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Zhang DQ, Liu XY, Qiu LF, Liu ZR, Yang YP, Huang L, Wang SY, Zhang JQ. Two chromosome-level genome assemblies of Rhodiola shed new light on genome evolution in rapid radiation and evolution of the biosynthetic pathway of salidroside. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:464-482. [PMID: 37872890 DOI: 10.1111/tpj.16501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/25/2023]
Abstract
Rhodiola L. is a genus that has undergone rapid radiation in the mid-Miocene and may represent a typic case of adaptive radiation. Many species of Rhodiola have also been widely used as an important adaptogen in traditional medicines for centuries. However, a lack of high-quality chromosome-level genomes hinders in-depth study of its evolution and biosynthetic pathway of secondary metabolites. Here, we assembled two chromosome-level genomes for two Rhodiola species with different chromosome number and sexual system. The assembled genome size of R. chrysanthemifolia (2n = 14; hermaphrodite) and R. kirilowii (2n = 22; dioecious) were of 402.67 and 653.62 Mb, respectively, with approximately 57.60% and 69.22% of transposable elements (TEs). The size difference between the two genomes was mostly due to proliferation of long terminal repeat-retrotransposons (LTR-RTs) in the R. kirilowii genome. Comparative genomic analysis revealed possible gene families responsible for high-altitude adaptation of Rhodiola, including a homolog of plant cysteine oxidase 2 gene of Arabidopsis thaliana (AtPCO2), which is part of the core molecular reaction to hypoxia and contributes to the stability of Group VII ethylene response factors (ERF-VII). We found extensive chromosome fusion/fission events and structural variations between the two genomes, which might have facilitated the initial rapid radiation of Rhodiola. We also identified candidate genes in the biosynthetic pathway of salidroside. Overall, our results provide important insights into genome evolution in plant rapid radiations, and possible roles of chromosome fusion/fission and structure variation played in rapid speciation.
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Affiliation(s)
- Dan-Qing Zhang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, China
| | - Xiao-Ying Liu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, China
| | - Lin-Feng Qiu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, China
| | - Zhao-Rui Liu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, China
| | - Ya-Peng Yang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, China
| | - Long Huang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, China
| | - Shi-Yu Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, China
| | - Jian-Qiang Zhang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, China
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Watkins JL, Li Q, Yeaman S, Facchini PJ. Elucidation of the mescaline biosynthetic pathway in peyote (Lophophora williamsii). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:635-649. [PMID: 37675639 DOI: 10.1111/tpj.16447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023]
Abstract
Peyote (Lophophora williamsii) is an entheogenic and medicinal cactus native to the Chihuahuan desert. The psychoactive and hallucinogenic properties of peyote are principally attributed to the phenethylamine derivative mescaline. Despite the isolation of mescaline from peyote over 120 years ago, the biosynthetic pathway in the plant has remained undiscovered. Here, we use a transcriptomics and homology-guided gene discovery strategy to elucidate a near-complete biosynthetic pathway from l-tyrosine to mescaline. We identified a cytochrome P450 that catalyzes the 3-hydroxylation of l-tyrosine to l-DOPA, a tyrosine/DOPA decarboxylase yielding dopamine, and four substrate-specific and regiospecific substituted phenethylamine O-methyltransferases. Biochemical assays with recombinant enzymes or functional analyses performed by feeding putative precursors to engineered yeast (Saccharomyces cerevisiae) strains expressing candidate peyote biosynthetic genes were used to determine substrate specificity, which served as the basis for pathway elucidation. Additionally, an N-methyltransferase displaying broad substrate specificity and leading to the production of N-methylated phenethylamine derivatives was identified, which could also function as an early step in the biosynthesis of tetrahydroisoquinoline alkaloids in peyote.
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Affiliation(s)
- Jacinta L Watkins
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Qiushi Li
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
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Hiura T, Yoshida H, Miyata U, Asami T, Suzuki Y. Conferring High IAA Productivity on Low-IAA-Producing Organisms with PonAAS2, an Aromatic Aldehyde Synthase of a Galling Sawfly, and Identification of Its Inhibitor. INSECTS 2023; 14:598. [PMID: 37504604 PMCID: PMC10380194 DOI: 10.3390/insects14070598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023]
Abstract
Gall-inducing insects often contain high concentrations of phytohormones, such as auxin and cytokinin, which are suggested to be involved in gall induction, but no conclusive evidence has yet been obtained. There are two possible approaches to investigating the importance of phytohormones in gall induction: demonstrating either that high phytohormone productivity can induce gall-inducing ability in non-gall-inducing insects or that the gall-inducing ability is inhibited when phytohormone productivity in galling insects is suppressed. In this study, we show that the overexpression of PonAAS2, which encodes an aromatic aldehyde synthase (AAS) responsible for the rate-limiting step in indoleacetic acid (IAA) biosynthesis in a galling sawfly (Pontania sp.) that contains high levels of endogenous IAA, conferred high IAA productivity on Caenorhabditis elegans, as the model system. This result strongly suggests that PonAAS2 can also confer high IAA productivity on low-IAA-producing insects. We also successfully identified an inhibitor of PonAAS2 in a chemical library. This highly selective inhibitor showed stronger inhibitory activity against AAS than against aromatic amino acid decarboxylase, which belongs to the same superfamily as AAS. We also confirm that this inhibitor clearly inhibited IAA productivity in the high-IAA-producing C. elegans engineered here.
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Affiliation(s)
- Takeshi Hiura
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-0054, Japan
- Department of Food and Life Sciences, College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami-machi, Inashiki-gun, Ibaraki 300-0393, Japan
| | - Hibiki Yoshida
- Department of Food and Life Sciences, College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami-machi, Inashiki-gun, Ibaraki 300-0393, Japan
| | - Umi Miyata
- Department of Food and Life Sciences, College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami-machi, Inashiki-gun, Ibaraki 300-0393, Japan
| | - Tadao Asami
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yoshihito Suzuki
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-0054, Japan
- Department of Food and Life Sciences, College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami-machi, Inashiki-gun, Ibaraki 300-0393, Japan
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Li X, Weth O, Haeberlein S, Grevelding CG. Molecular characterization of Sm tdc-1 and Sm ddc-1 discloses roles as male-competence factors for the sexual maturation of Schistosoma mansoni females. Front Cell Infect Microbiol 2023; 13:1173557. [PMID: 37305409 PMCID: PMC10252128 DOI: 10.3389/fcimb.2023.1173557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/27/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Schistosomes are the only mammalian flatworms that have evolved separate sexes. A key question of schistosome research is the male-dependent sexual maturation of the female since a constant pairing contact with a male is required for the onset of gonad development in the female. Although this phenomenon is long known, only recently a first peptide-based pheromone of males was identified that contributes to the control of female sexual development. Beyond this, our understanding of the molecular principles inducing the substantial developmental changes in a paired female is still rudimentary. Objectives Previous transcriptomic studies have consistently pointed to neuronal genes being differentially expressed and upregulated in paired males. These genes included Smp_135230 and Smp_171580, both annotated as aromatic-L-amino-acid decarboxylases (DOPA decarboxylases). Here, we characterized both genes and investigated their roles in male-female interaction of S. mansoni. Methodologies/findings Sequence analyses indicated that Smp_135230 represents an L-tyrosine decarboxylase (Smtdc-1), whereas Smp_171580 represents a DOPA decarboxylase (Smddc-1). By qRT-PCR, we confirmed the male-specific and pairing-dependent expression of both genes with a significant bias toward paired males. RNA-interference experiments showed a strong influence of each gene on gonad differentiation in paired females, which was enhanced by double knockdown. Accordingly, egg production was significantly reduced. By confocal laser scanning microscopy, a failure of oocyte maturation was found in paired knockdown females. Whole-mount in situ hybridization patterns exhibited the tissue-specific occurrence of both genes in particular cells at the ventral surface of the male, the gynecophoral canal, which represents the physical interface of both genders. These cells probably belong to the predicted neuronal cluster 2 of S. mansoni. Conclusion Our results suggest that Smtdc-1 and Smddc-2 are male-competence factors that are expressed in neuronal cells at the contact zone between the genders as a response of pairing to subsequently control processes of female sexual maturation.
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Huang H, He Y, Cui A, Sun L, Han M, Wang J, Rui C, Lei Y, Liu X, Xu N, Zhang H, Zhang Y, Fan Y, Feng X, Ni K, Jiang J, Zhang X, Chen C, Wang S, Chen X, Lu X, Wang D, Wang J, Yin Z, Qaraevna BZ, Guo L, Zhao L, Ye W. Genome-wide identification of GAD family genes suggests GhGAD6 functionally respond to Cd2+ stress in cotton. Front Genet 2022; 13:965058. [PMID: 36176295 PMCID: PMC9513066 DOI: 10.3389/fgene.2022.965058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/10/2022] [Indexed: 11/25/2022] Open
Abstract
Glutamate decarboxylase (GAD) mainly regulated the biosynthesis of γ-aminobutyric acid (GABA) and played an important role in plant growth and stress resistance. To explore the potential function of GAD in cotton growth, the genome-wide identification, structure, and expression analysis of GAD genes were performed in this study. There were 10, 9, 5, and 5 GAD genes identified in G. hirsutum, G. barbadense, G. arboreum, and G. raimondii, respectively. GAD was divided into four clades according to the protein motif composition, gene structure, and phylogenetic relationship. The segmental duplication was the main way of the GAD gene family evolution. Most GhGADs respond to abiotic stress. Clade Ⅲ GAD was induced by Cd2+ stress, especially GhGAD6, and silencing GhGAD6 would lead to more serious Cd2+ poisoning in cotton. The oxidative damage caused by Cd2+ stress was relieved by increasing the GABA content. It was speculated that the decreased expression of GhGAD6 reduced the content of GABA in vivo and caused the accumulation of ROS. This study will further expand our understanding of the relationship between the evolution and function of the GhGAD gene family and provide new genetic resources for cotton breeding under environmental stress and phytoremediation.
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Affiliation(s)
- Hui Huang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Yunxin He
- Hunan Institute of Cotton Science, Changde, China
| | - Aihua Cui
- Cotton Research Institute of Jiangxi Province, Jiujiang, China
| | - Liangqing Sun
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Mingge Han
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Jing Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Cun Rui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Yuqian Lei
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Xiaoyu Liu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Nan Xu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Hong Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Yuexin Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Yapeng Fan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Xixian Feng
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Kesong Ni
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Jie Jiang
- Hunan Institute of Cotton Science, Changde, China
| | | | - Chao Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Delong Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Junjuan Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Zujun Yin
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Bobokhonova Zebinisso Qaraevna
- Department Cotton Growing, Genetics, Breeding and Seed, Tajik Agrarian University Named Shirinsho Shotemur Dushanbe, Dushanbe, Tajikistan
| | - Lixue Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
- *Correspondence: Wuwei Ye,
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Qiao C, Chen F, Liu Z, Huang T, Li W, Zhang G, Luo Y. Functional characterization of a catalytically promiscuous tryptophan decarboxylase from camptothecin-producing Camptotheca acuminata. FRONTIERS IN PLANT SCIENCE 2022; 13:987348. [PMID: 36061783 PMCID: PMC9433702 DOI: 10.3389/fpls.2022.987348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Tryptophan decarboxylases (TDCs) are a group of pyridoxal 5'-phosphate-dependent enzymes involved in the enzymatic conversion of tryptophan into tryptamine, a critical biogenic amine. We herein mined and cloned a TDC-encoding gene, CaTDC3, from camptothecin-producing plant Camptotheca acuminata. The intact CaTDC3 was heterologously overexpressed in Escherichia coli and the recombinant CaTDC3 was purified to homogeneity. High-performance liquid chromatography (HPLC)-diode array detector (DAD) and high resolution mass spectrometry (HRMS) data analyses of the CaTDC3-catalyzed reaction mixture confirmed the catalytically decarboxylative activity of CaTDC3. CaTDC3 shows strict stereoselectivity for L-tryptophan. Homology modeling and molecular docking implied CaTDC3's recognition of L-tryptophan derivatives and analogs. Substrate scope investigations revealed that the appropriate substituent groups on the indole ring, i.e., hydroxylated and halogenated L-tryptophans, could be recognized by CaTDC3 and the decarboxylation reactions generated the corresponding tryptamines. The Cβ -methyl-L-tryptophans were decarboxylated by CaTDC3 efficiently. 1-Thio-L-tryptophan, the NH group of the indole ring replaced by an S atom, could be decarboxylated by CaTDC3. CaTDC3 catalyzed the decarboxylation of 7-aza-L-tryptophan, an N displacement of the C on the aromatic ring, to afford 7-aza-tryptamine. L-Kynurenine, an L-tryptophan degradation product, could be decarboxylated by CaTDC3. The present works uncover a catalytically promiscuous TDC and the TDC is a versatile decarboxylase in synthetic biology for specialized pharmaceutically important substances.
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Affiliation(s)
- Chong Qiao
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Chen
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhan Liu
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tianfang Huang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Wei Li
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Guolin Zhang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yinggang Luo
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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Han SW, Shin JS. Aromatic L-amino acid decarboxylases: mechanistic features and microbial applications. Appl Microbiol Biotechnol 2022; 106:4445-4458. [DOI: 10.1007/s00253-022-12028-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/04/2022] [Accepted: 06/10/2022] [Indexed: 11/02/2022]
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Rattan S, Kumar P, Kaur E, Sood A, Acharya V, Warghat AR. Comparative transcriptome and tissue-specific expression analysis of genes reveal tissue-cultured plants as an alternative source for phenylethanoids and phenylpropanoids in Rhodiola imbricata (Edgew.). Gene X 2022; 836:146672. [PMID: 35714804 DOI: 10.1016/j.gene.2022.146672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/30/2022] [Accepted: 06/10/2022] [Indexed: 11/29/2022] Open
Abstract
Rhodiola imbricata (Crassulaceae) is a traditional trans-Himalayan endangered medicinal herb with immense therapeutic applications. Over the years, over-exploitation, un-managed harvesting, and lack of captive cultivation procedures persuaded threat to its wild habitat. Plant tissue culture and RNA-Seq-based molecular bioprospection of key regulatory genes aid the understanding of molecular dynamics involved in specialized metabolites (phenylethanoids and phenylpropanoids) biosynthesis and its sustainable production. Hence, comparative transcriptomic analysis was performed using leaf and root tissues from the wild and tissue-cultured plants, revealing tissue-specific production of salidroside and rosavin. The transcriptome profiling resulted in 345 million high-quality reads yielding 92,380 unique transcripts with an N50 of 1260 bp. Tissue-specific gene expression analysis revealed that both phenylethanoids and phenylpropanoids biosynthesis are predominantly associated with the shikimate pathway. In addition to RNA-Seq data, the downstream biosynthesis pathways genes viz., phospho-2-dehydro-3-deoxyheptonate aldolase (DAHPS), 3-dehydroquinate synthase (DHQS), shikimate kinase (SK), chorismate mutase (CM), arogenate dehydrogenase (TYRAAT), aromatic-L-amino-acid decarboxylase (TDC), phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4-CL), cinnamoyl-CoA reductase (CCR), and cinnamyl alcohol dehydrogenase (CAD) showed higher expression pattern in wild plant tissues compared to tissue-cultured plants. The transcript fold expression determined by RT-qPCR results followed similar patterns as those observed in RNA-seq and targeted metabolite profiling data. Salidroside and rosavin content in wild plants exhibited 2.40 fold and 1.77 fold increase accumulation compared to the tissue-cultured plant. The present investigation explained the tissue and condition-specific significant differences between the expression of proposed biosynthetic pathway genes and salidroside and rosavin content. Additionally, NAC, bHLH, and ARF were the most abundant transcription factor families found in the transcriptomic analysis of R. imbricata. The generated transcriptome dataset provides a valuable gene(s)/transcription factors hub that can be used for the sustainable production of salidroside and rosavin in R. imbricata under tissue culture conditions.
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Affiliation(s)
- Shiv Rattan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Pankaj Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Ekjot Kaur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Archit Sood
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Vishal Acharya
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ashish R Warghat
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Machine learning discovery of missing links that mediate alternative branches to plant alkaloids. Nat Commun 2022; 13:1405. [PMID: 35296652 PMCID: PMC8927377 DOI: 10.1038/s41467-022-28883-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/16/2022] [Indexed: 01/12/2023] Open
Abstract
Engineering the microbial production of secondary metabolites is limited by the known reactions of correctly annotated enzymes. Therefore, the machine learning discovery of specialized enzymes offers great potential to expand the range of biosynthesis pathways. Benzylisoquinoline alkaloid production is a model example of metabolic engineering with potential to revolutionize the paradigm of sustainable biomanufacturing. Existing bacterial studies utilize a norlaudanosoline pathway, whereas plants contain a more stable norcoclaurine pathway, which is exploited in yeast. However, committed aromatic precursors are still produced using microbial enzymes that remain elusive in plants, and additional downstream missing links remain hidden within highly duplicated plant gene families. In the current study, machine learning is applied to predict and select plant missing link enzymes from homologous candidate sequences. Metabolomics-based characterization of the selected sequences reveals potential aromatic acetaldehyde synthases and phenylpyruvate decarboxylases in reconstructed plant gene-only benzylisoquinoline alkaloid pathways from tyrosine. Synergistic application of the aryl acetaldehyde producing enzymes results in enhanced benzylisoquinoline alkaloid production through hybrid norcoclaurine and norlaudanosoline pathways. Producing plant secondary metabolites by microbes is limited by the known enzymatic reactions. Here, the authors apply machine learning to predict missing link enzymes of benzylisoquinoline alkaloid (BIA) biosynthesis in Papaver somniferum, and validate the specialized activities through heterologous production.
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10
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Identification and Functional Characterization of Tyrosine Decarboxylase from Rehmannia glutinosa. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27051634. [PMID: 35268735 PMCID: PMC8912026 DOI: 10.3390/molecules27051634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 11/17/2022]
Abstract
Rehmannia glutinosa is an important medicinal plant that has long been used in Chinese traditional medicine. Acteoside, one of the bioactive components from R. glutinosa, possessed various pharmacological activities for human health; however, the molecular mechanism of acteoside formation is not fully understood. In the current study, a novel tyrosine decarboxylase (designated as RgTyDC2) was identified from the R. glutinosa transcriptome. Biochemical analysis of RgTyDC2 showed RgTyDC2 uses tyrosine and dopa as the substrate to produce tyramine and dopamine, respectively, and it displays higher catalytic efficiency toward tyrosine than dopa. Moreover, the transcript level of RgTyDC2 was consistent with the accumulation pattern of acteoside in R. glutinosa, supporting its possible role in the biosynthesis of acteoside in vivo.
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Choi Y, Han SW, Kim JS, Jang Y, Shin JS. Biochemical characterization and synthetic application of aromatic L-amino acid decarboxylase from Bacillus atrophaeus. Appl Microbiol Biotechnol 2021; 105:2775-2785. [PMID: 33713143 DOI: 10.1007/s00253-021-11122-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 01/04/2021] [Accepted: 01/16/2021] [Indexed: 12/29/2022]
Abstract
Aromatic L-amino acid decarboxylases (AADCs) are ubiquitously found in higher organisms owing to their physiological role in the synthesis of neurotransmitters and alkaloids. However, bacterial AADC has not attracted much attention because of its rather limited availability and narrow substrate range. Here, we examined the biochemical properties of AADC from Bacillus atrophaeus (AADC-BA) and assessed the synthetic feasibility of the enzyme for the preparation of monoamine neurotransmitters. AADC-BA was expressed in Escherichia coli BL21(DE3) and the purified enzyme showed a specific activity of 2.6 ± 0.4 U/mg for 10 mM L-phenylalanine (L-Phe) at 37 °C. AADC-BA showed optimal pH and temperature ranges at 7-8 and 37-45 °C, respectively. The KM and kcat values for L-Phe were 7.2 mM and 7.4 s-1, respectively, at pH 7.0 and 37 °C. Comparison of the kinetic constants at different temperatures revealed that the temperature dependency of the enzyme was mainly determined by catalytic turnover rather than substrate binding. AADC-BA showed a broad substrate scope for various aromatic amino acids, including L-Phe, L-tryptophan (610% relative to L-Phe), L-tyrosine (12%), 3,4-dihydroxyphenyl-L-alanine (24%), 5-hydroxy-L-tryptophan (L-HTP, 71%), 4-chloro-L-phenylalanine (520%), and 4-nitro-L-phenylalanine (450%). Homology modeling and docking simulations were carried out and were consistent with the observed substrate specificity. To demonstrate the synthetic potential of AADC-BA, we carried out the production of serotonin by decarboxylation of L-HTP. The reaction yield of serotonin reached 98% after 1 h at the reaction conditions of 50 mM L-HTP and 4 U/mL AADC-BA. Moreover, we carried out preparative-scale decarboxylation of L-Phe (100 mM in 40-mL reaction mixture) and isolated the resulting 2-phenylethylamine (51% recovery yield). We expect that the broad substrate specificity of AADC-BA can be exploited to produce various aromatic biogenic amines. KEY POINTS: • AADC-BA showed broad substrate specificity for various aromatic amino acids. • The substrate specificity was elucidated by in silico structural modeling. • The synthetic potential of AADC-BA was demonstrated for the production of biogenic amines.
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Affiliation(s)
- Yeri Choi
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Sang-Woo Han
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Jun-Sung Kim
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Youngho Jang
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Jong-Shik Shin
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea.
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Jadaun JS, Kushwaha AK, Sangwan NS, Narnoliya LK, Mishra S, Sangwan RS. WRKY1-mediated regulation of tryptophan decarboxylase in tryptamine generation for withanamide production in Withania somnifera (Ashwagandha). PLANT CELL REPORTS 2020; 39:1443-1465. [PMID: 32789542 DOI: 10.1007/s00299-020-02574-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/14/2020] [Accepted: 07/22/2020] [Indexed: 06/11/2023]
Abstract
WsWRKY1-mediated transcriptional modulation of Withania somnifera tryptophan decarboxylase gene (WsTDC) helps to regulate fruit-specific tryptamine generation for production of withanamides. Withania somnifera is a highly valued medicinal plant. Recent demonstration of novel indolyl metabolites called withanamides in its fruits (berries) prompted us to investigate its tryptophan decarboxylase (TDC), as tryptophan is invariably a precursor for indole moiety. TDC catalyzes conversion of tryptophan into tryptamine, and the catalytic reaction constitutes a committed metabolic step for synthesis of an array of indolyl metabolites. The TDC gene (WsTDC) was cloned from berries of the plant and expressed in E. coli. The recombinant enzyme was purified and characterized for its catalytic attributes. Catalytic and structural aspects of the enzyme indicated its regulatory/rate-limiting significance in generation of the indolyl metabolites. Novel tissue-wise and developmentally differential abundance of WsTDC transcripts reflected its preeminent role in withanamide biogenesis in the fruits. Transgenic lines overexpressing WsTDC gene showed accumulation of tryptamine at significantly higher levels, while lines silenced for WsTDC exhibited considerably depleted levels of tryptamine. Cloning and sequence analysis of promoter of WsTDC revealed the presence of W-box in it. Follow-up studies on isolation of WsWRKY1 transcription factor and its overexpression in W. somnifera revealed that WsTDC expression was substantially induced by WsWRKY1 resulting in overproduction of tryptamine. The study invokes a key role of TDC in regulating the indolyl secondary metabolites through enabling elevated flux/supply of tryptamine at multiple levels from gene expression to catalytic attributes overall coordinated by WsWRKY1. This is the first biochemical, molecular, structural, physiological and regulatory description of a fruit-functional TDC.
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Affiliation(s)
- Jyoti Singh Jadaun
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Amit Kumar Kushwaha
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Neelam S Sangwan
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India.
- Department of Biochemistry, Central University of Haryana, Mahendergarh, Haryana, 123031, India.
| | - Lokesh Kumar Narnoliya
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Smrati Mishra
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Rajender Singh Sangwan
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India.
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India.
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A single amino acid substitution converts a histidine decarboxylase to an imidazole acetaldehyde synthase. Arch Biochem Biophys 2020; 693:108551. [PMID: 32871134 DOI: 10.1016/j.abb.2020.108551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 12/25/2022]
Abstract
Histidine decarboxylase (HDC; EC 4.1.1.22), an enzyme that catalyzes histamine synthesis with high substrate specificity, is a member of the group II pyridoxal 5'-phosphate (PLP) -dependent decarboxylase family. Tyrosine is a conserved residue among group II PLP-dependent decarboxylases. Human HDC has a Y334 located on a catalytically important loop at the active site. In this study, we demonstrated that a HDC Y334F mutant is capable of catalyzing the decarboxylation-dependent oxidative deamination of histidine to yield imidazole acetaldehyde. Replacement of the active-site Tyr with Phe in group II PLP-dependent decarboxylases, including mammalian aromatic amino acid decarboxylase, plant tyrosine/DOPA decarboxylase, and plant tryptophan decarboxylase, is expected to result in the same functional change, given that a Y-to-F substitution at the corresponding residue (number 260) in the HDC of Morganella morganii, another group II PLP-dependent decarboxylase, yielded the same effect. Thus, it was suggested that the loss of the OH moiety from the active-site Tyr residue of decarboxylase uniquely converts the enzyme to an aldehyde synthase.
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Lichman BR. The scaffold-forming steps of plant alkaloid biosynthesis. Nat Prod Rep 2020; 38:103-129. [PMID: 32745157 DOI: 10.1039/d0np00031k] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Alkaloids from plants are characterised by structural diversity and bioactivity, and maintain a privileged position in both modern and traditional medicines. In recent years, there have been significant advances in elucidating the biosynthetic origins of plant alkaloids. In this review, I will describe the progress made in determining the metabolic origins of the so-called true alkaloids, specialised metabolites derived from amino acids containing a nitrogen heterocycle. By identifying key biosynthetic steps that feature in the majority of pathways, I highlight the key roles played by modifications to primary metabolism, iminium reactivity and spontaneous reactions in the molecular and evolutionary origins of these pathways.
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Affiliation(s)
- Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK.
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Zhou Y, Liao L, Liu X, Liu B, Chen X, Guo Y, Huang C, Zhao Y, Zeng Z. Crystal structure of Oryza sativa TDC reveals the substrate specificity for TDC-mediated melatonin biosynthesis. J Adv Res 2020; 24:501-511. [PMID: 32595985 PMCID: PMC7306523 DOI: 10.1016/j.jare.2020.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 04/20/2020] [Accepted: 06/08/2020] [Indexed: 01/01/2023] Open
Abstract
Plant tryptophan decarboxylase (TDC) is a type II Pyridoxal-5'-phosphate-dependent decarboxylase (PLP_DC) that could be used as a target to genetically improve crops. However, lack of accurate structural information on plant TDC hampers the understanding of its decarboxylation mechanisms. In the present study, the crystal structures of Oryza sativa TDC (OsTDC) in its complexes with pyridoxal-5'-phosphate, tryptamine and serotonin were determined. The structures provide detailed interaction information between TDC and its substrates. The Y359 residue from the loop gate is a proton donor and forms a Lewis acid-base pair with serotonin/tryptamine, which is associated with product release. The H214 residue is responsible for PLP binding and proton transfer, and its proper interaction with Y359 is essential for OsTDC enzyme activity. The extra hydrogen bonds formed between the 5-hydroxyl group of serotonin and the backbone carboxyl groups of F104 and P105 explain the discrepancy between the catalytic activity of TDC in tryptophan and in 5-hydroxytryptophan. In addition, an evolutionary analysis revealed that type II PLP_DC originated from glutamic acid decarboxylase, potentially as an adaptive evolution of mechanism in organisms in extreme environments. This study is, to our knowledge, the first to present a detailed analysis of the crystal structure of OsTDC in these complexes. The information regarding the catalytic mechanism described here could facilitate the development of protocols to regulate melatonin levels and thereby contribute to crop improvement efforts to improve food security worldwide.
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Affiliation(s)
- Yuanze Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijing Liao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xikai Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Biao Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinxin Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Chuanlong Huang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210014, China
| | - Yucheng Zhao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210014, China
| | - Zhixiong Zeng
- Shandong Provincial Key Laboratory of Microbial Engineering, College of Bioengineering, Qilu University of Technology, Jinan 250353, China
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Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins. Proc Natl Acad Sci U S A 2020; 117:10806-10817. [PMID: 32371491 DOI: 10.1073/pnas.1920097117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Radiation of the plant pyridoxal 5'-phosphate (PLP)-dependent aromatic l-amino acid decarboxylase (AAAD) family has yielded an array of paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either the decarboxylation or decarboxylation-dependent oxidative deamination of aromatic l-amino acids to produce aromatic monoamines or aromatic acetaldehydes, respectively. These compounds serve as key precursors for the biosynthesis of several important classes of plant natural products, including indole alkaloids, benzylisoquinoline alkaloids, hydroxycinnamic acid amides, phenylacetaldehyde-derived floral volatiles, and tyrosol derivatives. Here, we present the crystal structures of four functionally distinct plant AAAD paralogs. Through structural and functional analyses, we identify variable structural features of the substrate-binding pocket that underlie the divergent evolution of substrate selectivity toward indole, phenyl, or hydroxyphenyl amino acids in plant AAADs. Moreover, we describe two mechanistic classes of independently arising mutations in AAAD paralogs leading to the convergent evolution of the derived aldehyde synthase activity. Applying knowledge learned from this study, we successfully engineered a shortened benzylisoquinoline alkaloid pathway to produce (S)-norcoclaurine in yeast. This work highlights the pliability of the AAAD fold that allows change of substrate selectivity and access to alternative catalytic mechanisms with only a few mutations.
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Xu JJ, Fang X, Li CY, Yang L, Chen XY. General and specialized tyrosine metabolism pathways in plants. ABIOTECH 2020; 1:97-105. [PMID: 36304719 PMCID: PMC9590561 DOI: 10.1007/s42994-019-00006-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/06/2019] [Indexed: 11/25/2022]
Abstract
The tyrosine metabolism pathway serves as a starting point for the production of a variety of structurally diverse natural compounds in plants, such as tocopherols, plastoquinone, ubiquinone, betalains, salidroside, benzylisoquinoline alkaloids, and so on. Among these, tyrosine-derived metabolites, tocopherols, plastoquinone, and ubiquinone are essential to plant survival. In addition, this pathway provides us essential micronutrients (e.g., vitamin E and ubiquinone) and medicine (e.g., morphine, salidroside, and salvianolic acid B). However, our knowledge of the plant tyrosine metabolism pathway remains rudimentary, and genes encoding the pathway enzymes have not been fully defined. In this review, we summarize and discuss recent advances in the tyrosine metabolism pathway, key enzymes, and important tyrosine-derived metabolites in plants.
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Affiliation(s)
- Jing-Jing Xu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602 People’s Republic of China
| | - Xin Fang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences Kunming, Kunming, 650201 Yunnan People’s Republic of China
| | - Chen-Yi Li
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 People’s Republic of China
- University of Chinese Academy of Sciences, Shanghai, 200032 People’s Republic of China
| | - Lei Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602 People’s Republic of China
| | - Xiao-Ya Chen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602 People’s Republic of China
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 People’s Republic of China
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Wang H, Yu J, Satoh Y, Nakagawa Y, Tanaka R, Kato K, Yao M. Crystal structures clarify cofactor binding of plant tyrosine decarboxylase. Biochem Biophys Res Commun 2020; 523:500-505. [DOI: 10.1016/j.bbrc.2019.12.077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 12/16/2019] [Indexed: 10/25/2022]
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Torrens-Spence MP, Liu CT, Weng JK. Engineering New Branches of the Kynurenine Pathway To Produce Oxo-(2-aminophenyl) and Quinoline Scaffolds in Yeast. ACS Synth Biol 2019; 8:2735-2745. [PMID: 31714755 DOI: 10.1021/acssynbio.9b00368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The kynurenine pathway, named after its nonproteinogenic amino acid precursor l-kynurenine, is responsible for the de novo biosynthesis of nicotinamide adenine dinucleotide (NAD+) in eukaryotes. Oxo-(2-aminophenyl) and quinoline molecules downstream from l-kynurenine also serve as antagonists of several receptors of the central nervous system in mammals. In this study, we engineered new biosynthetic routes in yeast Saccharomyces cerevisiae to produce a suite of l-kynurenine-derived natural products. Overexpression of Homo sapiens l-tryptophan 2,3-dioxygenase (HsTDO2) in S. cerevisiae led to a marked increase in the production of l-kynurenine and downstream metabolites. Using this background, new branch points to the kynurenine pathway were added through the incorporation of a Psilocybe cubensis noncanonical L-aromatic amino acid decarboxylase (PcncAAAD) capable of catalyzing both decarboxylation and decarboxylation-dependent oxidative-deamination reactions of l-kynurenine and 3-hydroxy-l-kynurenine to yield their corresponding monoamines, aldehydes, and downstream nonenzymatically cyclized quinolines. The PcncAAAD-catalyzed decarboxylation products, kynuramine and 3-hydroxykynuramine, could further be converted to quinoline scaffolds through the addition of H. sapiens monoamine oxidase A (HsMAO-A). Finally, by incorporating upstream regiospecific l-tryptophan halogenases into the engineering scheme, we produced a number of halogenated oxo-(2-aminophenyl) and quinoline compounds. This work illustrates a synthetic biology approach to expand primary metabolic pathways in the production of novel natural-product-like scaffolds amenable for downstream functionalization.
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Affiliation(s)
| | - Chun-Ting Liu
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, Massachusetts 02142, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, Massachusetts 02142, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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An Aromatic Aldehyde Synthase Controls the Synthesis of Hydroxytyrosol Derivatives Present in Virgin Olive Oil. Antioxidants (Basel) 2019; 8:antiox8090352. [PMID: 31480559 PMCID: PMC6770214 DOI: 10.3390/antiox8090352] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 01/30/2023] Open
Abstract
The phenolic composition of virgin olive oil (VOO) is strongly determined by the content and distribution of secoiridoid phenolic glucosides present in the olive fruit. Among them, oleuropein is the most abundant in olive mesocarp and is characterized by containing an hydroxytyrosol residue in its chemical structure. Hydroxytyrosol-containing molecules are those that exhibit the most important biological activities in virgin olive oil. In this regard, we identified an aromatic aldehyde synthase gene (OeAAS) from an olive transcriptome, which was synthesized, expressed in Eschrichia coli, and purified its encoded protein. The recombinant OeAAS is a bifunctional enzyme catalyzing decarboxylation and amine-oxidation reactions in a single step. OeAAS displays strict substrate specificity for l-DOPA to form 2,4-dihydroxyphenylacetaldehyde, the immediate precursor of hydroxytyrosol. In addition to the biochemical characterization of the enzyme, the expression analysis carried out in different olive cultivars and ripening stages indicate that OeAAS gene is temporally regulated in a cultivar-dependent manner. High correlation coefficients were found between OeAAS expression levels and the phenolic content of olive fruits and oils, which supports a key role for OeAAS in the accumulation of hydroxytyrosol-derived secoiridoid compounds in olive fruit and virgin olive oil.
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Muñiz-Calvo S, Bisquert R, Fernández-Cruz E, García-Parrilla MC, Guillamón JM. Deciphering the melatonin metabolism in Saccharomyces cerevisiae by the bioconversion of related metabolites. J Pineal Res 2019; 66:e12554. [PMID: 30633359 DOI: 10.1111/jpi.12554] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/04/2019] [Accepted: 01/04/2019] [Indexed: 12/11/2022]
Abstract
Melatonin (Mel), originally considered a neurohormone, has been detected in beverages and food-fermented products in which yeast metabolism is highly important. This indolamine is synthesized from serotonin, with L-tryptophan being the initial substrate of both. Regarding Mel metabolism, the biosynthetic pathway in mammals consists in four-step reactions. However, six genes are implicated in the synthesis of Mel in plants, which suggest the presence of many pathways. The aim of this study was to provide new empirical data on the production of Mel and other indole-related compounds in the yeast Saccharomyces cerevisiae (S. cerevisiae). To this end, we performed the addition of the pathway intermediates in S. cerevisiae cells in different growth stages (exponential and arrested cells) to follow the bioconversion and new indolic compound production from them. The different bioconverted indolic compounds tested (L-tryptophan, 5-hydroxytryptophan, tryptamine, serotonin, N-acetylserotonin, 5-methoxytryptamine, and Mel) were analyzed by UHPLC-MS/MS from the extra- and intracellular contents. Our results showed that serotonin, in yeast, was prevalently formed via tryptophan decarboxylation, followed by tryptamine hydroxylation as in plants. Mel production from serotonin can be achieved by either N-acetylation, followed by O-methylation or O-methylation, in turn followed by N-acetylation. Accordingly, the classic pathway of Mel synthesis in vertebrates does not seems prevalent in yeast.
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Affiliation(s)
- Sara Muñiz-Calvo
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Paterna, Valencia, Spain
| | - Ricardo Bisquert
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Paterna, Valencia, Spain
| | - Edwin Fernández-Cruz
- Department of Food Science and Nutrition, Facultad de Farmacia, University of Seville, Seville, Spain
| | - María C García-Parrilla
- Department of Food Science and Nutrition, Facultad de Farmacia, University of Seville, Seville, Spain
| | - José M Guillamón
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Paterna, Valencia, Spain
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Facchiano A, Pignone D, Servillo L, Castaldo D, De Masi L. Structure and Ligands Interactions of Citrus Tryptophan Decarboxylase by Molecular Modeling and Docking Simulations. Biomolecules 2019; 9:biom9030117. [PMID: 30917613 PMCID: PMC6468663 DOI: 10.3390/biom9030117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 03/22/2019] [Indexed: 01/21/2023] Open
Abstract
In a previous work, we in silico annotated protein sequences of Citrus genus plants as putative tryptophan decarboxylase (pTDC). Here, we investigated the structural properties of Citrus pTDCs by using the TDC sequence of Catharanthus roseus as an experimentally annotated reference to carry out comparative modeling and substrate docking analyses. The functional annotation as TDC was verified by combining 3D molecular modeling and docking simulations, evidencing the peculiarities and the structural similarities with C. roseus TDC. Docking with l-tryptophan as a ligand showed specificity of pTDC for this substrate. These combined results confirm our previous in silico annotation of the examined protein sequences of Citrus as TDC and provide support for TDC activity in this plant genus.
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Affiliation(s)
- Angelo Facchiano
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Scienze dell'Alimentazione (ISA), 83100 Avellino, Italy.
| | - Domenico Pignone
- CNR, Istituto di Bioscienze e BioRisorse (IBBR), 70126 Bari, Italy.
| | - Luigi Servillo
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", 80138 Napoli, Italy.
| | - Domenico Castaldo
- Stazione Sperimentale per le Industrie delle Essenze e dei Derivati dagli Agrumi (SSEA), Azienda Speciale della Camera di Commercio di Reggio Calabria, 89125 Reggio Calabria, Italy.
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Melatonin: A Small Molecule but Important for Salt Stress Tolerance in Plants. Int J Mol Sci 2019; 20:ijms20030709. [PMID: 30736409 PMCID: PMC6387279 DOI: 10.3390/ijms20030709] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 02/03/2019] [Accepted: 02/04/2019] [Indexed: 01/09/2023] Open
Abstract
Salt stress is one of the most serious limiting factors in worldwide agricultural production, resulting in huge annual yield loss. Since 1995, melatonin (N-acetyl-5-methoxytryptamine)—an ancient multi-functional molecule in eukaryotes and prokaryotes—has been extensively validated as a regulator of plant growth and development, as well as various stress responses, especially its crucial role in plant salt tolerance. Salt stress and exogenous melatonin lead to an increase in endogenous melatonin levels, partly via the phyto-melatonin receptor CAND2/PMTR1. Melatonin plays important roles, as a free radical scavenger and antioxidant, in the improvement of antioxidant systems under salt stress. These functions improve photosynthesis, ion homeostasis, and activate a series of downstream signals, such as hormones, nitric oxide (NO) and polyamine metabolism. Melatonin also regulates gene expression responses to salt stress. In this study, we review recent literature and summarize the regulatory roles and signaling networks involving melatonin in response to salt stress in plants. We also discuss genes and gene families involved in the melatonin-mediated salt stress tolerance.
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Ni J, Xu G, Dai W, Zhao YL, Ni Y. Hyperconjugation promoted by hydrogen bonding between His98/His241 and a carboxyl group contributes to tyrosine decarboxylase catalysis. Catal Sci Technol 2019. [DOI: 10.1039/c9cy01290g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This article first demonstrates the utility of the σ → π* hyperconjugation by His98 and His241 in pyridoxal 5′-phosphate-dependent tyrosine decarboxylase.
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Affiliation(s)
- Jie Ni
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Guochao Xu
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Wei Dai
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- MOE-LSB and MOE-LSC
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
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Torrens-Spence MP, Pluskal T, Li FS, Carballo V, Weng JK. Complete Pathway Elucidation and Heterologous Reconstitution of Rhodiola Salidroside Biosynthesis. MOLECULAR PLANT 2018; 11:205-217. [PMID: 29277428 DOI: 10.1016/j.molp.2017.12.007] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/23/2017] [Accepted: 12/12/2017] [Indexed: 05/05/2023]
Abstract
Salidroside is a bioactive tyrosine-derived phenolic natural product found in medicinal plants under the Rhodiola genus. In addition to their anti-fatigue and anti-anoxia roles in traditional medicine, Rhodiola total extract and salidroside have also displayed medicinal properties as anti-cardiovascular diseases and anti-cancer agents. The resulting surge in global demand of Rhodiola plants and salidroside has driven some species close to extinction. Here, we report the full elucidation of the Rhodiola salidroside biosynthetic pathway utilizing the first comprehensive transcriptomics and metabolomics datasets for Rhodiola rosea. Unlike the previously proposed pathway involving separate decarboxylation and deamination enzymatic steps from tyrosine to the key intermediate 4-hydroxyphenylacetaldehyde (4-HPAA), Rhodiola contains a pyridoxal phosphate-dependent 4-HPAA synthase that directly converts tyrosine to 4-HPAA. We further identified genes encoding the subsequent 4-HPAA reductase and tyrosol:UDP-glucose 8-O-glucosyltransferase, respectively, to complete salidroside biosynthesis in Rhodiola. We show that heterologous production of salidroside can be achieved in the yeast Saccharomyces cerevisiae as well as the plant Nicotiana benthamiana through transgenic expression of Rhodiola salidroside biosynthetic genes. This study provides new tools for engineering sustainable production of salidroside in heterologous hosts.
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Affiliation(s)
| | - Tomáš Pluskal
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Fu-Shuang Li
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Valentina Carballo
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Fricke J, Blei F, Hoffmeister D. Enzymatic Synthesis of Psilocybin. Angew Chem Int Ed Engl 2017; 56:12352-12355. [PMID: 28763571 DOI: 10.1002/anie.201705489] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Indexed: 12/14/2022]
Abstract
Psilocybin is the psychotropic tryptamine-derived natural product of Psilocybe carpophores, the so-called "magic mushrooms". Although its structure has been known for 60 years, the enzymatic basis of its biosynthesis has remained obscure. We characterized four psilocybin biosynthesis enzymes, namely i) PsiD, which represents a new class of fungal l-tryptophan decarboxylases, ii) PsiK, which catalyzes the phosphotransfer step, iii) the methyltransferase PsiM, catalyzing iterative N-methyl transfer as the terminal biosynthetic step, and iv) PsiH, a monooxygenase. In a combined PsiD/PsiK/PsiM reaction, psilocybin was synthesized enzymatically in a step-economic route from 4-hydroxy-l-tryptophan. Given the renewed pharmaceutical interest in psilocybin, our results may lay the foundation for its biotechnological production.
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Affiliation(s)
- Janis Fricke
- Department Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Felix Blei
- Department Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Dirk Hoffmeister
- Department Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
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Affiliation(s)
- Janis Fricke
- Department Pharmazeutische Mikrobiologie am Hans-Knöll-Institut; Friedrich-Schiller-Universität; Beutenbergstraße 11a 07745 Jena Deutschland
| | - Felix Blei
- Department Pharmazeutische Mikrobiologie am Hans-Knöll-Institut; Friedrich-Schiller-Universität; Beutenbergstraße 11a 07745 Jena Deutschland
| | - Dirk Hoffmeister
- Department Pharmazeutische Mikrobiologie am Hans-Knöll-Institut; Friedrich-Schiller-Universität; Beutenbergstraße 11a 07745 Jena Deutschland
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Guan H, Song S, Robinson H, Liang J, Ding H, Li J, Han Q. Structural Basis of the Substrate Specificity and Enzyme Catalysis of a Papaver somniferum Tyrosine Decarboxylase. Front Mol Biosci 2017; 4:5. [PMID: 28232911 PMCID: PMC5299019 DOI: 10.3389/fmolb.2017.00005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 01/27/2017] [Indexed: 12/03/2022] Open
Abstract
Tyrosine decarboxylase (TyDC), a type II pyridoxal 5′-phosphate decarboxylase, catalyzes the decarboxylation of tyrosine. Due to a generally high sequence identity to other aromatic amino acid decarboxylases (AAADs), primary sequence information is not enough to understand substrate specificities with structural information. In this study, we selected a typical TyDC from Papaver somniferum as a model to study the structural basis of AAAD substrate specificities. Analysis of the native P. somniferum TyDC crystal structure and subsequent molecular docking and dynamics simulation provide some structural bases that explain substrate specificity for tyrosine. The result confirmed the previous proposed mechanism for the enzyme selectivity of indolic and phenolic substrates. Additionally, this study yields the first crystal structure for a plant type II pyridoxal-5'-phosphate decarboxylase.
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Affiliation(s)
- Huai Guan
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan UniversityHainan, China; Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan UniversityHainan, China; Laboratory of Tropical Veterinary Medicine and Vector Biology, Hainan UniversityHaikou, Hainan, China
| | - Shuaibao Song
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan UniversityHainan, China; Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan UniversityHainan, China; Laboratory of Tropical Veterinary Medicine and Vector Biology, Hainan UniversityHaikou, Hainan, China
| | - Howard Robinson
- Biology Department, Brookhaven National Laboratory, Upton New York, NY, USA
| | - Jing Liang
- Department of Biochemistry, Virginia Tech Blacksburg, VA, USA
| | - Haizhen Ding
- Department of Biochemistry, Virginia Tech Blacksburg, VA, USA
| | - Jianyong Li
- Department of Biochemistry, Virginia Tech Blacksburg, VA, USA
| | - Qian Han
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan UniversityHainan, China; Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan UniversityHainan, China; Laboratory of Tropical Veterinary Medicine and Vector Biology, Hainan UniversityHaikou, Hainan, China
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Kumar R. Evolutionary Trails of Plant Group II Pyridoxal Phosphate-Dependent Decarboxylase Genes. FRONTIERS IN PLANT SCIENCE 2016; 7:1268. [PMID: 27602045 PMCID: PMC4993783 DOI: 10.3389/fpls.2016.01268] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/10/2016] [Indexed: 05/24/2023]
Abstract
Type II pyridoxal phosphate-dependent decarboxylase (PLP_deC) enzymes play important metabolic roles during nitrogen metabolism. Recent evolutionary profiling of these genes revealed a sharp expansion of histidine decarboxylase genes in the members of Solanaceae family. In spite of the high sequence homology shared by PLP_deC orthologs, these enzymes display remarkable differences in their substrate specificities. Currently, limited information is available on the gene repertoires and substrate specificities of PLP_deCs which renders their precise annotation challenging and offers technical challenges in the immediate identification and biochemical characterization of their full gene complements in plants. Herein, we explored their evolutionary trails in a comprehensive manner by taking advantage of high-throughput data accessibility and computational approaches. We discussed the premise that has enabled an improved reconstruction of their evolutionary lineage and evaluated the factors offering constraints in their rapid functional characterization, till date. We envisage that the synthesized information herein would act as a catalyst for the rapid exploration of their biochemical specificity and physiological roles in more plant species.
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Torrens-Spence MP, Fallon TR, Weng JK. A Workflow for Studying Specialized Metabolism in Nonmodel Eukaryotic Organisms. Methods Enzymol 2016; 576:69-97. [PMID: 27480683 DOI: 10.1016/bs.mie.2016.03.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Eukaryotes contain a diverse tapestry of specialized metabolites, many of which are of significant pharmaceutical and industrial importance to humans. Nevertheless, exploration of specialized metabolic pathways underlying specific chemical traits in nonmodel eukaryotic organisms has been technically challenging and historically lagged behind that of the bacterial systems. Recent advances in genomics, metabolomics, phylogenomics, and synthetic biology now enable a new workflow for interrogating unknown specialized metabolic systems in nonmodel eukaryotic hosts with greater efficiency and mechanistic depth. This chapter delineates such workflow by providing a collection of state-of-the-art approaches and tools, ranging from multiomics-guided candidate gene identification to in vitro and in vivo functional and structural characterization of specialized metabolic enzymes. As already demonstrated by several recent studies, this new workflow opens up a gateway into the largely untapped world of natural product biochemistry in eukaryotes.
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Affiliation(s)
- M P Torrens-Spence
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States
| | - T R Fallon
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States; Massachusetts Institute of Technology, Cambridge, MA, United States
| | - J K Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States; Massachusetts Institute of Technology, Cambridge, MA, United States.
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Kumar R, Jiwani G, Pareek A, SravanKumar T, Khurana A, Sharma AK. Evolutionary Profiling of Group II Pyridoxal-Phosphate-Dependent Decarboxylases Suggests Expansion and Functional Diversification of Histidine Decarboxylases in Tomato. THE PLANT GENOME 2016; 9. [PMID: 27898758 DOI: 10.3835/plantgenome2015.07.0057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Pyridoxal phosphate (PLP)-dependent enzymes are one of the most important enzymes involved in plant N metabolism. Here, we explored the evolution of group II PLP-dependent decarboxylases (PLP_deC), including aromatic L-amino acid decarboxylase, glutamate decarboxylase, and histidine decarboxylase in the plant lineage. Gene identification analysis revealed a higher number of genes encoding PLP_deC in higher plants than in lower plants. Expression profiling of PLP_deC orthologs and syntelogs in (L.) Heynh., pepper ( L.), and tomato ( L.) pointed toward conserved as well as distinct roles in developmental processes such as fruit maturation and ripening and abiotic stress responses. We further characterized a putative promoter of tomato ripening-associated gene () operating in a complex regulatory circuit. Our analysis provides a firm basis for further in-depth exploration of the PLP_deC gene family, particularly in the economically important Solanaceae family.
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Hardeland R. Melatonin in Plants - Diversity of Levels and Multiplicity of Functions. FRONTIERS IN PLANT SCIENCE 2016; 7:198. [PMID: 26925091 PMCID: PMC4759497 DOI: 10.3389/fpls.2016.00198] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/04/2016] [Indexed: 05/18/2023]
Abstract
Melatonin has been detected in numerous plant species. A particularly surprising finding concerns the highly divergent levels of melatonin that vary between species, organs and environmental conditions, from a few pg/g to over 20 μg/g, reportedly up to 200 μg/g. Highest values have been determined in oily seeds and in plant organs exposed to high UV radiation. The divergency of melatonin concentrations is discussed under various functional aspects and focused on several open questions. This comprises differences in precursor availability, catabolism, the relative contribution of isoenzymes of the melatonin biosynthetic pathway, and differences in rate limitation by either serotonin N-acetyltransferase or N-acetylserotonin O-methyltransferase. Other differences are related to the remarkable pleiotropy of melatonin, which exhibits properties as a growth regulator and morphogenetic factor, actually debated in terms of auxin-like effects, and as a signaling molecule that modulates pathways of ethylene, abscisic, jasmonic and salicylic acids and is involved in stress tolerance, pathogen defense and delay of senescence. In the context of high light/UV intensities, elevated melatonin levels exceed those required for signaling via stress-related phytohormones and may comprise direct antioxidant and photoprotectant properties, perhaps with a contribution of its oxidatively formed metabolites, such as N (1)-acetyl-N (2)-formyl-5-methoxykynuramine and its secondary products. High melatonin levels in seeds may also serve antioxidative protection and have been shown to promote seed viability and germination capacity.
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Kalb D, Gressler J, Hoffmeister D. Active-Site Engineering Expands the Substrate Profile of the Basidiomycetel-Tryptophan Decarboxylase CsTDC. Chembiochem 2015; 17:132-6. [DOI: 10.1002/cbic.201500438] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Daniel Kalb
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute; Friedrich-Schiller-Universität; Beutenbergstrasse 11a 07745 Jena Germany
| | - Julia Gressler
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute; Friedrich-Schiller-Universität; Beutenbergstrasse 11a 07745 Jena Germany
| | - Dirk Hoffmeister
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute; Friedrich-Schiller-Universität; Beutenbergstrasse 11a 07745 Jena Germany
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Sim GY, Yang SM, Kim BG, Ahn JH. Bacterial synthesis of N-hydroxycinnamoyl phenethylamines and tyramines. Microb Cell Fact 2015; 14:162. [PMID: 26463041 PMCID: PMC4603808 DOI: 10.1186/s12934-015-0353-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/02/2015] [Indexed: 11/18/2022] Open
Abstract
Background Hydroxycinnamic acids (HCAs) including cinnamic acid, p-coumaric acid, caffeic acid, and ferulic acid, are C6–C3 phenolic compounds that are synthesized via the phenylpropanoid pathway. HCAs serve as precursors for the synthesis of lignins, flavonoids, anthocyanins, stilbenes and other phenolic compounds. HCAs can also be conjugated with diverse compounds including quinic acid, hydroxyl acids, and amines. Hydroxycinnamoyl (HC) amine conjugates such as N-HC tyramines and N-HC phenethylamines have been considered as potential starting materials to develop antiviral and anticancer drugs. Results We synthesized N-HC tyramines and N-HC phenethylamines using three different approaches in Escherichia coli. Five N-HC phenethylamines and eight N-HC tyramines were synthesized by feeding HCAs and phenethylamine or tyramine to E. coli harboring 4CL (encoding 4-coumarate CoA:ligase) and either SHT (encoding phenethylamine N-HC transferase) or THT (encoding tyramine N-HC transferase). Also, N-(p-coumaroyl) phenethylamine and N-(p-coumaroyl) tyramine were synthesized from p-coumaric acid using E. coli harboring an additional gene, PDC (encoding phenylalanine decarboxylase) or TDC (encoding tyrosine decarboxylase). Finally, we synthesized N-(p-coumaroyl) phenethylamine and N-(p-coumaroyl) tyramine from glucose by reconstructing the metabolic pathways for their synthesis in E. coli. Productivity was maximized by optimizing the cell concentration and incubation temperature. Conclusions We reconstructed the metabolic pathways for synthesis of N-HC tyramines and N-HC phenethylamines by expressing several genes including 4CL, TST or SHT, PDC or TDC, and TAL (encoding tyrosine ammonia lyase) and engineering the shikimate metabolic pathway to increase endogenous tyrosine concentration in E. coli. Approximately 101.9 mg/L N-(p-coumaroyl) phenethylamine and 495.4 mg/L N-(p-coumaroyl) tyramine were synthesized from p-coumaric acid. Furthermore, 152.5 mg/L N-(p-coumaroyl) phenethylamine and 94.7 mg/L N-(p-coumaroyl) tyramine were synthesized from glucose.
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Affiliation(s)
- Geun Young Sim
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul, 143-701, Republic of Korea.
| | - So-Mi Yang
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul, 143-701, Republic of Korea.
| | - Bong Gyu Kim
- Department of Forest Resources, Gyeongnam National University of Science and Technology, 33 Dongjin-ro, Jinju-si, Gyeongsangman-do, 660-758, Republic of Korea.
| | - Joong-Hoon Ahn
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul, 143-701, Republic of Korea.
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