80-3 Cells during Seed Germination. Molecules 2019; 24:E3092. [PMID: 31454945 PMCID: PMC6749336 DOI: 10.3390/molecules24173092] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/19/2019] [Accepted: 08/19/2019] [Indexed: 12/15/2022] Open
Abstract
Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn) is rich in functional compounds such as rutin, quercetin, d-chiro-inositol, dietary fiber, and essential amino acids. Electric field (EF) treatment before sprout germination results in physiological and chemical changes, and some alterations might lead to positive applications in plant seeds. MTT assay showed that the effect of total flavonoids on human gastric cancer cell line MGC80-3 was significantly changed after EF treatment for different germination days (3-7 days). Among them, the total flavonoids of tartary buckwheat (BWTF) on the third day had the most obvious inhibitory effect on MGC80-3 (p < 0.01). In addition, flow cytometry evidenced that different ratios of quercetin and rutin had effects on the proliferation of MGC80-3. The same content of quercetin and rutin had the best effect, reaching 6.18 ± 0.82%. The anti-cancer mechanism was mainly promoted by promoting the expression of apoptotic proteins. The expression of Bax/Bcl-2 and caspase-8 in MGC80-3 cells was mediated by BWTFs. This study has good research value for improving the biological and economic value of tartary buckwheat.
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Affiliation(s)
- Xiao-Li Zhou
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Zhi-Dong Chen
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Yi-Ming Zhou
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China.
| | - Rong-Hua Shi
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Zong-Jie Li
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
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19
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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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20
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Cloning, Characterization and Expression of the Phenylalanine Ammonia-Lyase Gene (PaPAL) from Spruce Picea asperata. FORESTS 2019. [DOI: 10.3390/f10080613] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Phenylalanine ammonia-lyase (PAL) is the crucial enzyme of the phenylpropanoid pathway, which plays an important role in plant disease resistance. To understand the function of PAL in Picea asperata, in this study, the full-length cDNA sequence of the PAL gene from this species was isolated and named PaPAL. The gene contains a 2160-bp open reading frame (ORF) encoding 720 amino acids with a calculated molecular weight of 78.7 kDa and a theoretical isoelectric point of 5.88. The deduced PaPAL protein possesses the specific signature motif (GTITASGDLVPLSYIA) of phenylalanine ammonia-lyases. Multiple alignment analysis revealed that PaPAL has high identity with other plant PALs. The tertiary structure of PaPAL was predicted using PcPAL from Petroselinum crispum as a template, and the results suggested that PaPAL may have a similar function to that of PcPAL. Furthermore, phylogenetic analysis indicated that PaPAL has a close relationship with other PALs from the Pinaceae species. The optimal expression condition of recombinant PaPAL in Escherichia coli BL21 (DE3) was 0.2 mM IPTG (isopropyl β-D-thiogalactoside) at 16 °C for 4 h, and the molecular weight of recombinant PaPAL was found to be approximately 82 kDa. Recombinant PaPAL was purified and exhibited high PAL activity at optimal conditions of pH 8.6 and 60 °C. Quantitative real-time PCR (qRT-PCR) showed the PaPAL gene to be expressed in all tissues of P. asperata tested, with the highest expression level in the needles. The PaPAL gene was induced by the pathogen (Lophodermium piceae), which caused needle cast disease, indicating that it might be involved in defense against needle cast disease. These results provide a basis for understanding the molecular mechanisms of the PAL gene in the process of P. asperata disease resistance.
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21
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Kia R, Mahmoudi S, Raithby PR. New rhenium-tricarbonyl complexes bearing halogen-substituted bidentate ligands: structural, computational and Hirshfeld surfaces studies. CrystEngComm 2019. [DOI: 10.1039/c8ce01860j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The intermolecular interactions in a series of new complexes Re(CO)3(N,N)X (N,N is a halogen substituted bidentate N–N donor and X is Cl or Br) have been studied crystallographically and computationally. Metal-bound halogens are more effective than carbon-bound halogens in forming significant intermolecular interactions.
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Affiliation(s)
- Reza Kia
- Chemistry Department
- Sharif University of Technology
- Tehran
- Iran
| | - Soheil Mahmoudi
- Chemistry Department
- Sharif University of Technology
- Tehran
- Iran
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22
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Yoshikawa M, Luo W, Tanaka G, Konishi Y, Matsuura H, Takahashi K. Wounding stress induces phenylalanine ammonia lyases, leading to the accumulation of phenylpropanoids in the model liverwort Marchantia polymorpha. PHYTOCHEMISTRY 2018; 155:30-36. [PMID: 30064058 DOI: 10.1016/j.phytochem.2018.07.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 07/19/2018] [Accepted: 07/21/2018] [Indexed: 06/08/2023]
Abstract
Wounding stress induces the biosynthesis of various specialized metabolites in plants. In this study, wounding induced the biosynthesis of luteolin, apigenin, and isoriccardin C, which are biosynthesized through the phenylpropanoid pathway, in the model liverwort Marchantia polymorpha L (Marchantiaceae). Recombinant M. polymorpha phenylalanine ammonia lyases (MpPALs) exhibited PAL activity in vitro and converted phenylalanine into trans-cinnamic acid. Based on semi-quantitative RT-PCR analysis, the expression levels of the MpPAL genes were up-regulated after wounding. α-Aminooxy-β-phenylpropionic acid, a PAL inhibitor, suppressed the production of wounding-induced phenolic compounds, luteolin, apigenin, and isoriccardin C, in M. polymorpha. Thus, PAL is a committed step in the biosynthesis of phenylpropanoids in response to wounding in M. polymorpha. This study suggests that wound-induced specialized metabolites such as phenylpropanoids comprise a conserved defense system in land plants.
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Affiliation(s)
- Mayu Yoshikawa
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Weifeng Luo
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Genta Tanaka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Yuka Konishi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Hideyuki Matsuura
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Kosaku Takahashi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
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23
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Levy HL, Sarkissian CN, Scriver CR. Phenylalanine ammonia lyase (PAL): From discovery to enzyme substitution therapy for phenylketonuria. Mol Genet Metab 2018; 124:223-229. [PMID: 29941359 DOI: 10.1016/j.ymgme.2018.06.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/06/2018] [Accepted: 06/07/2018] [Indexed: 01/17/2023]
Abstract
Phenylketonuria (PKU) is a genetic inborn error in metabolism that impacts many people globally, with profound individual and societal consequences when left untreated. The journey of phenylalanine ammonia lyase (PAL) from plant enzyme to enzyme substitution therapy for PKU is a fascinating story that illustrates the importance of collaboration between basic scientists and industry in the drug development process. The story begins with the curiosity of plant physiologists about the origin of lignin, a polymer involved in maintaining the rigidity of plants. They learned that the critical element in this synthesis was an intermediary enzyme that deaminates phenylalanine to cinnamic acid and ammonia (later called phenylalanine ammonia lyase or PAL). Recognition of this ability to metabolize phenylalanine led to subsequent consideration of PAL as a treatment for PKU. This was initially attempted as enteral therapy with extracted enzyme, but that showed only minimal efficacy. Crucially, further development of PAL as a therapy for PKU required quantities of enzyme that could only be obtained after successfully cloning the gene, expressing the enzyme in vitro and modifying the protein via PEGylation to enable parenteral administration of this non-mammalian enzyme. Ultimately, PEGylated PAL was developed as an enzyme substitution therapy for PKU now approved under the name "Palynziq." The multidisciplinary academic-industrial partnership engaged throughout this process has been key to the successful pursuit of this therapeutic possibility and serves as a model for the development of future innovative therapies.
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Affiliation(s)
- Harvey L Levy
- Division of Genetics and Genomics, Boston Children's Hospital, 1 Autumn St., Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
| | | | - Charles R Scriver
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada.
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24
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Wanat W, Talma M, Hurek J, Pawełczak M, Kafarski P. Substituted phosphonic analogues of phenylglycine as inhibitors of phenylalanine ammonia lyase from potatoes. Biochimie 2018; 151:119-127. [PMID: 29890205 DOI: 10.1016/j.biochi.2018.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/06/2018] [Indexed: 11/26/2022]
Abstract
A series of phosphonic acid analogues of phenylglycine variously substituted in phenyl ring have been synthesized and evaluated for their inhibitory activity towards potato l-phenylalanine ammonia lyase. Most of the compounds appeared to act as moderate (micromolar) inhibitors of the enzyme. Analysis of their binding performed using molecular modeling have shown that they might be bound either in active site of the enzyme or in the non-physiologic site. The latter one is located in adjoining deep site nearby the to the entrance channel for substrate into active site.
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Affiliation(s)
- Weronika Wanat
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Michał Talma
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Józef Hurek
- Department of Chemistry, University of Opole, ul. Oleska 48, 45-052, Opole, Poland
| | - Małgorzata Pawełczak
- Department of Chemistry, University of Opole, ul. Oleska 48, 45-052, Opole, Poland
| | - Paweł Kafarski
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
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25
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Li W, Yang Y, Qiao C, Zhang G, Luo Y. Functional characterization of phenylalanine ammonia-lyase- and cinnamate 4-hydroxylase-encoding genes from Lycoris radiata, a galanthamine-producing plant. Int J Biol Macromol 2018; 117:1264-1279. [PMID: 29894786 DOI: 10.1016/j.ijbiomac.2018.06.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 06/08/2018] [Accepted: 06/09/2018] [Indexed: 01/13/2023]
Abstract
Galanthamine (GAL), the well-known Amaryllidaceae alkaloid, is a clinically used drug for the treatment of Alzheimer's disease. L-Phenylalanine (Phe) and trans-cinnamic acid (CA) were enzymatically transformed into the catechol portion of GAL. Herein, a Phe ammonia-lyase-encoding gene LrPAL3 and a cinnamate 4-hydroxylase-encoding gene LrC4H were cloned from Lycoris radiata, a GAL-producing plant. LrPAL3 was overexpressed in Escherichia coli and purified to homogeneity. LrPAL3 catalyzes the forward deamination conversion of L-Phe into trans-CA. The 3-chloro- and 4-fluoro-L-Phe were deaminated to generate the corresponding 3-chloro- and 4-fluoro-trans-CA by LrPAL3. LrPAL3-catalyzed reverse hydroamination was confirmed by the conversion of trans-CA into L-Phe with exceptional regio- and stereo-selectivity. LrC4H was overexpressed in E. coli with tCamCPR, a cytochrome P450 reductase-encoding gene. LrC4H catalyzes the regioselective para-hydroxylation on trans-CA to form p-coumaric acid. The transcriptional levels of both LrPAL3 and LrC4H were positively associated with the GAL contents within the leaves and flowers of L. radiata, which suggested that their expression and function are co-regulated and involved in the biosynthesis of GAL. The present investigations on the biosynthetic genes of GAL will promote the development of synthetic biology platforms for this kind of important drug via metabolic engineering.
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Affiliation(s)
- Wei Li
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin Road South, Chengdu 610041, People's Republic of China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, People's Republic of China
| | - Yun Yang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin Road South, Chengdu 610041, People's Republic of China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, People's Republic of China
| | - Chong Qiao
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin Road South, Chengdu 610041, People's Republic of China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, People's Republic of China
| | - Guolin Zhang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin Road South, Chengdu 610041, People's Republic of China
| | - Yinggang Luo
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin Road South, Chengdu 610041, People's Republic of China; State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China.
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26
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Davidson VL. Protein-Derived Cofactors Revisited: Empowering Amino Acid Residues with New Functions. Biochemistry 2018; 57:3115-3125. [PMID: 29498828 DOI: 10.1021/acs.biochem.8b00123] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A protein-derived cofactor is a catalytic or redox-active site in a protein that is formed by post-translational modification of one or more amino acid residues. These post-translational modifications are irreversible and endow the modified amino acid residues with new functional properties. This Perspective focuses on the following advances in this area that have occurred during recent years. The biosynthesis of the tryptophan tryptophylquinone cofactor is catalyzed by a diheme enzyme, MauG. A bis-FeIV redox state of the hemes performs three two-electron oxidations of specific Trp residues via long-range electron transfer. In contrast, a flavoenzyme catalyzes the biosynthesis of the cysteine tryptophylquinone (CTQ) cofactor present in a newly discovered family of CTQ-dependent oxidases. Another carbonyl cofactor, the pyruvoyl cofactor found in classes of decarboxylases and reductases, is formed during an apparently autocatalytic cleavage of a precursor protein at the N-terminus of the cleavage product. It has been shown that in at least some cases, the cleavage is facilitated by binding to an accessory protein. Tyrosylquinonine cofactors, topaquinone and lysine tyrosylquinone, are found in copper-containing amine oxidases and lysyl oxidases, respectively. The physiological roles of different families of these enzymes in humans have been more clearly defined and shown to have significant implications with respect to human health. There has also been continued characterization of the roles of covalently cross-linked amino acid side chains that influence the reactivity of redox-active metal centers in proteins. These include Cys-Tyr species in galactose oxidase and cysteine dioxygenase and the Met-Tyr-Trp species in the catalase-peroxidase KatG.
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Affiliation(s)
- Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine , University of Central Florida , Orlando , Florida 32827 , United States
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27
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Xue YP, Cao CH, Zheng YG. Enzymatic asymmetric synthesis of chiral amino acids. Chem Soc Rev 2018; 47:1516-1561. [DOI: 10.1039/c7cs00253j] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This review summarizes the progress achieved in the enzymatic asymmetric synthesis of chiral amino acids from prochiral substrates.
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Affiliation(s)
- Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Cheng-Hao Cao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
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28
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Park YK, Nicaud JM, Ledesma-Amaro R. The Engineering Potential of Rhodosporidium toruloides as a Workhorse for Biotechnological Applications. Trends Biotechnol 2017; 36:304-317. [PMID: 29132754 DOI: 10.1016/j.tibtech.2017.10.013] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 12/30/2022]
Abstract
Moving our society towards a bioeconomy requires efficient and sustainable microbial production of chemicals and fuels. Rhodotorula (Rhodosporidium) toruloides is a yeast that naturally synthesizes substantial amounts of specialty chemicals and has been recently engineered to (i) enhance its natural production of lipids and carotenoids, and (ii) produce novel industrially relevant compounds. The use of R. toruloides by companies and research groups has exponentially increased in recent years as a result of recent improvements in genetic engineering techniques and the availability of multiomics information on its genome and metabolism. This review focuses on recent engineering approaches in R. toruloides for bioproduction and explores its potential as a biotechnological chassis.
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Affiliation(s)
- Young-Kyoung Park
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Jean-Marc Nicaud
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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29
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Parmeggiani F, Weise NJ, Ahmed ST, Turner NJ. Synthetic and Therapeutic Applications of Ammonia-lyases and Aminomutases. Chem Rev 2017; 118:73-118. [DOI: 10.1021/acs.chemrev.6b00824] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Fabio Parmeggiani
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Weise
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Syed T. Ahmed
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Turner
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
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30
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de Vries J, de Vries S, Slamovits CH, Rose LE, Archibald JM. How Embryophytic is the Biosynthesis of Phenylpropanoids and their Derivatives in Streptophyte Algae? PLANT & CELL PHYSIOLOGY 2017; 58:934-945. [PMID: 28340089 DOI: 10.1093/pcp/pcx037] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 03/08/2017] [Indexed: 05/21/2023]
Abstract
The origin of land plants from algae is a long-standing question in evolutionary biology. It is becoming increasingly clear that many characters that were once assumed to be 'embryophyte specific' can in fact be found in their closest algal relatives, the streptophyte algae. One such case is the phenylpropanoid pathway. While biochemical data indicate that streptophyte algae harbor lignin-like components, the phenylpropanoid core pathway, which serves as the backbone of lignin biosynthesis, has been proposed to have arisen at the base of the land plants. Here we revisit this hypothesis using a wealth of new sequence data from streptophyte algae. Tracing the biochemical pathway towards lignin biogenesis, we show that most of the genes required for phenylpropanoid synthesis and the precursors for lignin production were already present in streptophyte algae. Nevertheless, phylogenetic analyses and protein structure predictions of one of the key enzyme classes in lignin production, cinnamyl alcohol dehydrogenase (CAD), suggest that CADs of streptophyte algae are more similar to sinapyl alcohol dehydrogenases (SADs). This suggests that the end-products of the pathway leading to lignin biosynthesis in streptophyte algae may facilitate the production of lignin-like compounds and defense molecules. We hypothesize that streptophyte algae already possessed the genetic toolkit from which the capacity to produce lignin later evolved in vascular plants.
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Affiliation(s)
- Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Population Genetics, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Toronto, ON, Canada
| | - Laura E Rose
- Population Genetics, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- CEPLAS - Cluster of Excellence in Plant Sciences, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Toronto, ON, Canada
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31
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Dreßen A, Hilberath T, Mackfeld U, Billmeier A, Rudat J, Pohl M. Phenylalanine ammonia lyase from Arabidopsis thaliana (AtPAL2): A potent MIO-enzyme for the synthesis of non-canonical aromatic alpha-amino acids: Part I: Comparative characterization to the enzymes from Petroselinum crispum (PcPAL1) and Rhodosporidium toruloides (RtPAL). J Biotechnol 2017; 258:148-157. [PMID: 28392421 DOI: 10.1016/j.jbiotec.2017.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 10/19/2022]
Abstract
Phenylalanine ammonia lyase (PAL) from Arabidopsis thaliana (AtPAL2) was comparatively characterized to the well-studied enzyme from parsley (PcPAL1) and Rhodosporidium toruloides (RtPAL) with respect to kinetic parameters for the deamination and the amination reaction, pH- and temperature optima and the substrate range of the amination reaction. Whereas both plant enzymes are specific for phenylalanine, the bifunctional enzyme from Rhodosporidium toruloides shows KM-values for L-Phe and L-Tyr in the same order of magnitude and, compared to both plant enzymes, a 10-15-fold higher activity. At 30°C all enzymes were sufficiently stable with half-lives of 3.4days (PcPAL1), 4.6days (AtPAL2) and 9.7days (RtPAL/TAL). Very good results for the amination of various trans-cinnamic acid derivatives were obtained using E. coli cells as whole cell biocatalysts in ammonium carbonate buffer. Investigation of the substrate ranges gave interesting results for the newly tested enzymes from A. thaliana and R. toruloides. Only the latter accepts besides 4-hydroxy-CA also 3-methoxy-4-hydroxy-CA as a substrate, which is an interesting intermediate for the formation of pharmaceutically relevant L-Dopa. AtPAL2 is a very good catalyst for the formation of (S)-3-F-Phe, (S)-4-F-Phe and (S)-2-Cl-Phe. Such non-canonical amino acids are valuable building blocks for the formation of various drug molecules.
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Affiliation(s)
- Alana Dreßen
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
| | - Thomas Hilberath
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
| | - Ursula Mackfeld
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
| | - Arne Billmeier
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
| | - Jens Rudat
- Karlsruhe Institute of Technology (KIT), Institute of Process Engineering in Life Sciences, Section: Technical Biology, Engler-Bunte-Ring 3, D-76131 Karlsruhe, Germany.
| | - Martina Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
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32
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Lv C, Zhao G, Ning Y. Interactions between plant proteins/enzymes and other food components, and their effects on food quality. Crit Rev Food Sci Nutr 2017; 57:1718-1728. [PMID: 26192262 DOI: 10.1080/10408398.2015.1023762] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Plant proteins are the main sources of dietary protein for humans, especially for vegetarians. There are a variety of components with different properties coexisting in foodstuffs, so the interactions between these components are inevitable to occur, thereby affecting food quality. Among these interactions, the interplay between plant proteins/enzymes from fruits and vegetables, cereals, and legumes and other molecules plays an important role in food quality, which recently has gained a particular scientific interest. Such interactions not only affect the appearances of fruits and vegetables and the functionality of cereal products but also the nutritive properties of plant foods. Non-covalent forces, such as hydrogen bond, hydrophobic interaction, electrostatic interaction, and van der Waals forces, are mainly responsible for these interactions. Future outlook is highlighted with aim to suggest a research line to be followed in further studies.
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Affiliation(s)
- Chenyan Lv
- a Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University , Beijing , China.,b Key Laboratory of Functional Dairy, Ministry of Education , Beijing , China
| | - Guanghua Zhao
- a Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University , Beijing , China.,c School of Laboratory Medicine, Hubei University of Chinese Medicine , Wuhan , China
| | - Yong Ning
- c School of Laboratory Medicine, Hubei University of Chinese Medicine , Wuhan , China
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33
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Zhang F, Huang N, Zhou L, Cui W, Liu Z, Zhu L, Liu Y, Zhou Z. Modulating the pH Activity Profiles of Phenylalanine Ammonia Lyase from Anabaena variabilis by Modification of Center-Near Surface Residues. Appl Biochem Biotechnol 2017; 183:699-711. [DOI: 10.1007/s12010-017-2458-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 03/12/2017] [Indexed: 10/19/2022]
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Bell SM, Wendt DJ, Zhang Y, Taylor TW, Long S, Tsuruda L, Zhao B, Laipis P, Fitzpatrick PA. Formulation and PEGylation optimization of the therapeutic PEGylated phenylalanine ammonia lyase for the treatment of phenylketonuria. PLoS One 2017; 12:e0173269. [PMID: 28282402 PMCID: PMC5345807 DOI: 10.1371/journal.pone.0173269] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 02/11/2017] [Indexed: 01/03/2023] Open
Abstract
Phenylketonuria (PKU) is a genetic metabolic disease in which the decrease or loss of phenylalanine hydroxylase (PAH) activity results in elevated, neurotoxic levels of phenylalanine (Phe). Due to many obstacles, PAH enzyme replacement therapy is not currently an option. Treatment of PKU with an alternative enzyme, phenylalanine ammonia lyase (PAL), was first proposed in the 1970s. However, issues regarding immunogenicity, enzyme production and mode of delivery needed to be overcome. Through the evaluation of PAL enzymes from multiple species, three potential PAL enzymes from yeast and cyanobacteria were chosen for evaluation of their therapeutic potential. The addition of polyethylene glycol (PEG, MW = 20,000), at a particular ratio to modify the protein surface, attenuated immunogenicity in an animal model of PKU. All three PEGylated PAL candidates showed efficacy in a mouse model of PKU (BTBR Pahenu2) upon subcutaneous injection. However, only PEGylated Anabaena variabilis (Av) PAL-treated mice demonstrated sustained low Phe levels with weekly injection and was the only PAL evaluated that maintained full enzymatic activity upon PEGylation. A PEGylated recombinant double mutant version of AvPAL (Cys503Ser/Cys565Ser), rAvPAL-PEG, was selected for drug development based on its positive pharmacodynamic profile and favorable expression titers. PEGylation was shown to be critical for rAvPAL-PEG efficacy as under PEGylated rAvPAL had a lower pharmacodynamic effect. rAvPAL and rAvPAL-PEG had poor stability at 4°C. L-Phe and trans-cinnamate were identified as activity stabilizing excipients. rAvPAL-PEG is currently in Phase 3 clinical trials to assess efficacy in PKU patients.
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Affiliation(s)
- Sean M. Bell
- BioMarin Pharmaceutical, Novato, California, United States of America
- * E-mail:
| | - Dan J. Wendt
- BioMarin Pharmaceutical, Novato, California, United States of America
| | - Yanhong Zhang
- BioMarin Pharmaceutical, Novato, California, United States of America
| | - Timothy W. Taylor
- BioMarin Pharmaceutical, Novato, California, United States of America
| | - Shinong Long
- BioMarin Pharmaceutical, Novato, California, United States of America
| | - Laurie Tsuruda
- BioMarin Pharmaceutical, Novato, California, United States of America
| | - Bin Zhao
- BioMarin Pharmaceutical, Novato, California, United States of America
| | - Phillip Laipis
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America
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35
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Li L, Yan K, Huang S, Pan S, Chen G, Liang Z. A Novel Phenylalanine Ammonia-Lyase Purified from Rhodosporidium paludigenum PT3. Chem Nat Compd 2017. [DOI: 10.1007/s10600-017-2008-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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36
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Zoń J, Miziak P. 1-Aminobenzocyclobutene-1-phosphonic Acid and Related Compounds as Inhibitors of Phenylalanine Ammonia-Lyase. Chem Biodivers 2017; 14. [PMID: 28171693 DOI: 10.1002/cbdv.201600488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/03/2017] [Indexed: 11/11/2022]
Abstract
Five new geminal aminocycloalkanephosphonic acids (4 - 8) containing both an aromatic ring and a cycloalkane ring were synthesized and evaluated as potential inhibitors of buckwheat phenylalanine ammonia-lyase (PAL). Within the set of compounds which are related to 2-aminoindane-2-phosphonic acid (AIP, 3), a known powerful inhibitor of PAL, racemic 1-aminobenzocyclobutene-1-phosphonic acid (4), was six times weaker than AIP as an in vitro inhibitor of buckwheat PAL, but six times stronger than AIP as an in vivo inhibitor of phenylalanine-derived anthocyanin synthesis in buckwheat.
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Affiliation(s)
- Jerzy Zoń
- Department of Thermodynamics, Theory of Machine and Thermal Systems, Faculty of Mechanical and Power Engineering, Wrocław University of Science and Technology, 27 Wybrzeże Wyspiańskiego St., 50-370, Wrocław, Poland
| | - Piotr Miziak
- Department of Thermodynamics, Theory of Machine and Thermal Systems, Faculty of Mechanical and Power Engineering, Wrocław University of Science and Technology, 27 Wybrzeże Wyspiańskiego St., 50-370, Wrocław, Poland
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Sánchez-Murcia PA, Bueren-Calabuig JA, Camacho-Artacho M, Cortés-Cabrera Á, Gago F. Stepwise Simulation of 3,5-Dihydro-5-methylidene-4H-imidazol-4-one (MIO) Biogenesis in Histidine Ammonia-lyase. Biochemistry 2016; 55:5854-5864. [DOI: 10.1021/acs.biochem.6b00744] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pedro A. Sánchez-Murcia
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad de Alcalá, E-28805 Alcalá de Henares, Spain
| | - Juan A. Bueren-Calabuig
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad de Alcalá, E-28805 Alcalá de Henares, Spain
| | - Marta Camacho-Artacho
- Structural
Biology Department, Centro Nacional de Investigaciones Oncológicas (CNIO), E-28029 Madrid, Spain
| | - Álvaro Cortés-Cabrera
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad de Alcalá, E-28805 Alcalá de Henares, Spain
| | - Federico Gago
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad de Alcalá, E-28805 Alcalá de Henares, Spain
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38
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Sabela MI, Mpanza T, Kanchi S, Sharma D, Bisetty K. Electrochemical sensing platform amplified with a nanobiocomposite of L-phenylalanine ammonia-lyase enzyme for the detection of capsaicin. Biosens Bioelectron 2016; 83:45-53. [DOI: 10.1016/j.bios.2016.04.037] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 04/12/2016] [Accepted: 04/13/2016] [Indexed: 12/25/2022]
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39
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Characterization of mutants of a tyrosine ammonia-lyase from Rhodotorula glutinis. Appl Microbiol Biotechnol 2016; 100:10443-10452. [DOI: 10.1007/s00253-016-7672-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 05/09/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022]
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40
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Weiser D, Bencze LC, Bánóczi G, Ender F, Kiss R, Kókai E, Szilágyi A, Vértessy BG, Farkas Ö, Paizs C, Poppe L. Phenylalanine Ammonia-Lyase-Catalyzed Deamination of an Acyclic Amino Acid: Enzyme Mechanistic Studies Aided by a Novel Microreactor Filled with Magnetic Nanoparticles. Chembiochem 2015; 16:2283-8. [DOI: 10.1002/cbic.201500444] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Diána Weiser
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
| | - László Csaba Bencze
- Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
| | - Gergely Bánóczi
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
| | - Ferenc Ender
- Department of Electron Devices; Budapest University of Technology and Economics; Magyar tudósok körútja 2 1117 Budapest Hungary
| | - Róbert Kiss
- Gedeon Richter Plc. Gyömrői út 19-21; 1103 Budapest Hungary
| | - Eszter Kókai
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
| | - András Szilágyi
- Department of Physical Chemistry and Materials Science; Budapest University of Technology and Economics; Budafoki út 8 1111 Budapest Hungary
| | - Beáta G. Vértessy
- Institute of Enzymology; Research Centre for Natural Sciences of Hungarian Academy of Sciences; Magyar tudósok körútja 2 1117 Budapest Hungary
- Department of Biotechnology and Food Sciences; Budapest University of Technology and Economics; Szt. Gellért tér 4 1111 Budapest Hungary
| | - Ödön Farkas
- Department of Organic Chemistry; Eötvös Lóránd University; Pázmány Péter sétány 1A 1117 Budapest Hungary
| | - Csaba Paizs
- Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
| | - László Poppe
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
- SynBiocat Ltd.; Lázár deák u 4/1 1173 Budapest Hungary
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41
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Structure and expression of two phenylalanine ammonia-lyase genes of the basidiomycete mushroom Tricholoma matsutake. MYCOSCIENCE 2015. [DOI: 10.1016/j.myc.2015.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Cass CL, Peraldi A, Dowd PF, Mottiar Y, Santoro N, Karlen SD, Bukhman YV, Foster CE, Thrower N, Bruno LC, Moskvin OV, Johnson ET, Willhoit ME, Phutane M, Ralph J, Mansfield SD, Nicholson P, Sedbrook JC. Effects of PHENYLALANINE AMMONIA LYASE (PAL) knockdown on cell wall composition, biomass digestibility, and biotic and abiotic stress responses in Brachypodium. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4317-35. [PMID: 26093023 PMCID: PMC4493789 DOI: 10.1093/jxb/erv269] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The phenylpropanoid pathway in plants synthesizes a variety of structural and defence compounds, and is an important target in efforts to reduce cell wall lignin for improved biomass conversion to biofuels. Little is known concerning the trade-offs in grasses when perturbing the function of the first gene family in the pathway, PHENYLALANINE AMMONIA LYASE (PAL). Therefore, PAL isoforms in the model grass Brachypodium distachyon were targeted, by RNA interference (RNAi), and large reductions (up to 85%) in stem tissue transcript abundance for two of the eight putative BdPAL genes were identified. The cell walls of stems of BdPAL-knockdown plants had reductions of 43% in lignin and 57% in cell wall-bound ferulate, and a nearly 2-fold increase in the amounts of polysaccharide-derived carbohydrates released by thermochemical and hydrolytic enzymic partial digestion. PAL-knockdown plants exhibited delayed development and reduced root growth, along with increased susceptibilities to the fungal pathogens Fusarium culmorum and Magnaporthe oryzae. Surprisingly, these plants generally had wild-type (WT) resistances to caterpillar herbivory, drought, and ultraviolet light. RNA sequencing analyses revealed that the expression of genes associated with stress responses including ethylene biosynthesis and signalling were significantly altered in PAL knocked-down plants under non-challenging conditions. These data reveal that, although an attenuation of the phenylpropanoid pathway increases carbohydrate availability for biofuel, it can adversely affect plant growth and disease resistance to fungal pathogens. The data identify notable differences between the stress responses of these monocot pal mutants versus Arabidopsis (a dicot) pal mutants and provide insights into the challenges that may arise when deploying phenylpropanoid pathway-altered bioenergy crops.
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Affiliation(s)
- Cynthia L Cass
- School of Biological Sciences, Illinois State University, Normal, IL 61790 USA US Department of Energy Great Lakes Bioenergy Research Center, Madison, WI 53706, USA
| | - Antoine Peraldi
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Patrick F Dowd
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL 61604, USA
| | - Yaseen Mottiar
- US Department of Energy Great Lakes Bioenergy Research Center, Madison, WI 53706, USA Department of Wood Science, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Nicholas Santoro
- US Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA
| | - Steven D Karlen
- US Department of Energy Great Lakes Bioenergy Research Center, Madison, WI 53706, USA
| | - Yury V Bukhman
- US Department of Energy Great Lakes Bioenergy Research Center, Madison, WI 53706, USA
| | - Cliff E Foster
- US Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA
| | - Nick Thrower
- US Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA
| | - Laura C Bruno
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Oleg V Moskvin
- US Department of Energy Great Lakes Bioenergy Research Center, Madison, WI 53706, USA
| | - Eric T Johnson
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL 61604, USA
| | - Megan E Willhoit
- School of Biological Sciences, Illinois State University, Normal, IL 61790 USA US Department of Energy Great Lakes Bioenergy Research Center, Madison, WI 53706, USA
| | - Megha Phutane
- School of Biological Sciences, Illinois State University, Normal, IL 61790 USA US Department of Energy Great Lakes Bioenergy Research Center, Madison, WI 53706, USA
| | - John Ralph
- US Department of Energy Great Lakes Bioenergy Research Center, Madison, WI 53706, USA Department of Biochemistry, Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53706, USA
| | - Shawn D Mansfield
- US Department of Energy Great Lakes Bioenergy Research Center, Madison, WI 53706, USA Department of Wood Science, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Paul Nicholson
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - John C Sedbrook
- School of Biological Sciences, Illinois State University, Normal, IL 61790 USA US Department of Energy Great Lakes Bioenergy Research Center, Madison, WI 53706, USA
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43
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Kim J, Park H, Han JG, Oh J, Choi HK, Kim SH, Sung GH. Regulation of a phenylalanine ammonia lyase (BbPAL) by calmodulin in response to environmental changes in the entomopathogenic fungus Beauveria bassiana. Environ Microbiol 2015; 17:4484-94. [PMID: 25970691 DOI: 10.1111/1462-2920.12898] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/01/2015] [Accepted: 05/05/2015] [Indexed: 11/30/2022]
Abstract
Phenylalanine ammonia lyase (PAL, E.C. 4.3.1.5) catalyses the deamination of L -phenylalanine to trans-cinnamic acid and ammonia, facilitating a critical step in the phenylpropanoid pathway that produces a variety of secondary metabolites. In this study, we isolated BbPAL gene in the entomopathogenic fungus Beauveria bassiana. According to multiple sequence alignment, homology modelling and in vitro PAL activity, we demonstrated that BbPAL acts as a typical PAL enzyme in B. bassiana. BbPAL interacted with calmodulin (CaM) in vitro and in vivo, indicating that BbPAL is a novel CaM-binding protein. The functional role of CaM in BbPAL action was to negatively regulate the BbPAL activity in B. bassiana. High-performance liquid chromatography analysis revealed that L -phenylalanine was reduced and trans-cinnamic acid was increased in response to the CaM inhibitor W-7. Dark conditions suppressed BbPAL activity in B. bassiana, compared with light. In addition, heat and cold stresses inhibited BbPAL activity in B. bassiana. Interestingly, these negative effects of BbPAL activity by dark, heat and cold conditions were recovered by W-7 treatment, suggesting that the inhibitory mechanism is mediated through stimulation of CaM activity. Therefore, this work suggests that BbPAL plays a role in the phenylpropanoid pathway mediated by environmental stimuli via the CaM signalling pathway.
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Affiliation(s)
- Jiyoung Kim
- Institute of Life Science and Biotechnology, Sungkyunkwan University, Suwon, 440-746, Korea
| | - Hyesung Park
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, 369-873, Korea
| | - Jae-Gu Han
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, 369-873, Korea
| | - Junsang Oh
- College of Pharmacy, Chung-Ang University, Seoul, 156-756, Korea
| | - Hyung-Kyoon Choi
- College of Pharmacy, Chung-Ang University, Seoul, 156-756, Korea
| | - Seong Hwan Kim
- Department of Microbiology, Dankook University, Cheonan, 330-714, Korea
| | - Gi-Ho Sung
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do, 210-701, Korea.,Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City, 404-834, Korea
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44
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Abstract
The four-component intramembrane protease γ-secretase is intricately linked to the development of Alzheimer's disease. Despite recent structural advances, the transmembrane segments (TMs) of γ-secretase remain to be specifically assigned. Here we report a 3D structure of human γ-secretase at 4.32-Å resolution, determined by single-particle, electron cryomicroscopy in the presence of digitonin and with a T4 lysozyme fused to the amino terminus of presenilin 1 (PS1). The overall structure of this human γ-secretase is very similar to that of wild-type γ-secretase determined in the presence of amphipols. The 20 TMs are unambiguously assigned to the four components, revealing principles of subunit assembly. Within the transmembrane region, PS1 is centrally located, with its amino-terminal fragment (NTF) packing against Pen-2 and its carboxyl-terminal fragment (CTF) interacting with Aph-1. The only TM of nicastrin associates with Aph-1 at the thick end of the TM horseshoe, and the extracellular domain of nicastrin directly binds Pen-2 at the thin end. TM6 and TM7 in PS1, which harbor the catalytic aspartate residues, are located on the convex side of the TM horseshoe. This structure serves as an important framework for understanding the function and mechanism of γ-secretase.
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45
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Highly Active and Specific Tyrosine Ammonia-Lyases from Diverse Origins Enable Enhanced Production of Aromatic Compounds in Bacteria and Saccharomyces cerevisiae. Appl Environ Microbiol 2015; 81:4458-76. [PMID: 25911487 DOI: 10.1128/aem.00405-15] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 04/20/2015] [Indexed: 11/20/2022] Open
Abstract
Phenylalanine and tyrosine ammonia-lyases form cinnamic acid and p-coumaric acid, which are precursors of a wide range of aromatic compounds of biotechnological interest. Lack of highly active and specific tyrosine ammonia-lyases has previously been a limitation in metabolic engineering approaches. We therefore identified 22 sequences in silico using synteny information and aiming for sequence divergence. We performed a comparative in vivo study, expressing the genes intracellularly in bacteria and yeast. When produced heterologously, some enzymes resulted in significantly higher production of p-coumaric acid in several different industrially important production organisms. Three novel enzymes were found to have activity exclusively for phenylalanine, including an enzyme from the low-GC Gram-positive bacterium Brevibacillus laterosporus, a bacterial-type enzyme from the amoeba Dictyostelium discoideum, and a phenylalanine ammonia-lyase from the moss Physcomitrella patens (producing 230 μM cinnamic acid per unit of optical density at 600 nm [OD600]) in the medium using Escherichia coli as the heterologous host). Novel tyrosine ammonia-lyases having higher reported substrate specificity than previously characterized enzymes were also identified. Enzymes from Herpetosiphon aurantiacus and Flavobacterium johnsoniae resulted in high production of p-coumaric acid in Escherichia coli (producing 440 μM p-coumaric acid OD600 unit(-1) in the medium) and in Lactococcus lactis. The enzymes were also efficient in Saccharomyces cerevisiae, where p-coumaric acid accumulation was improved 5-fold over that in strains expressing previously characterized tyrosine ammonia-lyases.
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46
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Nguyen QNN, Lodewyk MW, Bezer S, Gagné MR, Waters ML, Tantillo DJ. Effects of Helix Macrodipole and Local Interactions on Catalysis of Acyl Transfer by α-Helical Peptides. ACS Catal 2015. [DOI: 10.1021/cs5019277] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Q. Nhu N. Nguyen
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
| | - Michael W. Lodewyk
- Physical Science Department, Butte College, Oroville, California 95965, United States
| | - Silvia Bezer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Michel R. Gagné
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Marcey L. Waters
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Dean J. Tantillo
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
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47
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Tonnessen BW, Manosalva P, Lang JM, Baraoidan M, Bordeos A, Mauleon R, Oard J, Hulbert S, Leung H, Leach JE. Rice phenylalanine ammonia-lyase gene OsPAL4 is associated with broad spectrum disease resistance. PLANT MOLECULAR BIOLOGY 2015; 87:273-86. [PMID: 25515696 DOI: 10.1007/s11103-014-0275-9] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 12/09/2014] [Indexed: 05/21/2023]
Abstract
Most agronomically important traits, including resistance against pathogens, are governed by quantitative trait loci (QTL). QTL-mediated resistance shows promise of being effective and long-lasting against diverse pathogens. Identification of genes controlling QTL-based disease resistance contributes to breeding for cultivars that exhibit high and stable resistance. Several defense response genes have been successfully used as good predictors and contributors to QTL-based resistance against several devastating rice diseases. In this study, we identified and characterized a rice (Oryza sativa) mutant line containing a 750 bp deletion in the second exon of OsPAL4, a member of the phenylalanine ammonia-lyase gene family. OsPAL4 clusters with three additional OsPAL genes that co-localize with QTL for bacterial blight and sheath blight disease resistance on rice chromosome 2. Self-pollination of heterozygous ospal4 mutant lines produced no homozygous progeny, suggesting that homozygosity for the mutation is lethal. The heterozygous ospal4 mutant line exhibited increased susceptibility to three distinct rice diseases, bacterial blight, sheath blight, and rice blast. Mutation of OsPAL4 increased expression of the OsPAL2 gene and decreased the expression of the unlinked OsPAL6 gene. OsPAL2 function is not redundant because the changes in expression did not compensate for loss of disease resistance. OsPAL6 co-localizes with a QTL for rice blast resistance, and is down-regulated in the ospal4 mutant line; this may explain enhanced susceptibility to Magnoporthe oryzae. Overall, these results suggest that OsPAL4 and possibly OsPAL6 are key contributors to resistance governed by QTL and are potential breeding targets for improved broad-spectrum disease resistance in rice.
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Affiliation(s)
- Bradley W Tonnessen
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523-1177, USA
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48
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Kong JQ. Phenylalanine ammonia-lyase, a key component used for phenylpropanoids production by metabolic engineering. RSC Adv 2015. [DOI: 10.1039/c5ra08196c] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Phenylalanine ammonia-lyase, a versatile enzyme with industrial and medical applications.
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Affiliation(s)
- Jian-Qiang Kong
- Institute of Materia Medica
- Chinese Academy of Medical Sciences & Peking Union Medical College
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products
- Beijing
- China
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49
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Zhang X, Liu CJ. Multifaceted regulations of gateway enzyme phenylalanine ammonia-lyase in the biosynthesis of phenylpropanoids. MOLECULAR PLANT 2015; 8:17-27. [PMID: 25578269 DOI: 10.1016/j.molp.2014.11.001] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 10/25/2014] [Indexed: 05/03/2023]
Abstract
Phenylpropanoid biosynthesis in plants engenders a vast variety of aromatic metabolites critically important for their growth, development, and environmental adaptation. Some of these aromatic compounds have high economic value. Phenylalanine ammonia-lyase (PAL) is the first committed enzyme in the pathway; it diverts the central flux of carbon from the primary metabolism to the synthesis of myriad phenolics. Over the decades, many studies have shown that exquisite regulatory mechanisms at multiple levels control the transcription and the enzymatic activity of PALs. In this review, a current overview of our understanding of the complicated regulatory mechanisms governing the activity of PAL is presented; recent progress in unraveling its post-translational modifications, its metabolite feedback regulation, and its enzyme organization is highlighted.
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Affiliation(s)
- Xuebin Zhang
- Biological, Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Chang-Jun Liu
- Biological, Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973, USA.
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50
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Biosynthesis of crocacin involves an unusual hydrolytic release domain showing similarity to condensation domains. ACTA ACUST UNITED AC 2014; 21:855-65. [PMID: 24981773 DOI: 10.1016/j.chembiol.2014.05.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/12/2014] [Accepted: 05/15/2014] [Indexed: 11/20/2022]
Abstract
The crocacins are potent antifungal and cytotoxic natural compounds from myxobacteria of the genus Chondromyces. Although total synthesis approaches have been reported, the molecular and biochemical basis guiding the formation of the linear crocacin scaffold has remained unknown. Along with the identification and functional analysis of the crocacin biosynthetic gene cluster from Chondromyces crocatus Cm c5, we here present the identification and biochemical characterization of an unusual chain termination domain homologous to condensation domains responsible for hydrolytic release of the product from the assembly line. In particular, gene inactivation studies and in vitro experiments using the heterologously produced domain CroK-C2 confirm this surprising role giving rise to the linear carboxylic acid. Additionally, we determined the kinetic parameters of CroK-C2 by monitoring hydrolytic cleavage of the substrate mimic N-acetylcysteaminyl-crocacin B using an innovative high-performance liquid chromatography mass spectrometry-based assay.
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