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Xu X, Wei H, Yao K, Wu H, Huang T, Han M, Su T, Cao F. Integrative omics studies revealed synergistic link between sucrose metabolic isogenes and carbohydrates in poplar roots infected by Fusarium wilt. PLANT MOLECULAR BIOLOGY 2024; 114:29. [PMID: 38502380 DOI: 10.1007/s11103-024-01426-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/01/2024] [Indexed: 03/21/2024]
Abstract
Advances in carbohydrate metabolism prompted its essential role in defense priming and sweet immunity during plant-pathogen interactions. Nevertheless, upstream responding enzymes in the sucrose metabolic pathway and associated carbohydrate derivatives underlying fungal pathogen challenges remain to be deciphered in Populus, a model tree species. In silico deduction of genomic features, including phylogenies, exon/intron distributions, cis-regulatory elements, and chromosomal localization, identified 59 enzyme genes (11 families) in the Populus genome. Spatiotemporal expression of the transcriptome and the quantitative real-time PCR revealed a minuscule number of isogenes that were predominantly expressed in roots. Upon the pathogenic Fusarium solani (Fs) exposure, dynamic changes in the transcriptomics atlas and experimental evaluation verified Susy (PtSusy2 and 3), CWI (PtCWI3), VI (PtVI2), HK (PtHK6), FK (PtFK6), and UGPase (PtUGP2) families, displaying promotions in their expressions at 48 and 72 h of post-inoculation (hpi). Using the gas chromatography-mass spectrometry (GC-MS)-based non-targeted metabolomics combined with a high-performance ion chromatography system (HPICS), approximately 307 metabolites (13 categories) were annotated that led to the quantification of 46 carbohydrates, showing marked changes between three compared groups. By contrast, some sugars (e.g., sorbitol, L-arabitol, trehalose, and galacturonic acid) exhibited a higher accumulation at 72 hpi than 0 hpi, while levels of α-lactose and glucose decreased, facilitating them as potential signaling molecules. The systematic overview of multi-omics approaches to dissect the effects of Fs infection provides theoretical cues for understanding defense immunity depending on fine-tuned Suc metabolic gene clusters and synergistically linked carbohydrate pools in trees.
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Affiliation(s)
- Xianglei Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Haikun Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Kejun Yao
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Hao Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Tingting Huang
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Mei Han
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
| | - Tao Su
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
| | - Fuliang Cao
- College of Foresty, Nanjing Forestry University, Nanjing, China
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2
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Wu N, Ge X, Yin X, Yang L, Chen L, Shao R, Xu W. A review on polysaccharide biosynthesis in Cordyceps militaris. Int J Biol Macromol 2024; 260:129336. [PMID: 38224811 DOI: 10.1016/j.ijbiomac.2024.129336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/05/2024] [Accepted: 01/06/2024] [Indexed: 01/17/2024]
Abstract
Cordyceps militaris (C. militaris) is an edible parasitic fungus with medicinal properties. Its bioactive polysaccharides are structurally diverse and exhibit various metabolic and biological activities, including antitumor, hypoglycemic, antioxidant, hypolipidemic, anti-inflammatory, immunostimulatory, and anti-atherosclerotic effects. These properties make C. militaris-derived polysaccharides a promising candidate for future development. Recent advancements in microbial fermentation technology have enabled successful laboratory cultivation and extraction of these polysaccharides. These polysaccharides are structurally diverse and exhibit various biological activities, such as immunostimulatory, antioxidant, antitumor, hypolipidemic, and anti-atherosclerotic effects. This review aims to summarize the structure and production mechanisms of polysaccharides from C. militaris, covering extraction methods, key genes and pathways involved in biosynthesis, and fermentation factors that influence yield and activity. Furthermore, the future potential and challenges of utilizing polysaccharides in the development of health foods and pharmaceuticals are addressed. This review serves as a valuable reference in the fields of food and medicine, and provides a theoretical foundation for the study of polysaccharides.
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Affiliation(s)
- Na Wu
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Xiaodong Ge
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Xuemei Yin
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Lei Yang
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Ligen Chen
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Rong Shao
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Wei Xu
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng 224051, PR China.
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3
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Saint-Vincent PMB, Furches A, Galanie S, Teixeira Prates E, Aldridge JL, Labbe A, Zhao N, Martin MZ, Ranjan P, Jones P, Kainer D, Kalluri UC, Chen JG, Muchero W, Jacobson DA, Tschaplinski TJ. Validation of a metabolite-GWAS network for Populus trichocarpa family 1 UDP-glycosyltransferases. FRONTIERS IN PLANT SCIENCE 2023; 14:1210146. [PMID: 37546246 PMCID: PMC10402742 DOI: 10.3389/fpls.2023.1210146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/05/2023] [Indexed: 08/08/2023]
Abstract
Metabolite genome-wide association studies (mGWASs) are increasingly used to discover the genetic basis of target phenotypes in plants such as Populus trichocarpa, a biofuel feedstock and model woody plant species. Despite their growing importance in plant genetics and metabolomics, few mGWASs are experimentally validated. Here, we present a functional genomics workflow for validating mGWAS-predicted enzyme-substrate relationships. We focus on uridine diphosphate-glycosyltransferases (UGTs), a large family of enzymes that catalyze sugar transfer to a variety of plant secondary metabolites involved in defense, signaling, and lignification. Glycosylation influences physiological roles, localization within cells and tissues, and metabolic fates of these metabolites. UGTs have substantially expanded in P. trichocarpa, presenting a challenge for large-scale characterization. Using a high-throughput assay, we produced substrate acceptance profiles for 40 previously uncharacterized candidate enzymes. Assays confirmed 10 of 13 leaf mGWAS associations, and a focused metabolite screen demonstrated varying levels of substrate specificity among UGTs. A substrate binding model case study of UGT-23 rationalized observed enzyme activities and mGWAS associations, including glycosylation of trichocarpinene to produce trichocarpin, a major higher-order salicylate in P. trichocarpa. We identified UGTs putatively involved in lignan, flavonoid, salicylate, and phytohormone metabolism, with potential implications for cell wall biosynthesis, nitrogen uptake, and biotic and abiotic stress response that determine sustainable biomass crop production. Our results provide new support for in silico analyses and evidence-based guidance for in vivo functional characterization.
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Affiliation(s)
- Patricia M. B. Saint-Vincent
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Anna Furches
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, United States
| | - Stephanie Galanie
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Protein Engineering, Merck & Co., Inc., Rahway, NJ, United States
| | - Erica Teixeira Prates
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jessa L. Aldridge
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Audrey Labbe
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Nan Zhao
- School of Electrical Engineering, Southeast University, Nanjing, China
| | - Madhavi Z. Martin
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Priya Ranjan
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Piet Jones
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, United States
| | - David Kainer
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Udaya C. Kalluri
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, United States
| | - Jin-Gui Chen
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, United States
| | - Wellington Muchero
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, United States
| | - Daniel A. Jacobson
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, United States
| | - Timothy J. Tschaplinski
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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Xia X, Fan M, Liu Y, Chang X, Wang J, Qian J, Yang Y. Genome-wide alternative polyadenylation dynamics underlying plant growth retardant-induced dwarfing of pomegranate. FRONTIERS IN PLANT SCIENCE 2023; 14:1189456. [PMID: 37223801 PMCID: PMC10200943 DOI: 10.3389/fpls.2023.1189456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 04/17/2023] [Indexed: 05/25/2023]
Abstract
Dwarfed stature is a desired agronomic trait for pomegranate (Punica granatum L.), with its advantages such as lower cost and increased yield. A comprehensive understanding of regulatory mechanisms underlying the growth repression would provide a genetic foundation to molecular-assisted dwarfing cultivation of pomegranate. Our previous study induced dwarfed pomegranate seedlings via exogenous application of plant growth retardants (PGRs) and highlighted the important roles of differential expression of plant growth-related genes in eliciting the dwarfed phenotype of pomegranate. Alternative polyadenylation (APA) is an important post-transcriptional mechanism and has been demonstrated to act as a key regulator in plant growth and development. However, no attention has been paid to the role of APA in PGR-induced dwarfing in pomegranate. In this study, we characterized and compared APA-mediated regulation events underlying PGR-induced treatments and normal growth condition. Genome-wide alterations in the usage of poly(A) sites were elicited by PGR treatments, and these changes were involved in modulating the growth and development of pomegranate seedlings. Importantly, ample specificities were observed in APA dynamics among the different PGR treatments, which mirrors their distinct nature. Despite the asynchrony between APA events and differential gene expression, APA was found to regulate transcriptome via influencing microRNA (miRNA)-mediated mRNA cleavage or translation inhibition. A global preference for lengthening of 3' untranslated regions (3' UTRs) was observed under PGR treatments, which was likely to host more miRNA target sites in 3' UTRs and thus suppress the expression of the corresponding genes, especially those associated with developmental growth, lateral root branching, and maintenance of shoot apical meristem. Together, these results highlighted the key role of APA-mediated regulations in fine-tuning the PGR-induced dwarfed stature of pomegranate, which provides new insights into the genetic basis underlying the growth and development of pomegranate.
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Affiliation(s)
- Xinhui Xia
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Minhong Fan
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yuqi Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Xinyue Chang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Jingting Wang
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Jingjing Qian
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Yuchen Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
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Wang Z, Ma L, Liu P, Luo Z, Li Z, Wu M, Xu X, Pu W, Huang P, Yang J. Transcription factor NtWRKY33a modulates the biosynthesis of polyphenols by targeting NtMYB4 and NtHCT genes in tobacco. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 326:111522. [PMID: 36332766 DOI: 10.1016/j.plantsci.2022.111522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/21/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
There are abundant polyphenols in tobacco leaves mainly including chlorogenic acid (CGA), rutin, and scopoletin, which not only influence plant growth, development, and environmental adaptation, but also have a great impact on the industrial utilization of tobacco leaves. Few transcription factors regulating the biosynthesis of polyphenols have been identified in tobacco so far. In this study, two NtWRKY33 genes were identified from N. tabacum genome. NtWRKY33a showed higher transcriptional activity than NtWRKY33b, and encoded a nuclear localized protein. Overexpression and knock-out of NtWRKY33a gene revealed that NtWRKY33a inhibited the accumulation of rutin, scopoletin, and total polyphenols, but meanwhile promoted the biosynthesis of CGA. Chromatin immunoprecipitation and Dual-Luc assays indicated that NtWRKY33a could directly bind to the promoters of NtMYB4 and NtHCT, and thus induced the transcription of these two genes. The contents of polyphenols in ntwrky33a, ntmy4, and ntwrky33a/ntmyb4 mutants further confirmed that the repression of NtWRKY33a on the biosynthesis of rutin, scopoletin, and total polyphenols depends on the activity of NtMYB4. Moreover, the promotion of NtHCT by NtWRKY33a modulates the distribution of metabolism flux into the synthesis of CGA. Ectopic expression of NtWRKY33a inhibit the expression of NtSAUR14, NtSAUR59, NtSAUR66, NtIAA4, NtIAA17, and NtIAA19 genes, indicating that NtWRKY33a might be involved in the regulation of plant auxin response. Our study revealed new functions of NtWRKY33a in regulating the synthesis of polyphenols, and provided a promising target for manipulating polyphenols contents in tobacco.
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Affiliation(s)
- Zhong Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Lanxin Ma
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Pingping Liu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Zhaopeng Luo
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Zefeng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Mingzhu Wu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Xin Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Wenxuan Pu
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China
| | - Pingjun Huang
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China.
| | - Jun Yang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China.
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Kim TL, Lim H, Chung H, Veerappan K, Oh C. Elevated CO 2 Alters the Physiological and Transcriptome Responses of Pinus densiflora to Long-Term CO 2 Exposure. PLANTS (BASEL, SWITZERLAND) 2022; 11:3530. [PMID: 36559641 PMCID: PMC9781706 DOI: 10.3390/plants11243530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Physiological response and transcriptome changes were observed to investigate the effects on the growth, metabolism and genetic changes of Pinus densiflora grown for a long time in an environment with an elevated atmospheric CO2 concentration. Pine trees were grown at ambient (400 ppm) and elevated (560 ppm and 720 ppm) CO2 concentrations for 10 years in open-top chambers. The content of nonstructural carbohydrates was significantly increased in elevated CO2. It was notable that the contents of chlorophylls significantly decreased at an elevated CO2. The activities of antioxidants were significantly increased at an elevated CO2 concentration of 720 ppm. We analyzed the differences in the transcriptomes of Pinus densiflora at ambient and elevated CO2 concentrations and elucidated the functions of the differentially expressed genes (DEGs). RNA-Seq analysis identified 2415 and 4462 DEGs between an ambient and elevated CO2 concentrations of 560 ppm and 720 ppm, respectively. Genes related to glycolysis/gluconeogenesis and starch/sucrose metabolism were unchanged or decreased at an elevated CO2 concentration of 560 ppm and tended to increase at an elevated CO2 concentration of 720 ppm. It was confirmed that the expression levels of genes related to photosynthesis and antioxidants were increased at an elevated CO2 concentration of 720 ppm.
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Affiliation(s)
- Tae-Lim Kim
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea
| | - Hyemin Lim
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea
| | - Hoyong Chung
- 3BIGS CO. Ltd., Hwaseong 18469, Republic of Korea
| | | | - Changyoung Oh
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea
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Liu G, Jin T, Xu Y, Yao F, Guan G, Zhou G. Exogenous citrate restores the leaf metabolic profiles of navel orange plants under boron deficiency. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 192:101-109. [PMID: 36219993 DOI: 10.1016/j.plaphy.2022.09.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Boron (B) is an essential micronutrient for higher plants, and its deficiency causes a change in the citrate concentration in leaves of young navel orange plants. Although citrate has been implicated in the regulation of gene expression for many transcripts, it is unclear whether citrate can affect metabolic profiling under B deficiency and if so, how many metabolites are affected. In this study, GC-TOF-MS-based untargeted metabolite profiling was used to identify the physiological effects of exogenous citrate on recovery of metabolites in B-deficient orange plants. There were 31 increased and 24 decreased metabolites in the boron-deficient (BD) group leaves relative to those of the boron-adequate (BA) group. Boron deficiency-induced changes in many metabolites were restored to the level of BA (control) group leaves or showed a recovery tendency at 1 week after citrate supply (foliar application of citrate, BDFC), including 11 organic acids, 9 sugars and polyols, 10 amino acids, and 4 other compounds. To compare with the metabolic recovery effects of exogenous citrate on B deficiency, exogenous application of B (borate) was also performed under same conditions (BDFB), and similar effects on the regulation of metabolic homeostasis under B deficiency were observed. Both the results of principal component analysis (PCA) and hierarchical cluster analysis (HCA) showed that BA, BDFC, and BDFB were relatively similar and clustered close to each other. There are different responsive and regulatory mechanisms to the additions of exogenous citrate in navel orange leaves under B adequate and deficient conditions. Based on these results, we suggest that citrate is an important component of the B deficiency stress response, and exogenous application of citrate generally restores the leaf metabolic profiles of navel orange plants under boron deficiency, which might play a positive role in this stress tolerance.
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Affiliation(s)
- Guidong Liu
- College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi Province, 341000, PR China; National Navel Orange Engineering Research Center, Ganzhou, Jiangxi Province, 341000, PR China.
| | - Tian Jin
- College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi Province, 341000, PR China.
| | - Yuemei Xu
- College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi Province, 341000, PR China.
| | - Fengxian Yao
- College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi Province, 341000, PR China; National Navel Orange Engineering Research Center, Ganzhou, Jiangxi Province, 341000, PR China.
| | - Guan Guan
- College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi Province, 341000, PR China; National Navel Orange Engineering Research Center, Ganzhou, Jiangxi Province, 341000, PR China.
| | - Gaofeng Zhou
- College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi Province, 341000, PR China; National Navel Orange Engineering Research Center, Ganzhou, Jiangxi Province, 341000, PR China.
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Xu Z, He J, Tehseen Azhar M, Zhang Z, Fan S, Jiang X, Jia T, Shang H, Yuan Y. UDP-glucose pyrophosphorylase: genome-wide identification, expression and functional analyses in Gossypium hirsutum. PeerJ 2022; 10:e13460. [PMID: 35663522 PMCID: PMC9161816 DOI: 10.7717/peerj.13460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/27/2022] [Indexed: 01/14/2023] Open
Abstract
In this study, a total of 66 UDP-glucose pyrophosphorylase (UGP) (EC 2.7.7.9) genes were identified from the genomes of four cotton species, which are the members of Pfam glycosyltransferase family (PF01702) and catalyze the reaction between glucose-1-phosphate and UTP to produce UDPG. The analysis of evolutionary relationship, gene structure, and expression provides the basis for studies on function of UGP genes in cotton. The evolutionary tree and gene structure analysis revealed that the UGP gene family is evolutionarily conserved. Collinearity and Ka/Ks analysis indicated that amplification of UGP genes is due to repetitive crosstalk generating between new family genes, while being under strong selection pressure. The analysis of cis-acting elements exhibited that UGP genes play important role in cotton growth, development, abiotic and hormonal stresses. Six UGP genes that were highly expressed in cotton fiber at 15 DPA were screened by transcriptome data and qRT-PCR analysis. The addition of low concentrations of IAA and GA3 to ovule cultures revealed that energy efficiency promoted the development of ovules and fiber clusters, and qRT-PCR showed that expression of these six UGP genes was differentially increased. These results suggest that the UGP gene may play an important role in fiber development, and provides the opportunity to plant researchers to explore the mechanisms involve in fiber development in cotton.
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Affiliation(s)
- Zhongyang Xu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiasen He
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Muhammad Tehseen Azhar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministryof Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministryof Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Xiao Jiang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministryof Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Tingting Jia
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministryof Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Haihong Shang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministryof Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
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Cao J, Liao Y, Yang W, Jiang X, Li M. Enhanced microalgal toxicity due to polystyrene nanoplastics and cadmium co-exposure: From the perspective of physiological and metabolomic profiles. JOURNAL OF HAZARDOUS MATERIALS 2022; 427:127937. [PMID: 34863563 DOI: 10.1016/j.jhazmat.2021.127937] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/09/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
As important emerging contaminants, nanoplastics can act as vectors for other environmental pollutants, resulting in their migration throughout ecosystems and altering their toxicity. In this study, the fluorescent dye label aggravated the toxicity of polystyrene (PS) nanoplastics (100 nm diameter particles) to microalgae Euglena gracilis. Therefore, the toxicity of non-fluorescent labelled PS alone and in combination with divalent cadmium (Cd2+) on Euglena gracilis in the environmentally relevant concentrations was investigated. Results revealed that co-exposure to 50 μg/L (1.1 × 1010 particles/L) PS and 50 μg/L Cd2+ resulted in synergistic effects, significantly inhibiting microalgal growth by 28.76%. Superoxide dismutase, peroxidase and extracellular polymeric substances were distinctly enhanced in co-exposure treatments compared to the control, indicating that cellular antioxidant defense responses were activated. LC-MS-based metabolomic analysis suggested that PS and Cd2+ exposure alone or in combination induced significant disruption to carbohydrate and purine metabolism-related pathways, as compared to controls. As part of the PS and Cd2+ stress response, differential metabolites involved in lipid metabolism and amino acid metabolism provide antioxidants and cell membrane protective molecules. Overall, this combined physiological and metabolomic analysis approach provides a better understanding of the potential risks posed by nanoplastics and heavy metal pollution in aquatic ecosystems.
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Affiliation(s)
- Jing Cao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Yuanchen Liao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Weishu Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xiaofeng Jiang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Mei Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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Patel MK, Pandey S, Kumar M, Haque MI, Pal S, Yadav NS. Plants Metabolome Study: Emerging Tools and Techniques. PLANTS (BASEL, SWITZERLAND) 2021; 10:2409. [PMID: 34834772 PMCID: PMC8621461 DOI: 10.3390/plants10112409] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 05/06/2023]
Abstract
Metabolomics is now considered a wide-ranging, sensitive and practical approach to acquire useful information on the composition of a metabolite pool present in any organism, including plants. Investigating metabolomic regulation in plants is essential to understand their adaptation, acclimation and defense responses to environmental stresses through the production of numerous metabolites. Moreover, metabolomics can be easily applied for the phenotyping of plants; and thus, it has great potential to be used in genome editing programs to develop superior next-generation crops. This review describes the recent analytical tools and techniques available to study plants metabolome, along with their significance of sample preparation using targeted and non-targeted methods. Advanced analytical tools, like gas chromatography-mass spectrometry (GC-MS), liquid chromatography mass-spectroscopy (LC-MS), capillary electrophoresis-mass spectrometry (CE-MS), fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) matrix-assisted laser desorption/ionization (MALDI), ion mobility spectrometry (IMS) and nuclear magnetic resonance (NMR) have speed up precise metabolic profiling in plants. Further, we provide a complete overview of bioinformatics tools and plant metabolome database that can be utilized to advance our knowledge to plant biology.
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Affiliation(s)
- Manish Kumar Patel
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
| | - Sonika Pandey
- Independent Researcher, Civil Line, Fathepur 212601, India;
| | - Manoj Kumar
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel;
| | - Md Intesaful Haque
- Fruit Tree Science Department, Newe Ya’ar Research Center, Agriculture Research Organization, Volcani Center, Ramat Yishay 3009500, Israel;
| | - Sikander Pal
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu 180006, India;
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
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Wang D, Zhang Z, Yang L, Tian S, Liu Y. ARPI, β-AS, and UGE regulate glycyrrhizin biosynthesis in Glycyrrhiza uralensis hairy roots. PLANT CELL REPORTS 2021; 40:1285-1296. [PMID: 34002270 DOI: 10.1007/s00299-021-02712-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/08/2021] [Indexed: 06/12/2023]
Abstract
ARPI, β-AS, and UGE were cloned from G. uralensis and their regulatory effects on glycyrrhizin biosynthesis were investigated. β-AS and UGE but not ARPI positively regulate the biosynthesis of glycyrrhizin. Glycyrrhiza uralensis Fisch. has been used to treat respiratory, gastric, and liver diseases since ancient China. The most important and widely studied active component in G. uralensis is glycyrrhizin (GC). Our pervious RNA-Seq study shows that GC biosynthesis is regulated by multiple biosynthetic pathways. In this study, three target genes, ARPI, β-AS, and UGE from different pathways were selected and their regulatory effects on GC biosynthesis were investigated using G. uralensis hairy roots. Our data show that hairy roots knocking out ARPI or UGE died soon after induction, indicating that the genes are essential for the growth of G. uralensis hairy roots. Hairy roots with β-AS knocked out grew healthily. However, they failed to produce GC, suggesting that β-AS is required for triterpenoid skeleton formation. Conversely, overexpression of UGE or β-AS significantly increased the GC content, whereas overexpression of ARPI had no obvious effects on GC accumulation in G. uralensis hairy roots. Our findings demonstrate that β-AS and UGE positively regulate the biosynthesis of GC.
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Affiliation(s)
- Doudou Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Yangguang South Street, Fangshan District, Beijing, 102401, China
| | - Zhixin Zhang
- School of Life Sciences, Beijing University of Chinese Medicine, Yangguang South Street, Fangshan District, Beijing, 102401, China
| | - Lin Yang
- School of Life Sciences, Beijing University of Chinese Medicine, Yangguang South Street, Fangshan District, Beijing, 102401, China
| | - Shaokai Tian
- School of Life Sciences, Beijing University of Chinese Medicine, Yangguang South Street, Fangshan District, Beijing, 102401, China
| | - Ying Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Yangguang South Street, Fangshan District, Beijing, 102401, China.
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Wang Y, Yang X, Chen P, Yang S, Zhang H. Homologous overexpression of genes in Cordyceps militaris improves the production of polysaccharides. Food Res Int 2021; 147:110452. [PMID: 34399454 DOI: 10.1016/j.foodres.2021.110452] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 05/03/2021] [Accepted: 05/23/2021] [Indexed: 11/15/2022]
Abstract
The maximum yield of EPS produced by mutant CM-pgm-H was 4.63 ± 0.23 g/L, whereas the yield of wild-type strain was 3.43 ± 0.26 g/L. In addition, the data obtained in the present study indicated that the yield of EPS produced by the engineered strain treated with the co-overexpression of phosphoglucomutase and UDP-glucose 6-dehydrogenase genes achieved 6.11 ± 0.21 g/L, which was increased by 78.13% compared with that by the wild-type strain. CM-pgm-H obtained the highest EPS content than that of gk, ugp, and ugdh mutants. This result indicated that the content of protein phosphoglucomutase was an important influencing factor on the CP production of C. militaris. Furthermore, the EPS production of CM-ugdh-pgm-M was significantly improved by 1.78-fold by co-overexpression. Therefore, our engineering strategies will play an important role in the development of C. militaris for the sustainable production of Cordyceps polysaccharides.
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Affiliation(s)
- Yifeng Wang
- The College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Xi Yang
- The College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Ping Chen
- The College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Shengli Yang
- The College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China.
| | - Hui Zhang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, People's Republic of China.
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Jeon JS, Carreno-Quintero N, van Eekelen HDLM, De Vos RCH, Raaijmakers JM, Etalo DW. Impact of root-associated strains of three Paraburkholderia species on primary and secondary metabolism of Brassica oleracea. Sci Rep 2021; 11:2781. [PMID: 33531553 PMCID: PMC7854645 DOI: 10.1038/s41598-021-82238-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/14/2021] [Indexed: 02/07/2023] Open
Abstract
Several root-colonizing bacterial species can simultaneously promote plant growth and induce systemic resistance. How these rhizobacteria modulate plant metabolism to accommodate the carbon and energy demand from these two competing processes is largely unknown. Here, we show that strains of three Paraburkholderia species, P. graminis PHS1 (Pbg), P. hospita mHSR1 (Pbh), and P. terricola mHS1 (Pbt), upon colonization of the roots of two Broccoli cultivars led to cultivar-dependent increases in biomass, changes in primary and secondary metabolism and induced resistance against the bacterial leaf pathogen Xanthomonas campestris. Strains that promoted growth led to greater accumulation of soluble sugars in the shoot and particularly fructose levels showed an increase of up to 280-fold relative to the non-treated control plants. Similarly, a number of secondary metabolites constituting chemical and structural defense, including flavonoids, hydroxycinnamates, stilbenoids, coumarins and lignins, showed greater accumulation while other resource-competing metabolite pathways were depleted. High soluble sugar generation, efficient sugar utilization, and suppression or remobilization of resource-competing metabolites potentially contributed to curb the tradeoff between the carbon and energy demanding processes induced by Paraburkholderia-Broccoli interaction. Collectively, our results provide a comprehensive and integrated view of the temporal changes in plant metabolome associated with rhizobacteria-mediated plant growth promotion and induced resistance.
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Affiliation(s)
- Je-Seung Jeon
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
- Institute of Biology, Leiden University, Leiden, 2333 BE, The Netherlands
| | - Natalia Carreno-Quintero
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
- KeyGene N.V., Wageningen, 6708 PW, The Netherlands
| | | | - Ric C H De Vos
- Wageningen Plant Research, Bioscience, Wageningen, 6708 PB, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
- Institute of Biology, Leiden University, Leiden, 2333 BE, The Netherlands
| | - Desalegn W Etalo
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, 6708 PB, The Netherlands.
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Becerra-Martínez E, Pacheco-Hernández Y, Lozoya-Gloria E, Betancourt-Jiménez MG, Hidalgo-Martínez D, Zepeda-Vallejo LG, Villa-Ruano N. 1 H-NMR metabolomics profiling of recombinant tobacco plants holding a promoter of a sesquiterpene cyclase. PHYTOCHEMICAL ANALYSIS : PCA 2020; 31:480-487. [PMID: 31908083 DOI: 10.1002/pca.2911] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 10/22/2019] [Accepted: 11/25/2019] [Indexed: 06/10/2023]
Abstract
INTRODUCTION Nicotiana tabacum is a plant model intensively used in the bio-engineering pharmaceutical industry as a platform to produce drugs and therapeutic agents. Currently, no information regarding the non-targeted metabolome of transgenic tobacco containing recombinant regulatory sequences is available. OBJECTIVE To compare the proton nuclear magnetic resonance (1 H-NMR) metabolomics profiling of a recombinant Nicotiana tabacum strain containing a promoter of a sesquiterpene cyclase from Capsicum annuum driving GUS expression, versus wild-type samples. Methodology The non-targeted 1 H-NMR metabolome was obtained and processed by principal component analysis (PCA) and orthogonal projection to latent structures discriminant analysis (OPLS-DA). The differential metabolites were quantified by quantitative NMR. RESULTS PCA and OPLS-DA revealed 37 metabolites including 16 discriminant compounds for transgenic samples. Ethanol (0.4 mg g-1 ), the main differential compound, was exclusively detected in transgenic tobacco; however, high levels of formate (0.28 mg g-1 ) and acetate (0.3 mg g-1 ) were simultaneously observed in the same group of samples. Cembratriene-4,6-diol, an antitumour and neuroprotective compound, and capsidiol, a known phytoalexin, increased by about 30% in transgenic samples. In addition, the endogenous levels of the antioxidant caffeoylquinic acid isomers increased by 50% in comparison to those of wild-type tobaccos. CONCLUSION Our results support the occurrence of metabolic differences between wild type and transgenic tobacco containing a promoter of a Capsicum sesquiterpene cyclase gene. Interestingly, the recombinant transgenic strain studied accumulated high amounts of added value compounds with biological activity.
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Affiliation(s)
- Elvia Becerra-Martínez
- Centro de Nanociencias y Micro y Nanotecnologías, Instituto Politécnico Nacional, Ciudad de México, México
| | | | - Edmundo Lozoya-Gloria
- Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Guanajuato, México
| | | | | | - Luis G Zepeda-Vallejo
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Nemesio Villa-Ruano
- CONACyT - Centro Universitario de Vinculación y Transferencia de Tecnología, Benemérita Universidad Autónoma de Puebla, Puebla, México
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Jammer A, Albacete A, Schulz B, Koch W, Weltmeier F, van der Graaff E, Pfeifhofer HW, Roitsch TG. Early-stage sugar beet taproot development is characterized by three distinct physiological phases. PLANT DIRECT 2020; 4:e00221. [PMID: 32766510 PMCID: PMC7395582 DOI: 10.1002/pld3.221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/04/2020] [Accepted: 04/13/2020] [Indexed: 05/21/2023]
Abstract
Despite the agronomic importance of sugar beet (Beta vulgaris L.), the early-stage development of its taproot has only been poorly investigated. Thus, the mechanisms that determine growth and sugar accumulation in sugar beet are largely unknown. In the presented study, a physiological characterization of early-stage sugar beet taproot development was conducted. Activities were analyzed for fourteen key enzymes of carbohydrate metabolism in developing taproots over the first 80 days after sowing. In addition, we performed in situ localizations of selected carbohydrate-metabolic enzyme activities, anatomical investigations, and quantifications of soluble carbohydrates, hexose phosphates, and phytohormones. Based on the accumulation dynamics of biomass and sucrose, as well as on anatomical parameters, the early phase of taproot development could be subdivided into three stages-prestorage, transition, secondary growth and sucrose accumulation stage-each of which was characterized by distinct metabolic and phytohormonal signatures. The enzyme activity signatures corresponding to these stages were also shown to be robustly reproducible in experiments conducted in two additional locations. The results from this physiological phenotyping approach contribute to the identification of the key regulators of sugar beet taproot development and open up new perspectives for sugar beet crop improvement concerning both physiological marker-based breeding and biotechnological approaches.
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Affiliation(s)
- Alexandra Jammer
- Institute of BiologyUniversity of GrazGrazAustria
- Department of Crop SciencesUFT TullnUniversity of Natural Resources and Life Sciences (BOKU)TullnAustria
| | - Alfonso Albacete
- Institute of BiologyUniversity of GrazGrazAustria
- Present address:
Department of Plant Production and AgrotechnologyInstitute for Agri‐Food Research and Development of Murcia (IMIDA)MurciaSpain
| | | | | | | | - Eric van der Graaff
- Institute of BiologyUniversity of GrazGrazAustria
- Department of Plant and Environmental SciencesCopenhagen Plant Science CentreUniversity of CopenhagenTaastrupDenmark
- Present address:
Koppert Cress B.V.MonsterThe Netherlands
| | | | - Thomas G. Roitsch
- Department of Crop SciencesUFT TullnUniversity of Natural Resources and Life Sciences (BOKU)TullnAustria
- Department of Plant and Environmental SciencesCopenhagen Plant Science CentreUniversity of CopenhagenTaastrupDenmark
- Department of Adaptive BiotechnologiesGlobal Change Research Institute CASBrnoCzech Republic
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Effects of light, sucrose concentration and repetitive subculture on callus growth and medically important production in Justicia gendarussa Burm.f. ACTA ACUST UNITED AC 2020; 27:e00473. [PMID: 32612941 PMCID: PMC7321969 DOI: 10.1016/j.btre.2020.e00473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/07/2020] [Accepted: 05/15/2020] [Indexed: 12/23/2022]
Abstract
Objective This research aimed at the discovering the effects of light, sucrose concentration and repetitive subculture on the growth of Justicia gendarussa Burm.f. calluses based on biomass, morphological characters and metabolic profiles. Methods The second and third leaves of young J. gendarussa Burm.f. were isolated and cultured in solid Murashige and Skoog (MS) medium with the addition of 1 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D) and 0.5 mg/L benzyl amino purine (BAP). Different sucrose concentrations, varying from 0 to 5%, were included in the medium. The cultures were incubated under light and dark conditions for 6 weeks. Repetitive subculture was carried out every 2 weeks for a total of four times, and 3% sucrose gave the best callus growth. Dry calluses were extracted with methanol, and their metabolic profiles were analyzed using gas chromatography/mass spectrometry (GC/MS). Compound identification was performed by comparing the mass spectra to references from the WILEY version 7n.1 library. Results Among the 12 conditions tested for the prolonged 6-week culture, the 2-5 % sucrose treatments under light and 3-5 % sucrose treatments under dark exhibited the highest dry weight. For repetitive subculture, the highest wet and dry weights were identically detected under both light and dark conditions after the second repetitive subculture. A total of 19 metabolites was identified by GC/MS, with major compounds being taraxasterol, monoplex D, 2-methoxy-4-vinylphenol, and palmitic acid. Conclusion Light, sucrose concentration, and repetitive subculture all significantly impacted the growth and metabolic profiles of J. gendarussa Burm.f. calluses. A concentration of 3% sucrose demonstrated the best growth of callus and could be further applied for mass production.
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Tschaplinski TJ, Abraham PE, Jawdy SS, Gunter LE, Martin MZ, Engle NL, Yang X, Tuskan GA. The nature of the progression of drought stress drives differential metabolomic responses in Populus deltoides. ANNALS OF BOTANY 2019; 124:617-626. [PMID: 30689716 PMCID: PMC6821281 DOI: 10.1093/aob/mcz002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 01/01/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS The use of woody crops for Quad-level (approx. 1 × 1018 J) energy production will require marginal agricultural lands that experience recurrent periods of water stress. Populus species have the capacity to increase dehydration tolerance by lowering osmotic potential via osmotic adjustment. The aim of this study was to investigate how the inherent genetic potential of a Populus clone to respond to drought interacts with the nature of the drought to determine the degree of biochemical response. METHODS A greenhouse drought stress study was conducted on Populus deltoides 'WV94' and the resulting metabolite profiles of leaves were determined by gas chromatography-mass spectrometry following trimethylsilylation for plants subjected to cyclic mild (-0.5 MPa pre-dawn leaf water potential) drought vs. cyclic severe (-1.26 MPa) drought in contrast to well-watered controls (-0.1 MPa) after two or four drought cycles, and in contrast to plants subjected to acute drought, where plants were desiccated for up to 8 d. KEY RESULTS The nature of drought (cyclic vs. acute), frequency of drought (number of cycles) and the severity of drought (mild vs. severe) all dictated the degree of osmotic adjustment and the nature of the organic solutes that accumulated. Whereas cyclic drought induced the largest responses in primary metabolism (soluble sugars, organic acids and amino acids), acute onset of prolonged drought induced the greatest osmotic adjustment and largest responses in secondary metabolism, especially populosides (hydroxycinnamic acid conjugates of salicin). CONCLUSIONS The differential adaptive metabolite responses in cyclic vs. acute drought suggest that stress acclimation occurs via primary metabolism in response to cyclic drought, whereas expanded metabolic plasticity occurs via secondary metabolism following severe, acute drought. The shift in carbon partitioning to aromatic metabolism with the production of a diverse suite of higher order salicylates lowers osmotic potential and increases the probability of post-stress recovery.
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Affiliation(s)
| | | | - Sara S Jawdy
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Lee E Gunter
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | | | - Xiaohan Yang
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
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Liu X, Wen J, Chen W, Du H. Physiological effects of nitrogen deficiency and recovery on the macroalga Gracilariopsis lemaneiformis (Rhodophyta). JOURNAL OF PHYCOLOGY 2019; 55:830-839. [PMID: 30916786 DOI: 10.1111/jpy.12862] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/05/2019] [Indexed: 05/07/2023]
Abstract
Algal metabolites are the most promising feedstocks for bio-energy production. Gracilariopsis lemaneiformis seems to be a good candidate red alga for polysaccharide production, especially relating to the agar production industry. Nitrogen deficiency is an efficient environmental pressure used to increase the accumulation of metabolites in algae. However, there are no studies on the physiological effects of G. lemaneiformis in response to nitrogen deficiency and its subsequent recovery. Here we integrated physiological data with molecular studies to explore the response strategy of G. lemaneiformis under nitrogen deficiency and recovery. Physiological measurements indicated that amino acids and protein biosynthesis were decreased, while endogenous NH4+ and soluble polysaccharides levels were increased under nitrogen stress. The expression of key genes involved in these pathways further suggested that G. lemaneiformis responded to nitrogen stress through up-regulation or down-regulation of genes related to nitrogen metabolism, and increased levels of endogenous NH4+ to complement the deficiency of exogenous nitrogen. Consistent with the highest accumulation of soluble polysaccharides, the gene encoding UDP-glucose pyrophosphorylase, a molecular marker used to evaluate agar content, was dramatically up-regulated more than 4-fold compared to the relative expression of actin after 4 d of nitrogen recovery. The present data provide important information on the mechanisms of nutrient balance in macroalgae.
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Affiliation(s)
- Xiaojuan Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology and STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou, Guangdong, 515063, China
| | - Jinyan Wen
- Guangdong Provincial Key Laboratory of Marine Biotechnology and STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou, Guangdong, 515063, China
| | - Weizhou Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology and STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou, Guangdong, 515063, China
| | - Hong Du
- Guangdong Provincial Key Laboratory of Marine Biotechnology and STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou, Guangdong, 515063, China
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Veach AM, Morris R, Yip DZ, Yang ZK, Engle NL, Cregger MA, Tschaplinski TJ, Schadt CW. Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin. MICROBIOME 2019; 7:76. [PMID: 31103040 PMCID: PMC6525979 DOI: 10.1186/s40168-019-0668-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/20/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Plants have developed defense strategies for phytopathogen and herbivore protection via coordinated metabolic mechanisms. Low-molecular weight metabolites produced within plant tissues, such as salicylic acid, represent one such mechanism which likely mediates plant - microbe interactions above and below ground. Salicylic acid is a ubiquitous phytohormone at low levels in most plants, yet are concentrated defense compounds in Populus, likely acting as a selective filter for rhizosphere microbiomes. We propagated twelve Populus trichocarpa genotypes which varied an order of magnitude in salicylic acid (SA)-related secondary metabolites, in contrasting soils from two different origins. After four months of growth, plant properties (leaf growth, chlorophyll content, and net photosynthetic rate) and plant root metabolomics specifically targeting SA metabolites were measured via GC-MS. In addition, rhizosphere microbiome composition was measured via Illumina MiSeq sequencing of 16S and ITS2 rRNA-genes. RESULTS Soil origin was the primary filter causing divergence in bacterial/archaeal and fungal communities with plant genotype secondarily influential. Both bacterial/archaeal and fungal evenness varied between soil origins and bacterial/archaeal diversity and evenness correlated with at least one SA metabolite (diversity: populin; evenness: total phenolics). The production of individual salicylic acid derivatives that varied by host genotype resulted in compositional differences for bacteria /archaea (tremuloidin) and fungi (salicylic acid) within one soil origin (Clatskanie) whereas soils from Corvallis did not illicit microbial compositional changes due to salicylic acid derivatives. Several dominant bacterial (e.g., Betaproteobacteria, Acidobacteria, Verrucomicrobia, Chloroflexi, Gemmatimonadete, Firmicutes) and one fungal phyla (Mortierellomycota) also correlated with specific SA secondary metabolites; bacterial phyla exhibited more negative interactions (declining abundance with increasing metabolite concentration) than positive interactions. CONCLUSIONS These results indicate microbial communities diverge most among soil origin. However, within a soil origin, bacterial/archaeal communities are responsive to plant SA production within greenhouse-based rhizosphere microbiomes. Fungal microbiomes are impacted by root SA-metabolites, but overall to a lesser degree within this experimental context. These results suggest plant defense strategies, such as SA and its secondary metabolites, may partially drive patterns of both bacterial/archaeal and fungal taxa-specific colonization and assembly.
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Affiliation(s)
- Allison M. Veach
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831-6038 USA
| | - Reese Morris
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831-6038 USA
| | - Daniel Z. Yip
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831-6038 USA
| | - Zamin K. Yang
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831-6038 USA
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831-6038 USA
| | - Melissa A. Cregger
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831-6038 USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831-6038 USA
| | - Christopher W. Schadt
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831-6038 USA
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996 USA
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Tuskan GA, Muchero W, Tschaplinski TJ, Ragauskas AJ. Population-level approaches reveal novel aspects of lignin biosynthesis, content, composition and structure. Curr Opin Biotechnol 2019; 56:250-257. [PMID: 30925430 DOI: 10.1016/j.copbio.2019.02.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/20/2019] [Accepted: 02/22/2019] [Indexed: 10/27/2022]
Abstract
Population-level studies enabled by high-throughput phenotyping have revealed significant variation in lignin characteristics including content, S:G:H ratio, inter-unit linkage distributions, and molecular weights across multiple plant species. Coupled with genome-wide association mapping studies (GWAS) targeted at linking genetic mutations to phenotype, significant progress has been made in associating putative causal mutations to variation in lignin characteristics. Despite this progress, there are few examples, in which these associations have been molecularly validated to provide new insights into the genetic regulation of lignin biosynthesis. Given a recent report of a GWAS-discovered 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase moonlighting as a transcriptional regulator of lignin biosynthesis, the potential to bridge scientific disciplines in order to uncover hidden elements of lignin biosynthesis has been demonstrated, offering a path to alter lignin characteristics via genetic manipulation in order to expedite lignin valorization. To maximize this potential, however, there is a crucial need for (1) broader surveys of naturally varying diverse plant populations and (2) analytical platforms that can resolve subtle properties at fine chemical and biological scales.
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Affiliation(s)
- Gerald A Tuskan
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States.
| | - Wellington Muchero
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Timothy J Tschaplinski
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Arthur J Ragauskas
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; University of Tennessee Governor's Chair, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
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Kundu A, Vadassery J. Chlorogenic acid-mediated chemical defence of plants against insect herbivores. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:185-189. [PMID: 30521134 DOI: 10.1111/plb.12947] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/28/2018] [Indexed: 05/18/2023]
Abstract
Chlorogenic acid is one of the most abundant beneficial polyphenols in plants and is well known as a nutritional antioxidant in plant-based foods. Apart from its dietary antioxidant activity, it has been proved to be an efficient defence molecule against a broad range of insect herbivores. In the last two decades, several reports have shown the effectiveness of chlorogenic acid in insect growth deterrence. The pathway for chlorogenic acid biosynthesis in plants was previously elucidated, and metabolic engineering of the principal pathway showed high chlorogenic acid production in tomato plants. Herbivore-mediated induction of chlorogenic acid biosynthesis was also demonstrated both at metabolite and transcript level, although herbivore-mediated molecular regulation of chlorogenic acid biosynthesis is not yet fully elucidated. In this communication, we present our views on the efficacy of chlorogenic acid as an anti-herbivore defence molecule in plants and also discuss its future outlook.
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Affiliation(s)
- A Kundu
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - J Vadassery
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
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22
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Response of Bioactive Metabolite and Biosynthesis Related Genes to Methyl Jasmonate Elicitation in Codonopsis pilosula. Molecules 2019; 24:molecules24030533. [PMID: 30717158 PMCID: PMC6385095 DOI: 10.3390/molecules24030533] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 02/06/2023] Open
Abstract
Bioactive metabolites in Codonopsis pilosula are of particular interest as an immunostimulant. Methyl jasmonate (MeJA) plays an important role in the elicitation of metabolite biosynthesis. Here, we explored the response of metabolites to MeJA elicitation in C. pilosula adventitious roots and multiple shoots. The results showed that the biomass, polysaccharide, and lobetyolin content of adventitious roots exhibited the highest increases with 100 µmol·L−1 MeJA at the 16th day of subculture, whereas the atractylenolide III (a terpenoid) content increased extremely with 50 µmol·L−1 MeJA treatment at the 7th day of subculture. In addition, the biomass and lobetyolin content significantly increased at the 4th day after treatment. Similarly, the polysaccharide and lobetyolin content increased in multiple shoots. Further identification of different metabolites responding to MeJA by 1H-NMR showed an extremely significant increase of the lobetyolinin level, which coincided with lobetyolin. Accordingly, the precursor, fatty acids, showed a highly significant decrease in their levels. Furthermore, a significant increase in β-d-fructose-butanol glycoside was detected, which was accompanied by a decrease in the sucrose level. Accordingly, the enzyme genes responsible for terpenoid and carbohydrate biosynthesis, CpUGPase, and CpPMK, were up regulated. In conclusion, MeJA promoted culture growth and accelerated bioactive metabolite accumulation by regulating the expression of the metabolite biosynthesis related genes, CpUGPase and CpPMK in C. pilosula.
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Decker D, Kleczkowski LA. UDP-Sugar Producing Pyrophosphorylases: Distinct and Essential Enzymes With Overlapping Substrate Specificities, Providing de novo Precursors for Glycosylation Reactions. FRONTIERS IN PLANT SCIENCE 2019; 9:1822. [PMID: 30662444 PMCID: PMC6329318 DOI: 10.3389/fpls.2018.01822] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/23/2018] [Indexed: 05/02/2023]
Abstract
Nucleotide sugars are the key precursors for all glycosylation reactions and are required both for oligo- and polysaccharides synthesis and protein and lipid glycosylation. Among all nucleotide sugars, UDP-sugars are the most important precursors for biomass production in nature (e.g., synthesis of cellulose, hemicellulose, and pectins for cell wall production). Several recent studies have already suggested a potential role for UDP-Glc in plant growth and development, and UDP-Glc has also been suggested as a signaling molecule, in addition to its precursor function. In this review, we will cover primary mechanisms of formation of UDP-sugars, by focusing on UDP-sugar metabolizing pyrophosphorylases. The pyrophosphorylases can be divided into three families: UDP-Glc pyrophosphorylase (UGPase), UDP-sugar pyrophosphorylase (USPase), and UDP-N-acetyl glucosamine pyrophosphorylase (UAGPase), which can be distinguished both by their amino acid sequences and by differences in substrate specificity. Substrate specificities of these enzymes are discussed, along with structure-function relationships, based on their crystal structures and homology modeling. Earlier studies with transgenic plants have revealed that each of the pyrophosphorylases is essential for plant survival, and their loss or a decrease in activity results in reproductive impairment. This constitutes a problem when studying exact in vivo roles of the enzymes using classical reverse genetics approaches. Thus, strategies involving the use of specific inhibitors (reverse chemical genetics) are also discussed. Further characterization of the properties/roles of pyrophosphorylases should address fundamental questions dealing with mechanisms and control of carbohydrate synthesis and may allow to identify targets for manipulation of biomass production in plants.
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Affiliation(s)
| | - Leszek A. Kleczkowski
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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24
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Badmi R, Payyavula RS, Bali G, Guo HB, Jawdy SS, Gunter LE, Yang X, Winkeler KA, Collins C, Rottmann WH, Yee K, Rodriguez M, Sykes RW, Decker SR, Davis MF, Ragauskas AJ, Tuskan GA, Kalluri UC. A New Calmodulin-Binding Protein Expresses in the Context of Secondary Cell Wall Biosynthesis and Impacts Biomass Properties in Populus. FRONTIERS IN PLANT SCIENCE 2018; 9:1669. [PMID: 30568662 PMCID: PMC6290091 DOI: 10.3389/fpls.2018.01669] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/26/2018] [Indexed: 05/21/2023]
Abstract
A greater understanding of biosynthesis, signaling and regulatory pathways involved in determining stem growth and secondary cell wall chemistry is important for enabling pathway engineering and genetic optimization of biomass properties. The present study describes a new functional role of PdIQD10, a Populus gene belonging to the IQ67-Domain1 family of IQD genes, in impacting biomass formation and chemistry. Expression studies showed that PdIQD10 has enhanced expression in developing xylem and tension-stressed tissues in Populus deltoides. Molecular dynamics simulation and yeast two-hybrid interaction experiments suggest interactions with two calmodulin proteins, CaM247 and CaM014, supporting the sequence-predicted functional role of the PdIQD10 as a calmodulin-binding protein. PdIQD10 was found to interact with specific Populus isoforms of the Kinesin Light Chain protein family, shown previously to function as microtubule-guided, cargo binding and delivery proteins in Arabidopsis. Subcellular localization studies showed that PdIQD10 localizes in the nucleus and plasma membrane regions. Promoter-binding assays suggest that a known master transcriptional regulator of secondary cell wall biosynthesis (PdWND1B) may be upstream of an HD-ZIP III gene that is in turn upstream of PdIQD10 gene in the transcriptional network. RNAi-mediated downregulation of PdIQD10 expression resulted in plants with altered biomass properties including higher cellulose, wall glucose content and greater biomass quantity. These results present evidence in support of a new functional role for an IQD gene family member, PdIQD10, in secondary cell wall biosynthesis and biomass formation in Populus.
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Affiliation(s)
- Raghuram Badmi
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Raja S. Payyavula
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Garima Bali
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Georgia Institute of Technology, Atlanta, GA, United States
| | - Hao-Bo Guo
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Sara S. Jawdy
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Lee E. Gunter
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Xiaohan Yang
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | | | | | | - Kelsey Yee
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Miguel Rodriguez
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert W. Sykes
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Stephen R. Decker
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Mark F. Davis
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Arthur J. Ragauskas
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Gerald A. Tuskan
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Udaya C. Kalluri
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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25
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Zhao L, Huang Y, Keller AA. Comparative Metabolic Response between Cucumber ( Cucumis sativus) and Corn ( Zea mays) to a Cu(OH) 2 Nanopesticide. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:6628-6636. [PMID: 28493687 DOI: 10.1021/acs.jafc.7b01306] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Due to their unique properties, copper-based nanopesticides are emerging in the market. Thus, understanding their effect on crop plants is very important. Metabolomics can capture a snapshot of cellular metabolic responses to a stressor. We selected maize and cucumber as model plants for exposure to different doses of Cu(OH)2 nanopesticide. GC-TOF-MS-based metabolomics was employed to determine the metabolic responses of these two species. Results revealed significant differences in metabolite profile changes between maize and cucumber. Furthermore, the Cu(OH)2 nanopesticide induced metabolic reprogramming in both species, but in different manners. In maize, several intermediate metabolites of the glycolysis pathway and tricarboxylic acid cycle (TCA) were up-regulated, indicating the energy metabolism was activated. In addition, the levels of aromatic compounds (4-hydroxycinnamic acid and 1,2,4-benzenetriol) and their precursors (phenylalanine, tyrosine) were enhanced, indicating the activation of shikimate-phenylpropanoid biosynthesis in maize leaves, which is an antioxidant defense-related pathway. In cucumber, arginine and proline metabolic pathways were the most significantly altered pathway. Both species exhibited altered levels of fatty acids and polysaccharides, suggesting the cell membrane and cell wall composition may change in response to Cu(OH)2 nanopesticide. Thus, metabolomics helps to deeply understand the differential response of these plants to the same nanopesticide stressor.
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Affiliation(s)
- Lijuan Zhao
- Bren School of Environmental Science & Management , University of California , Santa Barbara , California 93106-5131 , United States
- Center for Environmental Implications of Nanotechnology , University of California , Santa Barbara , California 93106-5131 , United States
| | - Yuxiong Huang
- Bren School of Environmental Science & Management , University of California , Santa Barbara , California 93106-5131 , United States
- Center for Environmental Implications of Nanotechnology , University of California , Santa Barbara , California 93106-5131 , United States
| | - Arturo A Keller
- Bren School of Environmental Science & Management , University of California , Santa Barbara , California 93106-5131 , United States
- Center for Environmental Implications of Nanotechnology , University of California , Santa Barbara , California 93106-5131 , United States
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26
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Xie M, Muchero W, Bryan AC, Yee K, Guo HB, Zhang J, Tschaplinski TJ, Singan VR, Lindquist E, Payyavula RS, Barros-Rios J, Dixon R, Engle N, Sykes RW, Davis M, Jawdy SS, Gunter LE, Thompson O, DiFazio SP, Evans LM, Winkeler K, Collins C, Schmutz J, Guo H, Kalluri U, Rodriguez M, Feng K, Chen JG, Tuskan GA. A 5-Enolpyruvylshikimate 3-Phosphate Synthase Functions as a Transcriptional Repressor in Populus. THE PLANT CELL 2018; 30:1645-1660. [PMID: 29891568 PMCID: PMC6096593 DOI: 10.1105/tpc.18.00168] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 04/17/2018] [Accepted: 06/05/2018] [Indexed: 05/21/2023]
Abstract
Long-lived perennial plants, with distinctive habits of inter-annual growth, defense, and physiology, are of great economic and ecological importance. However, some biological mechanisms resulting from genome duplication and functional divergence of genes in these systems remain poorly studied. Here, we discovered an association between a poplar (Populus trichocarpa) 5-enolpyruvylshikimate 3-phosphate synthase gene (PtrEPSP) and lignin biosynthesis. Functional characterization of PtrEPSP revealed that this isoform possesses a helix-turn-helix motif in the N terminus and can function as a transcriptional repressor that regulates expression of genes in the phenylpropanoid pathway in addition to performing its canonical biosynthesis function in the shikimate pathway. We demonstrated that this isoform can localize in the nucleus and specifically binds to the promoter and represses the expression of a SLEEPER-like transcriptional regulator, which itself specifically binds to the promoter and represses the expression of PtrMYB021 (known as MYB46 in Arabidopsis thaliana), a master regulator of the phenylpropanoid pathway and lignin biosynthesis. Analyses of overexpression and RNAi lines targeting PtrEPSP confirmed the predicted changes in PtrMYB021 expression patterns. These results demonstrate that PtrEPSP in its regulatory form and PtrhAT form a transcriptional hierarchy regulating phenylpropanoid pathway and lignin biosynthesis in Populus.
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Affiliation(s)
- Meng Xie
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Wellington Muchero
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Anthony C Bryan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Kelsey Yee
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Hao-Bo Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Jin Zhang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Timothy J Tschaplinski
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Vasanth R Singan
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Erika Lindquist
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Raja S Payyavula
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Jaime Barros-Rios
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76203
| | - Richard Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76203
| | - Nancy Engle
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Robert W Sykes
- Bioscience Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Mark Davis
- Bioscience Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Sara S Jawdy
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Lee E Gunter
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Olivia Thompson
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, West Virginia 26506
| | - Luke M Evans
- Department of Biology, West Virginia University, Morgantown, West Virginia 26506
| | | | | | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Udaya Kalluri
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Miguel Rodriguez
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Kai Feng
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Jin-Gui Chen
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Gerald A Tuskan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
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27
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Cotrim CA, Soares JSM, Kobe B, Menossi M. Crystal structure and insights into the oligomeric state of UDP-glucose pyrophosphorylase from sugarcane. PLoS One 2018; 13:e0193667. [PMID: 29494650 PMCID: PMC5832301 DOI: 10.1371/journal.pone.0193667] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/15/2018] [Indexed: 12/19/2022] Open
Abstract
UDP-glucose pyrophosphorylase (UGPase) is found in all organisms and catalyses the formation of UDP-glucose. In sugarcane, UDP-glucose is a branch-point in the carbon channelling into other carbohydrates, such as sucrose and cellulose, which are the major factors for sugarcane productivity. In most plants, UGPase has been described to be enzymatically active in the monomeric form, while in human and yeast, homo-octamers represent the active form of the protein. Here, we present the crystal structure of UGPase from sugarcane (ScUGPase-1) at resolution of 2.0 Å. The crystals of ScUGPase-1 reveal the presence of two molecules in the asymmetric unit and the multi-angle light scattering analysis shows that ScUGPase-1 forms a mixture of species ranging from monomers to larger oligomers in solution, suggesting similarities with the orthologs from yeast and human.
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Affiliation(s)
- Camila A. Cotrim
- School of Chemistry and Molecular Bioscience and Australia Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
- * E-mail: (MM); (CAC)
| | - Jose Sergio M. Soares
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Bostjan Kobe
- School of Chemistry and Molecular Bioscience and Australia Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Marcelo Menossi
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- * E-mail: (MM); (CAC)
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28
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Decker D, Öberg C, Kleczkowski LA. The structure-activity relationship of the salicylimide derived inhibitors of UDP-sugar producing pyrophosphorylases. PLANT SIGNALING & BEHAVIOR 2018; 13:e1507406. [PMID: 30125142 PMCID: PMC6149491 DOI: 10.1080/15592324.2018.1507406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 07/31/2018] [Indexed: 05/18/2023]
Abstract
UDP-sugars are key precursors for biomass production in nature (synthesis of cellulose, hemicellulose, etc.). They are produced de novo by distinct UDP-sugar producing pyrophosphorylases. Studies on the roles of these enzymes using genetic knockouts were hampered by sterility of the mutants and by functional-complementation from related enzyme(s), hindering clear interpretation of the results. In an attempt to override these difficulties, we turned to the reverse chemical genetics approaches to identify compounds which interfere with the activity of those enzymes in vivo. Hit expansion on one of such compounds, a salicylimide derivative, allowed us to identify several inhibitors with a range of activities. The present study provides a structure-activity relationship for these compounds.
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Affiliation(s)
- Daniel Decker
- Department of Plant Physiology, Umeå Plant Science Center, Umeå University, Umeå, Sweden
- CONTACT Leszek A. Kleczkowski Department of Plant Physiology, Umeå Plant Science Center, Umeå University, 90187 Umeå, Sweden
| | - Christopher Öberg
- Laboratories for Chemical Biology Umeå, Department of Chemistry, Umeå University, Umeå, Sweden
| | - Leszek A. Kleczkowski
- Department of Plant Physiology, Umeå Plant Science Center, Umeå University, Umeå, Sweden
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29
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Ning K, Ding C, Zhu W, Zhang W, Dong Y, Shen Y, Su X. Comparative Metabolomic Analysis of the Cambium Tissue of Non-transgenic and Multi-Gene Transgenic Poplar ( Populus × euramericana 'Guariento'). FRONTIERS IN PLANT SCIENCE 2018; 9:1201. [PMID: 30174679 PMCID: PMC6108131 DOI: 10.3389/fpls.2018.01201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 07/26/2018] [Indexed: 05/09/2023]
Abstract
Poplar, a model for woody plant research, is the most widely distributed tree species in the world. Metabolites are the basis of phenotypes, allowing an intuitive and effective understanding of biological processes and their mechanisms. However, metabolites in non-transgenic and multi-gene transgenic poplar remains poorly characterized, especially in regards of the influences on quantity and in the analysis of the relative abundance of metabolites after the introduction of multi stress-related genes. In this study, we investigated the cambium metabolomes of one non-transgenic (D5-0) and two multi-gene (vgb, SacB, ERF36, BtCry3A, and OC-I) transgenic lines (D5-20 and D5-21) of hybrid poplar (Populus × euramericana 'Guariento') using both gas chromatography-mass spectrometry (GC-MS) and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). We aimed to explore the effects of the exogenous genes on metabolite composition and to screen out metabolites with important biological functions. Finally, we identified 239 named metabolites and determined their relative abundance. Among these, 197 metabolites had a different abundance across the three lines. These methabolites spanned nine primary and 44 secondary metabolism pathways. Arginine and glutamate, as substrates and intermediates in nitrogen metabolism, and important in growth and stress-related processes, as well as sucrose, uridine diphosphate glucose, and their derivatives, precursors in cell wall pathways, and catechol, relevant to insect resistance, differed greatly between the genetically modified and non-transgenic poplar. These findings may provide a basis for further study of cambium metabolism, and fully understand metabolites associated with stress response.
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Affiliation(s)
- Kun Ning
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing, China
| | - Yufeng Dong
- Shandong Provincial Key Laboratory of Forest Tree Genetic Improvement, Shandong Academy of Forestry, Jinan, China
| | - Yingbai Shen
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- *Correspondence: Xiaohua Su,
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30
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Gilna P, Lynd LR, Mohnen D, Davis MF, Davison BH. Progress in understanding and overcoming biomass recalcitrance: a BioEnergy Science Center (BESC) perspective. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:285. [PMID: 29213324 PMCID: PMC5707806 DOI: 10.1186/s13068-017-0971-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/15/2017] [Indexed: 06/07/2023]
Abstract
The DOE BioEnergy Science Center has operated as a virtual center with multiple partners for a decade targeting overcoming biomass recalcitrance. BESC has redefined biomass recalcitrance from an observable phenotype to a better understood and manipulatable fundamental and operational property. These manipulations are the result of deeper biological understanding and can be combined with other advanced biotechnology improvements in biomass conversion to improve bioenergy processes and markets. This article provides an overview of key accomplishments in overcoming recalcitrance via better plants, better microbes, and better tools and combinations. A perspective on the aspects of successful center operation is presented.
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Affiliation(s)
- Paul Gilna
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Bldg. 1505, Rm. 100A, Oak Ridge, TN 37831-6037 USA
| | - Lee R. Lynd
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Bldg. 1505, Rm. 100A, Oak Ridge, TN 37831-6037 USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
| | - Debra Mohnen
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Bldg. 1505, Rm. 100A, Oak Ridge, TN 37831-6037 USA
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Mark F. Davis
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Bldg. 1505, Rm. 100A, Oak Ridge, TN 37831-6037 USA
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Brian H. Davison
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Bldg. 1505, Rm. 100A, Oak Ridge, TN 37831-6037 USA
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31
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Cao LY, Li XX, Wang D, Sun HF, Gao JP. Validation of Reliable Reference Genes for Accurate Normalization in RT-qPCR Analysis of Codonopsis pilosula. CHINESE HERBAL MEDICINES 2017. [DOI: 10.1016/s1674-6384(17)60099-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Yang Y, Yoo CG, Guo HB, Rottmann W, Winkeler KA, Collins CM, Gunter LE, Jawdy SS, Yang X, Guo H, Pu Y, Ragauskas AJ, Tuskan GA, Chen JG. Overexpression of a Domain of Unknown Function 266-containing protein results in high cellulose content, reduced recalcitrance, and enhanced plant growth in the bioenergy crop Populus. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:74. [PMID: 28344649 PMCID: PMC5364563 DOI: 10.1186/s13068-017-0760-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 03/18/2017] [Indexed: 05/17/2023]
Abstract
BACKGROUND Domain of Unknown Function 266 (DUF266) is a plant-specific domain. DUF266-containing proteins (DUF266 proteins) have been categorized as 'not classified glycosyltransferases (GTnc)' due to amino acid similarity with GTs. However, little is known about the function of DUF266 proteins. RESULTS Phylogenetic analysis revealed that DUF266 proteins are only present in the land plants including moss and lycophyte. We report the functional characterization of one member of DUF266 proteins in Populus, PdDUF266A. PdDUF266A was ubiquitously expressed with high abundance in the xylem. In Populus transgenic plants overexpressing PdDUF266A (OXPdDUF266A), the glucose and cellulose contents were significantly higher, while the lignin content was lower than that in the wild type. Degree of polymerization of cellulose in OXPdDUF266A transgenic plants was also higher, whereas cellulose crystallinity index remained unchanged. Gene expression analysis indicated that cellulose biosynthesis-related genes such as CESA and SUSY were upregulated in mature leaf and xylem of OXPdDUF266A transgenic plants. Moreover, PdDUF266A overexpression resulted in an increase of biomass production. Their glucose contents and biomass phenotypes were further validated via heterologous expression of PdDUF266A in Arabidopsis. Results from saccharification treatment demonstrated that the rate of sugar release was increased by approximately 38% in the OXPdDUF266A transgenic plants. CONCLUSIONS These results suggest that the overexpression of PdDUF266A can increase cellulose content, reduce recalcitrance, and enhance biomass production, and that PdDUF266A is a promising target for genetic manipulation for biofuel production.
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Affiliation(s)
- Yongil Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Chang Geun Yoo
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Hao-Bo Guo
- Department of Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996 USA
| | | | | | | | - Lee E. Gunter
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sara S. Jawdy
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Xiaohan Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Hong Guo
- Department of Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996 USA
| | - Yunqiao Pu
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Arthur J. Ragauskas
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering & Department of Forestry, Wildlife, and Fisheries, University of Tennessee, Knoxville, TN 37996 USA
| | - Gerald A. Tuskan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Jin-Gui Chen
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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Yang Y, Yoo CG, Winkeler KA, Collins CM, Hinchee MAW, Jawdy SS, Gunter LE, Engle NL, Pu Y, Yang X, Tschaplinski TJ, Ragauskas AJ, Tuskan GA, Chen JG. Overexpression of a Domain of Unknown Function 231-containing protein increases O-xylan acetylation and cellulose biosynthesis in Populus. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:311. [PMID: 29299061 PMCID: PMC5744390 DOI: 10.1186/s13068-017-0998-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/14/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Domain of Unknown Function 231-containing proteins (DUF231) are plant specific and their function is largely unknown. Studies in the model plants Arabidopsis and rice suggested that some DUF231 proteins act in the process of O-acetyl substitution of hemicellulose and esterification of pectin. However, little is known about the function of DUF231 proteins in woody plant species. RESULTS This study provides evidence supporting that one member of DUF231 family proteins in the woody perennial plant Populus deltoides (genotype WV94), PdDUF231A, has a role in the acetylation of xylan and affects cellulose biosynthesis. A total of 52 DUF231-containing proteins were identified in the Populus genome. In P. deltoides transgenic lines overexpressing PdDUF231A (OXPdDUF231A), glucose and cellulose contents were increased. Consistent with these results, the transcript levels of cellulose biosynthesis-related genes were increased in the OXPdDUF231A transgenic lines. Furthermore, the relative content of total acetylated xylan was increased in the OXPdDUF231A transgenic lines. Enzymatic saccharification assays revealed that the rate of glucose release increased in OXPdDUF231A transgenic lines. Plant biomass productivity was also increased in OXPdDUF231A transgenic lines. CONCLUSIONS These results suggest that PdDUF231A affects cellulose biosynthesis and plays a role in the acetylation of xylan. PdDUF231A is a promising target for genetic modification for biofuel production because biomass productivity and compositional quality can be simultaneously improved through overexpression.
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Affiliation(s)
- Yongil Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Chang Geun Yoo
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | | | | | | | - Sara S. Jawdy
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Lee E. Gunter
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Nancy L. Engle
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Yunqiao Pu
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Xiaohan Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Timothy J. Tschaplinski
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Arthur J. Ragauskas
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996 USA
- Department of Forestry, Wildlife, and Fisheries, University of Tennessee, Knoxville, TN 37996 USA
| | - Gerald A. Tuskan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Jin-Gui Chen
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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Kalluri UC, Payyavula RS, Labbé JL, Engle N, Bali G, Jawdy SS, Sykes RW, Davis M, Ragauskas A, Tuskan GA, Tschaplinski TJ. Down-Regulation of KORRIGAN-Like Endo-β-1,4-Glucanase Genes Impacts Carbon Partitioning, Mycorrhizal Colonization and Biomass Production in Populus. FRONTIERS IN PLANT SCIENCE 2016; 7:1455. [PMID: 27757116 PMCID: PMC5047894 DOI: 10.3389/fpls.2016.01455] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/12/2016] [Indexed: 05/17/2023]
Abstract
A greater understanding of the genetic regulation of plant cell wall remodeling and the impact of modified cell walls on plant performance is important for the development of sustainable biofuel crops. Here, we studied the impact of down-regulating KORRIGAN-like cell wall biosynthesis genes, belonging to the endo-β-1,4-glucanase gene family, on Populus growth, metabolism and the ability to interact with symbiotic microbes. The reductions in cellulose content and lignin syringyl-to-guaiacyl unit ratio, and increase in cellulose crystallinity of cell walls of PdKOR RNAi plants corroborated the functional role of PdKOR in cell wall biosynthesis. Altered metabolism and reduced growth characteristics of RNAi plants revealed new implications on carbon allocation and partitioning. The distinctive metabolome phenotype comprised of a higher phenolic and salicylic acid content, and reduced lignin, shikimic acid and maleic acid content relative to control. Plant sustainability implications of modified cell walls on beneficial plant-microbe interactions were explored via co-culture with an ectomycorrhizal fungus, Laccaria bicolor. A significant increase in the mycorrhization rate was observed in transgenic plants, leading to measurable beneficial growth effects. These findings present new evidence for functional interconnectedness of cellulose biosynthesis pathway, metabolism and mycorrhizal association in plants, and further emphasize the consideration of the sustainability implications of plant trait improvement efforts.
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Affiliation(s)
- Udaya C. Kalluri
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak RidgeTN, USA
| | - Raja S. Payyavula
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak RidgeTN, USA
| | - Jessy L. Labbé
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak RidgeTN, USA
| | - Nancy Engle
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak RidgeTN, USA
| | - Garima Bali
- BioEnergy Science Center, School of Chemistry and Biochemistry, Institute of Paper Science and Technology, Georgia Institute of Technology, AtlantaGA, USA
| | - Sara S. Jawdy
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak RidgeTN, USA
| | - Robert W. Sykes
- The Biosciences Center, National Renewable Energy Laboratory, GoldenCO, USA
| | - Mark Davis
- The Biosciences Center, National Renewable Energy Laboratory, GoldenCO, USA
| | - Arthur Ragauskas
- Oak Ridge National Laboratory – Department of Chemical and Biomolecular Engineering and Department of Forestry, Wildlife and Fisheries, University of Tennessee, KnoxvilleTN, USA
| | - Gerald A. Tuskan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak RidgeTN, USA
| | - Timothy J. Tschaplinski
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak RidgeTN, USA
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Chen Y, Chen C, Tan Z, Liu J, Zhuang L, Yang Z, Huang B. Functional Identification and Characterization of Genes Cloned from Halophyte Seashore Paspalum Conferring Salinity and Cadmium Tolerance. FRONTIERS IN PLANT SCIENCE 2016; 7:102. [PMID: 26904068 PMCID: PMC4746305 DOI: 10.3389/fpls.2016.00102] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/19/2016] [Indexed: 05/25/2023]
Abstract
Salinity-affected and heavy metal-contaminated soils limit the growth of glycophytic plants. Identifying genes responsible for superior tolerance to salinity and heavy metals in halophytes has great potential for use in developing salinity- and Cd-tolerant glycophytes. The objective of this study was to identify salinity- and Cd-tolerance related genes in seashore paspalum (Paspalum vaginatum), a halophytic perennial grass species, using yeast cDNA expression library screening method. Based on the Gateway-compatible vector system, a high-quality entry library was constructed, which contained 9.9 × 10(6) clones with an average inserted fragment length of 1.48 kb representing a 100% full-length rate. The yeast expression libraries were screened in a salinity-sensitive and a Cd-sensitive yeast mutant. The screening yielded 32 salinity-tolerant clones harboring 18 salinity-tolerance genes and 20 Cd-tolerant clones, including five Cd-tolerance genes. qPCR analysis confirmed that most of the 18 salinity-tolerance and five Cd-tolerance genes were up-regulated at the transcript level in response to salinity or Cd stress in seashore paspalum. Functional analysis indicated that salinity-tolerance genes from seashore paspalum could be involved mainly in photosynthetic metabolism, antioxidant systems, protein modification, iron transport, vesicle traffic, and phospholipid biosynthesis. Cd-tolerance genes could be associated with regulating pathways that are involved in phytochelatin synthesis, HSFA4-related stress protection, CYP450 complex, and sugar metabolism. The 18 salinity-tolerance genes and five Cd-tolerance genes could be potentially used as candidate genes for genetic modification of glycophytic grass species to improve salinity and Cd tolerance and for further analysis of molecular mechanisms regulating salinity and Cd tolerance.
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Affiliation(s)
- Yu Chen
- Department of Turfgrass Science, College of Agro-Grassland Science, Nanjing Agricultural UniversityNanjing, China
| | - Chuanming Chen
- Department of Turfgrass Science, College of Agro-Grassland Science, Nanjing Agricultural UniversityNanjing, China
| | - Zhiqun Tan
- Department of Turfgrass Science, College of Agro-Grassland Science, Nanjing Agricultural UniversityNanjing, China
| | - Jun Liu
- Department of Turfgrass Science, College of Agro-Grassland Science, Nanjing Agricultural UniversityNanjing, China
| | - Lili Zhuang
- Department of Turfgrass Science, College of Agro-Grassland Science, Nanjing Agricultural UniversityNanjing, China
| | - Zhimin Yang
- Department of Turfgrass Science, College of Agro-Grassland Science, Nanjing Agricultural UniversityNanjing, China
| | - Bingru Huang
- Department of Plant Biology and Pathology, Rutgers, The State University of New JerseyNew Brunswick, NJ, USA
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Gayen D, Ghosh S, Paul S, Sarkar SN, Datta SK, Datta K. Metabolic Regulation of Carotenoid-Enriched Golden Rice Line. FRONTIERS IN PLANT SCIENCE 2016; 7:1622. [PMID: 27840631 PMCID: PMC5083848 DOI: 10.3389/fpls.2016.01622] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/13/2016] [Indexed: 05/21/2023]
Abstract
Vitamin A deficiency (VAD) is the leading cause of blindness among children and is associated with high risk of maternal mortality. In order to enhance the bioavailability of vitamin A, high carotenoid transgenic golden rice has been developed by manipulating enzymes, such as phytoene synthase (psy) and phytoene desaturase (crtI). In this study, proteome and metabolite analyses were carried out to comprehend metabolic regulation and adaptation of transgenic golden rice after the manipulation of endosperm specific carotenoid pathways. The main alteration was observed in carbohydrate metabolism pathways of the transgenic seeds. The 2D based proteomic studies demonstrated that carbohydrate metabolism-related enzymes, such as pullulanase, UDP-glucose pyrophosphorylase, and glucose-1-phosphate adenylyltransferase, were primarily up-regulated in transgenic rice seeds. In addition, the enzyme PPDK was also elevated in transgenic seeds thus enhancing pyruvate biosynthesis, which is the precursor in the carotenoids biosynthetic pathway. GC-MS based metabolite profiling demonstrated an increase in the levels of glyceric acid, fructo-furanose, and galactose, while decrease in galactonic acid and gentiobiose in the transgenic rice compared to WT. It is noteworthy to mention that the carotenoid content, especially β-carotene level in transgenic rice (4.3 μg/g) was significantly enhanced. The present study highlights the metabolic adaptation process of a transgenic golden rice line (homozygous T4 progeny of SKBR-244) after enhancing carotenoid biosynthesis. The presented information would be helpful in the development of crops enriched in carotenoids by expressing metabolic flux of pyruvate biosynthesis.
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Affiliation(s)
- Dipak Gayen
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
- National Institute of Plant Genome ResearchNew Delhi, India
| | - Subhrajyoti Ghosh
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
| | - Soumitra Paul
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
| | - Sailendra N. Sarkar
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
| | - Swapan K. Datta
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
- Department of Crop Sciences, Institute of Agriculture, Visva Bharati UniversitySantiniketan, India
| | - Karabi Datta
- Laboratory for Translational Research on Transgenic Crops, Department of Botany, University of CalcuttaKolkata, India
- *Correspondence: Karabi Datta
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Sucrose metabolism gene families and their biological functions. Sci Rep 2015; 5:17583. [PMID: 26616172 PMCID: PMC4663468 DOI: 10.1038/srep17583] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/02/2015] [Indexed: 01/30/2023] Open
Abstract
Sucrose, as the main product of photosynthesis, plays crucial roles in plant development. Although studies on general metabolism pathway were well documented, less information is available on the genome-wide identification of these genes, their expansion and evolutionary history as well as their biological functions. We focused on four sucrose metabolism related gene families including sucrose synthase, sucrose phosphate synthase, sucrose phosphate phosphatase and UDP-glucose pyrophosphorylase. These gene families exhibited different expansion and evolutionary history as their host genomes experienced differentiated rates of the whole genome duplication, tandem and segmental duplication, or mobile element mediated gene gain and loss. They were evolutionarily conserved under purifying selection among species and expression divergence played important roles for gene survival after expansion. However, we have detected recent positive selection during intra-species divergence. Overexpression of 15 sorghum genes in Arabidopsis revealed their roles in biomass accumulation, flowering time control, seed germination and response to high salinity and sugar stresses. Our studies uncovered the molecular mechanisms of gene expansion and evolution and also provided new insight into the role of positive selection in intra-species divergence. Overexpression data revealed novel biological functions of these genes in flowering time control and seed germination under normal and stress conditions.
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Liu J, Hai G, Wang C, Cao S, Xu W, Jia Z, Yang C, Wang JP, Dai S, Cheng Y. Comparative proteomic analysis of Populus trichocarpa early stem from primary to secondary growth. J Proteomics 2015; 126:94-108. [DOI: 10.1016/j.jprot.2015.05.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 05/20/2015] [Accepted: 05/21/2015] [Indexed: 01/01/2023]
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Kleczkowski LA, Decker D. Sugar Activation for Production of Nucleotide Sugars as Substrates for Glycosyltransferases in Plants. J Appl Glycosci (1999) 2015. [DOI: 10.5458/jag.jag.jag-2015_003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
| | - Daniel Decker
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University
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