1
|
Han T, Mi Z, Chen Z, Zhao J, Zhang H, Lv Y, Du S, Bu R, Zhou J, Li X, Sun Z, Chen Z, Song Y, Zhang J, Hao R, Ge S. Multi-omics analysis reveals the influence of tetracycline on the growth of ryegrass root. JOURNAL OF HAZARDOUS MATERIALS 2022; 435:129019. [PMID: 35523093 DOI: 10.1016/j.jhazmat.2022.129019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/15/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Environmental factors, including antibiotics such as tetracycline, can alter biological processes in plants. To ascertain how cell/tissue response to tetracycline, a multi-omic analysis was implemented to explore the molecular mechanism of tetracycline influencing the growth of ryegrass root. Tetracycline induced extensive changes in the root metabolome in plants, particularly impacting metabolites of flavonoid metabolic pathways, which were supported through consistent differences between transcriptome and proteome. Cross-comparison between mRNA and protein contents considered the authentication of congruence with related metabolites and revealed changes of several biological processes under tetracycline stress. Overall, we present an undemanding multi-omic strategy to survey the significant influence on the root under tetracycline stress.
Collapse
Affiliation(s)
- Tao Han
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Henan Institute of Science and Technology, Xinxiang 453003, China; Postdoctoral Research Station, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhaorong Mi
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Zhe Chen
- College of Life Science, Qinghai Normal University, Xining 810008, China
| | - Jinjin Zhao
- The First Affiliated Hospital of Xinxiang Medical University, Weihui 453100, China
| | - Haiguang Zhang
- The First Affiliated Hospital of Xinxiang Medical University, Weihui 453100, China
| | - Yang Lv
- Shanghai Fengyuan Biotechnology Limited Company, Shanghai 200240, China
| | - Shouyang Du
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Ruifang Bu
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Junguo Zhou
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Xinzheng Li
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Zhiqiang Sun
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhuo Chen
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yiting Song
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Jun Zhang
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Ruijuan Hao
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Shidong Ge
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China.
| |
Collapse
|
2
|
Li Y, Xiong W, He F, Qi T, Sun Z, Liu Y, Bai S, Wang H, Wu Z, Fu C. Down-regulation of PvSAMS impairs S-adenosyl-L-methionine and lignin biosynthesis, and improves cell wall digestibility in switchgrass. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4157-4169. [PMID: 35383829 DOI: 10.1093/jxb/erac147] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
S-adenosyl- l-methionine (SAM) is the methyl donor involved in the biosynthesis of guaiacyl (G) and syringyl (S) lignins in vascular plants. SAM is synthesized from methionine through the catalysis of the enzyme S-adenosylmethionine synthase (SAMS). However, the detailed function of SAMS in lignin biosynthesis has not been widely investigated in plants, particularly in monocot species. In this study, we identified PvSAMS genes from switchgrass (Panicum virgatum L.), an important dual-purpose fodder and biofuel crop, and generated numerous transgenic switchgrass lines through PvSAMS RNA interference technology. Down-regulation of PvSAMS reduced the contents of SAM, G-lignins, and S-lignins in the transgenic switchgrass. The methionine and glucoside derivatives of caffeoyl alcohol were found to accumulate in the transgenic plants. Moreover, down-regulation of PvSAMS in switchgrass resulted in brownish stems associated with reduced lignin content and improved cell wall digestibility. Furthermore, transcriptomic analysis revealed that most sulfur deficiency-responsive genes were differentially expressed in the transgenic switchgrass, leading to a significant increase in total sulfur content; thus implying an important role of SAMS in the methionine cycle, lignin biosynthesis, and sulfur assimilation. Taken together, our results suggest that SAMS is a valuable target in lignin manipulation, and that manipulation of PvSAMS can simultaneously regulate the biosynthesis of SAM and methylated monolignols in switchgrass.
Collapse
Affiliation(s)
- Yu Li
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wangdan Xiong
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Feng He
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Tianxiong Qi
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Zhen Sun
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuchen Liu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu, 611731, China
| | - Honglun Wang
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Zhenying Wu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunxiang Fu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| |
Collapse
|
3
|
Mishra M, Rathore RS, Singla‐Pareek SL, Pareek A. High lysine and high protein‐containing salinity‐tolerant rice grains (
Oryza sativa cv
IR64). Food Energy Secur 2022. [DOI: 10.1002/fes3.343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Manjari Mishra
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
| | - Ray Singh Rathore
- Plant Stress Biology Laboratory International Centre for Genetic Engineering and Biotechnology New Delhi India
| | - Sneh L Singla‐Pareek
- Plant Stress Biology Laboratory International Centre for Genetic Engineering and Biotechnology New Delhi India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
- National Agri‐Food Biotechnology Institute Punjab India
| |
Collapse
|
4
|
Rao S, Yu T, Cong X, Xu F, Lai X, Zhang W, Liao Y, Cheng S. Integration analysis of PacBio SMRT- and Illumina RNA-seq reveals candidate genes and pathway involved in selenium metabolism in hyperaccumulator Cardamine violifolia. BMC PLANT BIOLOGY 2020; 20:492. [PMID: 33109081 PMCID: PMC7590678 DOI: 10.1186/s12870-020-02694-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/12/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Cardamine violifolia, native to China, is one of the selenium (Se) hyperaccumulators. The mechanism of Se metabolism and tolerance remains unclear, and only limited genetic information is currently available. Therefore, we combined a PacBio single-molecule real-time (SMRT) transcriptome library and the Illumina RNA-seq data of sodium selenate (Na2SeO4)-treated C. violifolia to further reveal the molecular mechanism of Se metabolism. RESULTS The concentrations of the total, inorganic, and organic Se in C. violifolia seedlings significantly increased as the Na2SeO4 treatment concentration increased. From SMRT full-length transcriptome of C. violifolia, we obtained 26,745 annotated nonredundant transcripts, 14,269 simple sequence repeats, 283 alternative splices, and 3407 transcription factors. Fifty-one genes from 134 transcripts were identified to be involved in Se metabolism, including transporter, assimilatory enzyme, and several specific genes. Analysis of Illumina RNA-Seq data showed that a total of 948 differentially expressed genes (DEGs) were filtered from the four groups with Na2SeO4 treatment, among which 11 DEGs were related to Se metabolism. The enrichment analysis of KEGG pathways of all the DEGs showed that they were significantly enriched in five pathways, such as hormone signal transduction and plant-pathogen interaction pathways. Four genes related to Se metabolism, adenosine triphosphate sulfurase 1, adenosine 5'-phosphosulfate reductase 3, cysteine (Cys) desulfurase 1, and serine acetyltransferase 2, were regulated by lncRNAs. Twenty potential hub genes (e.g., sulfate transporter 1;1, Cys synthase, methionine gamma-lyase, and Se-binding protein 1) were screened and identified to play important roles in Se accumulation and tolerance in C. violifolia as concluded by weighted gene correlation network analysis. Based on combinative analysis of expression profiling and annotation of genes as well as Se speciation and concentration in C. violifolia under the treatments with different Na2SeO4 concentrations, a putative Se metabolism and assimilation pathway in C. violifolia was proposed. CONCLUSION Our data provide abundant information on putative gene transcriptions and pathway involved in Se metabolism of C. violifolia. The findings present a genetic resource and provide novel insights into the mechanism of Se hyperaccumulation in C. violifolia.
Collapse
Affiliation(s)
- Shen Rao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 China
| | - Tian Yu
- National R&D for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, 430023 China
- Enshi Se-Run Health Tech Development Co., Ltd, Enshi, 445000 China
| | - Xin Cong
- National R&D for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, 430023 China
- Enshi Se-Run Health Tech Development Co., Ltd, Enshi, 445000 China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 China
| | - Xiaozhuo Lai
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025 China
| | - Shuiyuan Cheng
- National R&D for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, 430023 China
- National Selenium Rich Product Quality Supervision and Inspection Center, Enshi, 445000 Hubei China
| |
Collapse
|
5
|
Zhao X, Yuan X, Chen S, Meng L, Fu D. Role of the tomato TAGL1 gene in regulating fruit metabolites elucidated using RNA sequence and metabolomics analyses. PLoS One 2018; 13:e0199083. [PMID: 29894500 PMCID: PMC5997326 DOI: 10.1371/journal.pone.0199083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 05/31/2018] [Indexed: 01/08/2023] Open
Abstract
Fruit ripening is a complex biological process affecting fruit quality. In tomato the fruit ripening process is delicately regulated by transcription factors (TFs). Among these, the TOMATO AGAMOUS-LIKE 1 (TAGL1) gene plays an important role in both the development and ripening of fruit. In this study, the TAGL1 gene was successfully silenced by virus-induced gene silencing technology (VIGS), and the global gene expression and metabolites profiles of TAGL1-silenced fruits were analyzed by RNA-sequence analysis (RNA-seq) and liquid chromatography-mass spectrometry (LC-MS/MS). The TAGL1-silenced fruits phenotypically displayed an orange pericarp, which was in accordance with the results expected from the down-regulation of genes associated with carotenoid synthesis. Levels of several amino acids and organic acids were lower in the TAGL1-silenced fruits than in the wild-type fruits, whereas, α-tomatine content was greatly increased (more than 10-fold) in the TAGL1-silenced fruits compared to wild-type fruits. The findings of this study showed that TAGL1 not only regulates the ripening of tomato fruits, but also affects the synthesis and levels of nutrients in the fruit.
Collapse
Affiliation(s)
- Xiaodan Zhao
- School of Food and Chemical Engineering, Beijing Technology and Business University, Haidian District, Beijing, China
- * E-mail:
| | - Xinyu Yuan
- Laboratory of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Haidian District, Beijing, China
| | - Sha Chen
- Institute of Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanhuan Meng
- Laboratory of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Haidian District, Beijing, China
| | - Daqi Fu
- Laboratory of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Haidian District, Beijing, China
| |
Collapse
|
6
|
Zheng J, Chen L, Liu L, Li H, Liu B, Zheng D, Liu T, Dong J, Sun L, Zhu Y, Yang J, Zhang X, Jin Q. Proteogenomic Analysis and Discovery of Immune Antigens in Mycobacterium vaccae. Mol Cell Proteomics 2017; 16:1578-1590. [PMID: 28733429 DOI: 10.1074/mcp.m116.065813] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 07/05/2017] [Indexed: 11/06/2022] Open
Abstract
Tuberculosis (TB) is one of the leading causes of death worldwide, especially in developing countries. Neonatal BCG vaccination occurs in various regions, but the level of protection varies in different populations. Recently, Mycobacterium vaccae is found to be an immunomodulating therapeutic agent that could confer a significant level of protection against TB. It is the only vaccine in a phase III trial from WHO to assess its efficacy and safety in preventing TB disease in people with latent TB infection. However, the mechanism of immunotherapy of M. vaccae remains poorly understood. In this study, the full genome of M. vaccae was obtained by next-generation sequencing technology, and a proteogenomic approach was successfully applied to further perform genome annotation using high resolution and high accuracy MS data. A total of 3,387 proteins (22,508 unique peptides) were identified, and 581 proteins annotated as hypothetical proteins in the genome database were confirmed. Furthermore, 38 novel protein products not annotated at the genome level were detected and validated. Additionally, the translational start sites of 445 proteins were confirmed, and 98 proteins were validated through extension of their translational start sites based on N terminus-derived peptides. The physicochemical characteristics of the identified proteins were determined. Thirty-five immunogenic proteins of M. vaccae were identified by immunoproteomic analysis, and 20 of them were selected to be expressed and validated by Western blot for immunoreactivity to serum from patients infected with M. tuberculosis The results revealed that eight of them showed strong specific reactive signals on the immunoblots. Furthermore, cellular immune response was further examined and one protein displayed a higher cellular immune level in pulmonary TB patients. Twelve identified immunogenic proteins have orthologous in H37Rv and BCG. This is the first study to obtain the full genome and annotation of M. vaccae using a proteogenomic approach, and some immunogenic proteins that were validated by immunoproteomic analysis could contribute to the understanding of the mechanism of M. vaccae immunotherapy.
Collapse
Affiliation(s)
- Jianhua Zheng
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lihong Chen
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liguo Liu
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haifeng Li
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bo Liu
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dandan Zheng
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Liu
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Dong
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lilian Sun
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yafang Zhu
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jian Yang
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaobing Zhang
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Jin
- ‡From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
7
|
Abstract
To feed the world’s growing population, increasing the yield of crops is not the only important factor, improving crop quality is also important, and it presents a significant challenge. Among the important crops, horticultural crops (particularly fruits and vegetables) provide numerous health compounds, such as vitamins, antioxidants, and amino acids. Essential amino acids are those that cannot be produced by the organism and, therefore, must be obtained from diet, particularly from meat, eggs, and milk, as well as a variety of plants. Extensive efforts have been devoted to increasing the levels of essential amino acids in plants. Yet, these efforts have been met with very little success due to the limited genetic resources for plant breeding and because high essential amino acid content is generally accompanied by limited plant growth. With a deep understanding of the biosynthetic pathways of essential amino acids and their interactions with the regulatory networks in plants, it should be possible to use genetic engineering to improve the essential amino acid content of horticultural plants, rendering these plants more nutritionally favorable crops. In the present report, we describe the recent advances in the enhancement of essential amino acids in horticultural plants and possible future directions towards their bio-fortification.
Collapse
|
8
|
Rennenberg H, Herschbach C. A detailed view on sulphur metabolism at the cellular and whole-plant level illustrates challenges in metabolite flux analyses. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5711-24. [PMID: 25124317 DOI: 10.1093/jxb/eru315] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Understanding the dynamics of physiological process in the systems biology era requires approaches at the genome, transcriptome, proteome, and metabolome levels. In this context, metabolite flux experiments have been used in mapping metabolite pathways and analysing metabolic control. In the present review, sulphur metabolism was taken to illustrate current challenges of metabolic flux analyses. At the cellular level, restrictions in metabolite flux analyses originate from incomplete knowledge of the compartmentation network of metabolic pathways. Transport of metabolites through membranes is usually not considered in flux experiments but may be involved in controlling the whole pathway. Hence, steady-state and snapshot readings need to be expanded to time-course studies in combination with compartment-specific metabolite analyses. Because of species-specific differences, differences between tissues, and stress-related responses, the quantitative significance of different sulphur sinks has to be elucidated; this requires the development of methods for whole-sulphur metabolome approaches. Different cell types can contribute to metabolite fluxes to different extents at the tissue and organ level. Cell type-specific analyses are needed to characterize these contributions. Based on such approaches, metabolite flux analyses can be expanded to the whole-plant level by considering long-distance transport and, thus, the interaction of roots and the shoot in metabolite fluxes. However, whole-plant studies need detailed empirical and mathematical modelling that have to be validated by experimental analyses.
Collapse
Affiliation(s)
- Heinz Rennenberg
- Institute of Forest Sciences, Chair of Tree Physiology, University of Freiburg, Georges-Koehler-Allee 53, 79110 Freiburg, Germany Centre for Biosystems Analysis (ZBSA), University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany
| | - Cornelia Herschbach
- Institute of Forest Sciences, Chair of Tree Physiology, University of Freiburg, Georges-Koehler-Allee 53, 79110 Freiburg, Germany
| |
Collapse
|
9
|
Pratelli R, Pilot G. Regulation of amino acid metabolic enzymes and transporters in plants. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5535-56. [PMID: 25114014 DOI: 10.1093/jxb/eru320] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Amino acids play several critical roles in plants, from providing the building blocks of proteins to being essential metabolites interacting with many branches of metabolism. They are also important molecules that shuttle organic nitrogen through the plant. Because of this central role in nitrogen metabolism, amino acid biosynthesis, degradation, and transport are tightly regulated to meet demand in response to nitrogen and carbon availability. While much is known about the feedback regulation of the branched biosynthesis pathways by the amino acids themselves, the regulation mechanisms at the transcriptional, post-transcriptional, and protein levels remain to be identified. This review focuses mainly on the current state of our understanding of the regulation of the enzymes and transporters at the transcript level. Current results describing the effect of transcription factors and protein modifications lead to a fragmental picture that hints at multiple, complex levels of regulation that control and coordinate transport and enzyme activities. It also appears that amino acid metabolism, amino acid transport, and stress signal integration can influence each other in a so-far unpredictable fashion.
Collapse
Affiliation(s)
- Réjane Pratelli
- Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24060, USA
| | - Guillaume Pilot
- Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24060, USA
| |
Collapse
|
10
|
Co-expression of bacterial aspartate kinase and adenylylsulfate reductase genes substantially increases sulfur amino acid levels in transgenic alfalfa (Medicago sativa L.). PLoS One 2014; 9:e88310. [PMID: 24520364 PMCID: PMC3919742 DOI: 10.1371/journal.pone.0088310] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 01/07/2014] [Indexed: 11/19/2022] Open
Abstract
Alfalfa (Medicago sativa L.) is one of the most important forage crops used to feed livestock, such as cattle and sheep, and the sulfur amino acid (SAA) content of alfalfa is used as an index of its nutritional value. Aspartate kinase (AK) catalyzes the phosphorylation of aspartate to Asp-phosphate, the first step in the aspartate family biosynthesis pathway, and adenylylsulfate reductase (APR) catalyzes the conversion of activated sulfate to sulfite, providing reduced sulfur for the synthesis of cysteine, methionine, and other essential metabolites and secondary compounds. To reduce the feedback inhibition of other metabolites, we cloned bacterial AK and APR genes, modified AK, and introduced them into alfalfa. Compared to the wild-type alfalfa, the content of cysteine increased by 30% and that of methionine increased substantially by 60%. In addition, a substantial increase in the abundance of essential amino acids (EAAs), such as aspartate and lysine, was found. The results also indicated a close connection between amino acid metabolism and the tricarboxylic acid (TCA) cycle. The total amino acid content and the forage biomass tested showed no significant changes in the transgenic plants. This approach provides a new method for increasing SAAs and allows for the development of new genetically modified crops with enhanced nutritional value.
Collapse
|
11
|
Matityahu I, Godo I, Hacham Y, Amir R. Tobacco seeds expressing feedback-insensitive cystathionine gamma-synthase exhibit elevated content of methionine and altered primary metabolic profile. BMC PLANT BIOLOGY 2013; 13:206. [PMID: 24314105 PMCID: PMC3878949 DOI: 10.1186/1471-2229-13-206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 12/03/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND The essential sulfur-containing amino acid methionine plays a vital role in plant metabolism and human nutrition. In this study, we aimed to elucidate the regulatory role of the first committed enzyme in the methionine biosynthesis pathway, cystathionine γ-synthase (CGS), on methionine accumulation in tobacco seeds. We also studied the effect of this manipulation on the seed's metabolism. RESULTS Two forms of Arabidopsis CGS (AtCGS) were expressed under the control of the seeds-specific promoter of legumin B4: feedback-sensitive F-AtCGS (LF seeds), and feedback-insensitive T-AtCGS (LT seeds). Unexpectedly, the soluble content of methionine was reduced significantly in both sets of transgenic seeds. Amino acids analysis and feeding experiments indicated that although the level of methionine was reduced, the flux through its synthesis had increased. As a result, the level of protein-incorporated methionine had increased significantly in LT seeds by up to 60%, but this was not observed in LF seeds, whose methionine content is tightly regulated. This increase was accompanied by a higher content of other protein-incorporated amino acids, which led to 27% protein content in the seeds although this was statistically insignificantly. In addition, the levels of reducing sugars (representing starch) were slightly but significantly reduced, while that of oil was insignificantly reduced. To assess the impact of the high expression level of T-AtCGS in seeds on other primary metabolites, metabolic profiling using GC-MS was performed. This revealed significant alterations to the primary seed metabolism manifested by a significant increase in eight annotated metabolites (mostly sugars and their oxidized derivatives), while the levels of 12 other metabolites were reduced significantly in LT compared to wild-type seeds. CONCLUSION Expression of T-AtCGS leads to an increase in the level of total Met, higher contents of total amino acids, and significant changes in the levels of 20 annotated metabolites. The high level of oxidized metabolites, the two stress-associated amino acids, proline and serine, and low level of glutathione suggest oxidative stress that occurs during LT seed development. This study provides information on the metabolic consequence of increased CGS activity in seeds and how it affects the seed's nutritional quality.
Collapse
Affiliation(s)
- Ifat Matityahu
- Laboratory of Plant Science, Migal Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12100, Israel
| | - Itamar Godo
- Laboratory of Plant Science, Migal Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12100, Israel
| | - Yael Hacham
- Laboratory of Plant Science, Migal Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12100, Israel
| | - Rachel Amir
- Laboratory of Plant Science, Migal Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12100, Israel
- Tel Hai College, Upper Galilee, Israel
| |
Collapse
|
12
|
Zhang D, Ren L, Yue JH, Wang L, Zhuo LH, Shen XH. A comprehensive analysis of flowering transition in Agapanthus praecox ssp. orientalis (Leighton) Leighton by using transcriptomic and proteomic techniques. J Proteomics 2013; 80:1-25. [DOI: 10.1016/j.jprot.2012.12.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Revised: 11/20/2012] [Accepted: 12/15/2012] [Indexed: 10/27/2022]
|
13
|
Galili G. The aspartate-family pathway of plants: linking production of essential amino acids with energy and stress regulation. PLANT SIGNALING & BEHAVIOR 2011; 6:192-5. [PMID: 21512320 PMCID: PMC3121977 DOI: 10.4161/psb.6.2.14425] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 12/05/2010] [Accepted: 12/08/2010] [Indexed: 05/19/2023]
Abstract
The Asp family pathway of plants is highly important from a nutritional standpoint because it leads to the synthesis of the four essential amino acids Lys, Thr, Met and Ile. These amino acids are not synthesized by human and its monogastric livestock and should be supplemented in their diets. Among the Asp-family amino acids, Lys is considered as the nutritionally most important essential amino acid because its level is most limiting in cereal grains, representing the largest source of plant foods and feeds worldwide. Metabolic engineering approaches led to significant increase in Lys level in seeds by enhancing its synthesis and reducing its catabolism. However, results from the model plant Arabidopsis showed that this approach may retard seed germination due to a major negative effect on the levels of a number of TCA cycle metabolites that associate with cellular energy. In the present review, we discuss the regulatory metabolic link of the Asp-family pathway with the TCA cycle and its biological significance upon exposure to stress conditions that cause energy deprivation. In addition, we also discuss how deep understanding of the regulatory metabolic link of the Asp-family pathway with energy and stress regulation can be used to improve Lys level in seeds of important crop species, minimizing the interference with the cellular energy status and plant-stress interaction. This review thus provides an example showing how deep understanding the inter-regulation of metabolism with plant stress physiology can lead to successful nutritional improvements with minimal negative effect on plant growth and response to stressful environments.
Collapse
Affiliation(s)
- Gad Galili
- Department of Plant Science, the Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
14
|
Li Z, Moon BP, Xing A, Liu ZB, McCardell RP, Damude HG, Falco SC. Stacking multiple transgenes at a selected genomic site via repeated recombinase-mediated DNA cassette exchanges. PLANT PHYSIOLOGY 2010; 154:622-31. [PMID: 20720171 PMCID: PMC2949048 DOI: 10.1104/pp.110.160093] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 08/18/2010] [Indexed: 05/18/2023]
Abstract
Recombinase-mediated DNA cassette exchange (RMCE) has been successfully used to insert transgenes at previously characterized genomic sites in plants. Following the same strategy, groups of transgenes can be stacked to the same site through multiple rounds of RMCE. A gene-silencing cassette, designed to simultaneously silence soybean (Glycine max) genes fatty acid ω-6 desaturase 2 (FAD2) and acyl-acyl carrier protein thioesterase 2 (FATB) to improve oleic acid content, was first inserted by RMCE at a precharacterized genomic site in soybean. Selected transgenic events were subsequently retransformed with the second DNA construct containing a Yarrowia lipolytica diacylglycerol acyltransferase gene (DGAT1) to increase oil content by the enhancement of triacylglycerol biosynthesis and three other genes, a Corynebacterium glutamicum dihydrodipicolinate synthetase gene (DHPS), a barley (Hordeum vulgare) high-lysine protein gene (BHL8), and a truncated soybean cysteine synthase gene (CGS), to improve the contents of the essential amino acids lysine and methionine. Molecular characterization confirmed that the second RMCE successfully stacked the four overexpression cassettes to the previously integrated FAD2-FATB gene-silencing cassette. Phenotypic analyses indicated that all the transgenes expressed expected phenotypes.
Collapse
Affiliation(s)
- Zhongsen Li
- DuPont Agricultural Biotechnology, Experimental Station E353, Wilmington, Delaware 19880, USA.
| | | | | | | | | | | | | |
Collapse
|
15
|
High-lysine maize: the key discoveries that have made it possible. Amino Acids 2010; 39:979-89. [PMID: 20373119 DOI: 10.1007/s00726-010-0576-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 03/17/2010] [Indexed: 10/19/2022]
Abstract
Forty-five years ago, a paper published by Mertz et al. (Science 145:279-280, 1964) initiated a revolution in the history of plant protein quality and affected dramatically the study of cereal crop storage proteins. The observation of the high lysine content of the endosperm of the opaque-2 (o2) maize mutant was a key factor in bringing about a new concept in the production of cereal seeds with a high nutritional value. It has been a long and very interesting road with astonishing results over these 45 years. We are now probably about to see the release of commercially engineered high-lysine maize lines. We have decided to pinpoint some key contributions to the science behind high-lysine plants and concentrated on the research done on maize, which is possibly the most complete and simple example to illustrate the advances achieved. However, studies on other plant species such as barley and model species such as tobacco are totally relevant and will be briefly addressed.
Collapse
|
16
|
Current understanding of the factors regulating methionine content in vegetative tissues of higher plants. Amino Acids 2010; 39:917-31. [DOI: 10.1007/s00726-010-0482-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2009] [Accepted: 01/12/2010] [Indexed: 01/14/2023]
|
17
|
|
18
|
Jander G, Joshi V. Recent progress in deciphering the biosynthesis of aspartate-derived amino acids in plants. MOLECULAR PLANT 2010; 3:54-65. [PMID: 20019093 DOI: 10.1093/mp/ssp104] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plants are either directly or indirectly the source of most of the essential amino acids in animal diets. Four of these essential amino acids-methionine, threonine, isoleucine, and lysine-are all produced from aspartate via a well studied biosynthesis pathway. Given the nutritional interest in essential amino acids, the aspartate-derived amino acid pathway has been the subject of extensive research. Additionally, several pathway enzymes serve as targets for economically important herbicides, and some of the downstream products are biosynthetic precursors for other essential plant metabolites such as ethylene and S-adenosylmethionine. Recent and ongoing research on the aspartate-derived family of amino acids has identified new enzyme activities, regulatory mechanisms, and in vivo metabolic functions. Together, these discoveries will open up new possibilities for plant metabolic engineering.
Collapse
Affiliation(s)
- Georg Jander
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14850, USA.
| | | |
Collapse
|
19
|
Jander G, Joshi V. Aspartate-Derived Amino Acid Biosynthesis in Arabidopsis thaliana. THE ARABIDOPSIS BOOK 2009; 7:e0121. [PMID: 22303247 PMCID: PMC3243338 DOI: 10.1199/tab.0121] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The aspartate-derived amino acid pathway in plants leads to the biosynthesis of lysine, methionine, threonine, and isoleucine. These four amino acids are essential in the diets of humans and other animals, but are present in growth-limiting quantities in some of the world's major food crops. Genetic and biochemical approaches have been used for the functional analysis of almost all Arabidopsis thaliana enzymes involved in aspartate-derived amino acid biosynthesis. The branch-point enzymes aspartate kinase, dihydrodipicolinate synthase, homoserine dehydrogenase, cystathionine gamma synthase, threonine synthase, and threonine deaminase contain well-studied sites for allosteric regulation by pathway products and other plant metabolites. In contrast, relatively little is known about the transcriptional regulation of amino acid biosynthesis and the mechanisms that are used to balance aspartate-derived amino acid biosynthesis with other plant metabolic needs. The aspartate-derived amino acid pathway provides excellent examples of basic research conducted with A. thaliana that has been used to improve the nutritional quality of crop plants, in particular to increase the accumulation of lysine in maize and methionine in potatoes.
Collapse
Affiliation(s)
- Georg Jander
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853 USA
- Address correspondence to
| | - Vijay Joshi
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853 USA
| |
Collapse
|
20
|
Hacham Y, Matityahu I, Schuster G, Amir R. Overexpression of mutated forms of aspartate kinase and cystathionine gamma-synthase in tobacco leaves resulted in the high accumulation of methionine and threonine. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 54:260-71. [PMID: 18208521 DOI: 10.1111/j.1365-313x.2008.03415.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Methionine and threonine are two essential amino acids, the levels of which limit the nutritional quality of plants. Both amino acids diverge from the same branch of the aspartate family biosynthesis pathway; therefore, their biosynthesis pathways compete for the same carbon/amino substrate. To further elucidate the regulation of methionine biosynthesis and seek ways of increasing the levels of these two amino acids, we crossed transgenic tobacco plants overexpressing the bacterial feedback-insensitive aspartate kinase (bAK), containing a significantly higher threonine level, with plants overexpressing Arabidopsis cystathionine gamma-synthase (AtCGS), the first unique enzyme of methionine biosynthesis. Plants co-expressing bAK and the full-length AtCGS (F-AtCGS) have significantly higher methionine and threonine levels compared with the levels found in wild-type plants, but the methionine level does not increase beyond that found in plants expressing F-AtCGS alone. This finding can be explained through the feedback inhibition regulation mediated by the methionine metabolite on the transcript level of AtCGS. To test this assumption, plants expressing bAK were crossed with plants expressing two mutated forms of AtCGS in which the domains responsible for the feedback regulation have been deleted. Indeed, significantly higher methionine contents and its metabolites levels accumulated in the newly produced plants, and the levels of threonine were also significantly higher than in the wild-type plants. The transcript level of the two mutated forms of AtCGS significantly increased when there was a high content of threonine in the plants, suggesting that threonine modulates, probably indirectly, the transcript level of AtCGS.
Collapse
Affiliation(s)
- Yael Hacham
- Laboratory of Plant Science, Migal Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12 100, Israel
| | | | | | | |
Collapse
|
21
|
Lee M, Huang T, Toro-Ramos T, Fraga M, Last RL, Jander G. Reduced activity of Arabidopsis thaliana HMT2, a methionine biosynthetic enzyme, increases seed methionine content. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 54:310-20. [PMID: 18208517 DOI: 10.1111/j.1365-313x.2008.03419.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In the S-methylmethionine cycle of plants, homocysteine methyltransferase (HMT) catalyzes the formation of two molecules of methionine from homocysteine and S-methylmethionine, and methionine methyltransferase (MMT) catalyzes the formation of methionine from S-methylmethionine using S-adenosylmethionine as a methyl group donor. Somewhat surprisingly, two independently isolated knockdown mutations of HMT2 (At3g63250), one of three Arabidopsis thaliana genes encoding homocysteine methyltransferase, increased free methionine abundance in seeds. Crosses and flower stalk grafting experiments demonstrate that the maternal genotype at the top of the flower stalk determines the seed S-methylmethionine and methionine phenotype of hmt2 mutants. Uptake, transport and inter-conversion of [(13)C]S-methylmethionine and [(13)C]methionine in hmt2, mmt and wild-type plants show that S-methylmethionine is a non-essential intermediate in the movement of methionine from vegetative tissue to the seeds. Together, these results support a model whereby elevated S-methylmethionine in hmt2 vegetative tissue is transported to seeds and either directly or indirectly results in the biosynthesis of additional methionine. Manipulation of the S-methylmethionine cycle may provide a new approach for improving the nutritional value of major grain crops such as rice, as methionine is a limiting essential amino acid for mammalian diets.
Collapse
Affiliation(s)
- Minsang Lee
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA
| | | | | | | | | | | |
Collapse
|
22
|
Abstract
S-methylmethionine (SMM), a naturally occurring, biologically active compound, is a free amino acid derivative, which is increasingly recognised as playing an important part in the plant metabolism. SMM, which is synthesised from methionine, is involved in crucial processes in the S metabolism, such as the regulation of methionine and S-adenosyl methionine levels, the methylation processes taking place in cells, and the transport and storage of sulphur in certain phases of development. It is of great importance in the development of resistance to abiotic and biotic stress factors, as it is a direct precursor in the biosynthesis of the osmoprotectants and other S-containing compounds involved in defence mechanisms, while also influencing the biosynthesis of major plant hormones such as polyamines and ethylene. The present paper discusses our increasing understanding of the role played by SMM in the plant metabolism and its possible role in the improvement of traits that enable plants to overcome stress.
Collapse
Affiliation(s)
- D. Szegő
- 1 Eötvös Loránd University Department of Plant Physiology Budapest Hungary
| | - E. Kósa
- 2 Pannon University Department of Botany and Plant Physiology, Georgikon Faculty Keszthely Hungary
| | - E. Horváth
- 3 Agricultural Research Institute of the Hungarian Academy of Sciences Martonvásár Hungary
| |
Collapse
|