1
|
Tao J, Zuo J, Watkins CB, Bai C, He X, Liu S, Han L, Zhao X, Liu Y, Li J, Zheng Y. Low storage temperature affects quality and volatile compounds in fresh tomatoes. Food Chem 2024; 460:140400. [PMID: 39033633 DOI: 10.1016/j.foodchem.2024.140400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 06/21/2024] [Accepted: 07/07/2024] [Indexed: 07/23/2024]
Abstract
To investigate the impact of low temperature on the quality and flavor of ripe red tomatoes, we analyzed transcriptomes and volatile metabolomes of ripe red fruits stored at 0 °C and 20 °C for 8 days. The results showed that 0 °C maintained the sugar content by increasing the expression of sucrose synthetase (SUS) and sucrose transporter (SUT). Low expression of aroma synthesis-related genes, such as alcohol dehydrogenase 1 (ADH1), amino acid decarboxylase 1 A (AADC1A), and branched-chain amino acid aminotransferase 2 (BCAT2), were associated with reduced levels of pentanal, hexanal, 3-methylbutanal, 2-methylbutanal, and 2-phenylethanol. Additionally, the expression of pectinesterase (PE), beta-galactosidase (β-GAL), and beta-glucosidase (β-Glu), as well as phytoene synthase1 (PSY1) involved in carotenoid synthesis, was inhibited, thereby maintaining fruits texture and color. Furthermore, storage at 0 °C induced the expression of numerous genes regulating antioxidant and heat shock proteins, which further preserved the postharvest quality of tomatoes.
Collapse
Affiliation(s)
- Jiejie Tao
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Jinhua Zuo
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Christopher B Watkins
- School of Integrative Plant Science, Horticulture Section, College of Agriculture and Life Science, Cornell University, NY 14853, USA
| | - Chunmei Bai
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Xuelian He
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Shiyu Liu
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Lichun Han
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Xiaoyan Zhao
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Ye Liu
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Jian Li
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Yanyan Zheng
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China.
| |
Collapse
|
2
|
Chen C, Naveed H, Chen K. Research progress on branched-chain amino acid aminotransferases. Front Genet 2023; 14:1233669. [PMID: 38028625 PMCID: PMC10658711 DOI: 10.3389/fgene.2023.1233669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Branched-chain amino acid aminotransferases, widely present in natural organisms, catalyze bidirectional amino transfer between branched-chain amino acids and branched-chain α-ketoacids in cells. Branched-chain amino acid aminotransferases play an important role in the metabolism of branched-chain amino acids. In this paper, the interspecific evolution and biological characteristics of branched-chain amino acid aminotransferases are introduced, the related research of branched-chain amino acid aminotransferases in animals, plants, microorganisms and humans is summarized and the molecular mechanism of branched-chain amino acid aminotransferase is analyzed. It has been found that branched-chain amino acid metabolism disorders are closely related to various diseases in humans and animals and plants, such as diabetes, cardiovascular diseases, brain diseases, neurological diseases and cancer. In particular, branched-chain amino acid aminotransferases play an important role in the development of various tumors. Branched-chain amino acid aminotransferases have been used as potential targets for various cancers. This article reviews the research on branched-chain amino acid aminotransferases, aiming to provide a reference for clinical research on targeted therapy for various diseases and different cancers.
Collapse
Affiliation(s)
- Can Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Hassan Naveed
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| |
Collapse
|
3
|
Mellidou I, Koukounaras A, Frusciante S, Rambla JL, Patelou E, Ntoanidou S, Pons C, Kostas S, Nikoloudis K, Granell A, Diretto G, Kanellis AK. A metabolome and transcriptome survey to tap the dynamics of fruit prolonged shelf-life and improved quality within Greek tomato germplasm. FRONTIERS IN PLANT SCIENCE 2023; 14:1267340. [PMID: 37818313 PMCID: PMC10560995 DOI: 10.3389/fpls.2023.1267340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/05/2023] [Indexed: 10/12/2023]
Abstract
Introduction Tomato is a high economic value crop worldwide with recognized nutritional properties and diverse postharvest potential. Nowadays, there is an emerging awareness about the exploitation and utilization of underutilized traditional germplasm in modern breeding programs. In this context, the existing diversity among Greek accessions in terms of their postharvest life and nutritional value remains largely unexplored. Methods Herein, a detailed evaluation of 130 tomato Greek accessions for postharvest and nutritional characteristics was performed, using metabolomics and transcriptomics, leading to the selection of accessions with these interesting traits. Results The results showed remarkable differences among tomato Greek accessions for overall ripening parameters (color, firmness) and weight loss. On the basis of their postharvest performance, a balance between short shelf life (SSL) and long shelf life (LSL) accessions was revealed. Metabolome analysis performed on 14 selected accessions with contrasting shelf-life potential identified a total of 206 phytonutrients and volatile compounds. In turn, transcriptome analysis in fruits from the best SSL and the best LSL accessions revealed remarkable differences in the expression profiles of transcripts involved in key metabolic pathways related to fruit quality and postharvest potential. Discussion The pathways towards cell wall synthesis, polyamine synthesis, ABA catabolism, and steroidal alkaloids synthesis were mostly induced in the LSL accession, whereas those related to ethylene biosynthesis, cell wall degradation, isoprenoids, phenylpropanoids, ascorbic acid and aroma (TomloxC) were stimulated in the SSL accession. Overall, these data would provide valuable insights into the molecular mechanism towards enhancing shelf-life and improving flavor and aroma of modern tomato cultivars.
Collapse
Affiliation(s)
- Ifigeneia Mellidou
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization – DEMETER, Thessaloniki, Greece
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athanasios Koukounaras
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sarah Frusciante
- Italian National Agency for New Technologies, Energy, and Sustainable Development (ENEA), Biotechnology Laboratory, Casaccia Research Center, Rome, Italy
| | - José L. Rambla
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
- Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, Castellón de la Plana, Spain
| | - Efstathia Patelou
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Symela Ntoanidou
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Clara Pons
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Stefanos Kostas
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy, and Sustainable Development (ENEA), Biotechnology Laboratory, Casaccia Research Center, Rome, Italy
| | - Angelos K. Kanellis
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| |
Collapse
|
4
|
Sui Y, Che Y, Zhong Y, He L. Genome-Wide Association Studies Using 3VmrMLM Model Provide New Insights into Branched-Chain Amino Acid Contents in Rice Grains. PLANTS (BASEL, SWITZERLAND) 2023; 12:2970. [PMID: 37631180 PMCID: PMC10459631 DOI: 10.3390/plants12162970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
Rice (Oryza sativa L.) is a globally important food source providing carbohydrates, amino acids, and dietary fiber for humans and livestock. The branched-chain amino acid (BCAA) level is a complex trait related to the nutrient quality of rice. However, the genetic mechanism underlying the BCAA (valine, leucine, and isoleucine) accumulation in rice grains remains largely unclear. In this study, the grain BCAA contents and 239,055 SNPs of a diverse panel containing 422 rice accessions were adopted to perform a genome-wide association study (GWAS) using a recently proposed 3VmrMLM model. A total of 357 BCAA-content-associated main-effect quantitative trait nucleotides (QTNs) were identified from 15 datasets (12 BCAA content datasets and 3 BLUP datasets of BCAA). Furthermore, the allelic variation of two novel candidate genes, LOC_Os01g52530 and LOC_Os06g15420, responsible for the isoleucine (Ile) content alteration were identified. To reveal the genetic basis of the potential interactions between the gene and environmental factor, 53 QTN-by-environment interactions (QEIs) were detected using the 3VmrMLM model. The LOC_Os03g24460, LOC_Os01g55590, and LOC_Os12g31820 were considered as the candidate genes potentially contributing to the valine (Val), leucine (Leu), and isoleucine (Ile) accumulations, respectively. Additionally, 10 QTN-by-QTN interactions (QQIs) were detected using the 3VmrMLM model, which were putative gene-by-gene interactions related to the Leu and Ile contents. Taken together, these findings suggest that the implementation of the 3VmrMLM model in a GWAS may provide new insights into the deeper understanding of BCAA accumulation in rice grains. The identified QTNs/QEIs/QQIs serve as potential targets for the genetic improvement of rice with high BCAA levels.
Collapse
Affiliation(s)
| | | | | | - Liqiang He
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou 570228, China
| |
Collapse
|
5
|
Barqawi AA, Abulfaraj AA. Salt Stress-Related Mechanisms in Leaves of the Wild Barley Hordeum spontaneum Generated from RNA-Seq Datasets. Life (Basel) 2023; 13:1454. [PMID: 37511829 PMCID: PMC10381474 DOI: 10.3390/life13071454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/22/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
This study aims to detect salt stress-related genes and mechanisms of the wild barley Hordeum spontaneum. Among the generated RNA-Seq datasets, several regulated transcripts are influenced by levels of cellular carbon, nitrogen and oxygen. Some of the regulated genes act on photorespiration and ubiquitination processes, as well as promoting plant growth and development under salt stress. One of the genes, encoding alanine:glyoxylate aminotransferase (AGT), participates in signaling transduction and proline biosynthesis, while the gene encoding asparagine synthetase (ASN) influences nitrogen storage and transport in plants under stress. Meanwhile, the gene encoding glutamate dehydrogenase (GDH) promotes shoot and root biomass production as well as nitrate assimilation. The upregulated genes encoding alpha-aminoadipic semialdehyde synthase (AASAS) and small auxin-up RNA 40 (SAUR40) participate in the production of proline and signaling compounds, respectively, while the gene encoding E3 ubiquitin-protein ligase regulates the carbon/nitrogen-nutrient response and pathogen resistance, in addition to some physiological processes under biotic and abiotic stresses via signal transduction. The gene encoding the tetratricopeptide repeat (TPR)-domain suppressor of STIMPY (TSS) negatively regulates the carbon level in the cell. In conclusion, this study sheds light on possible molecular mechanisms underlying salt stress tolerance in wild barley that can be utilized further in genomics-based breeding programs of cultivated species.
Collapse
Affiliation(s)
- Aminah A Barqawi
- Department of Chemistry, Al-Leith University College, Umm Al-Qura University, Makkah 28434, Saudi Arabia
| | - Aala A Abulfaraj
- Biological Sciences Department, College of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
| |
Collapse
|
6
|
Kaur G, Abugu M, Tieman D. The dissection of tomato flavor: biochemistry, genetics, and omics. FRONTIERS IN PLANT SCIENCE 2023; 14:1144113. [PMID: 37346138 PMCID: PMC10281629 DOI: 10.3389/fpls.2023.1144113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/02/2023] [Indexed: 06/23/2023]
Abstract
Flavor and quality are the major drivers of fruit consumption in the US. However, the poor flavor of modern commercial tomato varieties is a major cause of consumer dissatisfaction. Studies in flavor research have informed the role of volatile organic compounds in improving overall liking and sweetness of tomatoes. These studies have utilized and applied the tools of molecular biology, genetics, biochemistry, omics, machine learning, and gene editing to elucidate the compounds and biochemical pathways essential for good tasting fruit. Here, we discuss the progress in identifying the biosynthetic pathways and chemical modifications of important tomato volatile compounds. We also summarize the advances in developing highly flavorful tomato varieties and future steps toward developing a "perfect tomato".
Collapse
Affiliation(s)
- Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Modesta Abugu
- Department of Horticulture Science, North Carolina State University, Raleigh, NC, United States
| | - Denise Tieman
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| |
Collapse
|
7
|
Shim JS, Jeong HI, Bang SW, Jung SE, Kim G, Kim YS, Redillas MCFR, Oh SJ, Seo JS, Kim JK. DROUGHT-INDUCED BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE enhances drought tolerance in rice. PLANT PHYSIOLOGY 2023; 191:1435-1447. [PMID: 36493384 PMCID: PMC9922417 DOI: 10.1093/plphys/kiac560] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/13/2022] [Indexed: 06/17/2023]
Abstract
Plants accumulate several metabolites in response to drought stress, including branched-chain amino acids (BCAAs). However, the roles of BCAAs in plant drought responses and the underlying molecular mechanisms for BCAA accumulation remain elusive. Here, we demonstrate that rice (Oryza sativa) DROUGHT-INDUCED BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE (OsDIAT) mediates the accumulation of BCAAs in rice in response to drought stress. An in vitro enzyme activity assay indicated that OsDIAT is a branched-chain amino acid aminotransferase, and subcellular localization analysis revealed that OsDIAT localizes to the cytoplasm. The expression of OsDIAT was induced in plants upon exposure to abiotic stress. OsDIAT-overexpressing (OsDIATOX) plants were more tolerant to drought stress, whereas osdiat plants were more susceptible to drought stress compared with nontransgenic (NT) plants. Amino acid analysis revealed that BCAA levels were higher in OsDIATOX but lower in osdiat compared with in NT plants. Finally, the exogenous application of BCAAs improved plant tolerance to osmotic stress compared with that in control plants. Collectively, these findings suggest that OsDIAT mediates drought tolerance by promoting the accumulation of BCAAs.
Collapse
Affiliation(s)
| | | | - Seung Woon Bang
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Se Eun Jung
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Goeun Kim
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Youn Shic Kim
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Mark Christian Felipe R Redillas
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
- Department of Biology, De La Salle University, Manila 1004, Philippines
| | - Se-Jun Oh
- LaSemilla Co. Ltd., Pyeongchang 25354, Korea
| | - Jun Sung Seo
- Author for correspondence: (J. S. S.); (J.-K. K.)
| | - Ju-Kon Kim
- Author for correspondence: (J. S. S.); (J.-K. K.)
| |
Collapse
|
8
|
Wang S, Qiang Q, Xiang L, Fernie AR, Yang J. Targeted approaches to improve tomato fruit taste. HORTICULTURE RESEARCH 2022; 10:uhac229. [PMID: 36643745 PMCID: PMC9832879 DOI: 10.1093/hr/uhac229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/30/2022] [Indexed: 06/17/2023]
Abstract
Tomato (Solanum lycopersicum) is the most valuable fruit and horticultural crop species worldwide. Compared with the fruits of their progenitors, those of modern tomato cultivars are, however, often described as having unsatisfactory taste or lacking flavor. The flavor of a tomato fruit arises from a complex mix of tastes and volatile metabolites, including sugars, acids, amino acids, and various volatiles. However, considerable differences in fruit flavor occur among tomato varieties, resulting in mixed consumer experiences. While tomato breeding has traditionally been driven by the desire for continual increases in yield and the introduction of traits that provide a long shelf-life, consumers are prepared to pay a reasonable premium for taste. Therefore, it is necessary to characterize preferences of tomato flavor and to define its underlying genetic basis. Here, we review recent conceptual and technological advances that have rendered this more feasible, including multi-omics-based QTL and association analyses, along with the use of trained testing panels, and machine learning approaches. This review proposes how the comprehensive datasets compiled to date could allow a precise rational design of tomato germplasm resources with improved organoleptic quality for the future.
Collapse
Affiliation(s)
- Shouchuang Wang
- To whom correspondence should be addressed. E-mail: , or . Tel: 86-0898-66184571. Fax number: 0898-66184571
| | | | - Lijun Xiang
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Alisdair R Fernie
- To whom correspondence should be addressed. E-mail: , or . Tel: 86-0898-66184571. Fax number: 0898-66184571
| | - Jun Yang
- To whom correspondence should be addressed. E-mail: , or . Tel: 86-0898-66184571. Fax number: 0898-66184571
| |
Collapse
|
9
|
Pham MT, Tran TTA, Zayabaatar E. Discovery of inhibitors against mycobacterium branched-chain amino acid aminotransferases through in silico screening and experimental evaluation. Lett Appl Microbiol 2022; 75:942-950. [PMID: 35687522 DOI: 10.1111/lam.13763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) is one of the most dangerous infectious diseases and is caused by Mycobacterium bovis (Mb) and Mycobacterium tuberculosis (Mt). Branched-chain amino acid aminotransferases (BCATs) were reported to be the key enzyme for methionine synthesis in Mycobacterium. Blocking the methionine synthesis in Mycobacterium can inhibit the growth of Mycobacterium. Therefore, in silico screening of inhibitors can be a good way to develop a potential drug for treating TB. A pyridoxal 5'-phosphate (PLP)-form of Mycobacterium bovis branched-chain amino acid aminotransferases (MbBCAT), an active form of MbBCAT, was constructed manually for docking approximately 150 000 compounds and the free energy was calculated in Autodock Vina. The 10 compounds which had the highest affinity to MbBCAT were further evaluated for their inhibitory effects against MbBCAT. Within the selected compounds, compound 4 (ZINC12359007) was found to be the best inhibitor against MbBCAT with the inhibitory constant Ki of 0·45 μmol l-1 and IC50 of 2·37 μmol l-1 . Our work provides potential candidates to develop effective drugs to prevent TB since the well-known structural information would be beneficial in the structure-based modification and design.
Collapse
Affiliation(s)
- M T Pham
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - T T A Tran
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology, Ho Chi Minh City, Vietnam
| | - E Zayabaatar
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| |
Collapse
|
10
|
Yang J, Liang B, Zhang Y, Liu Y, Wang S, Yang Q, Geng X, Liu S, Wu Y, Zhu Y, Lin T. Genome-wide association study of eigenvectors provides genetic insights into selective breeding for tomato metabolites. BMC Biol 2022; 20:120. [PMID: 35606872 PMCID: PMC9128223 DOI: 10.1186/s12915-022-01327-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/10/2022] [Indexed: 01/05/2023] Open
Abstract
Background Long-term domestication and intensive breeding of crop plants aim to establish traits desirable for human needs, and characteristics related to yield, disease resistance, and postharvest storage have traditionally received considerable attention. These processes have led also to negative consequences, as is the case of loss of variants controlling fruit quality, for instance in tomato. Tomato fruit quality is directly associated to metabolite content profiles; however, a full understanding of the genetics affecting metabolite content during tomato domestication and improvement has not been reached due to limitations of the single detection methods previously employed. Here, we aim to reach a broad understanding of changes in metabolite content using a genome-wide association study (GWAS) with eigenvector decomposition (EigenGWAS) on tomato accessions. Results An EigenGWAS was performed on 331 tomato accessions using the first eigenvector generated from the genomic data as a “phenotype” to understand the changes in fruit metabolite content during breeding. Two independent gene sets were identified that affected fruit metabolites during domestication and improvement in consumer-preferred tomatoes. Furthermore, 57 candidate genes related to polyphenol and polyamine biosynthesis were discovered, and a major candidate gene chlorogenate: glucarate caffeoyltransferase (SlCGT) was identified, which affected the quality and diseases resistance of tomato fruit, revealing the domestication mechanism of polyphenols. Conclusions We identified gene sets that contributed to consumer liking during domestication and improvement of tomato. Our study reports novel evidence of selective sweeps and key metabolites controlled by multiple genes, increasing our understanding of the mechanisms of metabolites variation during those processes. It also supports a polygenic selection model for the application of tomato breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01327-x.
Collapse
|
11
|
Lin LY, Chen KF, Changchien LL, Chen KC, Peng RY. Volatile Variation of Theobroma cacao Malvaceae L. Beans Cultivated in Taiwan Affected by Processing via Fermentation and Roasting. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27103058. [PMID: 35630547 PMCID: PMC9145787 DOI: 10.3390/molecules27103058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 12/02/2022]
Abstract
After being harvested, cacao beans are usually subjected to very complex processes in order to improve their chemical and physical characteristics, like tastefulness with chocolate characteristic flavors. The traditional process consists of three major processing stages: fermentation, drying, and roasting, while most of the fermentation is carried out by an on-farm in-box process. In Taiwan, we have two major cocoa beans, the red and the yellow. We proposed that the major factor affecting the variation in tastes and colors in the finished cocoa might be the difference between cultivars. To uncover this, we examined the effect of the three major processes including fermentation, drying and roasting on these two cocoa beans. Results indicated that the two cultivars really behaved differently (despite before or after processing with fermentation, drying, and roasting) with respect to the patterns of fatty acids (palmitic, stearic, oleic, and arachidonic); triacylglycerols:1,2,3-trioleoyl-glycerol (OOO); 1-stearoyl-2,3-oleoyl-glycerol (SOO); 1-stearoyl-sn-2-oleoyl-3-arachidoyl- glycerol (SOA); 1,3-distearyol-sn-2-oleoyl-glycerol (SOS); organic acids (citric, tartaric, acetic, and malic); soluble sugars (glucose and fructose); amino acids; total phenolics; total flavonoids; and volatiles. Our findings suggest that to choose specific processing conditions for each specific cocoa genotype is the crucial point of processing cocoa with consistent taste and color.
Collapse
Affiliation(s)
- Li-Yun Lin
- Department of Food and Applied Technology, Hungkuang University, No. 1018, Sec. 6, Taiwan Boulevard, Shalu District, Taichung City 43302, Taiwan; (L.-Y.L.); (K.-F.C.)
| | - Kwei-Fan Chen
- Department of Food and Applied Technology, Hungkuang University, No. 1018, Sec. 6, Taiwan Boulevard, Shalu District, Taichung City 43302, Taiwan; (L.-Y.L.); (K.-F.C.)
| | - Lin-Ling Changchien
- Department of Physical Therapy, Hungkuang University, No. 1018, Sec. 6, Taiwan Boulevard, Shalu District, Taichung City 43302, Taiwan;
| | - Kuan-Chou Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, No. 250, Wu-Xin St., Taipei 11031, Taiwan;
- Department of Urology, Taipei Medical University Shuang-Ho Hospital, 250, Wu-Xin St., Xin-Yi District, Taipei 11031, Taiwan
- Correspondence:
| | - Robert Y. Peng
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, No. 250, Wu-Xin St., Taipei 11031, Taiwan;
- Research Institute of Biotechnology, School of Health Care, Hungkuang University, 1018, Sec. 6, Taiwan Boulevard, Shalu District, Taichung City 43302, Taiwan
| |
Collapse
|
12
|
Han X, Wang X, Shen C, Mo Y, Tian R, Mao L, Luo Z, Yang H. Exogenous ABA promotes aroma biosynthesis of postharvest kiwifruit after low-temperature storage. PLANTA 2022; 255:82. [PMID: 35257207 DOI: 10.1007/s00425-022-03855-w] [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: 01/28/2022] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Exogenous ABA played a positive role in the accumulation and biosynthesis of aroma components of postharvest kiwifruit after low-temperature storage, especially the esters production during ripening. Low-temperature storage (LTS) generally affects the aroma formation associated with the decrease in aroma quality in kiwifruit. In this work, abscisic acid (ABA) treatment after LTS increased the production of aroma components in postharvest kiwifruit and enhanced the related enzyme activity, especially alcohol acyltransferase (AAT), branched amino acid transaminase (BCAT) and hydroperoxide lyase (HPL). Corresponding to the enzyme activity, the gene expression of AchnAAT, AchnADH, AchnBCAT and AchnHPL was significantly up-regulated by ABA. The principal component analysis further illustrated the differences in aroma components between ABA and the control. The positive correlation of aroma accumulation with the expression levels of AchnPDC and AchnLOX and the enzyme activities of BCAT and pyruvate decarboxylase (PDC) was also revealed by correlation analysis. In addition, the promoter sequences of the key genes involved in aroma biosynthesis contained multiple cis-elements (ABRE and G-box) of ABA-responsive proteins. Combining the transcriptome sequencing data, the promoting role of ABA signaling in the regulation of aroma biosynthesis of postharvest kiwifruit after LTS was discussed. This study would provide a reference for improving aroma quality of postharvest kiwifruit after LTS, as well the molecular mechanism of kiwifruit aroma fading after LTS.
Collapse
Affiliation(s)
- Xueyuan Han
- School of Life Science, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China
| | - Xiaoyu Wang
- School of Life Science, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China
| | - Chi Shen
- School of Life Science, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China
| | - Yiwei Mo
- School of Life Science, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China
| | - Rungang Tian
- School of Life Science, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China
| | - Linchun Mao
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
| | - Huanyi Yang
- School of Life Science, Shaoxing University, Shaoxing, 312000, Zhejiang Province, China.
| |
Collapse
|
13
|
Using Steady-State Kinetics to Quantitate Substrate Selectivity and Specificity: A Case Study with Two Human Transaminases. Molecules 2022; 27:molecules27041398. [PMID: 35209187 PMCID: PMC8875635 DOI: 10.3390/molecules27041398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 11/16/2022] Open
Abstract
We examined the ability of two human cytosolic transaminases, aspartate aminotransferase (GOT1) and alanine aminotransferase (GPT), to transform their preferred substrates whilst discriminating against similar metabolites. This offers an opportunity to survey our current understanding of enzyme selectivity and specificity in a biological context. Substrate selectivity can be quantitated based on the ratio of the kcat/KM values for two alternative substrates (the 'discrimination index'). After assessing the advantages, implications and limits of this index, we analyzed the reactions of GOT1 and GPT with alternative substrates that are metabolically available and show limited structural differences with respect to the preferred substrates. The transaminases' observed selectivities were remarkably high. In particular, GOT1 reacted ~106-fold less efficiently when the side-chain carboxylate of the 'physiological' substrates (aspartate and glutamate) was replaced by an amido group (asparagine and glutamine). This represents a current empirical limit of discrimination associated with this chemical difference. The structural basis of GOT1 selectivity was addressed through substrate docking simulations, which highlighted the importance of electrostatic interactions and proper substrate positioning in the active site. We briefly discuss the biological implications of these results and the possibility of using kcat/KM values to derive a global measure of enzyme specificity.
Collapse
|
14
|
Regulation of the Leucine Metabolism in Mortierella alpina. J Fungi (Basel) 2022; 8:jof8020196. [PMID: 35205950 PMCID: PMC8880518 DOI: 10.3390/jof8020196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022] Open
Abstract
The oleaginous fungus Mortierella alpina is a safe source of polyunsaturated fatty acids (PUFA) in industrial food and feed production. Besides PUFA production, pharmaceutically relevant surface-active and antimicrobial oligopeptides were isolated from this basal fungus. Both production of fatty acids and oligopeptides rely on the biosynthesis and high turnover of branched-chain-amino acids (BCAA), especially l-leucine. However, the regulation of BCAA biosynthesis in basal fungi is largely unknown. Here, we report on the regulation of the leucine, isoleucine, and valine metabolism in M. alpina. In contrast to higher fungi, the biosynthetic genes for BCAA are hardly transcriptionally regulated, as shown by qRT-PCR analysis, which suggests a constant production of BCAAs. However, the enzymes of the leucine metabolism are tightly metabolically regulated. Three enzymes of the leucine metabolism were heterologously produced in Escherichia coli, one of which is inhibited by allosteric feedback loops: The key regulator is the α-isopropylmalate synthase LeuA1, which is strongly disabled by l-leucine, α-ketoisocaproate, and propionyl-CoA, the precursor of the odd-chain fatty acid catabolism. Its gene is not related to homologs from higher fungi, but it has been inherited from a phototrophic ancestor by horizontal gene transfer.
Collapse
|
15
|
Hong K, Wang L, Johnpaul A, Lv C, Ma C. Key Enzymes Involved in the Synthesis of Hops Phytochemical Compounds: From Structure, Functions to Applications. Int J Mol Sci 2021; 22:9373. [PMID: 34502286 PMCID: PMC8430942 DOI: 10.3390/ijms22179373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/13/2022] Open
Abstract
Humulus lupulus L. is an essential source of aroma compounds, hop bitter acids, and xanthohumol derivatives mainly exploited as flavourings in beer brewing and with demonstrated potential for the treatment of certain diseases. To acquire a comprehensive understanding of the biosynthesis of these compounds, the primary enzymes involved in the three major pathways of hops' phytochemical composition are herein critically summarized. Hops' phytochemical components impart bitterness, aroma, and antioxidant activity to beers. The biosynthesis pathways have been extensively studied and enzymes play essential roles in the processes. Here, we introduced the enzymes involved in the biosynthesis of hop bitter acids, monoterpenes and xanthohumol derivatives, including the branched-chain aminotransferase (BCAT), branched-chain keto-acid dehydrogenase (BCKDH), carboxyl CoA ligase (CCL), valerophenone synthase (VPS), prenyltransferase (PT), 1-deoxyxylulose-5-phosphate synthase (DXS), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR), Geranyl diphosphate synthase (GPPS), monoterpene synthase enzymes (MTS), cinnamate 4-hydroxylase (C4H), chalcone synthase (CHS_H1), chalcone isomerase (CHI)-like proteins (CHIL), and O-methyltransferase (OMT1). Furthermore, research advancements of each enzyme in terms of reaction conditions, substrate recognition, enzyme structures, and use in engineered microbes are described in depth. Hence, an extensive review of the key enzymes involved in the phytochemical compounds of hops will provide fundamentals for their applications in beer production.
Collapse
Affiliation(s)
| | | | | | - Chenyan Lv
- College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qinghua Donglu Road, Haidian District, Beijing 100083, China; (K.H.); (L.W.); (A.J.)
| | - Changwei Ma
- College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qinghua Donglu Road, Haidian District, Beijing 100083, China; (K.H.); (L.W.); (A.J.)
| |
Collapse
|
16
|
Free Amino Acids Profile and Expression Analysis of Core Genes Involved in Branched-Chain Amino Acids Metabolism during Fruit Development of Longan ( Dimocarpus longan Lour.) Cultivars with Different Aroma Types. BIOLOGY 2021; 10:biology10080807. [PMID: 34440040 PMCID: PMC8389590 DOI: 10.3390/biology10080807] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary In this study, three longan cultivars, including non-aroma types ‘Shixia’ (SX), ‘Lidongben’ (LDB), and strong aroma type ‘Xiangcui’ (XC), were selected to analyze free amino acids (FAAs) variations at six distinct growth stages. The genome-wide identification and expression analysis of genes related to the branched-chain amino acids (BCAA) synthesis pathway were carried out. Results showed that thirty-six FAAs were identified, which increased drastically with fruit development until ripening. During the period of rapid fruit expansion, the aroma of XC changed from light to strong, and the contents of L-alanine and L-leucine were significantly higher than those of SX and LDB. The content of Leu was negatively correlated with the expression of DilBCAT1, -6, and -9 in three varieties, but positively correlated with DilBCAT16, indicating that these four genes may be responsible for the different synthesis and degradation of Leu among cultivars. Abstract Amino acids are important component of fruit nutrition and quality. In this study, three longan cultivars, including non-aroma types ‘Shixia’ (SX), ‘Lidongben’ (LDB), and strong aroma type ‘Xiangcui’ (XC), were selected to analyze free amino acids (FAAs) variations at six distinct growth stages (S1–S6). The genome-wide identification and expression analysis of genes related to the branched-chain amino acids (BCAA) synthesis pathway were carried out. Results showed that 36 FAAs were identified, and the total FAAs content ranged from 2601.0 to 9073.5 mg/kg, which increased drastically with fruit development until ripening. L-glutamic acid (Glu), L-alanine (Ala), L-arginine (Arg), γ-Aminobutyric acid (GABA), L-aspartic acid (Asp), L-leucine (Leu), hydroxyl-proline (Hypro), and L-serine (Ser) were the predominant FAAs (1619.9–7213.9 mg/kg) in pulp, accounting for 62.28–92.05% of the total amino acids. During the period of rapid fruit expansion (S2–S4), the aroma of XC changed from light to strong, and the contents of L-alanine (Ala) and L-leucine (Leu) were significantly higher than those of SX and LDB. Furthermore, a total of two 2-isopropyl malate synthase (IPMS), two 3-isopropyl malate dehydrogenase (IPMD), and 16 BCAA transferase (BCAT) genes were identified. The expression levels of DilBCAT1, -6, and -9 genes in XC were significantly higher than those in SX and LDB, while DilBCAT16 in XC was lower. The content of Leu was negatively correlated with the expression of DilBCAT1, -6, and -9 in three varieties, but positively correlated with DilBCAT16, indicating that these four genes may be responsible for the different synthesis and degradation of Leu among cultivars.
Collapse
|
17
|
Li S, Chen K, Grierson D. Molecular and Hormonal Mechanisms Regulating Fleshy Fruit Ripening. Cells 2021; 10:1136. [PMID: 34066675 PMCID: PMC8151651 DOI: 10.3390/cells10051136] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 12/17/2022] Open
Abstract
This article focuses on the molecular and hormonal mechanisms underlying the control of fleshy fruit ripening and quality. Recent research on tomato shows that ethylene, acting through transcription factors, is responsible for the initiation of tomato ripening. Several other hormones, including abscisic acid (ABA), jasmonic acid (JA) and brassinosteroids (BR), promote ripening by upregulating ethylene biosynthesis genes in different fruits. Changes to histone marks and DNA methylation are associated with the activation of ripening genes and are necessary for ripening initiation. Light, detected by different photoreceptors and operating through ELONGATED HYPOCOTYL 5(HY5), also modulates ripening. Re-evaluation of the roles of 'master regulators' indicates that MADS-RIN, NAC-NOR, Nor-like1 and other MADS and NAC genes, together with ethylene, promote the full expression of genes required for further ethylene synthesis and change in colour, flavour, texture and progression of ripening. Several different types of non-coding RNAs are involved in regulating expression of ripening genes, but further clarification of their diverse mechanisms of action is required. We discuss a model that integrates the main hormonal and genetic regulatory interactions governing the ripening of tomato fruit and consider variations in ripening regulatory circuits that operate in other fruits.
Collapse
Affiliation(s)
- Shan Li
- College of Agriculture & Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China;
| | - Kunsong Chen
- College of Agriculture & Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China;
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Donald Grierson
- College of Agriculture & Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China;
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
- Plant and Crop Sciences Division, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK
| |
Collapse
|
18
|
Martina M, Tikunov Y, Portis E, Bovy AG. The Genetic Basis of Tomato Aroma. Genes (Basel) 2021; 12:genes12020226. [PMID: 33557308 PMCID: PMC7915847 DOI: 10.3390/genes12020226] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023] Open
Abstract
Tomato (Solanum lycopersicum L.) aroma is determined by the interaction of volatile compounds (VOCs) released by the tomato fruits with receptors in the nose, leading to a sensorial impression, such as "sweet", "smoky", or "fruity" aroma. Of the more than 400 VOCs released by tomato fruits, 21 have been reported as main contributors to the perceived tomato aroma. These VOCs can be grouped in five clusters, according to their biosynthetic origins. In the last decades, a vast array of scientific studies has investigated the genetic component of tomato aroma in modern tomato cultivars and their relatives. In this paper we aim to collect, compare, integrate and summarize the available literature on flavour-related QTLs in tomato. Three hundred and 5ifty nine (359) QTLs associated with tomato fruit VOCs were physically mapped on the genome and investigated for the presence of potential candidate genes. This review makes it possible to (i) pinpoint potential donors described in literature for specific traits, (ii) highlight important QTL regions by combining information from different populations, and (iii) pinpoint potential candidate genes. This overview aims to be a valuable resource for researchers aiming to elucidate the genetics underlying tomato flavour and for breeders who aim to improve tomato aroma.
Collapse
Affiliation(s)
- Matteo Martina
- DISAFA, Plant Genetics and Breeding, University of Turin, 10095 Grugliasco, Italy;
| | - Yury Tikunov
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands;
| | - Ezio Portis
- DISAFA, Plant Genetics and Breeding, University of Turin, 10095 Grugliasco, Italy;
- Correspondence: (E.P.); (A.G.B.); Tel.: +39-011-6708807 (E.P.); +31-317-480762 (A.G.B.)
| | - Arnaud G. Bovy
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands;
- Correspondence: (E.P.); (A.G.B.); Tel.: +39-011-6708807 (E.P.); +31-317-480762 (A.G.B.)
| |
Collapse
|
19
|
Sangpong L, Khaksar G, Pinsorn P, Oikawa A, Sasaki R, Erban A, Watanabe M, Wangpaiboon K, Tohge T, Kopka J, Hoefgen R, Saito K, Sirikantaramas S. Assessing Dynamic Changes of Taste-Related Primary Metabolism During Ripening of Durian Pulp Using Metabolomic and Transcriptomic Analyses. FRONTIERS IN PLANT SCIENCE 2021; 12:687799. [PMID: 34220909 PMCID: PMC8250156 DOI: 10.3389/fpls.2021.687799] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/24/2021] [Indexed: 05/07/2023]
Abstract
Durian is an economically important fruit of Southeast Asia. There is, however, a lack of in-depth information on the alteration of its metabolic networks during ripening. Here, we annotated 94 ripening-associated metabolites from the pulp of durian cv. Monthong fruit at unripe and ripe stages, using capillary electrophoresis- and gas chromatography- time-of-flight mass spectrometry, specifically focusing on taste-related metabolites. During ripening, sucrose content increased. Change in raffinose-family oligosaccharides are reported herein for the first time. The malate and succinate contents increased, while those of citrate, an abundant organic acid, were unchanged. Notably, most amino acids increased, including isoleucine, leucine, and valine, whereas aspartate decreased, and glutamate was unchanged. Furthermore, transcriptomic analysis was performed to analyze the dynamic changes in sugar metabolism, glycolysis, TCA cycle, and amino acid pathways to identify key candidate genes. Taken together, our results elucidate the fundamental taste-related metabolism of durian, which can be exploited to develop durian metabolic and genetic markers in the future.
Collapse
Affiliation(s)
- Lalida Sangpong
- Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Gholamreza Khaksar
- Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Pinnapat Pinsorn
- Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Akira Oikawa
- Faculty of Agriculture, Yamagata University, Yamagata, Japan
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Ryosuke Sasaki
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Alexander Erban
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Mutsumi Watanabe
- Plant Secondary Metabolism, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Nara, Japan
| | - Karan Wangpaiboon
- Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Takayuki Tohge
- Plant Secondary Metabolism, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Nara, Japan
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Kazuki Saito
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Supaart Sirikantaramas
- Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Molecular Sensory Science Center, Chulalongkorn University, Bangkok, Thailand
- *Correspondence: Supaart Sirikantaramas,
| |
Collapse
|
20
|
Sun Y, Shi Y, Liu G, Yao F, Zhang Y, Yang C, Guo H, Liu X, Jin C, Luo J. Natural variation in the OsbZIP18 promoter contributes to branched-chain amino acid levels in rice. THE NEW PHYTOLOGIST 2020; 228:1548-1558. [PMID: 32654152 DOI: 10.1111/nph.16800] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 06/29/2020] [Indexed: 05/21/2023]
Abstract
Branched-chain amino acids (BCAAs) are essential amino acids that must be obtained from the diet for humans and animals, and they play important roles in various aspects of plant growth and development. Although BCAA biosynthetic pathways in higher plants have been uncovered, knowledge of their genetic control is still limited, and no positive regulators have been identified to date. Here, we showed that variation in BCAA levels in rice is attributable to differential transcription of OsbZIP18, a basic leucine zipper (bZIP) transcription factor, due to polymorphisms in its promoter. Functional analysis revealed that OsbZIP18 positively regulates BCAA synthesis by binding directly to the ACE and C-box cis-elements in the promoters of the biosynthetic genes branched-chain aminotransferase1 (OsBCAT1) and OsBCAT2. We further demonstrated that OsbZIP18 is strongly induced by nitrogen (N) deficiency and that N starvation results in enhanced BCAA levels in an OsbZIP18-dependent manner. Overall, we identified OsbZIP18, a positive regulator of BCAA biosynthesis, which contributed to natural variation in BCAA levels and mediated BCAA accumulation through de novo synthesis by directly modulating the key biosynthetic genes OsBCAT1 and OsBCAT2.
Collapse
Affiliation(s)
- Yangyang Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuheng Shi
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Guige Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Fang Yao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuanyuan Zhang
- College of Tropical Crops, Hainan University, Haikou, Hainan, 570288, China
| | - Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Guo
- College of Tropical Crops, Hainan University, Haikou, Hainan, 570288, China
| | - Xianqing Liu
- College of Tropical Crops, Hainan University, Haikou, Hainan, 570288, China
| | - Cheng Jin
- College of Tropical Crops, Hainan University, Haikou, Hainan, 570288, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- College of Tropical Crops, Hainan University, Haikou, Hainan, 570288, China
| |
Collapse
|
21
|
Alseekh S, Ofner I, Liu Z, Osorio S, Vallarino J, Last RL, Zamir D, Tohge T, Fernie AR. Quantitative trait loci analysis of seed-specialized metabolites reveals seed-specific flavonols and differential regulation of glycoalkaloid content in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2007-2024. [PMID: 32538521 DOI: 10.1111/tpj.14879] [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: 04/01/2019] [Revised: 06/05/2020] [Accepted: 06/12/2020] [Indexed: 05/07/2023]
Abstract
Given the potential health benefits (and adverse effects), of polyphenolic and steroidal glycoalkaloids in the diet there is a growing interest in fully elucidating the genetic control of their levels in foodstuffs. Here we carried out profiling of the specialized metabolites in the seeds of the Solanum pennellii introgression lines identifying 338 putative metabolite quantitative trait loci (mQTL) for flavonoids, steroidal glycoalkaloids and further specialized metabolites. Two putative mQTL for flavonols and one for steroidal glycoalkaloids were cross-validated by evaluation of the metabolite content of recombinants harboring smaller introgression in the corresponding QTL interval or by analysis of lines from an independently derived backcross inbred line population. The steroidal glycoalkaloid mQTL was localized to a chromosomal region spanning 14 genes, including a previously defined steroidal glycoalkaloid gene cluster. The flavonoid mQTL was further validated via the use of transient and stable overexpression of the Solyc12g098600 and Solyc12g096870 genes, which encode seed-specific uridine 5'-diphosphate-glycosyltransferases. The results are discussed in the context of our understanding of the accumulation of polyphenols and steroidal glycoalkaloids, and how this knowledge may be incorporated into breeding strategies aimed at improving nutritional aspects of plants as well as in fortifying them against abiotic stress.
Collapse
Affiliation(s)
- Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Itai Ofner
- Faculty of Agriculture, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Zhongyuan Liu
- Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL, 32611, USA
| | - Sonia Osorio
- Department of Molecular Biology and Biochemistry, Instituto de Hortofruiticultura Subtropical y Mediterranea "La Major" - University of Malaga - Consejo Superior de Investigaciones Cientificas (IHSM-UMA-CSIC), Campus de Teatinos, Malaga, 29071, Spain
| | - Jose Vallarino
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Dani Zamir
- Faculty of Agriculture, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| |
Collapse
|
22
|
Buffagni V, Vurro F, Janni M, Gullì M, Keller AA, Marmiroli N. Shaping Durum Wheat for the Future: Gene Expression Analyses and Metabolites Profiling Support the Contribution of BCAT Genes to Drought Stress Response. FRONTIERS IN PLANT SCIENCE 2020; 11:891. [PMID: 32719694 PMCID: PMC7350509 DOI: 10.3389/fpls.2020.00891] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Global climate change, its implications for agriculture, and the complex scenario presented by the scientific community are of worldwide concern. Drought is a major abiotic stress that can restrict plants growth and yields, thus the identification of genotypes with higher adaptability to drought stress represents one of the primary goals in breeding programs. During abiotic stress, metabolic adaptation is crucial for stress tolerance, and accumulation of specific amino acids and/or as secondary metabolites deriving from amino acid metabolism may correlate with the increased tolerance to adverse environmental conditions. This work, focused on the metabolism of branched chain-amino acids (BCAAs) in durum wheat and the role of branched-chain amino acid aminotransferases (BCATs) in stress response. The role of BCATs in plant response to drought was previously proposed for Arabidopsis, where the levels of BCAAs were altered at the transcriptional level under drought conditions, triggering the onset of defense response metabolism. However, in wheat the role of BCAAs as a trigger of the onset of the drought defense response has not been elucidated. A comparative genomic approach elucidated the composition of the BCAT gene family in durum wheat. Here we demonstrate a tissue and developmental stage specificity of BCATs regulation in the drought response. Moreover, a metabolites profiling was performed on two contrasting durum wheat cultivars Colosseo and Cappelli resulting in the detection of a specific pattern of metabolites accumulated among genotypes and, in particular, in an enhanced BCAAs accumulation in the tolerant cv Cappelli further supporting a role of BCAAs in the drought defense response. The results support the use of gene expression and target metabolomic in modern breeding to shape new cultivars more resilient to a changing climate.
Collapse
Affiliation(s)
- Valentina Buffagni
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Filippo Vurro
- Institute of Materials for Electronics and Magnetism (IMEM), National Research Council (CNR), Parma, Italy
| | - Michela Janni
- Institute of Materials for Electronics and Magnetism (IMEM), National Research Council (CNR), Parma, Italy
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Bari, Italy
| | - Mariolina Gullì
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Arturo A. Keller
- Bren School of Environmental Science & Management, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- CINSA Interuniversity Consortium for Environmental Sciences, Parma/Venice, Italy
| |
Collapse
|
23
|
Li S, Zhu B, Pirrello J, Xu C, Zhang B, Bouzayen M, Chen K, Grierson D. Roles of RIN and ethylene in tomato fruit ripening and ripening-associated traits. THE NEW PHYTOLOGIST 2020; 226:460-475. [PMID: 31814125 PMCID: PMC7154718 DOI: 10.1111/nph.16362] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/01/2019] [Indexed: 05/13/2023]
Abstract
RIPENING INHIBITOR (RIN)-deficient fruits generated by CRISPR/Cas9 initiated partial ripening at a similar time to wild-type (WT) fruits but only 10% WT concentrations of carotenoids and ethylene (ET) were synthesized. RIN-deficient fruit never ripened completely, even when supplied with exogenous ET. The low amount of endogenous ET that they did produce was sufficient to enable ripening initiation and this could be suppressed by the ET perception inhibitor 1-MCP. The reduced ET production by RIN-deficient tomatoes was due to an inability to induce autocatalytic system-2 ET synthesis, a characteristic feature of climacteric ripening. Production of volatiles and transcripts of key volatile biosynthetic genes also were greatly reduced in the absence of RIN. By contrast, the initial extent and rates of softening in the absence of RIN were similar to WT fruits, although detailed analysis showed that the expression of some cell wall-modifying enzymes was delayed and others increased in the absence of RIN. These results support a model where RIN and ET, via ERFs, are required for full expression of ripening genes. Ethylene initiates ripening of mature green fruit, upregulates RIN expression and other changes, including system-2 ET production. RIN, ET and other factors are required for completion of the full fruit-ripening programme.
Collapse
Affiliation(s)
- Shan Li
- College of Agriculture & BiotechnologyZhejiang UniversityZijingang CampusHangzhou310058China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyZhejiang UniversityZijingang CampusHangzhou310058China
| | - Benzhong Zhu
- College of Food Science and Nutritional EngineeringChina Agricultural UniversityBeijing100083China
| | - Julien Pirrello
- GBF LaboratoryUniversity of ToulouseINRACastanet‐Tolosan31320France
| | - Changjie Xu
- College of Agriculture & BiotechnologyZhejiang UniversityZijingang CampusHangzhou310058China
| | - Bo Zhang
- College of Agriculture & BiotechnologyZhejiang UniversityZijingang CampusHangzhou310058China
| | - Mondher Bouzayen
- GBF LaboratoryUniversity of ToulouseINRACastanet‐Tolosan31320France
| | - Kunsong Chen
- College of Agriculture & BiotechnologyZhejiang UniversityZijingang CampusHangzhou310058China
| | - Donald Grierson
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyZhejiang UniversityZijingang CampusHangzhou310058China
- Plant and Crop Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
| |
Collapse
|
24
|
Mandal S, Ji W, McKnight TD. Candidate Gene Networks for Acylsugar Metabolism and Plant Defense in Wild Tomato Solanum pennellii. THE PLANT CELL 2020; 32:81-99. [PMID: 31628166 PMCID: PMC6961621 DOI: 10.1105/tpc.19.00552] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/30/2019] [Accepted: 10/16/2019] [Indexed: 05/13/2023]
Abstract
Many solanaceous plants secrete acylsugars, which are branched-chain and straight-chain fatty acids esterified to Glu or Suc. These compounds have important roles in plant defense and potential commercial applications. However, several acylsugar metabolic genes remain unidentified, and little is known about regulation of this pathway. Comparative transcriptomics between low- and high-acylsugar-producing accessions of Solanum pennellii revealed that expression levels of known and novel candidate genes (putatively encoding beta-ketoacyl-(acyl-carrier-protein) synthases, peroxisomal acyl-activating enzymes, ATP binding cassette (ABC) transporters, and central carbon metabolic proteins) were positively correlated with acylsugar accumulation, except two genes previously reported to be involved in acylglucose biosynthesis. Genes putatively encoding oxylipin metabolic proteins, subtilisin-like proteases, and other antimicrobial defense proteins were upregulated in low-acylsugar-producing accessions. Transcriptome analysis after biochemical inhibition of biosynthesis of branched-chain amino acids (precursors to branched-chain fatty acids) by imazapyr showed concentration-dependent downregulation of known and most acylsugar candidate genes, but not defense genes. Weighted gene correlation network analysis identified separate coexpressed gene networks for acylsugar metabolism (including six transcription factor genes and flavonoid metabolic genes) and plant defense (including genes putatively encoding NB-ARC and leucine-rich repeat sequences, protein kinases and defense signaling proteins, and previously mentioned defense proteins). Additionally, virus-induced gene silencing of two trichomes preferentially expressed candidate genes for straight-chain fatty acid biosynthesis confirmed their role in acylsugar metabolism.
Collapse
Affiliation(s)
- Sabyasachi Mandal
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Wangming Ji
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Thomas D McKnight
- Department of Biology, Texas A&M University, College Station, Texas 77843
| |
Collapse
|
25
|
Cheng G, Chang P, Shen Y, Wu L, El-Sappah AH, Zhang F, Liang Y. Comparing the Flavor Characteristics of 71 Tomato ( Solanum lycopersicum) Accessions in Central Shaanxi. FRONTIERS IN PLANT SCIENCE 2020; 11:586834. [PMID: 33362814 PMCID: PMC7758415 DOI: 10.3389/fpls.2020.586834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/06/2020] [Indexed: 05/21/2023]
Abstract
Flavor is an important quality of mature tomato fruits. Compared with heirloom tomatoes, modern commercial tomato cultivars are considerably less flavorful. This study aimed to compare the flavor of 71 tomato accessions (8 pink cherry, PC; 11 red cherry, RC; 15 pink large-fruited, PL; and 37 red large-fruited, RL) using hedonism scores and odor activity values. Taste compounds were detected using high-performance liquid chromatography. Volatiles were detected using gas chromatography-olfactometry-mass spectrometry. The flavor of tomato accessions can be evaluated using the DTOPSIS analysis method. According to the results of DTOPSIS analysis, 71 tomato accessions can be divided into 4 classes. Tomato accessions PL11, PC4, PC2, PC8, RL35, RC6, and RC10 had better flavor; accessions PC4, PC8, RC10, RL2, and RL35 had better tomato taste; and accessions PL11, PC2, and RC6 had better tomato odor. The concentrations of total soluble solids, fructose, glucose, and citric acid were shown to positively contribute to tomato taste. Tomato odor was mainly derived from 15 volatiles, namely, 1-hexanol, (Z)-3-hexen-1-ol, hexanal, (E)-2-hexenal, (E)-2-heptenal, (E)-2-octenal, (E,E)-2,4-decadienal, (Z)-3,7-dimethyl-2,6-octadieal, 2,6,6-timethyl-1-cyclohexene-1-carboxaldehyde, (2E)-3-(3-pentyl-2-oxiranyl)acrylaldehyde, 6-methyl-5-hepten-2-one, (E)-6,10-dimetyl-5,9-undecadien-2-one, methyl salicylate, 4-allyl-2-methoxyphenol, and 2-isobutylthiazole. Significant positive correlations (P < 0.05) were detected between the compound concentrations and flavor scores. The above-mentioned compounds can be used as parameters for the evaluation of flavor characteristics and as potential targets to improve the flavor quality of tomato varieties.
Collapse
Affiliation(s)
- Guoting Cheng
- College of Horticulture, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology in Arid Regions, Northwest A&F University, Yangling, China
| | - Peipei Chang
- Institute of Agricultural Sciences, Dezhou, China
| | - Yuanbo Shen
- College of Horticulture, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology in Arid Regions, Northwest A&F University, Yangling, China
| | - Liting Wu
- College of Horticulture, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology in Arid Regions, Northwest A&F University, Yangling, China
| | - Ahmed H. El-Sappah
- College of Horticulture, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology in Arid Regions, Northwest A&F University, Yangling, China
- Department of Genetics, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Fei Zhang
- College of Horticulture, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology in Arid Regions, Northwest A&F University, Yangling, China
- *Correspondence: Fei Zhang,
| | - Yan Liang
- College of Horticulture, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology in Arid Regions, Northwest A&F University, Yangling, China
- Yan Liang,
| |
Collapse
|
26
|
Comparative Proteomics of Salt-Tolerant and Salt-Sensitive Maize Inbred Lines to Reveal the Molecular Mechanism of Salt Tolerance. Int J Mol Sci 2019; 20:ijms20194725. [PMID: 31554168 PMCID: PMC6801879 DOI: 10.3390/ijms20194725] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/31/2019] [Accepted: 09/12/2019] [Indexed: 12/15/2022] Open
Abstract
Salt stress is one of the key abiotic stresses that causes great loss of yield and serious decrease in quality in maize (Zea mays L.). Therefore, it is very important to reveal the molecular mechanism of salt tolerance in maize. To acknowledge the molecular mechanisms underlying maize salt tolerance, two maize inbred lines, including salt-tolerant 8723 and salt-sensitive P138, were used in this study. Comparative proteomics of seedling roots from two maize inbred lines under 180 mM salt stress for 10 days were performed by the isobaric tags for relative and absolute quantitation (iTRAQ) approach. A total of 1056 differentially expressed proteins (DEPs) were identified. In total, 626 DEPs were identified in line 8723 under salt stress, among them, 378 up-regulated and 248 down-regulated. There were 473 DEPs identified in P138, of which 212 were up-regulated and 261 were down-regulated. Venn diagram analysis showed that 17 DEPs were up-regulated and 12 DEPs were down-regulated in the two inbred lines. In addition, 8 DEPs were up-regulated in line 8723 but down-regulated in P138, 6 DEPs were down-regulated in line 8723 but up-regulated in P138. In salt-stressed 8723, the DEPs were primarily associated with phenylpropanoid biosynthesis, starch and sucrose metabolism, and the mitogen-activated protein kinase (MAPK) signaling pathway. Intriguingly, the DEPs were only associated with the nitrogen metabolism pathway in P138. Compared to P138, the root response to salt stress in 8723 could maintain stronger water retention capacity, osmotic regulation ability, synergistic effects of antioxidant enzymes, energy supply capacity, signal transduction, ammonia detoxification ability, lipid metabolism, and nucleic acid synthesis. Based on the proteome sequencing information, changes of 8 DEPs abundance were related to the corresponding mRNA levels by quantitative real-time PCR (qRT-PCR). Our results from this study may elucidate some details of salt tolerance mechanisms and salt tolerance breeding of maize.
Collapse
|
27
|
Pott DM, Osorio S, Vallarino JG. From Central to Specialized Metabolism: An Overview of Some Secondary Compounds Derived From the Primary Metabolism for Their Role in Conferring Nutritional and Organoleptic Characteristics to Fruit. FRONTIERS IN PLANT SCIENCE 2019; 10:835. [PMID: 31316537 PMCID: PMC6609884 DOI: 10.3389/fpls.2019.00835] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/11/2019] [Indexed: 05/23/2023]
Abstract
Fruit flavor and nutritional characteristics are key quality traits and ones of the main factors influencing consumer preference. Central carbon metabolism, also known as primary metabolism, contributes to the synthesis of intermediate compounds that act as precursors for plant secondary metabolism. Specific and specialized metabolic pathways that evolved from primary metabolism play a key role in the plant's interaction with its environment. In particular, secondary metabolites present in the fruit serve to increase its attractiveness to seed dispersers and to protect it against biotic and abiotic stresses. As a consequence, several important organoleptic characteristics, such as aroma, color, and fruit nutritional value, rely upon secondary metabolite content. Phenolic and terpenoid compounds are large and diverse classes of secondary metabolites that contribute to fruit quality and have their origin in primary metabolic pathways, while the delicate aroma of ripe fruits is formed by a unique combination of hundreds of volatiles that are derived from primary metabolites. In this review, we show that the manipulation of primary metabolism is a powerful tool to engineer quality traits in fruits, such as the phenolic, terpenoid, and volatile content. The enzymatic reactions responsible for the accumulation of primary precursors are bottlenecks in the transfer of metabolic flux from central to specialized metabolism and should be taken into account to increase the yield of the final products of the biosynthetic pathways. In addition, understanding the connection and regulation of the carbon flow between primary and secondary metabolism is a key factor for the development of fruit cultivars with enhanced organoleptic and nutritional traits.
Collapse
Affiliation(s)
| | - Sonia Osorio
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga – Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
| | - José G. Vallarino
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga – Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
| |
Collapse
|
28
|
Zhang WF, Gong ZH, Wu MB, Chan H, Yuan YJ, Tang N, Zhang Q, Miao MJ, Chang W, Li Z, Li ZG, Jin L, Deng W. Integrative comparative analyses of metabolite and transcript profiles uncovers complex regulatory network in tomato (Solanum lycopersicum L.) fruit undergoing chilling injury. Sci Rep 2019; 9:4470. [PMID: 30872788 PMCID: PMC6418210 DOI: 10.1038/s41598-019-41065-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 02/27/2019] [Indexed: 01/22/2023] Open
Abstract
Tomato fruit are especially susceptible to chilling injury (CI) when continuously exposed to temperatures below 12 °C. In this study, integrative comparative analyses of transcriptomics and metabolomics data were performed to uncover the regulatory network in CI tomato fruit. Metabolite profiling analysis found that 7 amino acids, 27 organic acids, 16 of sugars and 22 other compounds had a significantly different content while transcriptomics data showed 1735 differentially expressed genes (DEGs) were down-regulated and 1369 were up-regulated in cold-stored fruit. We found that the contents of citrate, cis-aconitate and succinate were increased, which were consistent with the expression of ATP-citrate synthase (ACS) and isocitrate dehydrogenase (IDH) genes in cold-treated tomato fruit. Cold stress promotes the expression of ACS and IDH which may increase the synthesis of citrate, cis-aconitate and succinate. Alanine and leucine had increased contents, which may result from alanine aminotransferase (ALT) and branched-chain amino acid aminotransferase (BcAT)'s high expression levels, respectively. Overall the transcriptomics and metabolomics data in our study explain the molecular mechanisms of the chilling injury and expands our understanding of the complex regulatory mechanisms of a metabolic network in response to chilling injury in tomato fruit.
Collapse
Affiliation(s)
- Wen-Fa Zhang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China
| | - Ze-Hao Gong
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China
| | - Meng-Bo Wu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China
| | - Helen Chan
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yu-Jin Yuan
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China
| | - Ning Tang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China
| | - Qiang Zhang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China
| | - Ming-Jun Miao
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Wei Chang
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Zhi Li
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Zheng-Guo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China
| | - Liang Jin
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China.
| | - Wei Deng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China.
| |
Collapse
|
29
|
Lee JH, Kim YC, Jung Y, Han JH, Zhang C, Yun CW, Lee S. The overexpression of cucumber (Cucumis sativus L.) genes that encode the branched-chain amino acid transferase modulate flowering time in Arabidopsis thaliana. PLANT CELL REPORTS 2019; 38:25-35. [PMID: 30298307 DOI: 10.1007/s00299-018-2346-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/28/2018] [Indexed: 06/08/2023]
Abstract
The overexpression of CsBCATs promotes flowering in Arabidopsis by regulating the expression of flowering time genes. The branched-chain amino acid transferases (BCATs) play an important role in the metabolism of branched-chain amino acids (BCAAs), such as isoleucine, leucine, and valine. They function in both the synthesis and the degradation of this class of amino acids. We identified and characterized the three BCAT genes in cucumber (Cucumis sativus L.). The tissue-specific expression profiling in cucumber plants revealed that CsBCAT2 and CsBCAT7 were highly expressed in the reproductive tissues, whereas CsBCAT3 expression was highly detected in the vegetative tissues. The subcellular localization patterns of three CsBCATs were observed in the mitochondria. The functional analyses of CsBCATs showed that CsBCAT2 and CsBCAT3 restored the growth of bat1Δ/bat2Δ double knockout yeast (Saccharomyces cerevisiae), and CsBCAT3 and CsBCAT7 with different substrate preferences acted in a reverse reaction. The transgenic approach demonstrated that the overexpression of the three CsBCATs resulted in early flowering phenotypes, which were associated with the upregulation of FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) in a manner in which they were dependent on GIGANTEA (GI)/CONSTANS (CO) and SHORT VEGETATIVE PHASE (SVP)/FLOWERING LOCUS C (FLC) modules. Our results, which are observed in conjunction, suggest that there is an interconnection between BCAT genes that function in BCAA metabolism and the flowering time in plants.
Collapse
Affiliation(s)
- Jeong Hwan Lee
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
- Division of Life Sciences, Chonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju, Jeollabuk-do, 54896, Republic of Korea
| | - Young-Cheon Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
| | - Youjin Jung
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
| | - Ji Hoon Han
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
| | - Chunying Zhang
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
| | - Cheol-Won Yun
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Sanghyeob Lee
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea.
| |
Collapse
|
30
|
Smith SD, Angelovici R, Heyduk K, Maeda HA, Moghe GD, Pires JC, Widhalm JR, Wisecaver JH. The renaissance of comparative biochemistry. AMERICAN JOURNAL OF BOTANY 2019; 106:3-13. [PMID: 30629738 DOI: 10.1002/ajb2.1216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Affiliation(s)
- Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Ruthie Angelovici
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Karolina Heyduk
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Joshua R Widhalm
- Department of Horticulture and Landscape Architecture and Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Jennifer H Wisecaver
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
31
|
Brog YM, Osorio S, Yichie Y, Alseekh S, Bensal E, Kochevenko A, Zamir D, Fernie AR. A Solanum neorickii introgression population providing a powerful complement to the extensively characterized Solanum pennellii population. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:391-403. [PMID: 30230636 PMCID: PMC7379295 DOI: 10.1111/tpj.14095] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 09/01/2018] [Accepted: 09/04/2018] [Indexed: 05/31/2023]
Abstract
We present a complementary resource for trait fine-mapping in tomato to those based on the intra-specific cross between cultivated tomato and the wild tomato species Solanum pennellii, which have been extensively used for quantitative genetics in tomato over the last 20 years. The current population of backcross inbred lines (BILs) is composed of 107 lines derived after three backcrosses of progeny of the wild species Solanum neorickii (LA2133) and cultivated tomato (cultivar TA209) and is freely available to the scientific community. These S. neorickii BILs were genotyped using the 10K SolCAP single nucleotide polymorphism chip, and 3111 polymorphic markers were used to map recombination break points relative to the physical map of Solanum lycopersicum. The BILs harbor on average 4.3 introgressions per line, with a mean introgression length of 34.7 Mbp, allowing partitioning of the genome into 340 bins and thereby facilitating rapid trait mapping. We demonstrate the power of using this resource in comparison with archival data from the S. pennellii resources by carrying out metabolic quantitative trait locus analysis following gas chromatography-mass spectrometry on fruits harvested from the S. neorickii BILs. The metabolic candidate genes phenylalanine ammonia-lyase and cystathionine gamma-lyase were then tested and validated in F2 populations and via agroinfiltration-based overexpression in order to exemplify the fidelity of this method in identifying the genes that drive tomato metabolic phenotypes.
Collapse
Affiliation(s)
- Yaacov Micha Brog
- Faculty of AgricultureThe Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of JerusalemRehovot76100Israel
| | - Sonia Osorio
- Department of Molecular Biology and BiochemistryInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’ – University of Malaga – Consejo Superior de Investigaciones Científicas (IHSM‐UMA‐CSIC)Campus de Teatinos29071MálagaSpain
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Mühlenberg 114476Potsdam‐GolmGermany
| | - Yoav Yichie
- Faculty of AgricultureThe Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of JerusalemRehovot76100Israel
| | - Saleh Alseekh
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Mühlenberg 114476Potsdam‐GolmGermany
- Center of Plant Systems Biology and Biotechnology4000PlovdivBulgaria
| | - Elad Bensal
- Faculty of AgricultureThe Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of JerusalemRehovot76100Israel
| | - Andriy Kochevenko
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Mühlenberg 114476Potsdam‐GolmGermany
| | - Dani Zamir
- Faculty of AgricultureThe Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of JerusalemRehovot76100Israel
| | - Alisdair R. Fernie
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Mühlenberg 114476Potsdam‐GolmGermany
- Center of Plant Systems Biology and Biotechnology4000PlovdivBulgaria
| |
Collapse
|
32
|
Wu Q, Tao X, Ai X, Luo Z, Mao L, Ying T, Li L. Contribution of abscisic acid to aromatic volatiles in cherry tomato (Solanum lycopersicum L.) fruit during postharvest ripening. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 130:205-214. [PMID: 29990773 DOI: 10.1016/j.plaphy.2018.06.039] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 06/27/2018] [Indexed: 05/21/2023]
Abstract
Fruit aroma development depends on ripening. Abscisic acid (ABA) has been reported to be involved in the regulation of tomato fruit ripening. In the present study, the effects of exogenous ABA on aromatic volatiles in tomato fruit during postharvest ripening were studied. The results showed that exogenous ABA accelerated color development and ethylene production as well as the accumulation of carotenoids, total phenolics and linoleic acid in tomato fruit during ripening. Moreover, exogenous ABA increased the accumulation of volatile compounds such as 1-peten-3-one (2.06-fold), β-damascenone (1.64-fold), benzaldehyde (3.29-fold) and benzyl cyanide (4.15-fold); induced the expression of key genes implicated in the biosynthesis pathways of aromatic volatiles, including TomloxC, HPL, ADH2, LeCCD1B and SlBCAT1 (the values of the log2 fold changes ranged from -3.02 to 2.97); and promoted the activities of lipoxygenase (LOX), hydroperoxide lyase (HPL) and alcohol dehydrogenase (ADH). In addition, the results of promoter analyses revealed that cis-acting elements involved in ABA responsiveness (ABREs) exist in 8 of the 12 key genes involved in volatile biosynthesis, suggesting that ABA potentially affects aromatic volatile emissions via the regulation of gene expression profiles.
Collapse
Affiliation(s)
- Qiong Wu
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Key Laboratory of Agriculture Ministry for Postharvest Handling of Agro-Products, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, Zhejiang Province, PR China
| | - Xiaoya Tao
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Key Laboratory of Agriculture Ministry for Postharvest Handling of Agro-Products, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, Zhejiang Province, PR China
| | - Xinzi Ai
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Key Laboratory of Agriculture Ministry for Postharvest Handling of Agro-Products, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, Zhejiang Province, PR China
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Key Laboratory of Agriculture Ministry for Postharvest Handling of Agro-Products, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, Zhejiang Province, PR China
| | - Linchun Mao
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Key Laboratory of Agriculture Ministry for Postharvest Handling of Agro-Products, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, Zhejiang Province, PR China
| | - Tiejin Ying
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Key Laboratory of Agriculture Ministry for Postharvest Handling of Agro-Products, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, Zhejiang Province, PR China.
| | - Li Li
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Key Laboratory of Agriculture Ministry for Postharvest Handling of Agro-Products, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, Zhejiang Province, PR China.
| |
Collapse
|
33
|
Wong DCJ, Pichersky E, Peakall R. The Biosynthesis of Unusual Floral Volatiles and Blends Involved in Orchid Pollination by Deception: Current Progress and Future Prospects. FRONTIERS IN PLANT SCIENCE 2017; 8:1955. [PMID: 29181016 PMCID: PMC5693887 DOI: 10.3389/fpls.2017.01955] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/30/2017] [Indexed: 05/23/2023]
Abstract
Flowers have evolved diverse strategies to attract animal pollinators, with visual and olfactory floral cues often crucial for pollinator attraction. While most plants provide reward (e.g., nectar, pollen) in return for the service of pollination, 1000s of plant species, particularly in the orchid family, offer no apparent reward. Instead, they exploit their often specific pollinators (one or few) by mimicking signals of female insects, food source, and oviposition sites, among others. A full understanding of how these deceptive pollination strategies evolve and persist remains an open question. Nonetheless, there is growing evidence that unique blends that often contain unusual compounds in floral volatile constituents are often employed to secure pollination by deception. Thus, the ability of plants to rapidly evolve new pathways for synthesizing floral volatiles may hold the key to the widespread evolution of deceptive pollination. Yet, until now the biosynthesis of these volatile compounds has been largely neglected. While elucidating the biosynthesis in non-model systems is challenging, nonetheless, these cases may also offer untapped potential for biosynthetic breakthroughs given that some of the compounds can be exclusive or dominant components of the floral scent and production is often tissue-specific. In this perspective article, we first highlight the chemical diversity underpinning some of the more widespread deceptive orchid pollination strategies. Next, we explore the potential metabolic pathways and biosynthetic steps that might be involved. Finally, we offer recommendations to accelerate the discovery of the biochemical pathways in these challenging but intriguing systems.
Collapse
Affiliation(s)
- Darren C. J. Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Eran Pichersky
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| |
Collapse
|
34
|
Deng M, Li D, Luo J, Xiao Y, Liu H, Pan Q, Zhang X, Jin M, Zhao M, Yan J. The genetic architecture of amino acids dissection by association and linkage analysis in maize. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1250-1263. [PMID: 28218981 PMCID: PMC5595712 DOI: 10.1111/pbi.12712] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 01/28/2017] [Accepted: 02/14/2017] [Indexed: 05/03/2023]
Abstract
Amino acids are both constituents of proteins, providing the essential nutrition for humans and animals, and signalling molecules regulating the growth and development of plants. Most cultivars of maize are deficient in essential amino acids such as lysine and tryptophan. Here, we measured the levels of 17 different total amino acids, and created 48 derived traits in mature kernels from a maize diversity inbred collection and three recombinant inbred line (RIL) populations. By GWAS, 247 and 281 significant loci were identified in two different environments, 5.1 and 4.4 loci for each trait, explaining 7.44% and 7.90% phenotypic variation for each locus in average, respectively. By linkage mapping, 89, 150 and 165 QTLs were identified in B73/By804, Kui3/B77 and Zong3/Yu87-1 RIL populations, 2.0, 2.7 and 2.8 QTLs for each trait, explaining 13.6%, 16.4% and 21.4% phenotypic variation for each QTL in average, respectively. It implies that the genetic architecture of amino acids is relative simple and controlled by limited loci. About 43.2% of the loci identified by GWAS were verified by expression QTL, and 17 loci overlapped with mapped QTLs in the three RIL populations. GRMZM2G015534, GRMZM2G143008 and one QTL were further validated using molecular approaches. The amino acid biosynthetic and catabolic pathways were reconstructed on the basis of candidate genes proposed in this study. Our results provide insights into the genetic basis of amino acid biosynthesis in maize kernels and may facilitate marker-based breeding for quality protein maize.
Collapse
Affiliation(s)
- Min Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xuehai Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Mingchao Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
35
|
Schaeffer SM, Christian R, Castro-Velasquez N, Hyden B, Lynch-Holm V, Dhingra A. Comparative ultrastructure of fruit plastids in three genetically diverse genotypes of apple (Malus × domestica Borkh.) during development. PLANT CELL REPORTS 2017; 36:1627-1640. [PMID: 28698906 PMCID: PMC5693628 DOI: 10.1007/s00299-017-2179-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 07/03/2017] [Indexed: 05/02/2023]
Abstract
Comparative ultrastructural developmental time-course analysis has identified discrete stages at which the fruit plastids undergo structural and consequently functional transitions to facilitate subsequent development-guided understanding of the complex plastid biology. Plastids are the defining organelle for a plant cell and are critical for myriad metabolic functions. The role of leaf plastid, chloroplast, is extensively documented; however, fruit plastids-chromoplasts-are poorly understood, especially in the context of the diverse metabolic processes operating in these diverse plant organs. Recently, in a comparative study of the predicted plastid-targeted proteomes across seven plant species, we reported that each plant species is predicted to harbor a unique set of plastid-targeted proteins. However, the temporal and developmental context of these processes remains unknown. In this study, an ultrastructural analysis approach was used to characterize fruit plastids in the epidermal and collenchymal cell layers at 11 developmental timepoints in three genotypes of apple (Malus × domestica Borkh.): chlorophyll-predominant 'Granny Smith', carotenoid-predominant 'Golden Delicious', and anthocyanin-predominant 'Top Red Delicious'. Plastids transitioned from a proplastid-like plastid to a chromoplast-like plastid in epidermis cells, while in the collenchyma cells, they transitioned from a chloroplast-like plastid to a chloro-chromo-amyloplast plastid. Plastids in the collenchyma cells of the three genotypes demonstrated a diverse array of structures and features. This study enabled the identification of discrete developmental stages during which specific functions are most likely being performed by the plastids as indicated by accumulation of plastoglobuli, starch granules, and other sub-organeller structures. Information regarding the metabolically active developmental stages is expected to facilitate biologically relevant omics studies to unravel the complex biochemistry of plastids in perennial non-model systems.
Collapse
Affiliation(s)
- Scott M Schaeffer
- Department of Horticulture, Washington State University, Pullman, WA, USA
- Molecular Plant Science Graduate Program, Washington State University, Pullman, WA, USA
- Indigo Agriculture, 500 Rutherford Ave, Suite 201, Charlestown, MA, 02129, USA
| | - Ryan Christian
- Department of Horticulture, Washington State University, Pullman, WA, USA
- Molecular Plant Science Graduate Program, Washington State University, Pullman, WA, USA
| | | | - Brennan Hyden
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Valerie Lynch-Holm
- Franchesci Microscopy and Imaging Center, Washington State University, Pullman, WA, USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, USA.
- Molecular Plant Science Graduate Program, Washington State University, Pullman, WA, USA.
| |
Collapse
|
36
|
Angelovici R, Batushansky A, Deason N, Gonzalez-Jorge S, Gore MA, Fait A, DellaPenna D. Network-Guided GWAS Improves Identification of Genes Affecting Free Amino Acids. PLANT PHYSIOLOGY 2017; 173:872-886. [PMID: 27872244 PMCID: PMC5210728 DOI: 10.1104/pp.16.01287] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/16/2016] [Indexed: 05/18/2023]
Abstract
Amino acids are essential for proper growth and development in plants. Amino acids serve as building blocks for proteins but also are important for responses to stress and the biosynthesis of numerous essential compounds. In seed, the pool of free amino acids (FAAs) also contributes to alternative energy, desiccation, and seed vigor; thus, manipulating FAA levels can significantly impact a seed's nutritional qualities. While genome-wide association studies (GWAS) on branched-chain amino acids have identified some regulatory genes controlling seed FAAs, the genetic regulation of FAA levels, composition, and homeostasis in seeds remains mostly unresolved. Hence, we performed GWAS on 18 FAAs from a 313-ecotype Arabidopsis (Arabidopsis thaliana) association panel. Specifically, GWAS was performed on 98 traits derived from known amino acid metabolic pathways (approach 1) and then on 92 traits generated from an unbiased correlation-based metabolic network analysis (approach 2), and the results were compared. The latter approach facilitated the discovery of additional novel metabolic interactions and single-nucleotide polymorphism-trait associations not identified by the former approach. The most prominent network-guided GWAS signal was for a histidine (His)-related trait in a region containing two genes: a cationic amino acid transporter (CAT4) and a polynucleotide phosphorylase resistant to inhibition with fosmidomycin. A reverse genetics approach confirmed CAT4 to be responsible for the natural variation of His-related traits across the association panel. Given that His is a semiessential amino acid and a potent metal chelator, CAT4 orthologs could be considered as candidate genes for seed quality biofortification in crop plants.
Collapse
Affiliation(s)
- Ruthie Angelovici
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.);
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.);
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.);
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Albert Batushansky
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Nicholas Deason
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Sabrina Gonzalez-Jorge
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Michael A Gore
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Aaron Fait
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Dean DellaPenna
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| |
Collapse
|
37
|
Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation. Proc Natl Acad Sci U S A 2016; 113:12580-12585. [PMID: 27791156 DOI: 10.1073/pnas.1613910113] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Commercial tomatoes are widely perceived by consumers as lacking flavor. A major part of that problem is a postharvest handling system that chills fruit. Low-temperature storage is widely used to slow ripening and reduce decay. However, chilling results in loss of flavor. Flavor-associated volatiles are sensitive to temperatures below 12 °C, and their loss greatly reduces flavor quality. Here, we provide a comprehensive view of the effects of chilling on flavor and volatiles associated with consumer liking. Reduced levels of specific volatiles are associated with significant reductions in transcripts encoding key volatile synthesis enzymes. Although expression of some genes critical to volatile synthesis recovers after a return to 20 °C, some genes do not. RNAs encoding transcription factors essential for ripening, including RIPENING INHIBITOR (RIN), NONRIPENING, and COLORLESS NONRIPENING are reduced in response to chilling and may be responsible for reduced transcript levels in many downstream genes during chilling. Those reductions are accompanied by major changes in the methylation status of promoters, including RIN Methylation changes are transient and may contribute to the fidelity of gene expression required to provide maximal beneficial environmental response with minimal tangential influence on broader fruit developmental biology.
Collapse
|
38
|
Galili G, Amir R, Fernie AR. The Regulation of Essential Amino Acid Synthesis and Accumulation in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:153-78. [PMID: 26735064 DOI: 10.1146/annurev-arplant-043015-112213] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Although amino acids are critical for all forms of life, only proteogenic amino acids that humans and animals cannot synthesize de novo and therefore must acquire in their diets are classified as essential. Nine amino acids-lysine, methionine, threonine, phenylalanine, tryptophan, valine, isoleucine, leucine, and histidine-fit this definition. Despite their nutritional importance, several of these amino acids are present in limiting quantities in many of the world's major crops. In recent years, a combination of reverse genetic and biochemical approaches has been used to define the genes encoding the enzymes responsible for synthesizing, degrading, and regulating these amino acids. In this review, we describe recent advances in our understanding of the metabolism of the essential amino acids, discuss approaches for enhancing their levels in plants, and appraise efforts toward their biofortification in crop plants.
Collapse
Affiliation(s)
- Gad Galili
- Department of Plant Science, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Rachel Amir
- Laboratory of Plant Science, MIGAL-Galilee Research Institute, Kiryat Shmona 11016, Israel;
| | - Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
| |
Collapse
|
39
|
Wang L, Baldwin EA, Bai J. Recent Advance in Aromatic Volatile Research in Tomato Fruit: The Metabolisms and Regulations. FOOD BIOPROCESS TECH 2015. [DOI: 10.1007/s11947-015-1638-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
40
|
Tohge T, Fernie AR. Metabolomics-Inspired Insight into Developmental, Environmental and Genetic Aspects of Tomato Fruit Chemical Composition and Quality. PLANT & CELL PHYSIOLOGY 2015; 56:1681-96. [PMID: 26228272 DOI: 10.1093/pcp/pcv093] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 06/12/2015] [Indexed: 05/20/2023]
Abstract
Tomato was one of the first plant species to be evaluated using metabolomics and remains one of the best characterized, with tomato fruit being both an important source of nutrition in the human diet and a valuable model system for the development of fleshy fruits. Additionally, given the broad habitat range of members of the tomato clade and the extensive use of exotic germplasm in tomato genetic research, it represents an excellent genetic model system for understanding both metabolism per se and the importance of various metabolites in conferring stress tolerance. This review summarizes technical approaches used to characterize the tomato metabolome to date and details insights into metabolic pathway structure and regulation that have been obtained via analysis of tissue samples taken under different developmental or environmental circumstance as well as following genetic perturbation. Particular attention is paid to compounds of importance for nutrition or the shelf-life of tomatoes. We propose furthermore how metabolomics information can be coupled to the burgeoning wealth of genome sequence data from the tomato clade to enhance further our understanding of (i) the shifts in metabolic regulation occurring during development and (ii) specialization of metabolism within the tomato clade as a consequence of either adaptive evolution or domestication.
Collapse
Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| |
Collapse
|
41
|
Lächler K, Imhof J, Reichelt M, Gershenzon J, Binder S. The cytosolic branched-chain aminotransferases of Arabidopsis thaliana influence methionine supply, salvage and glucosinolate metabolism. PLANT MOLECULAR BIOLOGY 2015; 88:119-31. [PMID: 25851613 DOI: 10.1007/s11103-015-0312-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/22/2015] [Indexed: 05/10/2023]
Abstract
Arabidopsis thaliana possesses six branched-chain aminotransferases (BCAT1-6). Previous studies revealed that some members of this protein family are involved in the biosynthesis of branched-chain amino acids and/or in the Met chain elongation pathway, the initial steps towards the biosynthesis of Met-derived glucosinolates. We now analyzed branched-chain aminotransferase 6 (BCAT6). In vivo GFP-tagging experiments strongly suggest this enzyme to be localized to the cytosol. Substrate specificity assays performed with recombinant enzyme revealed that BCAT6 transaminates Val, Leu and Ile as well as the corresponding 2-oxo acids but also transaminates Met and its cognate ketoacid 4-methyl-2-oxobutanoate. We established single (bcat6-1), double (bcat4-2/bcat6-1) and triple (bcat3-1/bcat4-2/bcat6-1) mutants involving BCAT6 with the latter exhibiting a clear macroscopic phenotype with smaller plants and abnormal leaf morphology. Metabolite profiling of these mutants demonstrated that BCAT6 can contribute to Met chain elongation with the triple mutant line lacking BCAT3, 4 and 6 showing a dramatic reduction of Met-derived glucosinolate species down to 32 and 14% of wild-type levels in plant foliage and seeds, respectively. This drop in glucosinolate levels is accompanied by a 46-fold increase of free Met, demonstrating the important role of the three branched-chain aminotransferases in converting Met to its 2-oxo acid for glucosinolate chain elongation. In addition, we determined the relative amounts of 5'-deoxy-5'-methylthioadenosine, an intermediate of the Met recycling pathway. This metabolite accumulated to relative high amounts in the absence of the cytosolic BCAT4 and BCAT6, suggesting that cytosolic Met salvage also contributes to the biosynthesis of glucosinolates.
Collapse
Affiliation(s)
- Kurt Lächler
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
| | | | | | | | | |
Collapse
|
42
|
Alseekh S, Tohge T, Wendenberg R, Scossa F, Omranian N, Li J, Kleessen S, Giavalisco P, Pleban T, Mueller-Roeber B, Zamir D, Nikoloski Z, Fernie AR. Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato. THE PLANT CELL 2015; 27:485-512. [PMID: 25770107 PMCID: PMC4558650 DOI: 10.1105/tpc.114.132266] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 01/27/2015] [Accepted: 02/16/2015] [Indexed: 05/18/2023]
Abstract
A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism.
Collapse
Affiliation(s)
- Saleh Alseekh
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Takayuki Tohge
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Regina Wendenberg
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Federico Scossa
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy
| | - Nooshin Omranian
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany Institute of Biochemistry and Biology, University of Potsdam, D-14476 Potsdam-Golm, Germany
| | - Jie Li
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Sabrina Kleessen
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Patrick Giavalisco
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Tzili Pleban
- Institute of Plant Sciences and Genetics and Otto Warburg Centre for Biotechnology, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Bernd Mueller-Roeber
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany Institute of Biochemistry and Biology, University of Potsdam, D-14476 Potsdam-Golm, Germany
| | - Dani Zamir
- Institute of Plant Sciences and Genetics and Otto Warburg Centre for Biotechnology, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Zoran Nikoloski
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| |
Collapse
|
43
|
Rambla JL, Tikunov YM, Monforte AJ, Bovy AG, Granell A. The expanded tomato fruit volatile landscape. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4613-23. [PMID: 24692651 DOI: 10.1093/jxb/eru128] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The present review aims to synthesize our present knowledge about the mechanisms implied in the biosynthesis of volatile compounds in the ripe tomato fruit, which have a key role in tomato flavour. The difficulties in identifiying not only genes or genomic regions but also individual target compounds for plant breeding are addressed. Ample variability in the levels of almost any volatile compound exists, not only in the populations derived from interspecific crosses but also in heirloom varieties and even in commercial hybrids. Quantitative trait loci (QTLs) for all tomato aroma volatiles have been identified in collections derived from both intraspecific and interspecific crosses with different wild tomato species and they (i) fail to co-localize with structural genes in the volatile biosynthetic pathways and (ii) reveal very little coincidence in the genomic regions characterized, indicating that there is ample opportunity to reinforce the levels of the volatiles of interest. Some of the identified genes may be useful as markers or as biotechnological tools to enhance tomato aroma. Current knowledge about the major volatile biosynthetic pathways in the fruit is summarized. Finally, and based on recent reports, it is stressed that conjugation to other metabolites such as sugars seems to play a key role in the modulation of volatile release, at least in some metabolic pathways.
Collapse
Affiliation(s)
- José L Rambla
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica Valencia, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Yury M Tikunov
- Wageningen UR Plant Breeding, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Antonio J Monforte
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica Valencia, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Arnaud G Bovy
- Wageningen UR Plant Breeding, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica Valencia, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| |
Collapse
|
44
|
Xu Z, Hansen MA, Hansen LH, Jacquiod S, Sørensen SJ. Bioinformatic approaches reveal metagenomic characterization of soil microbial community. PLoS One 2014; 9:e93445. [PMID: 24691166 PMCID: PMC3972102 DOI: 10.1371/journal.pone.0093445] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 02/28/2014] [Indexed: 11/22/2022] Open
Abstract
As is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the Earth. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. However, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. In the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, Arctic soil, and mangrove sediment) and integrated some state-of-the-art computational tools to explore the phylogenetic and functional characterizations of the microbial communities in soil. Microbial composition and metabolic potential in soils were comprehensively illustrated at the metagenomic level. A spectrum of metagenomic biomarkers containing 46 taxa and 33 metabolic modules were detected to be significantly differential that could be used as indicators to distinguish at least one of five soil communities. The co-occurrence associations between complex microbial compositions and functions were inferred by network-based approaches. Our results together with the established bioinformatic pipelines should provide a foundation for future research into the relation between soil biodiversity and ecosystem function.
Collapse
Affiliation(s)
- Zhuofei Xu
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Asser Hansen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lars H. Hansen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Samuel Jacquiod
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Søren J. Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
| |
Collapse
|
45
|
Klie S, Osorio S, Tohge T, Drincovich MF, Fait A, Giovannoni JJ, Fernie AR, Nikoloski Z. Conserved changes in the dynamics of metabolic processes during fruit development and ripening across species. PLANT PHYSIOLOGY 2014; 164:55-68. [PMID: 24243932 PMCID: PMC3875825 DOI: 10.1104/pp.113.226142] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 11/13/2013] [Indexed: 05/18/2023]
Abstract
Computational analyses of molecular phenotypes traditionally aim at identifying biochemical components that exhibit differential expression under various scenarios (e.g. environmental and internal perturbations) in a single species. High-throughput metabolomics technologies allow the quantification of (relative) metabolite levels across developmental stages in different tissues, organs, and species. Novel methods for analyzing the resulting multiple data tables could reveal preserved dynamics of metabolic processes across species. The problem we address in this study is 2-fold. (1) We derive a single data table, referred to as a compromise, which captures information common to the investigated set of multiple tables containing data on different fruit development and ripening stages in three climacteric (i.e. peach [Prunus persica] and two tomato [Solanum lycopersicum] cultivars, Ailsa Craig and M82) and two nonclimacteric (i.e. strawberry [Fragaria × ananassa] and pepper [Capsicum chilense]) fruits; in addition, we demonstrate the power of the method to discern similarities and differences between multiple tables by analyzing publicly available metabolomics data from three tomato ripening mutants together with two tomato cultivars. (2) We identify the conserved dynamics of metabolic processes, reflected in the data profiles of the corresponding metabolites that contribute most to the determined compromise. Our analysis is based on an extension to principal component analysis, called STATIS, in combination with pathway overenrichment analysis. Based on publicly available metabolic profiles for the investigated species, we demonstrate that STATIS can be used to identify the metabolic processes whose behavior is similarly affected during fruit development and ripening. These findings ultimately provide insights into the pathways that are essential during fruit development and ripening across species.
Collapse
Affiliation(s)
- Sebastian Klie
- Genes and Small Molecules Group (S.K.), Central Metabolism Group (T.T., A.R.F.), and Systems Biology and Mathematical Modeling Group (Z.N.), Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” University of Malaga-Consejo Superior de Investigaciones Científicas, Department of Molecular Biology and Biochemistry, Campus de Teatinos, 29071 Malaga, Spain (S.O.)
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Rosario 2000, Argentina (M.F.D.)
- French Associates Institute for Agriculture and Biotechnology of Dryland, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negrev, Sede Boquer 84990, Israel (A.F.); and
- Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Cornell University, Ithaca, New York 14853 (J.J.G.)
| | | | - Takayuki Tohge
- Genes and Small Molecules Group (S.K.), Central Metabolism Group (T.T., A.R.F.), and Systems Biology and Mathematical Modeling Group (Z.N.), Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” University of Malaga-Consejo Superior de Investigaciones Científicas, Department of Molecular Biology and Biochemistry, Campus de Teatinos, 29071 Malaga, Spain (S.O.)
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Rosario 2000, Argentina (M.F.D.)
- French Associates Institute for Agriculture and Biotechnology of Dryland, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negrev, Sede Boquer 84990, Israel (A.F.); and
- Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Cornell University, Ithaca, New York 14853 (J.J.G.)
| | - María F. Drincovich
- Genes and Small Molecules Group (S.K.), Central Metabolism Group (T.T., A.R.F.), and Systems Biology and Mathematical Modeling Group (Z.N.), Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” University of Malaga-Consejo Superior de Investigaciones Científicas, Department of Molecular Biology and Biochemistry, Campus de Teatinos, 29071 Malaga, Spain (S.O.)
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Rosario 2000, Argentina (M.F.D.)
- French Associates Institute for Agriculture and Biotechnology of Dryland, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negrev, Sede Boquer 84990, Israel (A.F.); and
- Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Cornell University, Ithaca, New York 14853 (J.J.G.)
| | - Aaron Fait
- Genes and Small Molecules Group (S.K.), Central Metabolism Group (T.T., A.R.F.), and Systems Biology and Mathematical Modeling Group (Z.N.), Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” University of Malaga-Consejo Superior de Investigaciones Científicas, Department of Molecular Biology and Biochemistry, Campus de Teatinos, 29071 Malaga, Spain (S.O.)
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Rosario 2000, Argentina (M.F.D.)
- French Associates Institute for Agriculture and Biotechnology of Dryland, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negrev, Sede Boquer 84990, Israel (A.F.); and
- Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Cornell University, Ithaca, New York 14853 (J.J.G.)
| | - James J. Giovannoni
- Genes and Small Molecules Group (S.K.), Central Metabolism Group (T.T., A.R.F.), and Systems Biology and Mathematical Modeling Group (Z.N.), Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” University of Malaga-Consejo Superior de Investigaciones Científicas, Department of Molecular Biology and Biochemistry, Campus de Teatinos, 29071 Malaga, Spain (S.O.)
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Rosario 2000, Argentina (M.F.D.)
- French Associates Institute for Agriculture and Biotechnology of Dryland, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negrev, Sede Boquer 84990, Israel (A.F.); and
- Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Cornell University, Ithaca, New York 14853 (J.J.G.)
| | - Alisdair R. Fernie
- Genes and Small Molecules Group (S.K.), Central Metabolism Group (T.T., A.R.F.), and Systems Biology and Mathematical Modeling Group (Z.N.), Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” University of Malaga-Consejo Superior de Investigaciones Científicas, Department of Molecular Biology and Biochemistry, Campus de Teatinos, 29071 Malaga, Spain (S.O.)
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Rosario 2000, Argentina (M.F.D.)
- French Associates Institute for Agriculture and Biotechnology of Dryland, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negrev, Sede Boquer 84990, Israel (A.F.); and
- Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Cornell University, Ithaca, New York 14853 (J.J.G.)
| | - Zoran Nikoloski
- Genes and Small Molecules Group (S.K.), Central Metabolism Group (T.T., A.R.F.), and Systems Biology and Mathematical Modeling Group (Z.N.), Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” University of Malaga-Consejo Superior de Investigaciones Científicas, Department of Molecular Biology and Biochemistry, Campus de Teatinos, 29071 Malaga, Spain (S.O.)
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Rosario 2000, Argentina (M.F.D.)
- French Associates Institute for Agriculture and Biotechnology of Dryland, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negrev, Sede Boquer 84990, Israel (A.F.); and
- Thompson Institute for Plant Research and United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Cornell University, Ithaca, New York 14853 (J.J.G.)
| |
Collapse
|
46
|
Angelovici R, Lipka AE, Deason N, Gonzalez-Jorge S, Lin H, Cepela J, Buell R, Gore MA, DellaPenna D. Genome-wide analysis of branched-chain amino acid levels in Arabidopsis seeds. THE PLANT CELL 2013; 25:4827-43. [PMID: 24368787 PMCID: PMC3903990 DOI: 10.1105/tpc.113.119370] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Revised: 11/26/2013] [Accepted: 12/10/2013] [Indexed: 05/18/2023]
Abstract
Branched-chain amino acids (BCAAs) are three of the nine essential amino acids in human and animal diets and are important for numerous processes in development and growth. However, seed BCAA levels in major crops are insufficient to meet dietary requirements, making genetic improvement for increased and balanced seed BCAAs an important nutritional target. Addressing this issue requires a better understanding of the genetics underlying seed BCAA content and composition. Here, a genome-wide association study and haplotype analysis for seed BCAA traits in Arabidopsis thaliana revealed a strong association with a chromosomal interval containing two branched-chain amino acid transferases, BCAT1 and BCAT2. Linkage analysis, reverse genetic approaches, and molecular complementation analysis demonstrated that allelic variation at BCAT2 is responsible for the natural variation of seed BCAAs in this interval. Complementation analysis of a bcat2 null mutant with two significantly different alleles from accessions Bayreuth-0 and Shahdara is consistent with BCAT2 contributing to natural variation in BCAA levels, glutamate recycling, and free amino acid homeostasis in seeds in an allele-dependent manner. The seed-specific phenotype of bcat2 null alleles, its strong transcription induction during late seed development, and its subcellular localization to the mitochondria are consistent with a unique, catabolic role for BCAT2 in BCAA metabolism in seeds.
Collapse
Affiliation(s)
- Ruthie Angelovici
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824–1319
| | - Alexander E. Lipka
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
| | - Nicholas Deason
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824–1319
| | - Sabrina Gonzalez-Jorge
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824–1319
| | | | - Jason Cepela
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Michael A. Gore
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853
| | - Dean DellaPenna
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824–1319
- Address correspondence to
| |
Collapse
|
47
|
Clark SM, Vaitheeswaran V, Ambrose SJ, Purves RW, Page JE. Transcriptome analysis of bitter acid biosynthesis and precursor pathways in hop (Humulus lupulus). BMC PLANT BIOLOGY 2013; 13:12. [PMID: 23347725 PMCID: PMC3564914 DOI: 10.1186/1471-2229-13-12] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 12/12/2012] [Indexed: 05/02/2023]
Abstract
BACKGROUND Bitter acids (e.g. humulone) are prenylated polyketides synthesized in lupulin glands of the hop plant (Humulus lupulus) which are important contributors to the bitter flavour and stability of beer. Bitter acids are formed from acyl-CoA precursors derived from branched-chain amino acid (BCAA) degradation and C5 prenyl diphosphates from the methyl-D-erythritol 4-phosphate (MEP) pathway. We used RNA sequencing (RNA-seq) to obtain the transcriptomes of isolated lupulin glands, cones with glands removed and leaves from high α-acid hop cultivars, and analyzed these datasets for genes involved in bitter acid biosynthesis including the supply of major precursors. We also measured the levels of BCAAs, acyl-CoA intermediates, and bitter acids in glands, cones and leaves. RESULTS Transcripts encoding all the enzymes of BCAA metabolism were significantly more abundant in lupulin glands, indicating that BCAA biosynthesis and subsequent degradation occurs in these specialized cells. Branched-chain acyl-CoAs and bitter acids were present at higher levels in glands compared with leaves and cones. RNA-seq analysis showed the gland-specific expression of the MEP pathway, enzymes of sucrose degradation and several transcription factors that may regulate bitter acid biosynthesis in glands. Two branched-chain aminotransferase (BCAT) enzymes, HlBCAT1 and HlBCAT2, were abundant, with gene expression quantification by RNA-seq and qRT-PCR indicating that HlBCAT1 was specific to glands while HlBCAT2 was present in glands, cones and leaves. Recombinant HlBCAT1 and HlBCAT2 catalyzed forward (biosynthetic) and reverse (catabolic) reactions with similar kinetic parameters. HlBCAT1 is targeted to mitochondria where it likely plays a role in BCAA catabolism. HlBCAT2 is a plastidial enzyme likely involved in BCAA biosynthesis. Phylogenetic analysis of the hop BCATs and those from other plants showed that they group into distinct biosynthetic (plastidial) and catabolic (mitochondrial) clades. CONCLUSIONS Our analysis of the hop transcriptome significantly expands the genomic resources available for this agriculturally-important crop. This study provides evidence for the lupulin gland-specific biosynthesis of BCAAs and prenyl diphosphates to provide precursors for the production of bitter acids. The biosynthetic pathway leading to BCAAs in lupulin glands involves the plastidial enzyme, HlBCAT2. The mitochondrial enzyme HlBCAT1 degrades BCAAs as the first step in the catabolic pathway leading to branched chain-acyl-CoAs.
Collapse
Affiliation(s)
- Shawn M Clark
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Vinidhra Vaitheeswaran
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Stephen J Ambrose
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Randy W Purves
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Jonathan E Page
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK, S7N 5E2, Canada
| |
Collapse
|
48
|
Abstract
For optimal plant growth and development, cellular nitrogen (N) metabolism must be closely coordinated with other metabolic pathways, and mitochondria are thought to play a central role in this process. Recent studies using genetically modified plants have provided insight into the role of mitochondria in N metabolism. Mitochondrial metabolism is linked with N assimilation by amino acid, carbon (C) and redox metabolism. Mitochondria are not only an important source of C skeletons for N incorporation, they also produce other necessary metabolites and energy used in N remobilization processes. Nitric oxide of mitochondrial origin regulates respiration and influences primary N metabolism. Here, we discuss the changes in mitochondrial metabolism during ammonium or nitrate nutrition and under low N conditions. We also describe the involvement of mitochondria in the redistribution of N during senescence. The aim of this review was to demonstrate the role of mitochondria as an integration point of N cellular metabolism.
Collapse
Affiliation(s)
- Bożena Szal
- Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | | |
Collapse
|
49
|
Kirma M, Araújo WL, Fernie AR, Galili G. The multifaceted role of aspartate-family amino acids in plant metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:4995-5001. [PMID: 22516796 DOI: 10.1093/jxb/ers119] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Plants represent the major sources of human foods and livestock feeds, worldwide. However, the limited content of the essential amino acid lysine in cereal grains represents a major nutritional problem for human and for livestock feeding in developed countries. Optimizing the level of lysine in cereal grains requires extensive knowledge on the biological processes regulating the homeostasis of this essential amino acid as well as the biological consequences of this homeostasis. Manipulating biosynthetic and catabolic enzymes of lysine metabolism enabled an enhanced accumulation of this essential amino acid in seeds. However, this approach had a major effect on the levels of various metabolites of the tricarboxylic acid (TCA) cycle, revealing a strong interaction between lysine metabolism and cellular energy metabolism. Recent studies discussed here have shed new light on the metabolic processes responsible for the catabolism of lysine, as well as isoleucine, another amino acid of the aspartate-family pathway, into the TCA cycle. Here we discuss progress being made to understand biological processes associated with the catabolism of amino acids of the aspartate-family pathway and its importance for optimal improvement of the nutritional quality of plants.
Collapse
Affiliation(s)
- Menny Kirma
- Department of Plant Science, The Weizmnn Institute of Science, Rehovot 76100, Israel
| | | | | | | |
Collapse
|
50
|
Allen DK, Laclair RW, Ohlrogge JB, Shachar-Hill Y. Isotope labelling of Rubisco subunits provides in vivo information on subcellular biosynthesis and exchange of amino acids between compartments. PLANT, CELL & ENVIRONMENT 2012; 35:1232-44. [PMID: 22292468 PMCID: PMC3556518 DOI: 10.1111/j.1365-3040.2012.02485.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Revised: 01/19/2012] [Accepted: 01/22/2012] [Indexed: 05/18/2023]
Abstract
The architecture of plant metabolism includes substantial duplication of metabolite pools and enzyme catalyzed reactions in different subcellular compartments. This poses challenges for understanding the regulation of metabolism particularly in primary metabolism and amino acid biosynthesis. To explore the extent to which amino acids are made in single compartments and to gain insight into the metabolic precursors from which they derive, we used steady state (13) C labelling and analysed labelling in protein amino acids from plastid and cytosol. Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a major component of green tissues and its large and small subunits are synthesized from different pools of amino acids in the plastid and cytosol, respectively. Developing Brassica napus embryos were cultured in the presence of [U-(13) C]-sucrose, [U-(13) C]-glucose, [U-(13) C]-glutamine or [U-(13) C]-alanine to generate proteins. The large subunits (LSU) and small subunits (SSU) of Rubisco were isolated and the labelling in their constituent amino acids was analysed by gas chromatography-mass spectrometry. Amino acids including alanine, glycine and serine exhibited different (13) C enrichment in the LSU and SSU, demonstrating that these pools have different metabolic origins and are not isotopically equilibrated between the plastid and cytosol on the time scale of cellular growth. Potential extensions of this novel approach to other macromolecules, organelles and cell types of eukaryotes are discussed.
Collapse
Affiliation(s)
- Doug K Allen
- USDA-ARS, Plant Genetics Research Unit, St Louis, MO 63132, USA Donald Danforth Plant Science Center, St Louis, MO 63132, USA.
| | | | | | | |
Collapse
|