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Xiong Z, Ding Z, Sun J, Jiang X, Cong H, Sun H, Qiao F. In vivo assembly in tobacco cells to elucidate and engineer the biosynthesis of 4-hydroxydihydrocinnamaldehyde from Gloriosa superba. PLANT CELL REPORTS 2024; 43:235. [PMID: 39299972 DOI: 10.1007/s00299-024-03318-4] [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: 08/05/2024] [Accepted: 09/10/2024] [Indexed: 09/22/2024]
Abstract
KEY MESSAGE This study described the biosynthesis of 4-hydroxydihydrocinnamaldehyde sharing with monolignol pathway and supplemented the biosynthesis of colchicine in G. superba, 4-hydroxydihydrocinnamaldehyde produced in tobacco BY2 cells provided an important stepstone. The precursor, 4-hydroxydihydrocinnamaldehyde (4-HDCA), participates in the biosynthesis of the carbon skeleton of colchicine, which is derived from L-phenylalanine. However, one hypothesis proposed that 4-HDCA is synthesized by sharing the early part of the monolignol pathway in G. superba. In this study, we validated this prediction and identified the enzymatic functions involved in this pathway. GsDBR1 is a crucial enzyme to illustrate 4-HDCA diverging from monolignol pathway, we first confirmed its reductase activity on 4-coumaraldehyde, an important intermediate compound in monolignol biosynthesis. Then, the biochemical function of recombinant enzymes belonging to the other four families were verified to elucidate the entire process of 4-HDCA biosynthesis from L-phenylalanine. After reconstruction, the 4-HDCA was 78.4 ng/g with fresh weight (FW) of transgenic tobacco cells, and the yield increased to 168.22 ng/g·FW after improved treatment with methyl jasmonate (MeJA). The elucidation of 4-HDCA biosynthesis sharing the monolignol pathway supplemented the biosynthesis of colchicine in G. superba, and the production of 4-HDCA in tobacco cells provides an important step in the development of plant cell cultures as heterologous bio-factories for secondary metabolite production.
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Affiliation(s)
- Zhiqiang Xiong
- National Key Laboratory for Tropical Crops Breeding, Sanya, 572024, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources, Key Laboratory for Quality Regulation of Tropical Horticultural Plants of Hainan Province, Sanya Nanfan Research Institute, College of Horticulture, Hainan University, Haikou, 570228, China
| | - Zhuoying Ding
- National Key Laboratory for Tropical Crops Breeding, Sanya, 572024, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources, Key Laboratory for Quality Regulation of Tropical Horticultural Plants of Hainan Province, Sanya Nanfan Research Institute, College of Horticulture, Hainan University, Haikou, 570228, China
| | - Jingyi Sun
- National Key Laboratory for Tropical Crops Breeding, Sanya, 572024, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources, Key Laboratory for Quality Regulation of Tropical Horticultural Plants of Hainan Province, Sanya Nanfan Research Institute, College of Horticulture, Hainan University, Haikou, 570228, China
| | - Xuefei Jiang
- Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources, Key Laboratory for Quality Regulation of Tropical Horticultural Plants of Hainan Province, Sanya Nanfan Research Institute, College of Horticulture, Hainan University, Haikou, 570228, China
| | - Hanqing Cong
- National Key Laboratory for Tropical Crops Breeding, Sanya, 572024, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Huapeng Sun
- National Key Laboratory for Tropical Crops Breeding, Sanya, 572024, China.
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
| | - Fei Qiao
- National Key Laboratory for Tropical Crops Breeding, Sanya, 572024, China.
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
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Ye P, Su J, Lin J, Li Y, Wu H. Identification of a cinnamoyl-CoA reductase from Cinnamomum cassia involved in trans-cinnamaldehyde biosynthesis. PLANTA 2024; 259:138. [PMID: 38687380 DOI: 10.1007/s00425-024-04419-w] [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: 11/30/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
MAIN CONCLUSION The identification of a functional cinnamoyl-CoA reductase enzyme from Cinnamomum cassia involved in trans-cinnamaldehyde biosynthesis offers the potential for enhancing trans-cinnamaldehyde production through genetic engineering. A significant accumulation of trans-cinnamaldehyde has been found in the bark tissues of C. cassia, used in traditional Chinese medicine. trans-Cinnamaldehyde exhibits various pharmacological properties such as anti-inflammatory, analgesic, and protection of the stomach and the digestive tract. However, further elucidation and characterization of the biosynthetic pathway for trans-cinnamaldehyde is required. In this study, we conducted an integrated analysis of trans-cinnamaldehyde accumulation profiles and transcriptomic data from five different C. cassia tissues to identify the genes involved in its biosynthesis. The transcriptome data we obtained included nearly all genes associated with the trans-cinnamaldehyde pathway, with the majority demonstrating high abundance in branch barks and trunk barks. We successfully cloned four C. cassia cinnamoyl-CoA reductases (CcCCRs), a key gene in trans-cinnamaldehyde biosynthesis. We found that the recombinant CcCCR1 protein was the only one that more efficiently converted cinnamoyl-CoA into trans-cinnamaldehyde. CcCCR1 exhibited approximately 14.7-fold higher catalytic efficiency (kcat/Km) compared to the Arabidopsis thaliana cinnamoyl-CoA reductase 1 (AtCCR1); therefore, it can be utilized for engineering higher trans-cinnamaldehyde production as previously reported. Molecular docking studies and mutagenesis experiments also validated the superior catalytic activity of CcCCR1 compared to AtCCR1. These findings provide valuable insights for the functional characterization of enzyme-coding genes and hold potential for future engineering of trans-cinnamaldehyde biosynthetic pathways.
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Affiliation(s)
- Peng Ye
- Center for Medicinal Plants Research, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jianmu Su
- Center for Medicinal Plants Research, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jianhao Lin
- Center for Medicinal Plants Research, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yanqun Li
- Center for Medicinal Plants Research, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry, South China Agricultural University, Guangzhou, 510642, China.
| | - Hong Wu
- Center for Medicinal Plants Research, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry, South China Agricultural University, Guangzhou, 510642, China.
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Li W, Hao Z, Yang L, Xia H, Tu Z, Cui Z, Wu J, Li H. Genome-wide identification and characterization of LcCCR13 reveals its potential role in lignin biosynthesis in Liriodendron chinense. FRONTIERS IN PLANT SCIENCE 2023; 13:1110639. [PMID: 36726672 PMCID: PMC9884966 DOI: 10.3389/fpls.2022.1110639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Introduction Wood formation is closely related to lignin biosynthesis. Cinnamoyl-CoA reductase (CCR) catalyzes the conversion of cinnamoyl-CoA to cinnamaldehydes, which is the initiation of the lignin biosynthesis pathway and a crucial point in the manipulation of associated traits. Liriodendron chinense is an economically significant timber tree. Nevertheless, the underlying mechanism of wood formation in it remains unknown; even the number of LcCCR family members in this species is unclear. Materials and Results This study aimed to perform a genome-wide identification of genes(s) involved in lignin biosynthesis in L. chinense via RT-qPCR assays and functional verification. Altogether, 13 LcCCR genes were identified that were divided into four major groups based on structural and phylogenetic features. The gene structures and motif compositions were strongly conserved between members of the same groups. Subsequently, the expression patterns analysis based on RNA-seq data indicated that LcCCR5/7/10/12/13 had high expression in the developing xylem at the stem (DXS). Furthermore, the RT-qPCR assays showed that LcCCR13 had the highest expression in the stem as compared to other tissues. Moreover, the overexpression of the LcCCR13 in transgenic tobacco plants caused an improvement in the CCR activity and lignin content, indicating that it plays a key role in lignin biosynthesis in the stems. Discussion Our research lays a foundation for deeper investigation of the lignin synthesis and uncovers the genetic basis of wood formation in L. chinense.
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Affiliation(s)
| | | | | | | | | | | | | | - Huogen Li
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Wang Y, Xu J, Zhao W, Li J, Chen J. Genome-wide identification, characterization, and genetic diversity of CCR gene family in Dalbergia odorifera. FRONTIERS IN PLANT SCIENCE 2022; 13:1064262. [PMID: 36600926 PMCID: PMC9806228 DOI: 10.3389/fpls.2022.1064262] [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: 10/08/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Lignin is a complex aromatic polymer plays major biological roles in maintaining the structure of plants and in defending them against biotic and abiotic stresses. Cinnamoyl-CoA reductase (CCR) is the first enzyme in the lignin-specific biosynthetic pathway, catalyzing the conversion of hydroxycinnamoyl-CoA into hydroxy cinnamaldehyde. Dalbergia odorifera T. Chen is a rare rosewood species for furniture, crafts and medicine. However, the CCR family genes in D. odorifera have not been identified, and their function in lignin biosynthesis remain uncertain. METHODS AND RESULTS Here, a total of 24 genes, with their complete domains were identified. Detailed sequence characterization and multiple sequence alignment revealed that the DoCCR protein sequences were relatively conserved. They were divided into three subfamilies and were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that seven DoCCRs were grouped together with functionally characterized CCRs of dicotyledons involved in developmental lignification. Synteny analysis showed that segmental and tandem duplications were crucial in the expansion of CCR family in D. odorifera, and purifying selection emerged as the main force driving these genes evolution. Cis-acting elements in the putative promoter regions of DoCCRs were mainly associated with stress, light, hormones, and growth/development. Further, analysis of expression profiles from the RNA-seq data showed distinct expression patterns of DoCCRs among different tissues and organs, as well as in response to stem wounding. Additionally, 74 simple sequence repeats (SSRs) were identified within 19 DoCCRs, located in the intron or untranslated regions (UTRs), and mononucleotide predominated. A pair of primers with high polymorphism and good interspecific generality was successfully developed from these SSRs, and 7 alleles were amplified in 105 wild D. odorifera trees from 17 areas covering its whole native distribution. DISCUSSION Overall, this study provides a basis for further functional dissection of CCR gene families, as well as breeding improvement for wood properties and stress resistance in D. odorifera.
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Affiliation(s)
- Yue Wang
- Hainan Yazhou Bay Seed Laboratory, School of Forestry, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Jieru Xu
- Hainan Yazhou Bay Seed Laboratory, School of Forestry, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Wenxiu Zhao
- Hainan Yazhou Bay Seed Laboratory, School of Forestry, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Jia Li
- Hainan Yazhou Bay Seed Laboratory, School of Forestry, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Jinhui Chen
- Hainan Yazhou Bay Seed Laboratory, School of Forestry, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
- Research Institute of Forestry, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, China
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Zhao Y, Su X, Wang X, Wang M, Feng X, Aamir Manzoor M, Cai Y. Comparative genomic analysis of the COBRA genes in six Rosaceae species and expression analysis in Chinese white pear ( Pyrus bretschneideri). PeerJ 2022; 10:e13723. [PMID: 35873912 PMCID: PMC9306554 DOI: 10.7717/peerj.13723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/22/2022] [Indexed: 01/17/2023] Open
Abstract
COBRA-Like (COBL) genes encode a glycosylphosphatidylinositol (GPI) anchoring protein unique to plants. In current study, 87 COBRA genes were identified in 6 Rosaceae species, including Pyrus bretschneideri (16 genes), Malus domestica (22 genes), Fragaria vesca (13 genes), Prunus mume (11 genes), Rubus occidentalis (13 genes) and Prunus avium (12 genes). We revealed the evolution of the COBRA gene in six Rosaceae species by phylogeny, gene structure, conservative sequence, hydrophobicity analysis, gene replication events and sliding window analysis. In addition, based on the analysis of expression patterns in pear fruit combined with bioinformatics, we identified PbCOBL12 and PbCOBL13 as potential genes regulating secondary cell wall (SCW) formation during pear stone cell development. This study aimed to understand the evolutionary relationship of the COBRA gene in Rosaceae species, clarify the potential function of COBRA in pear fruit development, and provide essential theoretical basis and gene resources for improving pear fruit quality through genetical modification mechanism.
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Affiliation(s)
- Yu Zhao
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Xueqiang Su
- Institute of Sericulture, Anhui Academy of Agricultural Sciences, HeFei, China
| | - Xinya Wang
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Mengna Wang
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Xiaofeng Feng
- School of Life Science, Anhui Agricultural University, Hefei, China
| | | | - Yongping Cai
- School of Life Science, Anhui Agricultural University, Hefei, China
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Characterization, Expression Profiling, and Biochemical Analyses of the Cinnamoyl-CoA Reductase Gene Family for Lignin Synthesis in Alfalfa Plants. Int J Mol Sci 2022; 23:ijms23147762. [PMID: 35887111 PMCID: PMC9316543 DOI: 10.3390/ijms23147762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/09/2022] [Accepted: 07/12/2022] [Indexed: 02/01/2023] Open
Abstract
Cinnamoyl-CoA reductase (CCR) is a pivotal enzyme in plant lignin synthesis, which has a role in plant secondary cell wall development and environmental stress defense. Alfalfa is a predominant legume forage with excellent quality, but the lignin content negatively affects fodder digestibility. Currently, there is limited information on CCR characteristics, gene expression, and its role in lignin metabolism in alfalfa. In this study, we identified 30 members in the CCR gene family of Medicago sativa. In addition, gene structure, conserved motif, and evolution analysis suggested MsCCR1–7 presumably functioned as CCR, while the 23 MsCCR-likes fell into three categories. The expression patterns of MsCCRs/MsCCR-likes suggested their role in plant development, response to environmental stresses, and phytohormone treatment. These results were consistent with the cis-elements in their promoters. Histochemical staining showed that lignin accumulation gradually deepened with the development, which was consistent with gene expression results. Furthermore, recombinant MsCCR1 and MsCCR-like1 were purified and the kinetic parameters were tested under four substrates. In addition, three-dimensional structure models of MsCCR1 and MsCCR-like1 proteins showed the difference in the substrate-binding motif H212(X)2K215R263. These results will be useful for further application for legume forage quality modification and biofuels industry engineering in the future.
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Comparative Genomic Analysis of SAUR Gene Family, Cloning and Functional Characterization of Two Genes (PbrSAUR13 and PbrSAUR52) in Pyrus bretschneideri. Int J Mol Sci 2022; 23:ijms23137054. [PMID: 35806062 PMCID: PMC9266570 DOI: 10.3390/ijms23137054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
The SAUR (small auxin-up RNA) gene family is the biggest family of early auxin response genes in higher plants and has been associated with the control of a variety of biological processes. Although SAUR genes had been identified in several genomes, no systematic analysis of the SAUR gene family has been reported in Chinese white pear. In this study, comparative and systematic genomic analysis has been performed in the SAUR gene family and identified a total of 116 genes from the Chinese white pear. A phylogeny analysis revealed that the SAUR family could be classified into four groups. Further analysis of gene structure (introns/exons) and conserved motifs showed that they are diverse functions and SAUR-specific domains. The most frequent mechanisms are whole-genome duplication (WGD) and dispersed duplication (DSD), both of which may be important in the growth of the SAUR gene family in Chinese white pear. Moreover, cis-acting elements of the PbrSAUR genes were found in promoter regions associated with the auxin-responsive elements that existed in most of the upstream sequences. Remarkably, the qRT-PCR and transcriptomic data indicated that PbrSAUR13 and PbrSAUR52 were significantly expressed in fruit ripening. Subsequently, subcellular localization experiments revealed that PbrSAUR13 and PbrSAUR52 were localized in the nucleus. Moreover, PbrSAUR13 and PbrSAUR52 were screened for functional verification, and Dangshan pear and frandi strawberry were transiently transformed. Finally, the effects of these two genes on stone cells and lignin were analyzed by phloroglucinol staining, Fourier infrared spectroscopy, and qRT-PCR. It was found that PbrSAUR13 promoted the synthesis and accumulation of stone cells and lignin, PbrSAUR52 inhibited the synthesis and accumulation of stone cells and lignin. In conclusion, these results indicate that PbrSAUR13 and PbrSAUR52 are predominantly responsible for lignin inhibit synthesis, which provides a basic mechanism for further study of PbrSAUR gene functions.
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Wang X, Chao N, Zhang A, Kang J, Jiang X, Gai Y. Systematic Analysis and Biochemical Characterization of the Caffeoyl Shikimate Esterase Gene Family in Poplar. Int J Mol Sci 2021; 22:ijms222413366. [PMID: 34948162 PMCID: PMC8704367 DOI: 10.3390/ijms222413366] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023] Open
Abstract
Caffeoyl shikimate esterase (CSE) hydrolyzes caffeoyl shikimate into caffeate and shikimate in the phenylpropanoid pathway. In this study, we performed a systematic analysis of the CSE gene family and investigated the possible roles of CSE and CSE-like genes in Populus. We conducted a genome-wide analysis of the CSE gene family, including functional and phylogenetic analyses of CSE and CSE-like genes, using the poplar (Populus trichocarpa) genome. Eighteen CSE and CSE-like genes were identified in the Populus genome, and five phylogenetic groups were identified from phylogenetic analysis. CSEs in Group Ia, which were proposed as bona fide CSEs, have probably been lost in most monocots except Oryza sativa. Primary functional classification showed that PoptrCSE1 and PoptrCSE2 had putative function in lignin biosynthesis. In addition, PoptrCSE2, along with PoptrCSE12, might also respond to stress with a function in cell wall biosynthesis. Enzymatic assay of PoptoCSE1 (Populus tomentosa), -2 and -12 showed that PoptoCSE1 and -2 maintained CSE activity. PoptoCSE1 and 2 had similar biochemical properties, tissue expression patterns and subcellular localization. Most of the PoptrCSE-like genes are homologs of AtMAGL (monoacylglycerol lipase) genes in Arabidopsis and may function as MAG lipase in poplar. Our study provides a systematic understanding of this novel gene family and suggests the function of CSE in monolignol biosynthesis in Populus.
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Affiliation(s)
- Xuechun Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Nan Chao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China
| | - Aijing Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Jiaqi Kang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Xiangning Jiang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Ying Gai
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
- Correspondence: ; Tel.: +86-10-6233-8063
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Lackus ND, Schmidt A, Gershenzon J, Köllner TG. A peroxisomal β-oxidative pathway contributes to the formation of C6-C1 aromatic volatiles in poplar. PLANT PHYSIOLOGY 2021; 186:891-909. [PMID: 33723573 PMCID: PMC8195509 DOI: 10.1093/plphys/kiab111] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/19/2021] [Indexed: 05/06/2023]
Abstract
Benzenoids (C6-C1 aromatic compounds) play important roles in plant defense and are often produced upon herbivory. Black cottonwood (Populus trichocarpa) produces a variety of volatile and nonvolatile benzenoids involved in various defense responses. However, their biosynthesis in poplar is mainly unresolved. We showed feeding of the poplar leaf beetle (Chrysomela populi) on P. trichocarpa leaves led to increased emission of the benzenoid volatiles benzaldehyde, benzylalcohol, and benzyl benzoate. The accumulation of salicinoids, a group of nonvolatile phenolic defense glycosides composed in part of benzenoid units, was hardly affected by beetle herbivory. In planta labeling experiments revealed that volatile and nonvolatile poplar benzenoids are produced from cinnamic acid (C6-C3). The biosynthesis of C6-C1 aromatic compounds from cinnamic acid has been described in petunia (Petunia hybrida) flowers where the pathway includes a peroxisomal-localized chain shortening sequence, involving cinnamate-CoA ligase (CNL), cinnamoyl-CoA hydratase/dehydrogenase (CHD), and 3-ketoacyl-CoA thiolase (KAT). Sequence and phylogenetic analysis enabled the identification of small CNL, CHD, and KAT gene families in P. trichocarpa. Heterologous expression of the candidate genes in Escherichia coli and characterization of purified proteins in vitro revealed enzymatic activities similar to those described in petunia flowers. RNA interference-mediated knockdown of the CNL subfamily in gray poplar (Populus x canescens) resulted in decreased emission of C6-C1 aromatic volatiles upon herbivory, while constitutively accumulating salicinoids were not affected. This indicates the peroxisomal β-oxidative pathway participates in the formation of volatile benzenoids. The chain shortening steps for salicinoids, however, likely employ an alternative pathway.
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Affiliation(s)
- Nathalie D Lackus
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Axel Schmidt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Tobias G Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
- Author for communication:
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Hodgson-Kratky K, Perlo V, Furtado A, Choudhary H, Gladden JM, Simmons BA, Botha F, Henry RJ. Association of gene expression with syringyl to guaiacyl ratio in sugarcane lignin. PLANT MOLECULAR BIOLOGY 2021; 106:173-192. [PMID: 33738678 DOI: 10.1007/s11103-021-01136-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/02/2021] [Indexed: 05/11/2023]
Abstract
A transcriptome analysis reveals the transcripts and alleles differentially expressed in sugarcane genotypes with contrasting lignin composition. Sugarcane bagasse is a highly abundant resource that may be used as a feedstock for the production of biofuels and bioproducts in order to meet increasing demands for renewable replacements for fossil carbon. However, lignin imparts rigidity to the cell wall that impedes the efficient breakdown of the biomass into fermentable sugars. Altering the ratio of the lignin units, syringyl (S) and guaiacyl (G), which comprise the native lignin polymer in sugarcane, may facilitate the processing of bagasse. This study aimed to identify genes and markers associated with S/G ratio in order to accelerate the development of sugarcane bioenergy varieties with modified lignin composition. The transcriptome sequences of 12 sugarcane genotypes that contrasted for S/G ratio were compared and there were 2019 transcripts identified as differentially expressed (DE) between the high and low S/G ratio groups. These included transcripts encoding possible monolignol biosynthetic pathway enzymes, transporters, dirigent proteins and transcriptional and post-translational regulators. Furthermore, the frequencies of single nucleotide polymorphisms (SNPs) were compared between the low and high S/G ratio groups to identify specific alleles expressed with the phenotype. There were 2063 SNP loci across 787 unique transcripts that showed group-specific expression. Overall, the DE transcripts and SNP alleles identified in this study may be valuable for breeding sugarcane varieties with altered S/G ratio that may provide desirable bioenergy traits.
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Affiliation(s)
- K Hodgson-Kratky
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - V Perlo
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - A Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - H Choudhary
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Sandia National Laboratories, Livermore, CA, 94550, USA
| | - J M Gladden
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Sandia National Laboratories, Livermore, CA, 94550, USA
| | - B A Simmons
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - F Botha
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - R J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia.
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11
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Chao N, Qi Q, Li S, Ruan B, Jiang X, Gai Y. Characterization and functional analysis of the Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) gene family in poplar. PeerJ 2021; 9:e10741. [PMID: 33665007 PMCID: PMC7916539 DOI: 10.7717/peerj.10741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 12/18/2020] [Indexed: 12/24/2022] Open
Abstract
Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) divides the mass flux to H, G and S units in monolignol biosynthesis and affects lignin content. Ten HCT homologs were identified in the Populus trichocarpa (Torr. & Gray) genome. Both genome duplication and tandem duplication resulted in the expansion of HCT orthologs in Populus. Comprehensive analysis including motif analysis, phylogenetic analysis, expression profiles and co-expression analysis revealed the divergence and putative function of these candidate PoptrHCTs. PoptrHCT1 and 2 were identified as likely involved in lignin biosynthesis. PoptrHCT9 and 10- are likely to be involved in plant development and the response to cold stress. Similar functional divergence was also identified in Populus tomentosa Carr. Enzymatic assay of PtoHCT1 showed that PtoHCT1 was able to synthesize caffeoyl shikimate using caffeoyl-CoA and shikimic acid as substrates.
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Affiliation(s)
- Nan Chao
- School of Life Science, Tsinghua University, Beijing, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Qi Qi
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,College of Horticulture, China Agricultural University, Beijing, China
| | - Shuang Li
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Brent Ruan
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana Champaign, Urbana Champaign, IL, USA
| | - Xiangning Jiang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, the Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, Beijing, China
| | - Ying Gai
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, the Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, Beijing, China
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12
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Expression Profiles of Alkaloid-Related Genes across the Organs of Narrow-Leafed Lupin ( Lupinus angustifolius L.) and in Response to Anthracnose Infection. Int J Mol Sci 2021; 22:ijms22052676. [PMID: 33800929 PMCID: PMC7962062 DOI: 10.3390/ijms22052676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/06/2021] [Accepted: 03/03/2021] [Indexed: 11/21/2022] Open
Abstract
The main restraint obstructing the wider adoption of lupins as protein crops is the presence of bitter and toxic quinolizidine alkaloids (QAs), whose contents might increase under exposure to stressful environmental conditions. A poor understanding of how QAs accumulate hinders the breeding of sweet varieties. Here, we characterize the expression profiles of QA-related genes, along with the alkaloid content, in various organs of sweet and bitter narrow-leafed lupin (NLL, Lupinus angustifolius L.). Special attention is paid to the RAP2-7 transcription factor, a candidate regulator of the QA pathway. We demonstrate the upregulation of RAP2-7 and other QA-related genes, across the aerial organs of a bitter cultivar and the significant correlations between their expression levels, thus supporting the role of RAP2-7 as an important regulatory gene in NLL. Moreover, we showed that the initial steps of QA synthesis might occur independently in all aerial plant organs sharing common regulatory mechanisms. Nonetheless, other regulatory steps might be involved in RAP2-7-triggered QA accumulation, given its expression pattern in leaves. Finally, the examination of QA-related gene expression in plants infected with Colletotrichum lupini evidenced no connection between QA synthesis and anthracnose resistance, in contrast to the important role of polyamines during plant–pathogen interactions.
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13
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De Meester B, Madariaga Calderón B, de Vries L, Pollier J, Goeminne G, Van Doorsselaere J, Chen M, Ralph J, Vanholme R, Boerjan W. Tailoring poplar lignin without yield penalty by combining a null and haploinsufficient CINNAMOYL-CoA REDUCTASE2 allele. Nat Commun 2020; 11:5020. [PMID: 33024118 PMCID: PMC7538556 DOI: 10.1038/s41467-020-18822-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/16/2020] [Indexed: 01/09/2023] Open
Abstract
Lignin causes lignocellulosic biomass recalcitrance to enzymatic hydrolysis. Engineered low-lignin plants have reduced recalcitrance but often exhibit yield penalties, offsetting their gains in fermentable sugar yield. Here, CRISPR/Cas9-generated CCR2(−/*) line 12 poplars have one knockout CCR2 allele while the other contains a 3-bp deletion, resulting in a 114I115A-to-114T conversion in the corresponding protein. Despite having 10% less lignin, CCR2(−/*) line 12 grows normally. On a plant basis, the saccharification efficiency of CCR2(−/*) line 12 is increased by 25–41%, depending on the pretreatment. Analysis of monoallelic CCR2 knockout lines shows that the reduced lignin amount in CCR2(−/*) line 12 is due to the combination of a null and the specific haploinsufficient CCR2 allele. Analysis of another CCR2(−/*) line shows that depending on the specific CCR2 amino-acid change, lignin amount and growth can be affected to different extents. Our findings open up new possibilities for stably fine-tuning residual gene function in planta. Plants with reduced amounts of lignin typically suffer from dwarfed growth, which offsets their gain in fermentable sugar yield. Here, the authors show that genome-edited poplar lines with a null and a haploinsufficient allele of CINNAMOYL-COA REDUCTASE2 (CCR2) can be obtained that have a reduced lignin level and normal growth.
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Affiliation(s)
- Barbara De Meester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Barbara Madariaga Calderón
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Lisanne de Vries
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Jacob Pollier
- VIB Metabolomics Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Geert Goeminne
- VIB Metabolomics Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Jan Van Doorsselaere
- Higher Institute for Nursing and Biotechnology, VIVES University College, Wilgenstraat 32, 8800, Roeselare, Belgium
| | - Mingjie Chen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.,US Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, 53726, USA
| | - John Ralph
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.,US Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, 53726, USA
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium. .,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.
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15
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Chao N, Jiang WT, Wang XC, Jiang XN, Gai Y. Novel motif is capable of determining CCR and CCR-like proteins based on the divergence of CCRs in plants. TREE PHYSIOLOGY 2019; 39:2019-2026. [PMID: 31748812 DOI: 10.1093/treephys/tpz098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/23/2019] [Accepted: 09/09/2019] [Indexed: 05/22/2023]
Abstract
Cinnamoyl-coenzyme A reductases (CCRs) have been reported as key enzymes involved in monolignol biosynthesis. In this study, a motif-aware workflow based on a new signature motif effectively distinguished CCRs from CCR-like proteins. The divergence of CCRs and CCR-like sequences in Populus tomentosa Carr, Panicum virgatum L, Oryza sativa L and Selaginella moellendorffii Hieron suggests that NWYCY is not efficient for CCR recognition. The novel motif H202(X)2K205 (CCR-SBM or CCR substrate binding motif) was introduced to distinguish between CCRs and CCR-like proteins. The site-directed mutant R205K in Os(I)CCR-like and H202 in PtoCCR7 resulted in the rescue and loss of activity, respectively, further validating the fact that CCR-SBM is critical for maintaining CCR activity. The molecular docking using feruloyl-cinnamoyl-coenzyme A (CoA) as the ligand and binary PhCCR-NADP structures as receptors indicated an interaction between H202 and K205 with CoA moiety. The genuine CCRs and CCR-like proteins from several angiosperms and gymnosperms were screened using a motif-aware workflow and were validated using a biochemical assay. Our results suggest that the motif-aware workflow is efficient and effective for the identification of CCRs and CCR-like proteins in land plants and can be used as a more accurate way of identifying genuine CCRs among land plants.
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Affiliation(s)
- Nan Chao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083, People's Republic of China
- School of Biotechnology, Jiangsu University of Science and Technology, ZhenJiang, Jiangsu 212003, People's Republic of China
| | - Wen-Ting Jiang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083, People's Republic of China
| | - Xue-Chun Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083, People's Republic of China
| | - Xiang-Ning Jiang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083, People's Republic of China
- National Engineering Laboratory for Tree Breeding, the Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, Beijing 100083, People's Republic of China
| | - Ying Gai
- College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083, People's Republic of China
- National Engineering Laboratory for Tree Breeding, the Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, Beijing 100083, People's Republic of China
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16
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Su X, Zhao Y, Wang H, Li G, Cheng X, Jin Q, Cai Y. Transcriptomic analysis of early fruit development in Chinese white pear (Pyrus bretschneideri Rehd.) and functional identification of PbCCR1 in lignin biosynthesis. BMC PLANT BIOLOGY 2019; 19:417. [PMID: 31604417 PMCID: PMC6788021 DOI: 10.1186/s12870-019-2046-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/20/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND The content of stone cells and lignin is one of the key factors affecting the quality of pear fruit. In a previous study, we determined the developmental regularity of stone cells and lignin in 'Dangshan Su' pear fruit 15-145 days after pollination (DAP). However, the development of fruit stone cells and lignin before 15 DAP has not been heavily researched. RESULTS In this study, we found that primordial stone cells began to appear at 7 DAP and that the fruit had formed a large number of stone cells at 15 DAP. Subsequently, transcriptome sequencing was performed on fruits at 0, 7, and 15 DAP and identified 3834 (0 vs. 7 DAP), 4049 (7 vs. 15 DAP) and 5763 (0 vs. 15 DAP) DEGs. During the 7-15 DAP period, a large number of key enzyme genes essential for lignin biosynthesis are gradually up-regulated, and their expression pattern is consistent with the accumulation of lignin in this period. Further analysis found that the biosynthesis of S-type lignin in 'Dangshan Su' pear does not depend on the catalytic activity of PbSAD but is primarily generated by the catalytic activity of caffeoyl-CoA through CCoAOMT, CCR, F5H, and CAD. We cloned PbCCR1, 2 and analysed their functions in Chinese white pear lignin biosynthesis. PbCCR1 and 2 have a degree of functional redundancy; both demonstrate the ability to participate in lignin biosynthesis. However, PbCCR1 may be the major gene for lignin biosynthesis, while PbCCR2 has little effect on lignin biosynthesis. CONCLUSIONS Our results revealed that 'Dangshan Su' pear began to form a large number of stone cells and produce lignin after 7 DAP and mainly accumulated materials from 0 to 7 DAP. PbCCR1 is mainly involved in the biosynthesis of lignin in 'Dangshan Su' pear and plays a positive role in lignin biosynthesis.
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Affiliation(s)
- Xueqiang Su
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Yu Zhao
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Han Wang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Guohui Li
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Xi Cheng
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Qing Jin
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
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17
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Guo Y, Zhu C, Zhao S, Zhang S, Wang W, Fu H, Li X, Zhou C, Chen L, Lin Y, Lai Z. De novo transcriptome and phytochemical analyses reveal differentially expressed genes and characteristic secondary metabolites in the original oolong tea (Camellia sinensis) cultivar 'Tieguanyin' compared with cultivar 'Benshan'. BMC Genomics 2019; 20:265. [PMID: 30943892 PMCID: PMC6446291 DOI: 10.1186/s12864-019-5643-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/25/2019] [Indexed: 01/16/2023] Open
Abstract
Background The two original plants of the oolong tea cultivar (‘Tieguanyin’) are “Wei shuo” ‘Tieguanyin’—TGY (Wei) and “Wang shuo” ‘Tieguanyin’—TGY (Wang). Another cultivar, ‘Benshan’ (BS), is similar to TGY in its aroma, taste, and genetic make-up, but it lacks the “Yin Rhyme” flavor. We aimed to identify differences in biochemical characteristics and gene expression among these tea plants. Results The results of spectrophotometric, high performance liquid chromatography (HPLC), and gas chromatography-mass spectrometry (GC-MS) analyses revealed that TGY (Wei) and TGY (Wang) had deeper purple-colored leaves and higher contents of anthocyanin, catechins, caffeine, and limonene compared with BS. Analyses of transcriptome data revealed 12,420 differentially expressed genes (DEGs) among the cultivars. According to a Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the flavonoid, caffeine, and limonene metabolic pathways were highly enriched. The transcript levels of the genes involved in these three metabolic pathways were not significantly different between TGY (Wei) and TGY (Wang), except for two unigenes encoding IMPDH and SAMS, which are involved in caffeine metabolism. The comparison of TGY vs. BS revealed eight up-regulated genes (PAL, C4H, CHS, F3’H, F3H, DFR, ANS, and ANR) and two down-regulated genes (FLS and CCR) in flavonoid metabolism, four up-regulated genes (AMPD, IMPDH, SAMS, and 5′-Nase) and one down-regulated XDH gene in caffeine metabolism; and two down-regulated genes (ALDH and HIBADH) in limonene degradation. In addition, the expression levels of the transcription factor (TF) PAP1 were significantly higher in TGY than in BS. Therefore, high accumulation of flavonoids, caffeine, and limonene metabolites and the expression patterns of their related genes in TGY might be beneficial for the formation of the “Yin Rhyme” flavor. Conclusions Transcriptomic, HPLC, and GC-MS analyses of TGY (Wei), TGY (Wang), and BS indicated that the expression levels of genes related to secondary metabolism and high contents of catechins, anthocyanin, caffeine, and limonene may contribute to the formation of the “Yin Rhyme” flavor in TGY. These findings provide new insights into the relationship between the accumulation of secondary metabolites and sensory quality, and the molecular mechanisms underlying the formation of the unique flavor “Yin Rhyme” in TGY. Electronic supplementary material The online version of this article (10.1186/s12864-019-5643-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shanshan Zhao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuting Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenjian Wang
- Anxi Tea Research Institute, Anxi, 362400, China
| | - Haifeng Fu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaozhen Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lan Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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18
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Su X, Meng T, Zhao Y, Li G, Cheng X, Abdullah M, Sun X, Cai Y, Lin Y. Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear ( Pyrus bretschneideri). PeerJ 2019; 7:e6628. [PMID: 30941270 PMCID: PMC6440465 DOI: 10.7717/peerj.6628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/15/2019] [Indexed: 12/12/2022] Open
Abstract
The INDETERMINATE DOMAIN (IDD) gene family encodes hybrid transcription factors with distinct zinc finger motifs and appears to be found in all higher plant genomes. IDD genes have been identified throughout the genomes of the model plants Arabidopsis thaliana and Oryza sativa, and the functions of many members of this gene family have been studied. However, few studies have investigated the IDD gene family in Rosaceae species (among these species, a genome-wide identification of the IDD gene family has only been completed in Malus domestica). This study focuses on a comparative genomic analysis of the IDD gene family in five Rosaceae species (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Rubus occidentalis and Prunus avium). We identified a total of 68 IDD genes: 16 genes in Chinese white pear, 14 genes in F. vesca, 13 genes in Prunus mume, 14 genes in R. occidentalis and 11 genes in Prunus avium. The evolution of the IDD genes in these five Rosaceae species was revealed by constructing a phylogenetic tree, tracking gene duplication events, and performing a sliding window analysis and a conserved microsynteny analysis. The expression analysis of different organs showed that most of the pear IDD genes are found at a very high transcription level in fruits, flowers and buds. Based on our results with those obtained in previous research, we speculated that PbIDD2 and PbIDD8 might participate in flowering induction in pear. A temporal expression analysis showed that the expression patterns of PbIDD3 and PbIDD5 were completely opposite to the accumulation pattern of fruit lignin and the stone cell content. The results of the composite phylogenetic tree and expression pattern analysis indicated that PbIDD3 and PbIDD5 might be involved in the metabolism of lignin and secondary cell wall (SCW) formation. In summary, we provide basic information about the IDD genes in five Rosaceae species and thereby provide a theoretical basis for studying the function of these IDD genes.
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Affiliation(s)
- Xueqiang Su
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Tiankai Meng
- School of Life Sciences and Technology, TongJi University, Shanghai, China
| | - Yu Zhao
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Guohui Li
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Xi Cheng
- School of Life Science, Anhui Agricultural University, Hefei, China
| | | | - Xu Sun
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yi Lin
- School of Life Science, Anhui Agricultural University, Hefei, China
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Chao N, Li S, Li N, Qi Q, Jiang WT, Jiang XN, Gai Y. Two distinct cinnamoyl-CoA reductases in Selaginella moellendorffii offer insight into the divergence of CCRs in plants. PLANTA 2017; 246:33-43. [PMID: 28321576 DOI: 10.1007/s00425-017-2678-8] [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: 02/06/2017] [Accepted: 03/10/2017] [Indexed: 06/06/2023]
Abstract
Two distinct cinnamoyl-coenzyme A reductases (CCRs) from Selaginella moellendorffii were evaluated, and of these, SmCCR2-1, which has both distinct sequence motifs and catalytic properties, was clustered into a new CCR subgroup. Cinnamoyl-coenzyme A reductases (CCRs) have been reported in many land plants to have critical functions in monolignol biosynthesis. In this study, we performed a genome-wide screen and obtained two distinct SmCCRs from S. moellendorffii. Phylogenetic analysis indicated that SmCCR2 (both SmCCR2-1 and 2-2) and SmCCR3 together with PpaCCR belong to a distinct subgroup of genuine CCRs with variations in the NAD(P)H-binding motif. Enzymatic assays showed detectable activity by both SmCCR1 and SmCCR2-1 toward four hydroxycinnamoyl-CoA esters. SmCCR1, which clustered with reported CCRs from angiosperms and gymnosperms, exhibited specificity toward feruloyl-CoA, while SmCCR2-1 showed a preference for sinapoyl-CoA. Interestingly, the reaction temperature profiles for SmCCR1 and SmCCR2-1 are complementary. Homology models and molecular simulations suggest that the variations in NADPH-binding motifs, especially R(X)6K instead of R(X)5K, affect the NADP+ conformation. Notably, the signature motif NWYCY was replaced with NGYCL in SmCCR1 and with EWYCL in SmCCR2-1, while the signature residues H202 and R253, reported in a previous study, were conserved in SmCCR1 and SmCCR2-1 but varied in SmCCR-like genes. It is likely that NWYCY is not a reliable signature for CCRs in plants. The detectable activity of site-direct mutant S123T of SmCCR1 suggested that S123 which consists of catalytic triad is changeable. Possible evolution process for the emergence of two subgroups of genuine CCRs was also revealed. Altogether, these findings revise our understanding of CCRs with regard to divergence and active sites.
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Affiliation(s)
- Nan Chao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Shuang Li
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Ning Li
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Qi Qi
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Wen-Ting Jiang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xiang-Ning Jiang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, National Engineering Laboratory for Tree Breeding, Beijing, 100083, China
| | - Ying Gai
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, National Engineering Laboratory for Tree Breeding, Beijing, 100083, China.
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Liu S, Liu J, Hou J, Chao N, Gai Y, Jiang X. Three steps in one pot: biosynthesis of 4-hydroxycinnamyl alcohols using immobilized whole cells of two genetically engineered Escherichia coli strains. Microb Cell Fact 2017; 16:104. [PMID: 28606145 PMCID: PMC5468945 DOI: 10.1186/s12934-017-0722-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 06/07/2017] [Indexed: 11/13/2022] Open
Abstract
Background 4-Hydroxycinnamyl alcohols are a class of natural plant secondary metabolites that include p-coumaryl alcohol, caffeyl alcohol, coniferyl alcohol and sinapyl alcohol, and have physiological, ecological and biomedical significance. While it is necessary to investigate the biological pathways and economic value of these alcohols, research is hindered because of their limited availability and high cost. Traditionally, these alcohols are obtained by chemical synthesis and plant extraction. However, synthesis by biotransformation with immobilized microorganisms is of great interest because it is environmentally friendly and offers high stability and regenerable cofactors. Therefore, we produced 4-hydroxycinnamyl alcohols using immobilized whole cells of engineered Escherichia coli as the biocatalyst. Results In this study, we used the recombinant E. coli strain, M15–4CL1–CCR, expressing the fusion protein 4-coumaric acid: coenzyme A ligase and the cinnamoyl coenzyme A reductase and a recombinant E. coli strain, M15–CAD, expressing cinnamyl alcohol dehydrogenase from Populus tomentosa (P. tomentosa). High performance liquid chromatography and mass spectrometry showed that the immobilized whole cells of the two recombinant E. coli strains could effectively convert the phenylpropanoic acids to their corresponding 4-hydroxycinnamyl alcohols. Further, the optimum buffer pH and the reaction temperature were pH 7.0 and 30 °C. Under these conditions, the molar yield of the p-coumaryl alcohol, the caffeyl alcohol and the coniferyl alcohol was around 58, 24 and 60%, respectively. Moreover, the highly sensitive and selective HPLC–PDA–ESI–MSn method used in this study could be applied to the identification and quantification of these aromatic polymers. Conclusions We have developed a dual-cell immobilization system for the production of 4-hydroxycinnamyl alcohols from inexpensive phenylpropanoic acids. This biotransformation method is both simple and environmental-friendly, which is promising for the practical and cost effective synthesis of natural products.Biotransformation process of phenylpropanoic acids by immobilized whole-cells ![]()
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Affiliation(s)
- Shuxin Liu
- College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Jiabin Liu
- College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Jiayin Hou
- College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Nan Chao
- College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Ying Gai
- College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China.,The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, National Engineering Laboratory for Tree Breeding, Beijing, 100083, People's Republic of China
| | - Xiangning Jiang
- College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China. .,The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, National Engineering Laboratory for Tree Breeding, Beijing, 100083, People's Republic of China.
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Park HL, Bhoo SH, Kwon M, Lee SW, Cho MH. Biochemical and Expression Analyses of the Rice Cinnamoyl-CoA Reductase Gene Family. FRONTIERS IN PLANT SCIENCE 2017; 8:2099. [PMID: 29312373 PMCID: PMC5732984 DOI: 10.3389/fpls.2017.02099] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/24/2017] [Indexed: 05/06/2023]
Abstract
Cinnamoyl-CoA reductase (CCR) is the first committed enzyme in the monolignol pathway for lignin biosynthesis and catalyzes the conversion of hydroxycinnamoyl-CoAs into hydroxycinnamaldehydes. In the rice genome, 33 genes are annotated as CCR and CCR-like genes, collectively called OsCCRs. To elucidate the functions of OsCCRs, their phylogenetic relationships, expression patterns at the transcription levels and biochemical characteristics were thoroughly analyzed. Of the 33 OsCCRs, 24 of them encoded polypeptides of lengths similar to those of previously identified plant CCRs. The other nine OsCCRs had much shorter peptide lengths. Phylogenetic tree and sequence similarities suggested OsCCR4, 5, 17, 18, 19, 20, and 21 as likely candidates for functional CCRs in rice. To elucidate biochemical functions, OsCCR1, 5, 17, 19, 20, 21, and 26 were heterologously expressed in Escherichia coli and the resulting recombinant OsCCRs were purified to apparent homogeneity. Activity assays of the recombinant OsCCRs with hydroxycinnamoyl-CoAs revealed that OsCCR17, 19, 20, and 21 were biochemically active CCRs, in which the NAD(P)-binding and NADP-specificity motifs as well as the CCR signature motif were fully conserved. The kinetic parameters of enzyme reactions revealed that feruloyl-CoA, a precursor for the guaiacyl (G)-unit of lignin, is the most preferred substrate of OsCCR20 and 21. This result is consistent with a high content (about 70%) of G-units in rice lignins. Phylogenetic analysis revealed that OsCCR19 and 20 were grouped with other plant CCRs involved in developmental lignification, whereas OsCCR17 and 21 were closely related to stress-responsible CCRs identified from other plant species. In agreement with the phylogenetic analysis, expression analysis demonstrated that OsCCR20 was constitutively expressed throughout the developmental stages of rice, showing particularly high expression levels in actively lignifying tissues, such as roots and stems. These results suggest that OsCCR20 is primarily involved in developmental deposition of lignins in secondary cell walls. As expected, the expressions of OsCCR17 and 21 were induced in response to biotic and abiotic stresses, such as Magnaporthe grisea and Xanthomonas oryzae pv. oryzae (Xoo) infections, UV-irradiation and high salinity, suggesting that these genes play a role in defense-related processes in rice.
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Affiliation(s)
- Hye Lin Park
- Graduate School of Biotechnology and College of Life Sciences, Kyung Hee University, Yongin, South Korea
| | - Seong Hee Bhoo
- Graduate School of Biotechnology and College of Life Sciences, Kyung Hee University, Yongin, South Korea
| | - Mi Kwon
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Sang-Won Lee
- Graduate School of Biotechnology and College of Life Sciences, Kyung Hee University, Yongin, South Korea
- *Correspondence: Sang-Won Lee
| | - Man-Ho Cho
- Graduate School of Biotechnology and College of Life Sciences, Kyung Hee University, Yongin, South Korea
- Man-Ho Cho
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