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Zheng W, Zhao G, Zhang W, Lian C, Zhang H, Hou X. iTRAQ proteome analysis reveals the underling mechanisms of foliage zinc-spraying to improve photosynthetic capacity and seed yields of Peaonia ostii 'Fengdan'. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109082. [PMID: 39217824 DOI: 10.1016/j.plaphy.2024.109082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 07/30/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
Zinc (Zn) deficiency is a significant nutritional limitation to crop yield globally, particularly in calcareous soil environments. Tree peony of Peaonia ostii 'Fengdan' is regarded as an oil crop due to its seeds rich in alpha-linolenic acid, a beneficial compound for health promotion. However, low seed yield remains a primary challenge in attaining sufficient seed oil from tree peony. In this study, Zn fertilization was applied to soil or foliage of P. ostii 'Fengdan' in the growth period before fruit development. Our findings reveal that foliar Zn-spraying, as opposed to soil application, proves to be a more effective method for augmenting seed yield, Zn accumulation and photosynthetic capacity in 'Fengdan'. Comparative analyses of the leaf proteome of 'Fengdan' using iTRAQ profiling under foliar Zn-spraying identified 115 differentially expressed proteins (DEPs), including 36 upregulated proteins, which likely contribute to the observed increase in seed yields of 'Fengdan' caused by foliage Zn-spraying. Specifically, Zn2+ stimulation of phosphatidylinositol signaling initiates a cascade of metabolic regulations. Firstly, ATP synthesis promotes leaf photosynthetic capacity, facilitated by improved sucrose metabolism through upregulated pullulanase and 1,4-alpha-glucan-branching enzyme. Furthermore, lipid synthesis and transport are facilitated by upregulated lipoyl synthase and plastid lipid-associated proteins. Additionally, DEPs involved in secondary metabolism are upregulated in the production of various metabolites conducive to 'Fengdan' growth. Overall, our results demonstrate that foliage Zn-spraying enhances seed yield in P. ostii 'Fengdan' by elevating Zn content and secondary metabolite synthesis in leaves, thereby augmenting leaf photosynthetic capacity and lipid synthesis. This study provides an effective way to increase seed yield of tree peony by exogenous Zn application.
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Affiliation(s)
- Wenwen Zheng
- College of Agriculture, Henan University of Science and Technology, Luoyang, 471000, China
| | - Guodong Zhao
- Luoyang National Peony Park, Luoyang, 471000, China
| | - Wanqing Zhang
- College of Agriculture, Henan University of Science and Technology, Luoyang, 471000, China
| | - Chunlan Lian
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo, Tokyo, 188-0002, Japan
| | - Hongxiao Zhang
- College of Agriculture, Henan University of Science and Technology, Luoyang, 471000, China.
| | - Xiaogai Hou
- College of Agriculture, Henan University of Science and Technology, Luoyang, 471000, China.
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2
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Yang F, Zhang L, Zhang X, Guan J, Wang B, Wu X, Song M, Wei A, Liu Z, Huo D. Genome-wide investigation of UDP-Glycosyltransferase family in Tartary buckwheat (Fagopyrum tataricum). BMC PLANT BIOLOGY 2024; 24:249. [PMID: 38580941 PMCID: PMC10998406 DOI: 10.1186/s12870-024-04926-8] [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: 10/05/2023] [Accepted: 03/18/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND Tartary buckwheat (Fagopyrum tataricum) belongs to Polygonaceae family and has attracted increasing attention owing to its high nutritional value. UDP-glycosyltransferases (UGTs) glycosylate a variety of plant secondary metabolites to control many metabolic processes during plant growth and development. However, there have been no systematic reports of UGT superfamily in F. tataricum. RESULTS We identified 173 FtUGTs in F. tataricum based on their conserved UDPGT domain. Phylogenetic analysis of FtUGTs with 73 Arabidopsis UGTs clustered them into 21 families. FtUGTs from the same family usually had similar gene structure and motif compositions. Most of FtUGTs did not contain introns or had only one intron. Tandem repeats contributed more to FtUGTs amplification than segmental duplications. Expression analysis indicates that FtUGTs are widely expressed in various tissues and likely play important roles in plant growth and development. The gene expression analysis response to different abiotic stresses showed that some FtUGTs were involved in response to drought and cadmium stress. Our study provides useful information on the UGTs in F. tataricum, and will facilitate their further study to better understand their function. CONCLUSIONS Our results provide a theoretical basis for further exploration of the functional characteristics of FtUGTs and for understanding the growth, development, and metabolic model in F. tataricum.
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Affiliation(s)
- Fan Yang
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Lei Zhang
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Xiao Zhang
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Jingru Guan
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Bo Wang
- MARA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoying Wu
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Minli Song
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Aili Wei
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Zhang Liu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China
| | - Dongao Huo
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China.
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Sun X, Ke Z, Zheng D, She M, Wu Z, Li QX, Zhang Z. Cloning, Expression, and Functional Characterization of Two Highly Efficient Flavonoid-di- O-glycosyltransferases ZmUGT84A1 and ZmUGT84A2 from Maize ( Zea mays L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7354-7363. [PMID: 38511857 DOI: 10.1021/acs.jafc.3c06327] [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: 03/22/2024]
Abstract
The maize (Zea mays L.) glycosyltransferase family 1 comprises many uridine diphosphate glycosyltransferase (UGT) members. However, UGT activities and biochemical functions have seldom been revealed. In this study, the genes of two flavonoid di-O-glycosyltransferases ZmUGT84A1 and ZmUGT84A2 were cloned from maize plant and expressed in Escherichia coli. Phylogenetic analysis showed that the two enzymes were homologous to AtUGT84A1 and AtUGT84A3. The two recombinant enzymes showed a high conversion rate of luteolin to its glucosides, mainly 4',7-di-O-glucoside and minorly 3',7-di-O-glucoside in two-step glycosylation reactions in vitro. Moreover, the recombinant ZmUGT84A1 and ZmUGT84A2 had a broad substrate spectrum, converting eriodictyol, naringenin, apigenin, quercetin, and kaempferol to monoglucosides and diglucosides. The highly efficient ZmUGT84A1 and ZmUGT84A2 may be used as a tool for the effective synthesis of various flavonoid O-glycosides and as markers for crop breeding to increase O-glycosyl flavonoid content in food.
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Affiliation(s)
- Xiaorong Sun
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Zhao Ke
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 100096, China
| | - Dengyu Zheng
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Meng She
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- College of Agriculture, Yangtze University, Jingzhou, Hubei 434022, China
| | - Zhongyi Wu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Honolulu, Hawaii 96822, United States
| | - Zhongbao Zhang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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Wang Y, Xun H, Wang L, Aktar S, Lei Y, Zhang R, Wang L, Wei K. Identification of Key Genes Associated with 1,2,6-Tri-O-galloyl-β-D-glucopyranose Accumulation in Camellia sinensis Based on Transcriptome Sequencing. Foods 2024; 13:495. [PMID: 38338630 PMCID: PMC10855904 DOI: 10.3390/foods13030495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Hydrolyzed tannin 1,2,6-tri-O-galloyl-β-D-glucopyranose (1,2,6-TGGP) possesses significant medicinal properties. However, little is known about its underlying molecular mechanisms. In this study, the levels of 1,2,6-TGGP in tea materials from different cultivars and leaf positions were compared. Additionally, one leaf and one bud sample from six tea cultivars with significant variations in 1,2,6-TGGP levels were analyzed using transcriptome high-throughput sequencing to identify the genes that are responsible for 1,2,6-TGGP accumulation. The sequencing results were mapped to the reference tea genome, revealing a total of 2735 differentially expressed genes (DEGs). This set included four UDP glycosyltransferase (UGTs) and six serine carboxypeptidases-like (SCPLs) genes. Among them, the upregulated SCPLs (CSS0032817) may directly participate in the acylation reaction of 1,2,6-TGGP. In addition, several classes of DEGs, including cytochrome P450, were significantly associated with the 1,2,6-TGGP content, which is potentially involved in their regulation. Overall, these results provide new insights into the molecular mechanism of 1,2,6-TGGP accumulation.
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Affiliation(s)
| | | | | | | | | | | | | | - Kang Wei
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; (Y.W.); (H.X.); (L.W.); (S.A.); (Y.L.); (R.Z.); (L.W.)
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5
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Gan Y, Yu B, Liu R, Shu B, Liang Y, Zhao Y, Qiu Z, Yan S, Cao B. Systematic analysis of the UDP-glucosyltransferase family: discovery of a member involved in rutin biosynthesis in Solanum melongena. FRONTIERS IN PLANT SCIENCE 2023; 14:1310080. [PMID: 38197083 PMCID: PMC10774229 DOI: 10.3389/fpls.2023.1310080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/21/2023] [Indexed: 01/11/2024]
Abstract
Eggplant (Solanum melongena) is an economically important crop and rich in various nutrients, among which rutin that has positive effects on human health is found in eggplant. Glycosylation mediated by UDP-glycosyltransferases (UGTs) is a key step in rutin biosynthesis. However, the UGT gene has not been reported in eggplant to date. Herein, 195 putative UGT genes were identified in eggplant by genome-wide analysis, and they were divided into 17 subgroups (Group A-P and Group R) according to the phylogenetic evolutionary tree. The members of Groups A, B, D, E and L were related to flavonol biosynthesis, and rutin was the typical flavonol. The expression profile showed that the transcriptional levels of SmUGT genes in Clusters 7-10 were closely related to those of rutin biosynthetic pathway genes. Notably, SmUGT89B2 was classified into Cluster 7 and Group B; its expression was consistent with rutin accumulation in different tissues and different leaf stages of eggplant. SmUGT89B2 was located in the nucleus and cell membrane. Virus-induced gene silencing (VIGS) and transient overexpression assays showed that SmUGT89B2 can promote rutin accumulation in eggplant. These findings provide new insights into the UGT genes in eggplant, indicating that SmUGT89B2 is likely to encode the final enzyme in rutin biosynthesis.
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Affiliation(s)
| | | | | | | | | | | | | | - Shuangshuang Yan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetable Engineering and Technology Research Center/College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Bihao Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetable Engineering and Technology Research Center/College of Horticulture, South China Agricultural University, Guangzhou, China
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6
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Pei T, Zhu S, Liao W, Fang Y, Liu J, Kong Y, Yan M, Cui M, Zhao Q. Gap-free genome assembly and CYP450 gene family analysis reveal the biosynthesis of anthocyanins in Scutellaria baicalensis. HORTICULTURE RESEARCH 2023; 10:uhad235. [PMID: 38156283 PMCID: PMC10753160 DOI: 10.1093/hr/uhad235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/01/2023] [Indexed: 12/30/2023]
Abstract
Scutellaria baicalensis Georgi, a member of the Lamiaceae family, is a widely utilized medicinal plant. The flavones extracted from S. baicalensis contribute to numerous health benefits, including anti-inflammatory, antiviral, and anti-tumor activities. However, the incomplete genome assembly hinders biological studies on S. baicalensis. This study presents the first telomere-to-telomere (T2T) gap-free genome assembly of S. baicalensis through the integration of Pacbio HiFi, Nanopore ultra-long and Hi-C technologies. A total of 384.59 Mb of genome size with a contig N50 of 42.44 Mb was obtained, and all sequences were anchored into nine pseudochromosomes without any gap or mismatch. In addition, we analysed the major cyanidin- and delphinidin-based anthocyanins involved in the determination of blue-purple flower using a widely-targeted metabolome approach. Based on the genome-wide identification of Cytochrome P450 (CYP450) gene family, three genes (SbFBH1, 2, and 5) encoding flavonoid 3'-hydroxylases (F3'Hs) and one gene (SbFBH7) encoding flavonoid 3'5'-hydroxylase (F3'5'H) were found to hydroxylate the B-ring of flavonoids. Our studies enrich the genomic information available for the Lamiaceae family and provide a toolkit for discovering CYP450 genes involved in the flavonoid decoration.
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Affiliation(s)
- Tianlin Pei
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Sanming Zhu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
| | - Weizhi Liao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yumin Fang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Jie Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yu Kong
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Mengxiao Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Mengying Cui
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Qing Zhao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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Caygill S, Dolan L. ATP binding cassette transporters and uridine diphosphate glycosyltransferases are ancient protein families that evolved roles in herbicide resistance through exaptation. PLoS One 2023; 18:e0287356. [PMID: 37733747 PMCID: PMC10513242 DOI: 10.1371/journal.pone.0287356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/25/2023] [Indexed: 09/23/2023] Open
Abstract
ATP-binding cassette (ABC) transporters actively transport various substances across membranes, while uridine diphosphate (UDP) glycosyltransferases (UGTs) are proteins that catalyse the chemical modification of various organic compounds. Both of these protein superfamilies have been associated with conferring herbicide resistance in weeds. Little is known about the evolutionary history of these protein families in the Archaeplastida. To infer the evolutionary histories of these protein superfamilies, we compared protein sequences collected from 10 species which represent distinct lineages of the Archaeplastida-the lineage including glaucophyte algae, rhodophyte algae, chlorophyte algae and the streptophytes-and generated phylogenetic trees. We show that ABC transporters were present in the last common ancestor of the Archaeplastida which lived 1.6 billion years ago, and the major clades identified in extant plants were already present then. Conversely, we only identified UGTs in members of the streptophyte lineage, which suggests a loss of these proteins in earlier diverging Archaeplastida lineages or arrival of UGTs into a common ancestor of the streptophyte lineage through horizontal gene transfer from a non-Archaeplastida eukaryote lineage. We found that within the streptophyte lineage, most diversification of the UGT protein family occurred in the vascular lineage, with 17 of the 20 clades identified in extant plants present only in vascular plants. Based on our findings, we conclude that ABC transporters and UGTs are ancient protein families which diversified during Archaeplastida evolution, which may have evolved for developmental functions as plants began to occupy new environmental niches and are now being selected to confer resistance to a diverse range of herbicides in weeds.
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Affiliation(s)
- Samuel Caygill
- Gregor Mendel Institute, Vienna, Austria
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Liam Dolan
- Gregor Mendel Institute, Vienna, Austria
- Department of Biology, University of Oxford, Oxford, United Kingdom
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8
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Zhang H, Dean L, Wang ML, Dang P, Lamb M, Chen C. GWAS with principal component analysis identify QTLs associated with main peanut flavor-related traits. FRONTIERS IN PLANT SCIENCE 2023; 14:1204415. [PMID: 37780495 PMCID: PMC10540862 DOI: 10.3389/fpls.2023.1204415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023]
Abstract
Peanut flavor is a complex and important trait affected by raw material and processing technology owing to its significant impact on consumer preference. In this research, principal component analysis (PCA) on 33 representative traits associated with flavor revealed that total sugars, sucrose, and total tocopherols provided more information related to peanut flavor. Genome-wide association studies (GWAS) using 102 U.S. peanut mini-core accessions were performed to study associations between 12,526 single nucleotide polymorphic (SNP) markers and the three traits. A total of 7 and 22 significant quantitative trait loci (QTLs) were identified to be significantly associated with total sugars and sucrose, respectively. Among these QTLs, four and eight candidate genes for the two traits were mined. In addition, two and five stable QTLs were identified for total sugars and sucrose in both years separately. No significant QTLs were detected for total tocopherols. The results from this research provide useful knowledge about the genetic control of peanut flavor, which will aid in clarifying the molecular mechanisms of flavor research in peanuts.
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Affiliation(s)
- Hui Zhang
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Lisa Dean
- USDA-ARS Food Science and Market Quality and Handling Research Unit, Raleigh, NC, United States
| | - Ming Li Wang
- US Department of Agriculture-Agricultural Research Service Plant Genetic Resources Conservation, Griffin, GA, United States
| | - Phat Dang
- US Department of Agriculture-Agricultural Research Service National Peanut Research Laboratory, Dawson, GA, United States
| | - Marshall Lamb
- US Department of Agriculture-Agricultural Research Service National Peanut Research Laboratory, Dawson, GA, United States
| | - Charles Chen
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, United States
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9
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Solanki M, Shukla LI. Recent advances in auxin biosynthesis and homeostasis. 3 Biotech 2023; 13:290. [PMID: 37547917 PMCID: PMC10400529 DOI: 10.1007/s13205-023-03709-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 07/18/2023] [Indexed: 08/08/2023] Open
Abstract
The plant proliferation is linked with auxins which in turn play a pivotal role in the rate of growth. Also, auxin concentrations could provide insights into the age, stress, and events leading to flowering and fruiting in the sessile plant kingdom. The role in rejuvenation and plasticity is now evidenced. Interest in plant auxins spans many decades, information from different plant families for auxin concentrations, transcriptional, and epigenetic evidences for gene regulation is evaluated here, for getting an insight into pattern of auxin biosynthesis. This biosynthesis takes place via an tryptophan-independent and tryptophan-dependent pathway. The independent pathway initiated before the tryptophan (trp) production involves indole as the primary substrate. On the other hand, the trp-dependent IAA pathway passes through the indole pyruvic acid (IPyA), indole-3-acetaldoxime (IAOx), and indole acetamide (IAM) pathways. Investigations on trp-dependent pathways involved mutants, namely yucca (1-11), taa1, nit1, cyp79b and cyp79b2, vt2 and crd, and independent mutants of tryptophan, ins are compiled here. The auxin conjugates of the IAA amide and ester-linked mutant gh3, iar, ilr, ill, iamt1, ugt, and dao are remarkable and could facilitate the assimilation of auxins. Efforts are made herein to provide an up-to-date detailed information about biosynthesis leading to plant sustenance. The vast information about auxin biosynthesis and homeostasis is consolidated in this review with a simplified model of auxin biosynthesis with keys and clues for important missing links since auxins can enable the plants to proliferate and override the environmental influence and needs to be probed for applications in sustainable agriculture. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03709-6.
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Affiliation(s)
- Manish Solanki
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry, 605014 India
- Puducherry, India
| | - Lata Israni Shukla
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry, 605014 India
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10
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Chen HY, Li X, Chapple C, Dilkes B, Li X. UGT76F1 glycosylates an isomer of the C7-necic acid component of pyrrolizidine alkaloids in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 36995355 DOI: 10.1111/tpj.16211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/11/2023] [Indexed: 06/19/2023]
Abstract
Identification of unknown metabolites and their biosynthetic genes is an active research area in plant specialized metabolism. By following a gene-metabolite association from a genome-wide association study of Arabidopsis stem metabolites, we report a previously unknown metabolite, 2-hydroxy-2-(1-hydroxyethyl)pentanoic acid glucoside, and demonstrated that UGT76F1 is responsible for its production in Arabidopsis. The chemical structure of the glucoside was determined by a series of analyses, including tandem MS, acid and base hydrolysis, and NMR spectrometry. T-DNA knockout mutants of UGT76F1 are devoid of the glucoside but accumulate increased levels of the aglycone. 2-hydroxy-2-(1-hydroxyethyl)pentanoic acid is structurally related to the C7-necic acid component of lycopsamine-type pyrrolizidine alkaloids such as trachelantic acid and viridifloric acid. Feeding norvaline greatly enhances the accumulation of 2-hydroxy-2-(1-hydroxyethyl)pentanoic acid glucoside in wild-type but not the UGT76F1 knockout mutant plants, providing evidence for an orthologous C7-necic acid biosynthetic pathway in Arabidopsis despite the apparent lack of pyrrolizidine alkaloids.
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Affiliation(s)
- Han-Yi Chen
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, 28081, USA
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Xin Li
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, 28081, USA
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Brian Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Xu Li
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, 28081, USA
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
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11
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Htwe CSS, Rajkumar S, Pathania P, Agrawal A. Transcriptome Profiling during Sequential Stages of Cryopreservation in Banana ( Musa AAA cv Borjahaji) Shoot Meristem. PLANTS (BASEL, SWITZERLAND) 2023; 12:1165. [PMID: 36904022 PMCID: PMC10005800 DOI: 10.3390/plants12051165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Cryopreservation approaches have been implemented in gene banks as a strategy to back up plant genetic resource collections that are vegetatively propagated. Different strategies have been employed to effectively cryopreserve plant tissue. There is little information on the cellular processes and molecular adjustments that confer resilience to the multiple stresses imposed during a cryoprotocol. In the present work, the cryobionomics of banana (Musa sp.), a non-model species, was investigated through the transcriptomic approach using RNA-Seq. Proliferating meristems of in vitro explants (Musa AAA cv 'Borjahaji') were cryopreserved using the droplet-vitrification technique. Transcriptome profiling analysis of eight cDNA libraries including the bio-replicates for T0 (stock cultures (control tissue), T1 (high sucrose pre-cultured), T2 (vitrification solution-treated) and T3 (liquid nitrogen-treated) meristem tissues was carried out. The raw reads obtained were mapped with a Musa acuminata reference genome sequence. A total of 70 differentially expressed genes (DEGs) comprising 34 upregulated and 36 downregulated were identified in all three phases as compared to control (T0). Among the significant DEGs (>log FC 2.0), during sequential steps, 79 in T1, 3 in T2 and the 4 in T3 were upregulated and 122 in T1, 5 in T2 and 9 in T3 were downregulated. Gene ontology (GO) enrichment analysis showed that these significant DEGs were involved in the upregulation of biological process (BP-170), cellular component (CC-10) and molecular function (MF-94) and downregulation of biological process (BP-61), cellular component (CC-3) and molecular function (MF-56). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs were involved in the biosynthesis of secondary metabolites, glycolysis/gluconeogenesis, MAPK signaling, EIN 3-lke 1 protein, 3-ketoacy-CoA synthase 6-like, and fatty acid elongation during cryopreservation. For the first time, a comprehensive transcript profiling during four stages of cryopreservation in banana were carried out, which will pave the way for devising an effective cryopreservation protocol.
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Affiliation(s)
- Chaw Su Su Htwe
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
- Division of Plant Genetic Resources, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | - Subramani Rajkumar
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Pooja Pathania
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Anuradha Agrawal
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
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12
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UDP-Glycosyltransferases in Edible Fungi: Function, Structure, and Catalytic Mechanism. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
UDP-glycosyltransferases (UGTs) are the most studied glycosyltransferases, and belong to large GT1 family performing the key roles in antibiotic synthesis, the development of bacterial glycosyltransferase inhibitors, and in animal inflammation. They transfer the glycosyl groups from nucleotide UDP-sugars (UDP-glucose, UDP-galactose, UDP-xylose, and UDP-rhamnose) to the acceptors including saccharides, proteins, lipids, and secondary metabolites. The present review summarized the recent of UDP-glycosyltransferases, including their structures, functions, and catalytic mechanism, especially in edible fungi. The future perspectives and new challenges were also summarized to understand of their structure–function relationships in the future. The outputs in this field could provide a reference to recognize function, structure, and catalytic mechanism of UDP-glycosyltransferases for understanding the biosynthesis pathways of secondary metabolites, such as hydrocarbons, monoterpenes, sesquiterpene, and polysaccharides in edible fungi.
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Li Y, Yang H, Li Z, Li S, Li J. Advances in the Biosynthesis and Molecular Evolution of Steroidal Saponins in Plants. Int J Mol Sci 2023; 24:ijms24032620. [PMID: 36768941 PMCID: PMC9917158 DOI: 10.3390/ijms24032620] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Steroidal saponins are an important type of plant-specific metabolite that are essential for plants' responses to biotic and abiotic stresses. Because of their extensive pharmacological activities, steroidal saponins are also important industrial raw materials for the production of steroidal drugs. In recent years, more and more studies have explored the biosynthesis of steroidal saponins in plants, but most of them only focused on the biosynthesis of their molecular skeleton, diosgenin, and their subsequent glycosylation modification mechanism needs to be further studied. In addition, the biosynthetic regulation mechanism of steroidal saponins, their distribution pattern, and their molecular evolution in plants remain unclear. In this review, we summarized and discussed recent studies on the biosynthesis, molecular regulation, and function of steroidal saponins. Finally, we also reviewed the distribution and molecular evolution of steroidal saponins in plants. The elucidation of the biosynthesis, regulation, and molecular evolutionary mechanisms of steroidal saponins is crucial to provide new insights and references for studying their distribution, diversity, and evolutionary history in plants. Furthermore, a deeper understanding of steroidal saponin biosynthesis will contribute to their industrial production and pharmacological applications.
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Affiliation(s)
| | | | | | | | - Jiaru Li
- Correspondence: ; Tel.: +86-27-6875-3599
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14
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Wang ZF, Rouard M, Droc G, Heslop-Harrison P(JS, Ge XJ. Genome assembly of Musa beccarii shows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes. Gigascience 2022; 12:giad005. [PMID: 36807539 PMCID: PMC9941839 DOI: 10.1093/gigascience/giad005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/24/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023] Open
Abstract
BACKGROUND Musa beccarii (Musaceae) is a banana species native to Borneo, sometimes grown as an ornamental plant. The basic chromosome number of Musa species is x = 7, 10, or 11; however, M. beccarii has a basic chromosome number of x = 9 (2n = 2x = 18), which is the same basic chromosome number of species in the sister genera Ensete and Musella. Musa beccarii is in the section Callimusa, which is sister to the section Musa. We generated a high-quality chromosome-scale genome assembly of M. beccarii to better understand the evolution and diversity of genomes within the family Musaceae. FINDINGS The M. beccarii genome was assembled by long-read and Hi-C sequencing, and genes were annotated using both long Iso-seq and short RNA-seq reads. The size of M. beccarii was the largest among all known Musaceae assemblies (∼570 Mbp) due to the expansion of transposable elements and increased 45S ribosomal DNA sites. By synteny analysis, we detected extensive genome-wide chromosome fusions and fissions between M. beccarii and the other Musa and Ensete species, far beyond those expected from differences in chromosome number. Within Musaceae, M. beccarii showed a reduced number of terpenoid synthase genes, which are related to chemical defense, and enrichment in lipid metabolism genes linked to the physical defense of the cell wall. Furthermore, type III polyketide synthase was the most abundant biosynthetic gene cluster (BGC) in M. beccarii. BGCs were not conserved in Musaceae genomes. CONCLUSIONS The genome assembly of M. beccarii is the first chromosome-scale genome assembly in the Callimusa section in Musa, which provides an important genetic resource that aids our understanding of the evolution of Musaceae genomes and enhances our knowledge of the pangenome.
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Affiliation(s)
- Zheng-Feng Wang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Key Laboratory of Carbon Sequestration in Terrestrial Ecosystem, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | - Gaetan Droc
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Pat (J S) Heslop-Harrison
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Xue-Jun Ge
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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15
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Chen Y, Fu M, Li H, Wang L, Liu R, Liu Z. Genome-wide characterization of the UDP-glycosyltransferase gene family reveals their potential roles in leaf senescence in cotton. Int J Biol Macromol 2022; 222:2648-2660. [DOI: 10.1016/j.ijbiomac.2022.10.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/05/2022]
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16
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Sun L, Zhao L, Huang H, Zhang Y, Wang J, Lu X, Wang S, Wang D, Chen X, Chen C, Guo L, Xu N, Zhang H, Wang J, Rui C, Han M, Fan Y, Nie T, Ye W. Genome-wide identification, evolution and function analysis of UGTs superfamily in cotton. Front Mol Biosci 2022; 9:965403. [PMID: 36177349 PMCID: PMC9513525 DOI: 10.3389/fmolb.2022.965403] [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: 06/09/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Glycosyltransferases mainly catalyse the glycosylation reaction in living organisms and widely exists in plants. UGTs have been identified from G. raimondii, G. arboreum and G. hirsutum. However, Genome-wide systematic analysis of UGTs superfamily have not been studied in G. barbadense. 752 UGTs were identified from four cotton species and grouped into 18 clades, of which R was newly discovered clades. Most UGTs were clustered at both ends of the chromosome and showed a heterogeneous distribution. UGT proteins were widely distributed in cells, with the highest distribution in chloroplasts. UGTs of the same clade shared similar intron/exon structural features. During evolution, the gene family has undergone strong selection for purification. UGTs were significantly enriched in “transcriptional activity (GO:0016758)” and “metabolic processes (GO:0008152)”. Genes from the same clade differed in function under various abiotic stresses. The analysis of cis-acting element and qRT–PCR may indicate that GHUGTs play important roles in plant growth, development and abiotic stress. We further found that GHUGT74-2 plays an important role under submergence. The study broadens the understanding of UGTs in terms of gene characteristics, evolutionary processes, and gene function in cotton and provides a new way to systematically and globally understand the structure–function relationship of multigene families in the evolutionary process.
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Affiliation(s)
- Liangqing Sun
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
- Cotton Research Institute of Jiangxi Province, Jiujiang, China
| | - Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Hui Huang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Yuexin Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Junjuan Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Delong Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Chao Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Lixue Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Nan Xu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Hong Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Jing Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Cun Rui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Mingge Han
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Yapeng Fan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
| | - Taili Nie
- Cotton Research Institute of Jiangxi Province, Jiujiang, China
- *Correspondence: Wuwei Ye, ; Taili Nie,
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, China
- *Correspondence: Wuwei Ye, ; Taili Nie,
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17
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Yu G, Chen Q, Chen F, Liu H, Lin J, Chen R, Ren C, Wei J, Zhang Y, Yang F, Sheng Y. Glutathione Promotes Degradation and Metabolism of Residual Fungicides by Inducing UDP-Glycosyltransferase Genes in Tomato. FRONTIERS IN PLANT SCIENCE 2022; 13:893508. [PMID: 35860529 PMCID: PMC9289782 DOI: 10.3389/fpls.2022.893508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/23/2022] [Indexed: 05/28/2023]
Abstract
Reduced glutathione (GSH) is a key antioxidant, which plays a crucial role in the detoxification of xenobiotics in plants. In the present study, glutathione could reduce chlorothalonil (CHT) residues in tomatoes by inducing the expression of the UDP-glycosyltransferase (UGT) gene. In plants, UGT is an important glycosylation catalyst, which can respond to stresses in time by activating plant hormones and defense compounds. Given the importance of plant growth and development, the genome-wipe analyses of Arabidopsis and soybean samples have been carried out, though not on the tomato, which is a vital vegetable crop. In this study, we identified 143 UGT genes in the tomato that were unevenly distributed on 12 chromosomes and divided into 16 subgroups and found that a variety of plant hormones and stress response cis-elements were discovered in the promoter region of the SlUGT genes, indicating that the UGT genes were involved in several aspects of the tomato stress response. Transcriptome analysis and results of qRT-PCR showed that most SlUGT genes could be induced by CHT, and the expression of these genes was regulated by glutathione. In addition, we found that SlUGT genes could participate in plant detoxification through interaction with transcription factors. These findings further clarify the potential function of the UGT gene family in the detoxification of exogenous substances in tomatoes and provide valuable information for the future study of functional genomics of tomatoes.
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Affiliation(s)
- Gaobo Yu
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Qiusen Chen
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Fengqiong Chen
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Hanlin Liu
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jiaxin Lin
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Runan Chen
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, China
- College of Tropical Crop, Hainan University, Haikou, China
| | - Chunyuan Ren
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jinpeng Wei
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
- Ministry of Agriculture and Rural Affairs Agro-products and Processed Products Quality Supervision, Inspection and Testing Center, Daqing, China
| | - Yuxian Zhang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Fengjun Yang
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yunyan Sheng
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, China
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18
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Ao B, Han Y, Wang S, Wu F, Zhang J. Genome-Wide Analysis and Profile of UDP-Glycosyltransferases Family in Alfalfa (Medicago sativa L.) under Drought Stress. Int J Mol Sci 2022; 23:ijms23137243. [PMID: 35806246 PMCID: PMC9266349 DOI: 10.3390/ijms23137243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/07/2022] [Accepted: 06/23/2022] [Indexed: 12/04/2022] Open
Abstract
Drought stress is one of the major constraints that decreases global crop productivity. Alfalfa, planted mainly in arid and semi-arid areas, is of crucial importance in sustaining the agricultural system. The family 1 UDP-glycosyltransferases (UGT) is indispensable because it takes part in the regulation of plant growth and stress resistance. However, a comprehensive insight into the participation of the UGT family in adaptation of alfalfa to drought environments is lacking. In the present study, a genome-wide analysis and profiling of the UGT in alfalfa were carried out. A total of 409 UGT genes in alfalfa (MsUGT) were identified and they are clustered into 13 groups. The expression pattern of MsUGT genes were analyzed by RNA-seq data in six tissues and under different stresses. The quantitative real-time PCR verification genes suggested the distinct role of the MsUGT genes under different drought stresses and abscisic acid (ABA) treatment. Furthermore, the function of MsUGT003 and MsUGT024, which were upregulated under drought stress and ABA treatment, were characterized by heterologous expression in yeast. Taken together, this study comprehensively analyzed the UGT gene family in alfalfa for the first time and provided useful information for improving drought tolerance and in molecular breeding of alfalfa.
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Song W, Zhang C, Wu J, Qi J, Hua X, Kang L, Yuan Q, Yuan J, Xue Z. Characterization of Three Paris polyphylla Glycosyltransferases from Different UGT Families for Steroid Functionalization. ACS Synth Biol 2022; 11:1669-1680. [PMID: 35286065 DOI: 10.1021/acssynbio.2c00103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plant steroid glycosides, such as phytosterol glycosides, steroidal saponins, and steroidal glycoalkaloids, are natural products with great pharmaceutical values. In this study, we characterized three UDP-glycosyltransferases (UGTs) involved in the glycosylation of steroidal sapogenin from Paris polyphylla. Substrate specificity analysis revealed that UGT73CR1 could glycosylate steroidal sapogenins and steroidal alkaloids, with the highest affinity for diosgenin. The residues His27 and Asp129 of UGT73CR1 are conserved in corresponding positions of plant glycosyltransferases, which are crucial for activating the C-3 OH of the receptor substrates. In comparison, UGT80A33 and UGT80A34 exhibited a higher affinity for cholesterol than other steroids. UGT80s have a larger active pocket, which allows them to accommodate the side chain of sterols. In summary, we assessed three P. polyphylla glycosyltransferases from two UGT families for the functionalization of steroidal molecules, which will provide a basis for the future biomanufacturing of diverse bioactive steroid glycosides.
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Affiliation(s)
- Wei Song
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Zhejiang 310053, China
| | - Chunchun Zhang
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Zhejiang 310053, China
| | - Jiali Wu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Zhejiang 310053, China
| | - Jianzhao Qi
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization College of Life Science, Northeast Forestry University, Heilongjiang 150040, China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Shaanxi 712100, China
| | - Xin Hua
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization College of Life Science, Northeast Forestry University, Heilongjiang 150040, China
| | - Liping Kang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qiang Yuan
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Zhejiang 310053, China
| | - Jifeng Yuan
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361102, China
| | - Zheyong Xue
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization College of Life Science, Northeast Forestry University, Heilongjiang 150040, China
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High Resistance to Quinclorac in Multiple-Resistant Echinochloa colona Associated with Elevated Stress Tolerance Gene Expression and Enriched Xenobiotic Detoxification Pathway. Genes (Basel) 2022; 13:genes13030515. [PMID: 35328069 PMCID: PMC8949966 DOI: 10.3390/genes13030515] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/01/2022] [Accepted: 03/09/2022] [Indexed: 02/04/2023] Open
Abstract
Echinochloa colona and other species in this genus are a threat to global rice production and food security. Quinclorac, an auxin mimic, is a common herbicide for grass weed control in rice, and Echinochloa spp. have evolved resistance to it. The complete mode of quinclorac action and subsequent evolution of resistance is not fully understood. We analyzed the de novo transcriptome of multiple-herbicide-resistant (ECO-R) and herbicide-susceptible genotypes in response to quinclorac. Several biological processes were constitutively upregulated in ECO-R, including carbon metabolism, photosynthesis, and ureide metabolism, indicating improved metabolic efficiency. The transcriptional change in ECO-R following quinclorac treatment indicates an efficient response, with upregulation of trehalose biosynthesis, which is also known for abiotic stress mitigation. Detoxification-related genes were induced in ECO-R, mainly the UDP-glycosyltransferase (UGT) family, most likely enhancing quinclorac metabolism. The transcriptome data also revealed that many antioxidant defense elements were uniquely elevated in ECO-R to protect against the auxin-mediated oxidative stress. We propose that upon quinclorac treatment, ECO-R detoxifies quinclorac utilizing UGT genes, which modify quinclorac using the sufficient supply of UDP-glucose from the elevated trehalose pathway. Thus, we present the first report of upregulation of trehalose synthesis and its association with the herbicide detoxification pathway as an adaptive mechanism to herbicide stress in Echinochloa, resulting in high resistance.
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Pei T, Yan M, Li T, Li X, Yin Y, Cui M, Fang Y, Liu J, Kong Y, Xu P, Zhao Q. Characterization of UDP-glycosyltransferase family members reveals how major flavonoid glycoside accumulates in the roots of Scutellaria baicalensis. BMC Genomics 2022; 23:169. [PMID: 35232374 PMCID: PMC8888134 DOI: 10.1186/s12864-022-08391-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/15/2022] [Indexed: 01/01/2023] Open
Abstract
Background Flavonoid glycosides extracted from roots of Scutellaria baicalensis exhibit strong pharmaceutical antitumor, antioxidative, anti-inflammatory, and antiviral activities. UDP glycosyltransferase (UGT) family members are responsible for the transfer of a glycosyl moiety from UDP sugars to a wide range of acceptor flavonoids. Baicalin is the major flavonoid glycoside found in S. baicalensis roots, and its aglycone baicalein is synthesized from a specially evolved pathway that has been elucidated. However, it is necessary to carry out a genome-wide study of genes involved in 7-O-glucuronidation, the final biosynthesis step of baicalin, which might elucidate the relationship between the enzymes and the metabolic accumulation patterns in this medicinal plant. Results We reported the phylogenetic analysis, tissue-specific expression, biochemical characterization and evolutionary analysis of glucosyltransferases (SbUGTs) and glucuronosyltransferases (SbUGATs) genes based on the recently released genome of S. baicalensis. A total of 124 UGTs were identified, and over one third of them were highly expressed in roots. In vitro enzyme assays showed that 6 SbUGTs could use UDP-glucose as a sugar donor and convert baicalein to oroxin A (baicalein 7-O-glucoside), while 4 SbUGATs used only UDP-glucuronic acid as the sugar donor and catalyzed baicalein to baicalin. SbUGAT4 and SbUGT2 are the most highly expressed SbUGAT and SbUGT genes in root tissues, respectively. Kinetic measurements revealed that SbUGAT4 had a lower Km value and higher Vmax/Km ratio to baicalein than those of SbUGT2. Furthermore, tandem duplication events were detected in SbUGTs and SbUGATs. Conclusions This study demonstrated that glucosylation and glucuronidation are two major glycosylated decorations in the roots of S. baicalensis. Higher expression level and affinity to substrate of SbUGAT4, and expansion of this gene family contribute high accumulation of baicalin in the root of S. baicalensis. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08391-1.
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Affiliation(s)
- Tianlin Pei
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.,National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Mengxiao Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Tian Li
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Science, Shanghai, 201602, China
| | - Xiaoqiang Li
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Science, Shanghai, 201602, China
| | - Yijia Yin
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Mengying Cui
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yumin Fang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Jie Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yu Kong
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Ping Xu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Qing Zhao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China. .,National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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22
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Genome-Wide Identification of the TIFY Gene Family in Brassiceae and Its Potential Association with Heavy Metal Stress in Rapeseed. PLANTS 2022; 11:plants11050667. [PMID: 35270137 PMCID: PMC8912736 DOI: 10.3390/plants11050667] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 11/16/2022]
Abstract
The TIFY gene family plays important roles in various plant biological processes and responses to stress and hormones. The chromosome-level genome of the Brassiceae species has been released, but knowledge concerning the TIFY family is lacking in the Brassiceae species. The current study performed a bioinformatics analysis on the TIFY family comparing three diploid (B. rapa, B. nigra, and B. oleracea) and two derived allotetraploid species (B. juncea, and B. napus). A total of 237 putative TIFY proteins were identified from five Brassiceae species, and classified into ten subfamilies (six JAZ types, one PPD type, two TIFY types, and one ZML type) based on their phylogenetic relationships with TIFY proteins in A. thaliana and Brassiceae species. Duplication and synteny analysis revealed that segmental and tandem duplications led to the expansion of the TIFY family genes during the process of polyploidization, and most of these TIFY family genes (TIFYs) were subjected to purifying selection after duplication based on Ka/Ks values. The spatial and temporal expression patterns indicated that different groups of BnaTIFYs have distinct spatiotemporal expression patterns under normal conditions and heavy metal stresses. Most of the JAZIII subfamily members were highest in all tissues, but JAZ subfamily members were strongly induced by heavy metal stresses. BnaTIFY34, BnaTIFY59, BnaTIFY21 and BnaTIFY68 were significantly upregulated mostly under As3+ and Cd2+ treatment, indicating that they could be actively induced by heavy metal stress. Our results may contribute to further exploration of TIFYs, and provided valuable information for further studies of TIFYs in plant tolerance to heavy metal stress.
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Zhu T, Zhang M, Su H, Li M, Wang Y, Jin L, Li M. Integrated Metabolomic and Transcriptomic Analysis Reveals Differential Mechanism of Flavonoid Biosynthesis in Two Cultivars of Angelica sinensis. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27010306. [PMID: 35011537 PMCID: PMC8746331 DOI: 10.3390/molecules27010306] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/30/2021] [Accepted: 01/02/2022] [Indexed: 12/13/2022]
Abstract
Angelica sinensis is a traditional Chinese medicinal plant that has been primarily used as a blood tonic. It largely relies on its bioactive metabolites, which include ferulic acid, volatile oils, polysaccharides and flavonoids. In order to improve the yield and quality of A. sinensis, the two cultivars Mingui 1 (M1), with a purple stem, and Mingui 2 (M2), with a green stem, have been selected in the field. Although a higher root yield and ferulic acid content in M1 than M2 has been observed, the differences of flavonoid biosynthesis and stem-color formation are still limited. In this study, the contents of flavonoids and anthocyanins were determined by spectrophotometer, the differences of flavonoids and transcripts in M1 and M2 were conducted by metabolomic and transcriptomic analysis, and the expression level of candidate genes was validated by qRT-PCR. The results showed that the contents of flavonoids and anthocyanins were 1.5- and 2.6-fold greater in M1 than M2, respectively. A total of 26 differentially accumulated flavonoids (DAFs) with 19 up-regulated (UR) and seven down-regulated (DR) were obtained from the 131 identified flavonoids (e.g., flavonols, flavonoid, isoflavones, and anthocyanins) in M1 vs. M2. A total 2210 differentially expressed genes (DEGs) were obtained from the 34,528 full-length isoforms in M1 vs. M2, and 29 DEGs with 24 UR and 5 DR were identified to be involved in flavonoid biosynthesis, with 25 genes (e.g., CHS1, CHI3, F3H, DFR, ANS, CYPs and UGTs) mapped on the flavonoid biosynthetic pathway and four genes (e.g., RL1, RL6, MYB90 and MYB114) belonging to transcription factors. The differential accumulation level of flavonoids is coherent with the expression level of candidate genes. Finally, the network of DAFs regulated by DEGs was proposed. These findings will provide references for flavonoid production and cultivars selection of A. sinensis.
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Affiliation(s)
- Tiantian Zhu
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730101, China; (T.Z.); (M.Z.); (Y.W.)
- Northwest Collaborative Innovation Center for Traditional Chinese Medicine, Lanzhou 730000, China
| | - Minghui Zhang
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730101, China; (T.Z.); (M.Z.); (Y.W.)
| | - Hongyan Su
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (H.S.); (M.L.)
| | - Meiling Li
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (H.S.); (M.L.)
| | - Yuanyuan Wang
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730101, China; (T.Z.); (M.Z.); (Y.W.)
- Northwest Collaborative Innovation Center for Traditional Chinese Medicine, Lanzhou 730000, China
| | - Ling Jin
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730101, China; (T.Z.); (M.Z.); (Y.W.)
- Northwest Collaborative Innovation Center for Traditional Chinese Medicine, Lanzhou 730000, China
- Correspondence: (L.J.); (M.L.)
| | - Mengfei Li
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (H.S.); (M.L.)
- Correspondence: (L.J.); (M.L.)
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24
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Mateo-Bonmatí E, Casanova-Sáez R, Šimura J, Ljung K. Broadening the roles of UDP-glycosyltransferases in auxin homeostasis and plant development. THE NEW PHYTOLOGIST 2021; 232:642-654. [PMID: 34289137 DOI: 10.1111/nph.17633] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/03/2021] [Indexed: 05/02/2023]
Abstract
The levels of the important plant growth regulator indole-3-acetic acid (IAA) are tightly controlled within plant tissues to spatiotemporally orchestrate concentration gradients that drive plant growth and development. Metabolic inactivation of bioactive IAA is known to participate in the modulation of IAA maxima and minima. IAA can be irreversibly inactivated by oxidation and conjugation to aspartate and glutamate. Usually overlooked because of its reversible nature, the most abundant inactive IAA form is the IAA-glucose (IAA-glc) conjugate. Glycosylation of IAA in Arabidopsis thaliana is reported to be carried out by UDP-glycosyltransferase 84B1 (UGT84B1), while UGT74D1 has been implicated in the glycosylation of the irreversibly formed IAA catabolite oxIAA. Here we demonstrated that both UGT84B1 and UGT74D1 modulate IAA levels throughout plant development by dual IAA and oxIAA glycosylation. Moreover, we identified a novel UGT subfamily whose members redundantly mediate the glycosylation of oxIAA and modulate skotomorphogenic growth.
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Affiliation(s)
- Eduardo Mateo-Bonmatí
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE-901 83, Sweden
| | - Rubén Casanova-Sáez
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE-901 83, Sweden
| | - Jan Šimura
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE-901 83, Sweden
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE-901 83, Sweden
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25
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Kurze E, Wüst M, Liao J, McGraphery K, Hoffmann T, Song C, Schwab W. Structure-function relationship of terpenoid glycosyltransferases from plants. Nat Prod Rep 2021; 39:389-409. [PMID: 34486004 DOI: 10.1039/d1np00038a] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2021Terpenoids are physiologically active substances that are of great importance to humans. Their physicochemical properties are modified by glycosylation, in terms of polarity, volatility, solubility and reactivity, and their bioactivities are altered accordingly. Significant scientific progress has been made in the functional study of glycosylated terpenes and numerous plant enzymes involved in regio- and enantioselective glycosylation have been characterized, a reaction that remains chemically challenging. Crucial clues to the mechanism of terpenoid glycosylation were recently provided by the first crystal structures of a diterpene glycosyltransferase UGT76G1. Here, we review biochemically characterized terpenoid glycosyltransferases, compare their functions and primary structures, discuss their acceptor and donor substrate tolerance and product specificity, and elaborate features of the 3D structures of the first terpenoid glycosyltransferases from plants.
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Affiliation(s)
- Elisabeth Kurze
- Biotechnology of Natural Products, TUM School of Life Sciences, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany.
| | - Matthias Wüst
- Chair of Food Chemistry, Institute of Nutritional and Food Sciences, University of Bonn, Endenicher Allee 19C, 53115 Bonn, Germany.
| | - Jieren Liao
- Biotechnology of Natural Products, TUM School of Life Sciences, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany.
| | - Kate McGraphery
- Biotechnology of Natural Products, TUM School of Life Sciences, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany.
| | - Thomas Hoffmann
- Biotechnology of Natural Products, TUM School of Life Sciences, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany.
| | - Chuankui Song
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University Hefei, Anhui 230036, People's Republic of China.
| | - Wilfried Schwab
- Biotechnology of Natural Products, TUM School of Life Sciences, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany. .,State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University Hefei, Anhui 230036, People's Republic of China.
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26
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Wu C, Dai J, Chen Z, Tie W, Yan Y, Yang H, Zeng J, Hu W. Comprehensive analysis and expression profiles of cassava UDP-glycosyltransferases (UGT) family reveal their involvement in development and stress responses in cassava. Genomics 2021; 113:3415-3429. [PMID: 34371100 DOI: 10.1016/j.ygeno.2021.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 07/12/2021] [Accepted: 08/03/2021] [Indexed: 11/30/2022]
Abstract
UDP-glycosyltransferases (UGTs) are widely involved in plant growth and stress responses. However, UGT family are not well understood in cassava. Here, we identified 121 MeUGT genes and classified them into 14 subfamilies by phylogenetic analysis. All MeUGT proteins have typical feature of the UGTs family. Tandem duplications are the crucial driving force for the expansion of MeUGT family. Cis-Acting elements analysis uncovered those 14 kinds of cis-elements associated with biotic and abiotic stress responses. Transcriptomic and qRT-PCR analyses indicated that MeUGT genes participate in postharvest physiological deterioration of storage root and the responses of biotic and abiotic stresses. Of which, MeUGT-14/41 were significantly induced after Xam treatment. Silencing of MeUGT-14 or MeUGT-41 reduced cassava resistance to Xam, verifying the accuracy of transcriptomic data for function prediction. Together, this study characterized the MeUGTs family and revealed their potential functions, which build a solid foundation for MeUGTs associated genetic improvement of cassava.
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Affiliation(s)
- Chunlai Wu
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jing Dai
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhisheng Chen
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Weiwei Tie
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China,.
| | - Yan Yan
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
| | - Hai Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Jian Zeng
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, China.
| | - Wei Hu
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China,.
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27
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Ma L, Dong C, Song C, Wang X, Zheng X, Niu Y, Chen S, Feng W. De novo genome assembly of the potent medicinal plant Rehmannia glutinosa using nanopore technology. Comput Struct Biotechnol J 2021; 19:3954-3963. [PMID: 34377362 PMCID: PMC8318827 DOI: 10.1016/j.csbj.2021.07.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/30/2021] [Accepted: 07/06/2021] [Indexed: 01/16/2023] Open
Abstract
Rehmannia glutinosa is a potent medicinal plant with a significant importance in traditional Chinese medicine. Its root is enriched with various bioactive molecules mainly iridoids, possessing important pharmaceutical properties. However, the molecular biology and evolution of R. glutinosa have been largely unexplored. Here, we report a reference genome of R. glutinosa using Nanopore technology, Illumina and Hi-C sequencing. The assembly genome is 2.49 Gb long with a scaffold N50 length of 70 Mb and high heterozygosity (2%). Since R. glutinosa is an autotetraploid (4n = 56), the difference between each set of chromosomes is very small, and it is difficult to distinguish the two sets of chromosomes using Hi-C. Hence, only one set of the genome size was mounted to the chromosome level. Scaffolds covering 52.61% of the assembled genome were anchored on 14 pseudochromosomes. Over 67% of the genome consists of repetitive sequences dominated by Copia long terminal repeats and 48,475 protein-coding genes were predicted. Phylogenetic analysis corroborates the placement of R. glutinosa in the Orobanchaceae family. Our results indicated an independent and very recent whole genome duplication event that occurred 3.64 million year ago in the R. glutinosa lineage. Comparative genomics analysis demonstrated expansion of the UDP-dependent glycosyltransferases and terpene synthase gene families, known to be involved in terpenoid biosynthesis and diversification. Furthermore, the molecular biosynthetic pathway of iridoids has been clarified in this work. Collectively, the generated reference genome of R. glutinosa will facilitate discovery and development of important pharmacological compounds.
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Affiliation(s)
- Ligang Ma
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Zhengzhou 450046, China
| | - Chengming Dong
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Zhengzhou 450046, China
| | - Chi Song
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiaolan Wang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Zhengzhou 450046, China
| | - Xiaoke Zheng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Zhengzhou 450046, China
| | - Yan Niu
- Wuhan Benagen Tech Solutions Company Limited, Wuhan 430070, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Weisheng Feng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Zhengzhou 450046, China
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28
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Wang Y, Xiang F, Zhang Z, Hou Q, Guo Z. Characterization of bacterial community and flavor differences of different types of Douchi. Food Sci Nutr 2021; 9:3460-3469. [PMID: 34262706 PMCID: PMC8269581 DOI: 10.1002/fsn3.2280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 12/11/2022] Open
Abstract
According to the appearance and technology, traditional fermented Douchi can be divided into dried Douchi and wet Douchi. However, there are few reports on the difference of bacterial community structure between them or the influence of bacterial community on product flavor. In this study, high-throughput sequencing technology and electronic nose were used to measure the bacterial diversity and flavor of 40 Douchi samples, and the correlation between them was explored by multivariate statistical means combined with COG database. Results showed that the cumulative average relative abundance of Firmicutes and Proteobacteria in the samples was as high as 95.93%, and the former was the core bacteria phylum. On the whole, the dominant bacteria in Douchi were Bacillus (50.67%), Staphylococcus (14.07%), Enterococcus (2.54%), Proteus (1.61%), Brevibacillus (1.46%), Providencia (1.26%), Weissella (1.24%), and Ureibacillus (1.19%). LEfSe analysis indicated that Bacillus can be used as a biomarker in dried fermented soybeans. Meanwhile, dried samples contained more intensive aromatic substances, but were significantly lower in W6S (selectivity to hydrogen) and W3S (methane-aliph) compared with the wet samples. Aneurinibacillus and Brevibacillus were helpful to the formation of aromatic flavor in Douchi, but Vagococcus and Corynebacterium were the opposite. Gene and microbial phenotypic prediction showed that microorganisms in dried Douchi use protein more efficiently, while in wet Douchi, microbial energy metabolism was more vigorous. The pathogenic potential of microorganisms in dried samples was higher than that in wet. This study can sound the alarm for improving the safety of home-brewed Douchi and provide guidance for the subsequent screening of strains that enhance the flavor of fermented soybeans.
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Affiliation(s)
- Yurong Wang
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
| | - Fanshu Xiang
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
| | - Zhendong Zhang
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
| | - Qiangchuan Hou
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
| | - Zhuang Guo
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
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29
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Genome-Wide Analysis of the YABBY Transcription Factor Family in Rapeseed ( Brassica napus L.). Genes (Basel) 2021; 12:genes12070981. [PMID: 34199012 PMCID: PMC8306101 DOI: 10.3390/genes12070981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022] Open
Abstract
The YABBY family of plant-specific transcription factors play important regulatory roles during the development of leaves and floral organs, but their functions in Brassica species are incompletely understood. Here, we identified 79 YABBY genes from Arabidopsis thaliana and five Brassica species (B. rapa, B. nigra, B. oleracea, B. juncea, and B. napus). A phylogenetic analysis of YABBY proteins separated them into five clusters (YAB1–YAB5) with representatives from all five Brassica species, suggesting a high degree of conservation and similar functions within each subfamily. We determined the gene structure, chromosomal location, and expression patterns of the 21 BnaYAB genes identified, revealing extensive duplication events and gene loss following polyploidization. Changes in exon–intron structure during evolution may have driven differentiation in expression patterns and functions, combined with purifying selection, as evidenced by Ka/Ks values below 1. Based on transcriptome sequencing data, we selected nine genes with high expression at the flowering stage. qRT-PCR analysis further indicated that most BnaYAB family members are tissue-specific and exhibit different expression patterns in various tissues and organs of B. napus. This preliminary study of the characteristics of the YABBY gene family in the Brassica napus genome provides theoretical support and reference for the later functional identification of the family genes.
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30
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Zhang K, Li J, Zhou Z, Huang R, Lin S. Roles of Alkaline Phosphatase PhoA in Algal Metabolic Regulation under Phosphorus-replete Conditions. JOURNAL OF PHYCOLOGY 2021; 57:703-707. [PMID: 33608874 DOI: 10.1111/jpy.13151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/24/2021] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
Alkaline phosphatase (AP) in plants and algae is known to hydrolyze dissolved organophosphate (DOP) in order to obtain phosphorus when the preferred dissolved inorganic phosphorus (DIP) is present in limited supply. By conducting comparative analyses of physiologies and transcriptomes on a mutant of PhoA type AP (mPhoA) and wild type (WT) of the marine diatom Phaeodactylum tricornutum CCAP 1055/1 under P-replete and P-depleted conditions, we document other roles of this gene than DOP scavenging. PhoA mutation created by CRISPR/Cas9 diminished its DOP hydrolase activity but led to significant increases in cellular contents of pigment, carbon, and lipids, photosynthetic rate, growth rate, and the transcriptional levels of their corresponding metabolic pathways. All the results in concert indicate that besides P-nutrient scavenging under DIP deficiency, AP also functions, under the P-replete condition, to constrain pigment biosynthesis, photosynthesis, fatty acid biosynthesis, and cell division. These functions have important implications in maintaining metabolic homeostasis and preventing premature cell division.
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Affiliation(s)
- Kaidian Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
| | - Jiashun Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Zhi Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China
| | - Ruiping Huang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
- Laboratory of Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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31
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Park JC, Kim DH, Kim MS, Hagiwara A, Lee JS. The genome of the euryhaline rotifer Brachionus paranguensis: Potential use in molecular ecotoxicology. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100836. [PMID: 33940320 DOI: 10.1016/j.cbd.2021.100836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/03/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
Brachionus spp. rotifers have been proposed as model organisms for ecotoxicological studies. We analyzed the whole-genome sequence of B. paranguensis through NextDenovo, resulting in a total length of 106.2 Mb and 71 contigs. The N50 and the GC content were 4.13 Mb and 28%, respectively. A total of 18,501 genes were predicted within the genome of B. paranguensis. Prominent detoxification-related gene families of phase I and II detoxifications have been investigated. In parallel with other Brachionus rotifers, high gene expansion was observed in CYP clan 3 and GST sigma class in B. paranguensis. Moreover, species-specific expansion of sulfotransferase (SULTs) and gain of UDP-glucuronosyltransferases (UGTs) through horizontal gene transfer has been specifically found within B. plicatilis complex. This whole-genome analysis of B. paranguensis provides a basis for molecular ecotoxicological studies and provides useful information for comparative studies of the evolution of detoxification mechanisms in Brachionus spp.
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Affiliation(s)
- Jun Chul Park
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Sub Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Atsushi Hagiwara
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki 852-8521, Japan; Organization for Marine Science and Technology, Nagasaki University, Nagasaki 852-8521, Japan
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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Wang Y, Cai W, Wang W, Shu N, Zhang Z, Hou Q, Shan C, Guo Z. Analysis of microbial diversity and functional differences in different types of high-temperature Daqu. Food Sci Nutr 2021; 9:1003-1016. [PMID: 33598183 PMCID: PMC7866569 DOI: 10.1002/fsn3.2068] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/07/2020] [Accepted: 12/02/2020] [Indexed: 12/29/2022] Open
Abstract
Bacterial communities that enrich in high-temperature Daqu are important for the Chinese maotai-flavor liquor brewing process. However, the bacterial communities in three different types of high-temperature Daqu (white Daqu, black Daqu, and yellow Daqu) are still undercharacterized. In this study, the bacterial diversity of three different types of high-temperature Daqu was investigated using Illumina MiSeq high-throughput sequencing. The bacterial community of high-temperature Daqu is mainly composed of thermophilic bacteria, and seven bacterial phyla along with 262 bacterial genera were identified in all 30 high-temperature Daqu samples. Firmicutes, Actinobacteria, Proteobacteria, and Acidobacteria were the dominant bacterial phyla in high-temperature Daqu samples, while Thermoactinomyces, Staphylococcus, Lentibacillus, Bacillus, Kroppenstedtia, Saccharopolyspora, Streptomyces, and Brevibacterium were the dominant bacterial genera. The bacterial community structure of three different types of high-temperature Daqu was significantly different (p < .05). In addition, the results of microbiome phenotype prediction by BugBase and bacterial functional potential prediction using PICRUSt show that bacteria from different types of high-temperature Daqu have similar functions as well as phenotypes, and bacteria in high-temperature Daqu have vigorous metabolism in the transport and decomposition of amino acids and carbohydrates. These results offer a reference for the comprehensive understanding of bacterial diversity of high-temperature Daqu.
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Affiliation(s)
- Yurong Wang
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
| | - Wenchao Cai
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
- School of Food ScienceShihezi UniversityShiheziChina
| | - Wenping Wang
- Hubei Yaozhihe Chuwengquan Liquor Industry Co., Ltd.XiangyangChina
| | - Na Shu
- Hubei Yaozhihe Chuwengquan Liquor Industry Co., Ltd.XiangyangChina
| | - Zhendong Zhang
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
| | - Qiangchuan Hou
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
| | - Chunhui Shan
- School of Food ScienceShihezi UniversityShiheziChina
| | - Zhuang Guo
- Hubei Provincial Engineering and Technology Research Center for Food IngredientsHubei University of Arts and ScienceXiangyangChina
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Cai W, Tang F, Wang Y, Zhang Z, Xue Y, Zhao X, Guo Z, Shan C. Bacterial diversity and flavor profile of Zha-Chili, a traditional fermented food in China. Food Res Int 2021; 141:110112. [PMID: 33641979 DOI: 10.1016/j.foodres.2021.110112] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/18/2020] [Accepted: 01/05/2021] [Indexed: 12/20/2022]
Abstract
Zha-chili is a traditional Chinese fermented food with special flavor, which is often used as an appetizer in condiments and an important energy source. The final quality of zha-chili is closely related to its microbial community structure. However, the differences of bacterial diversity in zha-chili from different regions and how bacterial species affect zha-chili fermentation process and flavor quality have not been reported. In this study, the bacterial diversity and flavor quality of zha-chili samples from different regions were analyzed using Illumina Miseq high-throughput sequencing, electronic nose and electronic tongue technology. Twenty-three bacterial phyla and 665 bacterial genera were identified in all zha-chili samples. Firmicutes, Proteobacteria and Actinobacteria were the dominant bacterial phyla in zha-chili samples, while Lactobacillus, Pseudomonas, Pediococcus, Weissella and Staphylococcus were the dominant bacterial genera. The bacterial community structure of zha-chili samples from different regions was significantly diverse (p < 0.05). The flavor of zha-chili samples also varied in different regions, and the discrepancy of taste was much greater than that of aroma. Moreover, there were significant correlations (p < 0.05) between 6 dominant bacterial genera and 8 flavor indicators (3 aroma indicators, 5 taste indicators). In addition, the results of microbiome phenotypes prediction by BugBase and bacterial functional potential prediction using PICRUSt showed that eight out of nine predicted phenotypic functions of zha-chili samples from different regions were significantly different (p < 0.05), bacterial metabolism was vigorous in the zha-chili samples, and Lactobacillus was the dominant bacterial genus involved in metabolism during fermentation.
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Affiliation(s)
- Wenchao Cai
- School of Food Science, Shihezi University, Xinjiang Autonomous Region, Shihezi, PR China; Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Xinjiang Autonomous Region, Shihezi, PR China
| | - Fengxian Tang
- School of Food Science, Shihezi University, Xinjiang Autonomous Region, Shihezi, PR China; Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Xinjiang Autonomous Region, Shihezi, PR China
| | - Yurong Wang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Sciences, Xiangyang, Hubei Province, PR China
| | - Zhendong Zhang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Sciences, Xiangyang, Hubei Province, PR China
| | - Yuang Xue
- School of Food Science, Shihezi University, Xinjiang Autonomous Region, Shihezi, PR China; Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Xinjiang Autonomous Region, Shihezi, PR China
| | - Xinxin Zhao
- School of Food Science, Shihezi University, Xinjiang Autonomous Region, Shihezi, PR China; Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Xinjiang Autonomous Region, Shihezi, PR China
| | - Zhuang Guo
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Sciences, Xiangyang, Hubei Province, PR China.
| | - Chunhui Shan
- School of Food Science, Shihezi University, Xinjiang Autonomous Region, Shihezi, PR China; Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, Shihezi University, Xinjiang Autonomous Region, Shihezi, PR China.
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Wu B, Liu X, Xu K, Zhang B. Genome-wide characterization, evolution and expression profiling of UDP-glycosyltransferase family in pomelo (Citrus grandis) fruit. BMC PLANT BIOLOGY 2020; 20:459. [PMID: 33028214 PMCID: PMC7542425 DOI: 10.1186/s12870-020-02655-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/20/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND Pomelo is one of the three major species of citrus. The fruit accumulates a variety of abundant secondary metabolites that affect the flavor. UDP-glycosyltransferases (UGTs) are involved in the glycosylation of secondary metabolites. RESULTS In the present study, we performed a genome-wide analysis of pomelo UGT family, a total of 145 UGTs was identified based on the conserved plant secondary product glycosyltransferase (PSPG) motif. These UGT genes were clustered into 16 major groups through phylogenetic analysis of these genes with other plant UGTs (A-P). Pomelo UGTs were distributed unevenly among the chromosomes. At least 10 intron insertion events were observed in these UGT genome sequences, and I-5 was identified to be the highest conserved one. The expression profile analysis of pomelo UGT genes in different fruit tissues during development and ripening was carried out by RNA-seq. CONCLUSIONS We identified 145 UGTs in pomelo fruit through transcriptome data and citrus genome database. Our research provides available information on UGTs studies in pomelo, and provides an important research foundation for screening and identification of functional UGT genes.
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Affiliation(s)
- Boping Wu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Xiaohong Liu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology / Laboratory of Fruit Quality Biology, Zhejiang University, Hangzhou, 310058, China
| | - Kai Xu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China.
| | - Bo Zhang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology / Laboratory of Fruit Quality Biology, Zhejiang University, Hangzhou, 310058, China.
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Qiao C, Yang J, Wan Y, Xiang S, Guan M, Du H, Tang Z, Lu K, Li J, Qu C. A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling Their Expression Profiles under Abiotic Stress in Rapeseed. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1072. [PMID: 32825473 PMCID: PMC7569899 DOI: 10.3390/plants9091072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 01/22/2023]
Abstract
The multidrug and toxic compound extrusion (MATE) protein family is important in the export of toxins and other substrates, but detailed information on this family in the Brassicaceae has not yet been reported compared to Arabidopsis thaliana. In this study, we identified 57, 124, 81, 85, 130, and 79 MATE genes in A. thaliana, Brassica napus, Brassica oleracea, Brassica rapa, Brassica juncea, and Brassica nigra, respectively, which were unevenly distributed on chromosomes owing to both tandem and segmental duplication events. Phylogenetic analysis showed that these genes could be classified into four subgroups, shared high similarity and conservation within each group, and have evolved mainly through purifying selection. Furthermore, numerous B. napusMATE genes showed differential expression between tissues and developmental stages and between plants treated with heavy metals or hormones and untreated control plants. This differential expression was especially pronounced for the Group 2 and 3 BnaMATE genes, indicating that they may play important roles in stress tolerance and hormone induction. Our results provide a valuable foundation for the functional dissection of the different BnaMATE homologs in B. napus and its parental lines, as well as for the breeding of more stress-tolerant B. napus genotypes.
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Affiliation(s)
- Cailin Qiao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (C.Q.); (J.Y.); (Y.W.); (S.X.); (M.G.); (H.D.); (Z.T.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jing Yang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (C.Q.); (J.Y.); (Y.W.); (S.X.); (M.G.); (H.D.); (Z.T.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Yuanyuan Wan
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (C.Q.); (J.Y.); (Y.W.); (S.X.); (M.G.); (H.D.); (Z.T.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Sirou Xiang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (C.Q.); (J.Y.); (Y.W.); (S.X.); (M.G.); (H.D.); (Z.T.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Mingwei Guan
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (C.Q.); (J.Y.); (Y.W.); (S.X.); (M.G.); (H.D.); (Z.T.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Hai Du
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (C.Q.); (J.Y.); (Y.W.); (S.X.); (M.G.); (H.D.); (Z.T.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Zhanglin Tang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (C.Q.); (J.Y.); (Y.W.); (S.X.); (M.G.); (H.D.); (Z.T.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (C.Q.); (J.Y.); (Y.W.); (S.X.); (M.G.); (H.D.); (Z.T.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (C.Q.); (J.Y.); (Y.W.); (S.X.); (M.G.); (H.D.); (Z.T.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (C.Q.); (J.Y.); (Y.W.); (S.X.); (M.G.); (H.D.); (Z.T.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
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Genome-wide identification AINTEGUMENTA-like (AIL) genes in Brassica species and expression patterns during reproductive development in Brassica napus L. PLoS One 2020; 15:e0234411. [PMID: 32511257 PMCID: PMC7279594 DOI: 10.1371/journal.pone.0234411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/24/2020] [Indexed: 12/05/2022] Open
Abstract
The AINTEGUMENTA-like (AIL) proteins, which belong to the AP2 family, play important roles in regulating the growth and development of plant organs. The AIL family has not yet been comprehensively studied in rapeseed (Brassica napus), an allotetraploid and model organism for the study of polyploid evolution. In the present study, 99 AIL family genes were identified and characterized from B. rapa, B. oleracea, B. napus, B. juncea, and B. nigra using a comprehensive genome-wide study, including analyses of phylogeny, gene structure, chromosomal localization, and expression pattern. Using a phylogenetic analysis, the AIL genes were divided into eight groups, which were closely related to the eight AtAIL genes, and which shared highly conserved structural features within the same subfamily. The non-synonymous/synonymous substitution ratios of the paralogs and orthologs were less than 1, suggesting that the AIL genes mainly experienced purifying selection during evolution. In addition, the RNA sequencing data and qRT-PCR analysis revealed that the B. napus AIL genes exhibited organ- and developmental stage-specific expression patterns. Certain genes were highly expressed in the developing seeds (BnaAIL1, BnaAIL2, BnaAIL5, and BnaAIL6), the roots (BnaANT, BnaAIL5, and BnaAIL6), and the stem (BnaAIL7B). Our results provide valuable information for further functional analysis of the AIL family in B. napus and related Brassica species.
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Cheng Y, Liu H, Tong X, Liu Z, Zhang X, Li D, Jiang X, Yu X. Identification and analysis of CYP450 and UGT supergene family members from the transcriptome of Aralia elata (Miq.) seem reveal candidate genes for triterpenoid saponin biosynthesis. BMC PLANT BIOLOGY 2020; 20:214. [PMID: 32404131 PMCID: PMC7218531 DOI: 10.1186/s12870-020-02411-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 04/28/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND Members of the cytochrome P450 (CYP450) and UDP-glycosyltransferase (UGT) gene superfamily have been shown to play essential roles in regulating secondary metabolite biosynthesis. However, the systematic identification of CYP450s and UGTs has not been reported in Aralia elata (Miq.) Seem, a highly valued medicinal plant. RESULTS In the present study, we conducted the RNA-sequencing (RNA-seq) analysis of the leaves, stems, and roots of A. elata, yielding 66,713 total unigenes. Following annotation and KEGG pathway analysis, we were able to identify 64 unigenes related to triterpenoid skeleton biosynthesis, 254 CYP450s and 122 UGTs, respectively. A total of 150 CYP450s and 92 UGTs encoding > 300 amino acid proteins were utilized for phylogenetic and tissue-specific expression analyses. This allowed us to cluster 150 CYP450s into 9 clans and 40 families, and then these CYP450 proteins were further grouped into two primary branches: A-type (53%) and non-A-type (47%). A phylogenetic analysis of 92 UGTs and other plant UGTs led to clustering into 16 groups (A-P). We further assessed the expression patterns of these CYP450 and UGT genes across A. elata tissues, with 23 CYP450 and 16 UGT members being selected for qRT-PCR validation, respectively. From these data, we identified CYP716A295 and CYP716A296 as the candidate genes most likely to be associated with oleanolic acid synthesis, while CYP72A763 and CYP72A776 were identified as being the most likely to play roles in hederagenin biosynthesis. We also selected five unigenes as the best candidates for oleanolic acid 3-O-glucosyltransferase. Finally, we assessed the subcellular localization of three CYP450 proteins within Arabidopsis protoplasts, highlighting the fact that they localize to the endoplasmic reticulum. CONCLUSIONS This study presents a systematic analysis of the CYP450 and UGT gene family in A. elata and provides a foundation for further functional characterization of these two multigene families.
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Affiliation(s)
- Yao Cheng
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Hanbing Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Xuejiao Tong
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Zaimin Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Xin Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Dalong Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Xinmei Jiang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China.
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China.
| | - Xihong Yu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China.
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China.
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Wan Y, Wang Z, Xia J, Shen S, Guan M, Zhu M, Qiao C, Sun F, Liang Y, Li J, Lu K, Qu C. Genome-Wide Analysis of Phosphorus Transporter Genes in Brassica and Their Roles in Heavy Metal Stress Tolerance. Int J Mol Sci 2020; 21:E2209. [PMID: 32210032 PMCID: PMC7139346 DOI: 10.3390/ijms21062209] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 11/18/2022] Open
Abstract
Phosphorus transporter (PHT) genes encode H2PO4-/H+ co-transporters that absorb and transport inorganic nutrient elements required for plant development and growth and protect plants from heavy metal stress. However, little is known about the roles of PHTs in Brassica compared to Arabidopsis thaliana. In this study, we identified and extensively analyzed 336 PHTs from three diploid (B. rapa, B. oleracea, and B. nigra) and two allotetraploid (B. juncea and B. napus) Brassica species. We categorized the PHTs into five phylogenetic clusters (PHT1-PHT5), including 201 PHT1 homologs, 15 PHT2 homologs, 40 PHT3 homologs, 54 PHT4 homologs, and 26 PHT5 homologs, which are unevenly distributed on the corresponding chromosomes of the five Brassica species. All PHT family genes from Brassica are more closely related to Arabidopsis PHTs in the same vs. other clusters, suggesting they are highly conserved and have similar functions. Duplication and synteny analysis revealed that segmental and tandem duplications led to the expansion of the PHT gene family during the process of polyploidization and that members of this family have undergone purifying selection during evolution based on Ka/Ks values. Finally, we explored the expression profiles of BnaPHT family genes in specific tissues, at various developmental stages, and under heavy metal stress via RNA-seq analysis and qRT-PCR. BnaPHTs that were induced by heavy metal treatment might mediate the response of rapeseed to this important stress. This study represents the first genome-wide analysis of PHT family genes in Brassica species. Our findings improve our understanding of PHT family genes and provide a basis for further studies of BnaPHTs in plant tolerance to heavy metal stress.
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Affiliation(s)
- Yuanyuan Wan
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Zhen Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jichun Xia
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Shulin Shen
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Mingwei Guan
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Meichen Zhu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Cailin Qiao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Fujun Sun
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Ying Liang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.W.); (Z.W.); (J.X.); (S.S.); (M.G.); (M.Z.); (C.Q.); (F.S.); (Y.L.); (J.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
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Identification of Differentially Expressed Proteins in Sugarcane in Response to Infection by Xanthomonas albilineans Using iTRAQ Quantitative Proteomics. Microorganisms 2020; 8:microorganisms8010076. [PMID: 31947808 PMCID: PMC7023244 DOI: 10.3390/microorganisms8010076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/16/2019] [Accepted: 12/28/2019] [Indexed: 01/02/2023] Open
Abstract
Sugarcane can suffer severe yield losses when affected by leaf scald, a disease caused by Xanthomonas albilineans. This bacterial pathogen colonizes the vascular system of sugarcane, which can result in reduced plant growth and plant death. In order to better understand the molecular mechanisms involved in the resistance of sugarcane to leaf scald, a comparative proteomic study was performed with two sugarcane cultivars inoculated with X. albilineans: one resistant (LCP 85-384) and one susceptible (ROC20) to leaf scald. The iTRAQ (isobaric tags for relative and absolute quantification) approach at 0 and 48 h post-inoculation (hpi) was used to identify and annotate differentially expressed proteins (DEPs). A total of 4295 proteins were associated with 1099 gene ontology (GO) terms by GO analysis. Among those, 285 were DEPs during X. albilineans infection in cultivars LCP 85-384 and ROC20. One hundred seventy-two DEPs were identified in resistant cultivar LCP 85-384, and 113 of these proteins were upregulated and 59 were downregulated. One hundred ninety-two DEPs were found in susceptible cultivar ROC20 and half of these (92) were upregulated, whereas the other half corresponded to downregulated proteins. The significantly upregulated DEPs in LCP 85-384 were involved in metabolic pathways, the biosynthesis of secondary metabolites, and the phenylpropanoid biosynthesis pathway. Additionally, the expression of seven candidate genes related to photosynthesis and glycolytic pathways, plant innate immune system, glycosylation process, plant cytochrome P450, and non-specific lipid transfer protein was verified based on transcription levels in sugarcane during infection by X. albilineans. Our findings shed new light on the differential expression of proteins in sugarcane cultivars in response to infection by X. albilineans. The identification of these genes provides important information for sugarcane variety improvement programs using molecular breeding strategies.
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Wilson AE, Tian L. Phylogenomic analysis of UDP-dependent glycosyltransferases provides insights into the evolutionary landscape of glycosylation in plant metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1273-1288. [PMID: 31446648 DOI: 10.1111/tpj.14514] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/09/2019] [Accepted: 08/19/2019] [Indexed: 05/05/2023]
Abstract
Glycosylated metabolites generated by UDP-dependent glycosyltransferases (UGTs) play critical roles in plant interactions with the environment as well as human and animal nutrition. The evolution of plant UGTs has previously been explored, but with a limited taxon sampling. In this study, 65 fully sequenced plant genomes were analyzed, and stringent criteria for selection of candidate UGTs were applied to ensure a more comprehensive taxon sampling and reliable sequence inclusion. In addition to revealing the overall evolutionary landscape of plant UGTs, the phylogenomic analysis also resolved the phylogenetic association of UGTs from free-sporing plants and gymnosperms, and identified an additional UGT group (group R) in seed plants. Furthermore, lineage-specific expansions and contractions of UGT groups were detected in angiosperms, with the total number of UGTs per genome remaining constant generally. The loss of group Q UGTs in Poales and Brassicales, rather than functional convergence in the group Q containing species, was supported by a gene tree of group Q UGTs sampled from many species, and further corroborated by the absence of group Q homologs on the syntenic chromosomal regions in Arabidopsis thaliana (Brassicales). Branch-site analyses of the group Q UGT gene tree allowed for identification of branches and amino acid sites that experienced episodic positive selection. The positively selected sites are located on the surface of a representative group Q UGT (PgUGT95B2), away from the active site, suggesting their role in protein folding/stability or protein-protein interactions.
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Affiliation(s)
- Alexander E Wilson
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Li Tian
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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Hu Z, He J, Chen K, Wang Z, Liu J, Qiao X, Ye M. Molecular cloning and biochemical characterization of a new flavonoid glycosyltransferase from the aquatic plant lotus. Biochem Biophys Res Commun 2019; 510:315-321. [PMID: 30709586 DOI: 10.1016/j.bbrc.2019.01.099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 01/23/2019] [Indexed: 11/26/2022]
Abstract
Lotus (Nelumbo nucifera Gaertn.), one of the earliest plants in angiosperms, is a perennial aquatic herb widely distributed throughout Eastern Asia. Quercetin and its glycosides are the most abundant phenolic compounds in lotus with multiple pharmacological activities. Although many flavonoid O-glycosyltransferases involved in the biosynthesis of quercetin glycosides have been identified from terrestrial plants, no glycosyltransferase has been identified in aquatic plants. In this study, a new glycosyltransferase (NpUGT6) was identified from the embryo of Nelumbo nucifera (Nelumbinis Plumula). Function characterization demonstrated that NpUGT6 exhibited a robust capability to regio- and stereo-specific O-glycosylation at the 3-hydroxy group of quercetin scaffolds with UDP-glucose. Moreover, the O-glycosylation catalyzed by NpUGT6 was reversible. NpUGT6 is the first identified flavonoid O-glycosyltransferase from aquatic plants. Its sequence will provide useful guidance for the discovery of additional flavonoid glycosyltransferses in Nymphaeaceae and other aquatic plants.
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Affiliation(s)
- Zhimin Hu
- The State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Junbin He
- The State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Kuan Chen
- The State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Zilong Wang
- The State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Jiyang Liu
- The State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Xue Qiao
- The State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.
| | - Min Ye
- The State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.
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Molecular Regulation of Catalpol and Acteoside Accumulation in Radial Striation and non-Radial Striation of Rehmannia glutinosa Tuberous Root. Int J Mol Sci 2018; 19:ijms19123751. [PMID: 30486279 PMCID: PMC6321003 DOI: 10.3390/ijms19123751] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/08/2018] [Accepted: 11/22/2018] [Indexed: 12/19/2022] Open
Abstract
Rehmannia glutinosa L., a perennial plant of Scrophulariaceae, is one of the most commonly used herbs in traditional Chinese medicine (TCM) that have been widely cultivated in China. However, to date, the biosynthetic pathway of its two quality-control components, catalpol and acteoside, are only partially elucidated and the mechanism for their tissue-specific accumulation remains unknown. To facilitate the basic understanding of the key genes and transcriptional regulators involved in the biosynthesis of catalpol and acteoside, transcriptome sequencing of radial striation (RS) and non-radial striation (nRS) from four R. glutinosa cultivars was performed. A total of 715,158,202 (~107.27 Gb) high quality reads obtained using paired-end Illumina sequencing were de novo assembled into 150,405 transcripts. Functional annotation with multiple public databases identified 155 and 223 unigenes involved in catalpol and acteoside biosynthesis, together with 325 UGTs, and important transcription factor (TF) families. Comparative analysis of the transcriptomes identified 362 unigenes, found to be differentially expressed in all RS vs. nRS comparisons, with 143 upregulated unigenes, including those encoding enzymes of the catalpol and acteoside biosynthetic pathway, such as geranyl diphosphate synthase (RgGPPS), geraniol 8-hydroxylase (RgG10H), and phenylalanine ammonia-lyase (RgPAL). Other differentially expressed unigenes predicted to be related to catalpol and acteoside biosynthesis fall into UDP-dependent glycosyltransferases (UGTs), as well as transcription factors. In addition, 16 differentially expressed genes were selectively confirmed by real-time PCR. In conclusion, a large unigene dataset of R. glutinosa generated in the current study will serve as a resource for the identification of potential candidate genes for investigation of the tuberous root development and biosynthesis of active components.
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Thodberg S, Del Cueto J, Mazzeo R, Pavan S, Lotti C, Dicenta F, Jakobsen Neilson EH, Møller BL, Sánchez-Pérez R. Elucidation of the Amygdalin Pathway Reveals the Metabolic Basis of Bitter and Sweet Almonds ( Prunus dulcis). PLANT PHYSIOLOGY 2018; 178:1096-1111. [PMID: 30297455 PMCID: PMC6236625 DOI: 10.1104/pp.18.00922] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/18/2018] [Indexed: 05/15/2023]
Abstract
Almond (Prunus dulcis) is the principal Prunus species in which the consumed and thus commercially important part of the fruit is the kernel. As a result of continued selection, the vast majority of almonds have a nonbitter kernel. However, in the field, there are trees carrying bitter kernels, which are toxic to humans and, consequently, need to be removed. The toxicity of bitter almonds is caused by the accumulation of the cyanogenic diglucoside amygdalin, which releases toxic hydrogen cyanide upon hydrolysis. In this study, we identified and characterized the enzymes involved in the amygdalin biosynthetic pathway: PdCYP79D16 and PdCYP71AN24 as the cytochrome P450 (CYP) enzymes catalyzing phenylalanine-to-mandelonitrile conversion, PdUGT94AF3 as an additional monoglucosyl transferase (UGT) catalyzing prunasin formation, and PdUGT94AF1 and PdUGT94AF2 as the two enzymes catalyzing amygdalin formation from prunasin. This was accomplished by constructing a sequence database containing UGTs known, or predicted, to catalyze a β(1→6)-O-glycosylation reaction and a Basic Local Alignment Search Tool search of the draft version of the almond genome versus these sequences. Functional characterization of candidate genes was achieved by transient expression in Nicotiana benthamiana Reverse transcription quantitative polymerase chain reaction demonstrated that the expression of PdCYP79D16 and PdCYP71AN24 was not detectable or only reached minute levels in the sweet almond genotype during fruit development, while it was high and consistent in the bitter genotype. Therefore, the basis for the sweet kernel phenotype is a lack of expression of the genes encoding the two CYPs catalyzing the first steps in amygdalin biosynthesis.
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Affiliation(s)
- Sara Thodberg
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871, Frederiksberg C, Denmark
| | - Jorge Del Cueto
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Arboriculture Research Group. Agroscope, Conthey, Switzerland
- Plant Breeding Department, Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), Campus Universitario de Espinardo, E-30100, Espinardo, Murcia, Spain
| | - Rosa Mazzeo
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871, Frederiksberg C, Denmark
- Department of Soil, Plant and Food Science, University of Bari "Aldo Moro", Via Amendola 165/A, 70126 Bari, Italy
| | - Stefano Pavan
- Department of Soil, Plant and Food Science, University of Bari "Aldo Moro", Via Amendola 165/A, 70126 Bari, Italy
- Institute of Biomedical Technologies, National Research Council (CNR), Via Amendola 122/D, 70126 Bari, Italy
| | - Concetta Lotti
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, 71100 Foggia, Italy
| | - Federico Dicenta
- Plant Breeding Department, Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), Campus Universitario de Espinardo, E-30100, Espinardo, Murcia, Spain
| | - Elizabeth H Jakobsen Neilson
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871, Frederiksberg C, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871, Frederiksberg C, Denmark
| | - Raquel Sánchez-Pérez
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- VILLUM Research Center for Plant Plasticity, DK-1871, Frederiksberg C, Denmark
- Plant Breeding Department, Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), Campus Universitario de Espinardo, E-30100, Espinardo, Murcia, Spain
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Comparative Genomic and Transcriptomic Analyses of Family-1 UDP Glycosyltransferase in Prunus Mume. Int J Mol Sci 2018; 19:ijms19113382. [PMID: 30380641 PMCID: PMC6274698 DOI: 10.3390/ijms19113382] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/09/2018] [Accepted: 10/12/2018] [Indexed: 12/02/2022] Open
Abstract
Glycosylation mediated by Family-1 UDP-glycosyltransferases (UGTs) plays crucial roles in plant growth and adaptation to various stress conditions. Prunus mume is an ideal crop for analyzing flowering for its early spring flowering characteristics. Revealing the genomic and transcriptomic portfolio of the UGT family in P. mume, a species in which UGTs have not yet been investigated, is therefore important. In this study, 130 putative UGT genes were identified and phylogenetically clustered into 14 groups. These PmUGTs were distributed unevenly across eight chromosomes and 32 tandem duplication and 8 segmental duplication pairs were revealed. A highly conserved intron insertion event was revealed on the basis of intron/exon patterns within PmUGTs. According to RNA-seq data, these PmUGTs were specifically expressed in different tissues and during the bud dormancy process. In addition, we confirmed the differential expression of some representative genes in response to abscisic acid treatment. Our results will provide important information on the UGT family in P. mume that should aid further characterization of their biological roles in response to environmental stress.
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He Y, Ahmad D, Zhang X, Zhang Y, Wu L, Jiang P, Ma H. Genome-wide analysis of family-1 UDP glycosyltransferases (UGT) and identification of UGT genes for FHB resistance in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2018; 18:67. [PMID: 29673318 PMCID: PMC5909277 DOI: 10.1186/s12870-018-1286-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/10/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Fusarium head blight (FHB), a devastating disease in wheat worldwide, results in yield loses and mycotoxin, such as deoxynivalenol (DON), accumulation in infected grains. DON also facilitates the pathogen colonization and spread of FHB symptoms during disease development. UDP-glycosyltransferase enzymes (UGTs) are known to contribute to detoxification and enhance FHB resistance by glycosylating DON into DON-3-glucoside (D3G) in wheat. However, a comprehensive investigation of wheat (Triticum aestivum) UGT genes is still lacking. RESULTS In this study, we carried out a genome-wide analysis of family-1 UDP glycosyltransferases in wheat based on the PSPG conserved box that resulted in the identification of 179 putative UGT genes. The identified genes were clustered into 16 major phylogenetic groups with a lack of phylogenetic group K. The UGT genes were invariably distributed among all the chromosomes of the 3 genomes. At least 10 intron insertion events were found in the UGT sequences, where intron 4 was observed as the most conserved intron. The expression analysis of the wheat UGT genes using both online microarray data and quantitative real-time PCR verification suggested the distinct role of UGT genes in different tissues and developmental stages. The expression of many UGT genes was up-regulated after Fusarium graminearum inoculation, and six of the genes were further verified by RT-qPCR. CONCLUSION We identified 179 UGT genes from wheat using the available sequenced wheat genome. This study provides useful insight into the phylogenetic structure, distribution, and expression patterns of family-1 UDP glycosyltransferases in wheat. The results also offer a foundation for future work aimed at elucidating the molecular mechanisms underlying the resistance to FHB and DON accumulation.
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Affiliation(s)
- Yi He
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - Dawood Ahmad
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Xu Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - Yu Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - Lei Wu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - Peng Jiang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - Hongxiang Ma
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
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Tan J, Miao Z, Ren C, Yuan R, Tang Y, Zhang X, Han Z, Ma C. Evolution of intron-poor clades and expression patterns of the glycosyltransferase family 47. PLANTA 2018; 247:745-760. [PMID: 29196940 DOI: 10.1007/s00425-017-2821-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 11/24/2017] [Indexed: 05/26/2023]
Abstract
A large-scale bioinformatics analysis revealed the origin and evolution of GT47 gene family, and identified two clades of intron-poor genes with putative functions in drought stress responses and seed development in maize. Glycosyltransferase family 47 (GT47) genes encode β-galactosyltransferases and β-glucuronyltransferases that synthesize pectin, xyloglucans and xylan, which are important components of the plant cell wall. In this study, we performed a systematic and large-scale bioinformatics analysis of GT47 gene family using 352 GT47 proteins from 15 species ranging from cyanobacteria to seed plants. The analysis results showed that GT47 family may originate in cyanobacteria and expand along the evolutionary trajectory to moss. Further analysis of 47 GT47 genes in maize revealed that they can divide into five clades with diverse exon-intron structures. Among these five clades, two were mainly composed with intron-poor genes, which may originate in the moss. Gene duplication analysis revealed that the expansion of GT47 gene family in maize was significantly driven from tandem duplication events and segmental duplication events. Significantly, almost all duplicated genes are intron-poor genes. Expression analysis indicated that several intron-poor GT47 genes may be involved in the drought stress response and seed development in maize. This work provides insight into the origin and evolutionary process, expansion mechanisms and expression patterns of GT47 genes, thus facilitating their functional investigations in the future.
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Affiliation(s)
- Junfeng Tan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhenyan Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chengzhi Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ruxia Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yunjia Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaorong Zhang
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhaoxue Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Chuang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Rehman HM, Nawaz MA, Shah ZH, Ludwig-Müller J, Chung G, Ahmad MQ, Yang SH, Lee SI. Comparative genomic and transcriptomic analyses of Family-1 UDP glycosyltransferase in three Brassica species and Arabidopsis indicates stress-responsive regulation. Sci Rep 2018; 8:1875. [PMID: 29382843 PMCID: PMC5789830 DOI: 10.1038/s41598-018-19535-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 01/03/2018] [Indexed: 12/25/2022] Open
Abstract
In plants, UGTs (UDP-glycosyltransferases) glycosylate various phytohormones and metabolites in response to biotic and abiotic stresses. Little is known about stress-responsive glycosyltransferases in plants. Therefore, it is important to understand the genomic and transcriptomic portfolio of plants with regard to biotic and abiotic stresses. Here, we identified 140, 154, and 251 putative UGTs in Brassica rapa, Brassica oleracea, and Brassica napus, respectively, and clustered them into 14 major phylogenetic groups (A–N). Fourteen major KEGG pathways and 24 biological processes were associated with the UGTs, highlighting them as unique modulators against environmental stimuli. Putative UGTs from B. rapa and B. oleracea showed a negative selection pressure and biased gene fractionation pattern during their evolution. Polyploidization increased the intron proportion and number of UGT-containing introns among Brassica. The putative UGTs were preferentially expressed in developing tissues and at the senescence stage. Differential expression of up- and down-regulated UGTs in response to phytohormone treatments, pathogen responsiveness and abiotic stresses, inferred from microarray and RNA-Seq data in Arabidopsis and Brassica broaden the glycosylation impact at the molecular level. This study identifies unique candidate UGTs for the manipulation of biotic and abiotic stress pathways in Brassica and Arabidopsis.
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Affiliation(s)
- Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea
| | - Zahid Hussain Shah
- Department of Arid Land Agriculture, King Abdul-Aziz University, Jeddah, Saudi Arabia
| | - Jutta Ludwig-Müller
- Institut für Botanik, Technische Universität Dresden, 01062, Dresden, Germany
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea
| | - Muhammad Qadir Ahmad
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, 6000, Pakistan
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea.
| | - Soo In Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju, 54874, Republic of Korea.
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Han Z, Zhang J, Cai S, Chen X, Quan X, Zhang G. Association mapping for total polyphenol content, total flavonoid content and antioxidant activity in barley. BMC Genomics 2018; 19:81. [PMID: 29370751 PMCID: PMC5784657 DOI: 10.1186/s12864-018-4483-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/16/2018] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The interest has been increasing on the phenolic compounds in plants because of their nutritive function as food and the roles regulating plant growth. However, their underlying genetic mechanism in barley is still not clear. RESULTS A genome-wide association study (GWAS) was conducted for total phenolic content (TPC), total flavonoid content (FLC) and antioxidant activity (AOA) in 67 cultivated and 156 Tibetan wild barley genotypes. Most markers associated with phenolic content were different in cultivated and wild barleys. The markers bPb-0572 and bPb-4531 were identified as the major QTLs controlling phenolic compounds in Tibetan wild barley. Moreover, the marker bPb-4531 was co-located with the UDP- glycosyltransferase gene (HvUGT), which is a homolog to Arabidopsis UGTs and involved in biosynthesis of flavonoid glycosides . CONCLUSIONS GWAS is an efficient tool for exploring the genetic architecture of phenolic compounds in the cultivated and Tibetan wild barleys. The DArT markers applied in this study can be used in barley breeding for developing new barley cultivars with higher phenolics content. The candidate gene (HvUGT) provides a potential route for deep understanding of the molecular mechanism of flavonoid synthesis.
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Affiliation(s)
- Zhigang Han
- Department of Agronomy, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058 China
| | - Jingjie Zhang
- Department of Agronomy, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058 China
| | - Shengguan Cai
- Department of Agronomy, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058 China
| | - Xiaohui Chen
- Department of Agronomy, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058 China
| | - Xiaoyan Quan
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Guoping Zhang
- Department of Agronomy, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058 China
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