1
|
Chen Y, Wang T, Liang H, Ma D, Zhan R, Yang J, Yang P. Functional Characterization and Catalytic Activity Improvement of Borneol Acetyltransferase from Wurfbainia longiligularis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:13250-13261. [PMID: 38813660 DOI: 10.1021/acs.jafc.4c02915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
In plant secondary metabolite biosynthesis, acylation is a diverse physiological process, with BAHD acyltransferases playing an essential role. Borneol acetyltransferase (BAT) is an alcohol acetyltransferase, which catalyzes borneol and acetyl-CoA to synthesize bornyl acetate (BA). However, the enzymes involved in the biosynthesis of BA have so far only been characterized in Wurfbainia villosa, the studies on the WvBATs have only been conducted in vitro, and the catalytic activity was relatively low. In this research, three genes (WlBAT1, WlBAT2, and WlBAT3) have been identified to encode BATs that are capable of acetylating borneol to synthesize BA in vitro. We also determined that WlBAT1 has the highest catalytic efficiency for borneol-type substrates, including (+)-borneol, (-)-borneol, and isoborneol. Furthermore, we found that BATs could catalyze a wide range of substrate types in vitro, but in vivo, they exclusively catalyzed borneol-type substrates. Through molecular simulations and site-directed mutagenesis, it was revealed that residues D32, N36, H168, N297, N355, and H384 are crucial for the catalytic activity of WlBAT1, while the R382I-D385R double mutant of WlBAT1 exhibited an increasing acylation efficiency for borneol-type substrates in vitro and in vivo. These findings offer key genetic elements for the metabolic engineering of plants and synthetic biology to produce BA.
Collapse
Affiliation(s)
- Yuanxia Chen
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Tiantian Wang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Huilin Liang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Dongming Ma
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Ruoting Zhan
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Jinfen Yang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Peng Yang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua 418000, China
| |
Collapse
|
2
|
Zhao J, Xu Y, Li H, An W, Yin Y, Wang B, Wang L, Wang B, Duan L, Ren X, Liang X, Wang Y, Wan R, Huang T, Zhang B, Li Y, Luo J, Cao Y. Metabolite-based genome-wide association studies enable the dissection of the genetic bases of flavonoids, betaine and spermidine in wolfberry (Lycium). PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1435-1452. [PMID: 38194521 PMCID: PMC11123438 DOI: 10.1111/pbi.14278] [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: 12/22/2021] [Revised: 10/28/2023] [Accepted: 12/14/2023] [Indexed: 01/11/2024]
Abstract
Wolfberry is a plant with medicinal and food values. However, its bioactive ingredients and the corresponding genetic bases have not been determined. Here, we de novo generated a chromosome-level genome assembly for wolfberry, yielding a genome sequence of ~1.77 Gb with contig N50 of 50.55 Mb and 39 224 predicted gene models. A variation map, using 307 re-sequenced accessions, was called based on this genome assembly. Furthermore, the fruit metabolome of these accessions was profiled using 563 annotated metabolites, which separated Lycium barbarum L. and non-L. barbarum L. The flavonoids, coumarins, alkaloids and nicotinic acid contents were higher in the former than in the latter. A metabolite-based genome-wide association study mapped 156 164 significant single nucleotide polymorphisms corresponding to 340 metabolites. This included 19 219 unique lead single nucleotide polymorphisms in 1517 significant association loci, of which three metabolites, flavonoids, betaine and spermidine, were highlighted. Two candidate genes, LbUGT (evm.TU.chr07.2692) and LbCHS (evm.TU.chr07.2738), with non-synonymous mutations, were associated with the flavonoids content. LbCHS is a structural gene that interacts with a nearby MYB transcription factor (evm.TU.chr07.2726) both in L. barbarum and L. ruthenicum. Thus, these three genes might be involved in the biosynthesis/metabolism of flavonoids. LbSSADH (evm.TU.chr09.627) was identified as possibly participating in betaine biosynthesis/metabolism. Four lycibarbarspermidines (E-G and O) were identified, and only the lycibarbarspermidines O content was higher in L. barbarum varieties than in non-L. barbarum varieties. The evm.TU.chr07.2680 gene associated with lycibarbarspermidines O was annotated as an acetyl-CoA-benzylalcohol acetyltransferase, suggesting that it is a candidate gene for spermidine biosynthesis. These results provide novel insights into the specific metabolite profile of non-L. barbarum L. and the genetic bases of flavonoids, betaine and spermidine biosynthesis/metabolism.
Collapse
Affiliation(s)
- Jianhua Zhao
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd.UrumchiChina
| | - Haoxia Li
- Desertification Control Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Wei An
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Yue Yin
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Bin Wang
- Wuhan Matware Biotechnology Co., Ltd.WuhanChina
| | - Liping Wang
- School of breeding and multiplcation (Sanya Institute of Breeding and Multiplication)Hainan, UniversitySanyaChina
| | - Bi Wang
- School of breeding and multiplcation (Sanya Institute of Breeding and Multiplication)Hainan, UniversitySanyaChina
| | - Linyuan Duan
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Xiaoyue Ren
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Xiaojie Liang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Yajun Wang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Ru Wan
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Ting Huang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Bo Zhang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Yanlong Li
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Jie Luo
- School of breeding and multiplcation (Sanya Institute of Breeding and Multiplication)Hainan, UniversitySanyaChina
| | - Youlong Cao
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| |
Collapse
|
3
|
Mano NA, Shaikh MA, Widhalm JR, Yoo CY, Mickelbart MV. Transcriptional repression of GTL1 under water-deficit stress promotes anthocyanin biosynthesis to enhance drought tolerance. PLANT DIRECT 2024; 8:e594. [PMID: 38799417 PMCID: PMC11117050 DOI: 10.1002/pld3.594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024]
Abstract
The transcription factor GT2-LIKE 1 (GTL1) has been implicated in orchestrating a transcriptional network of diverse physiological, biochemical, and developmental processes. In response to water-limiting conditions, GTL1 is a negative regulator of stomatal development, but its potential rolein other water-deficit responses is unknown. We hypothesized that GTL1 regulates transcriptome changes associated with drought tolerance over leaf developmental stages. To test the hypothesis, gene expression was profiled by RNA-seq analysis in emerging and expanding leaves of wild-type and a drought-tolerant gtl1-4 knockout mutant under well-watered and water-deficit conditions. Our comparative analysis of genotype-treatment combinations within leaf developmental age identified 459 and 1073 differentially expressed genes in emerging and expanding leaves, respectively, as water-deficit responsive GTL1-regulated genes. Transcriptional profiling identified a potential role of GTL1 in two important pathways previously linked to drought tolerance: flavonoid and polyamine biosynthesis. In expanding leaves, negative regulation of GTL1 under water-deficit conditions promotes biosynthesis of flavonoids and anthocyanins that may contribute to drought tolerance. Quantification of polyamines did not support a role for GTL1 in these drought-responsive pathways, but this is likely due to the complex nature of polyamine synthesis and turnover. Our global transcriptome analysis suggests that transcriptional repression of GTL1 by water deficit allows plants to activate diverse pathways that collectively contribute to drought tolerance.
Collapse
Affiliation(s)
- Noel Anthony Mano
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteIndianaUSA
- Center for Plant BiologyPurdue UniversityWest LafayetteIndianaUSA
- Department of Biological and Environmental SciencesHeidelberg UniversityTiffinOhioUSA
- Present address:
School of Biological SciencesThe University of UtahSalt Lake CityUtahUSA
| | - Mearaj A. Shaikh
- Center for Plant BiologyPurdue UniversityWest LafayetteIndianaUSA
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayetteIndianaUSA
| | - Joshua R. Widhalm
- Center for Plant BiologyPurdue UniversityWest LafayetteIndianaUSA
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayetteIndianaUSA
| | - Chan Yul Yoo
- Present address:
School of Biological SciencesThe University of UtahSalt Lake CityUtahUSA
| | - Michael V. Mickelbart
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteIndianaUSA
- Center for Plant BiologyPurdue UniversityWest LafayetteIndianaUSA
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayetteIndianaUSA
| |
Collapse
|
4
|
de Carvalho CC, Murray IP, Nguyen H, Nguyen T, Cantu DC. Acyltransferase families that act on thioesters: Sequences, structures, and mechanisms. Proteins 2024; 92:157-169. [PMID: 37776148 DOI: 10.1002/prot.26599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 10/01/2023]
Abstract
Acyltransferases (AT) are enzymes that catalyze the transfer of acyl group to a receptor molecule. This review focuses on ATs that act on thioester-containing substrates. Although many ATs can recognize a wide variety of substrates, sequence similarity analysis allowed us to classify the ATs into fifteen distinct families. Each AT family is originated from enzymes experimentally characterized to have AT activity, classified according to sequence similarity, and confirmed with tertiary structure similarity for families that have crystallized structures available. All the sequences and structures of the AT families described here are present in the thioester-active enzyme (ThYme) database. The AT sequences and structures classified into families and available in the ThYme database could contribute to enlightening the understanding acyl transfer to thioester-containing substrates, most commonly coenzyme A, which occur in multiple metabolic pathways, mostly with fatty acids.
Collapse
Affiliation(s)
- Caio C de Carvalho
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada, USA
| | - Ian P Murray
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada, USA
| | - Hung Nguyen
- Department of Computer Science and Software Engineering, Auburn University, Auburn, Alabama, USA
| | - Tin Nguyen
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada, USA
- Department of Computer Science and Software Engineering, Auburn University, Auburn, Alabama, USA
| | - David C Cantu
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada, USA
| |
Collapse
|
5
|
Yuan J, Ma L, Wang Y, Xu X, Zhang R, Wang C, Meng W, Tian Z, Zhou Y, Wang G. A recently evolved BAHD acetyltransferase, responsible for bitter soyasaponin A production, is indispensable for soybean seed germination. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2490-2504. [PMID: 37548097 DOI: 10.1111/jipb.13553] [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: 06/16/2023] [Accepted: 08/04/2023] [Indexed: 08/08/2023]
Abstract
Soyasaponins are major small molecules that accumulate in soybean (Glycine max) seeds. Among them, type-A soyasaponins, fully acetylated at the terminal sugar of their C22 sugar chain, are responsible for the bitter taste of soybean-derived foods. However, the molecular basis for the acetylation of type-A soyasaponins remains unclear. Here, we identify and characterize GmSSAcT1, encoding a BADH-type soyasaponin acetyltransferase that catalyzes three or four consecutive acetylations on type-A soyasaponins in vitro and in planta. Phylogenetic analysis and biochemical assays suggest that GmSSAcT1 likely evolved from acyltransferases present in leguminous plants involved in isoflavonoid acylation. Loss-of-function mutants of GmSSAcT1 exhibited impaired seed germination, which attribute to the excessive accumulation of null-acetylated type-A soyasaponins. We conclude that GmSSAcT1 not only functions as a detoxification gene for high accumulation of type-A soyasaponins in soybean seeds but is also a promising target for breeding new soybean varieties with lower bitter soyasaponin content.
Collapse
Affiliation(s)
- Jia Yuan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Liya Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Xindan Xu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Rui Zhang
- State Key Laboratory of Molecular Developmental Biology, the Chinese Academy of Sciences, Beijing, 100190, China
| | - Chengyuan Wang
- The Center for Microbes, Development and Health, Institute of Pasteur of Shanghai, the Chinese Academy of Sciences, Shanghai, 200031, China
| | - Wenxiang Meng
- State Key Laboratory of Molecular Developmental Biology, the Chinese Academy of Sciences, Beijing, 100190, China
| | - Zhixi Tian
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
| |
Collapse
|
6
|
Wang L, Jiang Z, Zhang J, Chen K, Zhang M, Wang Z, Wang B, Ye M, Qiao X. Characterization and structure-based protein engineering of a regiospecific saponin acetyltransferase from Astragalus membranaceus. Nat Commun 2023; 14:5969. [PMID: 37749089 PMCID: PMC10519980 DOI: 10.1038/s41467-023-41599-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/12/2023] [Indexed: 09/27/2023] Open
Abstract
Acetylation contributes to the bioactivity of numerous medicinally important natural products. However, little is known about the acetylation on sugar moieties. Here we report a saponin acetyltransferase from Astragalus membranaceus. AmAT7-3 is discovered through a stepwise gene mining approach and characterized as the xylose C3'/C4'-O-acetyltransferse of astragaloside IV (1). To elucidate its catalytic mechanism, complex crystal structures of AmAT7-3/1 and AmAT7-3A310G/1 are obtained, which reveal a large active pocket decided by a specific sequence AADAG. Combining with QM/MM computation, the regiospecificity of AmAT7-3 is determined by sugar positioning modulated by surrounding amino acids including #A310 and #L290. Furthermore, a small mutant library is built using semi-rational design, where variants A310G and A310W are found to catalyze specific C3'-O and C4'-O acetylation, respectively. AmAT7-3 and its variants are also employed to acetylate other bioactive saponins. This work expands the understanding of saponin acetyltransferases, and provide efficient catalytic tools for saponin acetylation.
Collapse
Affiliation(s)
- Linlin Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Zhihui Jiang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, China
| | - Jiahe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Kuan Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Meng Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Zilong Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, China.
| | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.
- Peking University-Yunnan Baiyao International Medical Research Center, 38 Xueyuan Road, Beijing, 100191, China.
| | - Xue Qiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.
- Peking University-Yunnan Baiyao International Medical Research Center, 38 Xueyuan Road, Beijing, 100191, China.
| |
Collapse
|
7
|
Liu H, Liu Y, Han H, Lu C, Chen H, Chai Y. Identification and characterization of phenolamides in tea (Camellia sinensis) flowers using ultra-high-performance liquid chromatography/Q-Exactive orbitrap mass spectrometry. Food Chem 2023; 424:136402. [PMID: 37216782 DOI: 10.1016/j.foodchem.2023.136402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/24/2023]
Abstract
Phenolamides (PAs) are important secondary metabolites present in plants with multiple bioactivities. This study aims to comprehensively identify and characterize PAs in tea (Camellia sinensis) flowers using ultra-high-performance liquid chromatography/Q-Exactive orbitrap mass spectrometry based on a lab-developed in-silico accurate-mass database. The PAs found in tea flowers were conjugates of Z/E-hydroxycinnamic acids (p-coumaric, caffeic and ferulic acids) with polyamines (putrescine, spermidine and agmatine). The positional and Z/E isomers were distinguished through characteristic MS2 fragmentation rules and chromatographic retention behavior summarized from some synthetic PAs. 21 types of PAs consisting of over 80 isomers were identified, and the majority of them were found in tea flowers for the first time. Among 12 tea flower varieties studied, they all possessed tris-(p-coumaroyl)-spermidine with the highest relative content, and C. sinensis 'Huangjinya' had the highest total relative contents of PAs. This study shows the richness and structural diversity of PAs in tea flowers.
Collapse
Affiliation(s)
- Hongxia Liu
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingying Liu
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haolei Han
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chengyin Lu
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Hangzhou 310008, China
| | - Hongping Chen
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Hangzhou 310008, China.
| | - Yunfeng Chai
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Hangzhou 310008, China.
| |
Collapse
|
8
|
Kruse LH, Fehr B, Chobirko JD, Moghe GD. Phylogenomic analyses across land plants reveals motifs and coexpression patterns useful for functional prediction in the BAHD acyltransferase family. FRONTIERS IN PLANT SCIENCE 2023; 14:1067613. [PMID: 36844084 PMCID: PMC9950517 DOI: 10.3389/fpls.2023.1067613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
The BAHD acyltransferase family is one of the largest enzyme families in flowering plants, containing dozens to hundreds of genes in individual genomes. Highly prevalent in angiosperm genomes, members of this family contribute to several pathways in primary and specialized metabolism. In this study, we performed a phylogenomic analysis of the family using 52 genomes across the plant kingdom to gain deeper insights into its functional evolution and enable function prediction. We found that BAHD expansion in land plants was associated with significant changes in various gene features. Using pre-defined BAHD clades, we identified clade expansions in different plant groups. In some groups, these expansions coincided with the prominence of metabolite classes such as anthocyanins (flowering plants) and hydroxycinnamic acid amides (monocots). Clade-wise motif-enrichment analysis revealed that some clades have novel motifs fixed on either the acceptor or the donor side, potentially reflecting historical routes of functional evolution. Co-expression analysis in rice and Arabidopsis further identified BAHDs with similar expression patterns, however, most co-expressed BAHDs belonged to different clades. Comparing BAHD paralogs, we found that gene expression diverges rapidly after duplication, suggesting that sub/neo-functionalization of duplicate genes occurs quickly via expression diversification. Analyzing co-expression patterns in Arabidopsis in conjunction with orthology-based substrate class predictions and metabolic pathway models led to the recovery of metabolic processes of most of the already-characterized BAHDs as well as definition of novel functional predictions for some uncharacterized BAHDs. Overall, this study provides new insights into the evolution of BAHD acyltransferases and sets up a foundation for their functional characterization.
Collapse
Affiliation(s)
- Lars H. Kruse
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Benjamin Fehr
- Computational Biology Department, Cornell University, Ithaca, NY, United States
| | - Jason D. Chobirko
- Molecular Biology and Genetics Department, Cornell University, Ithaca, NY, United States
| | - Gaurav D. Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| |
Collapse
|
9
|
Yulianti Y, Adawiyah DR, Herawati D, Indrasti D, Andarwulan N. Detection of Markers in Green Beans and Roasted Beans of Kalosi-Enrekang Arabica Coffee with Different Postharvest Processing Using LC-MS/MS. INTERNATIONAL JOURNAL OF FOOD SCIENCE 2023; 2023:6696808. [PMID: 37007842 PMCID: PMC10063361 DOI: 10.1155/2023/6696808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 04/04/2023]
Abstract
Our study is aimed at evaluating the effect of postharvest processing (natural, honey, and fully washed) on the compounds profile in green beans and roasted beans of Kalosi-Enrekang Arabica coffee and determining the marker compounds for each process. These beans were extracted using boiling water, and the extract was analyzed using LC-MS/MS. The results of this work confirmed the significant impact of postharvest processing on compounds in the coffee beans, and each process has a marker compound. Green beans by natural processing have 3 marker compounds, honey processing has 6 marker compounds, and fully washed processing has 2 marker compounds. Meanwhile, roasted beans by natural processing have 4 marker compounds, honey processing has 5 marker compounds, and fully washed processing has 7 marker compounds. In addition, our research identified caffeoyl tyrosine in green beans from natural and honey processing, which was previously only identified in Robusta coffee. These marker compounds can differentiate postharvest processing (natural, honey, and fully washed). These results can also help understand the effect of postharvest processing on the chemical composition of green and roasted beans.
Collapse
Affiliation(s)
- Yulianti Yulianti
- Department of Food Science and Technology, Faculty of Agricultural Engineering and Technology, IPB University, IPB Dramaga Campus, Bogor 16680, Indonesia
- South-East Asia Food & Agricultural Science and Technology (SEAFAST) Center, IPB University, IPB Dramaga Campus, Bogor 16680, Indonesia
- Department of Agricultural Technology, Faculty of Agriculture, Gorontalo University, Gorontalo 96211, Indonesia
| | - Dede Robiatul Adawiyah
- Department of Food Science and Technology, Faculty of Agricultural Engineering and Technology, IPB University, IPB Dramaga Campus, Bogor 16680, Indonesia
- South-East Asia Food & Agricultural Science and Technology (SEAFAST) Center, IPB University, IPB Dramaga Campus, Bogor 16680, Indonesia
| | - Dian Herawati
- Department of Food Science and Technology, Faculty of Agricultural Engineering and Technology, IPB University, IPB Dramaga Campus, Bogor 16680, Indonesia
- South-East Asia Food & Agricultural Science and Technology (SEAFAST) Center, IPB University, IPB Dramaga Campus, Bogor 16680, Indonesia
| | - Dias Indrasti
- Department of Food Science and Technology, Faculty of Agricultural Engineering and Technology, IPB University, IPB Dramaga Campus, Bogor 16680, Indonesia
- South-East Asia Food & Agricultural Science and Technology (SEAFAST) Center, IPB University, IPB Dramaga Campus, Bogor 16680, Indonesia
| | - Nuri Andarwulan
- Department of Food Science and Technology, Faculty of Agricultural Engineering and Technology, IPB University, IPB Dramaga Campus, Bogor 16680, Indonesia
- South-East Asia Food & Agricultural Science and Technology (SEAFAST) Center, IPB University, IPB Dramaga Campus, Bogor 16680, Indonesia
| |
Collapse
|
10
|
Beltrame LC, Thompson CE, Freitas LB. Molecular evolution and structural analyses of proteins involved in metabolic pathways of volatile organic compounds in Petunia hybrida (Solanaceae). Genet Mol Biol 2022; 46:e20220114. [PMID: 36534952 PMCID: PMC9762610 DOI: 10.1590/1678-4685-gmb-2022-0114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022] Open
Abstract
The association between plants and their pollinators is essential for increasing the diversity in angiosperms. Morphological and physiological traits, mainly floral scent, can influence the pollination dynamics and select pollinators for each plant species. In this work, we studied two proteins involved in producing volatile organic compounds in plants, conyferyl alcohol acyltransferase (CFAT) and benzoyl-CoA:benzyl alcohol/phenyl ethanol benzoyl transferase (BPBT) genes. We aimed to understand these proteins with respect to evolutionary and structural aspects and functions in Solanaceae using phylogenetic methods and comparative molecular modeling. We used Bayesian inference to describe the proteins' evolutionary history using Petunia x hybrida as a query to search for homologs in the Solanaceae family. Theoretical 3D models were obtained for both proteins using Panicum virgatum as a template. The phylogenetic tree included several different enzymes with diverse biological roles in Solanaceae, displaying the transferase domain. We identified only one sequence of CFAT in the databases, which belongs to Petunia x hybrida, and found several BPBT sequences from the genera Nicotiana, Solanum, and Capsicum. The 3D structures of CFAT and BPBT have two different domains, and we have identified the amino acid residues essential for the enzymatic activity and interaction with substrates.
Collapse
Affiliation(s)
- Lucas C. Beltrame
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Claudia E. Thompson
- Universidade Federal de Ciências da Saúde de Porto Alegre, Departamento de Farmacociências, Porto Alegre, RS, Brazil
| | - Loreta B. Freitas
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| |
Collapse
|
11
|
Hong B, Grzech D, Caputi L, Sonawane P, López CER, Kamileen MO, Hernández Lozada NJ, Grabe V, O'Connor SE. Biosynthesis of strychnine. Nature 2022; 607:617-622. [PMID: 35794473 PMCID: PMC9300463 DOI: 10.1038/s41586-022-04950-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/08/2022] [Indexed: 11/08/2022]
Abstract
Strychnine is a natural product that, through isolation, structural elucidation and synthetic efforts, shaped the field of organic chemistry. Currently, strychnine is used as a pesticide to control rodents1 because of its potent neurotoxicity2,3. The polycyclic architecture of strychnine has inspired chemists to develop new synthetic transformations and strategies to access this molecular scaffold4, yet it is still unknown how plants create this complex structure. Here we report the biosynthetic pathway of strychnine, along with the related molecules brucine and diaboline. Moreover, we successfully recapitulate strychnine, brucine and diaboline biosynthesis in Nicotiana benthamiana from an upstream intermediate, thus demonstrating that this complex, pharmacologically active class of compounds can now be harnessed through metabolic engineering approaches.
Collapse
Affiliation(s)
- Benke Hong
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Dagny Grzech
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Prashant Sonawane
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Carlos E Rodríguez López
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Mohamed Omar Kamileen
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Néstor J Hernández Lozada
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Veit Grabe
- Microscopic Imaging Service Group, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany.
| |
Collapse
|
12
|
Liu X, Dai S, Zhou Y, Liu J, Li D, Zhang J, Zhu Y, Zhao Q, Feng Y, Zhang Y. Crystal structure of the plant feruloyl-coenzyme A monolignol transferase provides insights into the formation of monolignol ferulate conjugates. Biochem Biophys Res Commun 2022; 594:8-14. [PMID: 35066379 DOI: 10.1016/j.bbrc.2022.01.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/10/2022] [Indexed: 11/02/2022]
Abstract
Lignin is a highly complex phenolic polymer which is essential for plants, but also makes it difficult for industrial processing. Engineering lignin by introducing relatively labile linkages into the lignin backbone can render it more amenable to chemical depolymerization. It has been reported that introducing a feruloyl-coenzyme A monolignol transferase from Angelica sinensis (AsFMT) into poplar could incorporate monolignol ferulate conjugates (ML-FAs) into lignin polymers, suggesting a promising way to manipulate plants for readily deconstructing. FMT catalyzes a reaction between monolignols and feruloyl-CoA to produce ML-FAs and free CoA-SH. However, the mechanisms of substrate specificity and catalytic process of FMT remains poorly understood. Here we report the structure of AsFMT, which adopts a typical fold of BAHD acyltransferase family. Structural comparisons with other BAHD homologs reveal several unique structural features of AsFMT, different from those of the BAHD homologs. Further molecular docking studies showed that T375 in AsFMT may function as an oxyanion hole to stabilize the reaction intermediate and also proposed a role of H278 in the binding of the nucleophilic hydroxyl group of monolignols. Together, this study provides important structural insights into the reactions catalyzed by AsFMT and will shed light on its future application in lignin engineering.
Collapse
Affiliation(s)
- Xi Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shuliu Dai
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yu Zhou
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Jinyue Liu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Dong Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jun Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yushan Zhu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Qiao Zhao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yue Feng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yi Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| |
Collapse
|
13
|
Kumar G, Kumar P, Kapoor R, Lore JS, Bhatia D, Kumar A. Characterization of evolutionarily distinct rice BAHD-Acyltransferases provides insight into their plausible role in rice susceptibility to Rhizoctonia solani. THE PLANT GENOME 2021; 14:e20140. [PMID: 34498798 DOI: 10.1002/tpg2.20140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/01/2021] [Indexed: 05/06/2023]
Abstract
Plants produce diverse secondary metabolites in response to different environmental cues including pathogens. The modification of secondary metabolites, including acylation, modulates their biological activity, stability, transport, and localization. A plant-specific BAHD-acyltransferase (BAHD-AT) gene family members catalyze the acylation of secondary metabolites. Here we characterized the rice (Oryza sativa L.) BAHD-ATs at the genome-wide level and endeavor to define their plausible role in the tolerance against Rhizoctonia solani AG1-IA. We identified a total of 85 rice OsBAHD-AT genes and classified them into five canonical clades based on their phylogenetic relationship with characterized BAHD-ATs from other plant species. The time-course RNA sequencing (RNA-seq) analysis of OsBAHD-AT genes and qualitative real-time polymerase chain reaction (qRT-PCR) validation showed higher expression in sheath blight susceptible rice genotype. Furthermore, the DNA methylation analysis revealed higher hypomethylation of OsBAHD-AT genes that corresponds to their higher expression in susceptible rice genotype, indicating epigenetic regulation of OsBAHD-AT genes in response to R. solani AG1-IA inoculation. The results shown here indicate that BAHD-ATs may have a negative role in rice tolerance against R. solani AG1-IA possibly mediated through the brassinosteroid (BR) signaling pathway. Altogether, the present analysis suggests the putative functions of several OsBAHD-AT genes, which will provide a blueprint for their functional characterization and to understand the rice-R. solani AG1-IA interaction.
Collapse
Affiliation(s)
- Gulshan Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- National Agri-Food Biotechnology Institute, Mohali, Punjab, 140306, India
| | - Pankaj Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Ritu Kapoor
- National Agri-Food Biotechnology Institute, Mohali, Punjab, 140306, India
| | - Jagjeet Singh Lore
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141 004, India
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141 004, India
| | - Arun Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| |
Collapse
|