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Do TD, Vuong TD, Dunn D, Clubb M, Valliyodan B, Patil G, Chen P, Xu D, Nguyen HT, Shannon JG. Identification of new loci for salt tolerance in soybean by high-resolution genome-wide association mapping. BMC Genomics 2019; 20:318. [PMID: 31023240 PMCID: PMC6485111 DOI: 10.1186/s12864-019-5662-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/31/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Salinity is an abiotic stress that negatively affects soybean [Glycine max (L.) Merr.] seed yield. Although a major gene for salt tolerance was identified and consistently mapped to chromosome (Chr.) 3 by linkage mapping studies, it does not fully explain genetic variability for tolerance in soybean germplasm. In this study, a genome-wide association study (GWAS) was performed to map genomic regions for salt tolerance in a diverse panel of 305 soybean accessions using a single nucleotide polymorphism (SNP) dataset derived from the SoySNP50K iSelect BeadChip. A second GWAS was also conducted in a subset of 234 accessions using another 3.7 M SNP dataset derived from a whole-genome resequencing (WGRS) study. In addition, three gene-based markers (GBM) of the known gene, Glyma03g32900, on Chr. 3 were also integrated into the two datasets. Salt tolerance among soybean lines was evaluated by leaf scorch score (LSS), chlorophyll content ratio (CCR), leaf sodium content (LSC), and leaf chloride content (LCC). RESULTS For both association studies, a major locus for salt tolerance on Chr. 3 was confirmed by a number of significant SNPs, of which three gene-based SNP markers, Salt-20, Salt14056 and Salt11655, had the highest association with all four traits studied. Also, additional genomic regions on Chrs. 1, 8, and 18 were found to be associated with various traits measured in the second GWAS using the WGRS-derived SNP dataset. CONCLUSIONS A region identified on Chr. 8 was identified to be associated with all four traits and predicted as a new minor locus for salt tolerance in soybean. The candidate genes harbored in this minor locus may help reveal the molecular mechanism involved in salt tolerance and to improve tolerance in soybean cultivars. The significant SNPs will be useful for marker-assisted selection for salt tolerance in soybean breeding programs.
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Affiliation(s)
- Tuyen D. Do
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
- Present address: The Cuu Long Delta Rice Research Institute, Thoi Lai District, Can Tho City, Vietnam
| | - Tri D. Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - David Dunn
- Division of Plant Sciences, University of Missouri, Portageville, MO 63873 USA
| | - Michael Clubb
- Division of Plant Sciences, University of Missouri, Portageville, MO 63873 USA
| | - Babu Valliyodan
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Gunvant Patil
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
- Present Address: Department Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 USA
| | - Pengyin Chen
- Division of Plant Sciences, University of Missouri, Portageville, MO 63873 USA
| | - Dong Xu
- Department of Electric Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211 USA
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - J. Grover Shannon
- Division of Plant Sciences, University of Missouri, Portageville, MO 63873 USA
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Kalladan R, Lasky JR, Sharma S, Kumar MN, Juenger TE, Des Marais DL, Verslues PE. Natural Variation in 9-Cis-Epoxycartenoid Dioxygenase 3 and ABA Accumulation. PLANT PHYSIOLOGY 2019; 179:1620-1631. [PMID: 30710052 PMCID: PMC6446753 DOI: 10.1104/pp.18.01185] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 01/23/2019] [Indexed: 05/18/2023]
Abstract
The stress hormone abscisic acid (ABA) is critical for drought resistance; however, mechanisms controlling ABA levels are unclear. At low water potential, ABA accumulation in the Arabidopsis (Arabidopsis thaliana) accession Shahdara (Sha) was less than that in Landsberg erecta (Ler) or Columbia. Analysis of a Ler × Sha recombinant inbred line population revealed a single major-effect quantitative trait locus for ABA accumulation, which included 9-cis-epoxycarotenoid dioxygenase3 (NCED3) as a candidate gene. NCED3 encodes a rate-limiting enzyme for stress-induced ABA synthesis. Complementation experiments indicated that Sha has a reduced-function NCED3 allele. Compared with Ler, Sha did not have reduced NCED3 gene expression or protein level but did have four amino acid substitutions within NCED3. Sha differed from Ler in the apparent molecular mass of NCED3, indicative of altered NCED3 proteolytic processing in the chloroplast. Site-directed mutagenesis demonstrated that substitution at amino acid 271 was critical for the altered NCED3 molecular mass pattern, while the other Sha NCED3 polymorphisms were also involved in the reduced ABA accumulation. Sha did not have a reduced level of thylakoid-bound NCED3 but did differ from Ler in the apparent molecular mass of stromal NCED3. As Sha was not impaired in known factors critical for NCED3 function in ABA synthesis (expression, chloroplast import, and thylakoid binding), the differences between Ler and Sha NCED3 may affect NCED3 activity or other factors influencing NCED3 function. These results identify functionally important sites on NCED3 and indicate a complex pattern of NCED3 posttranslational regulation in the chloroplast.
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Affiliation(s)
- Rajesh Kalladan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Sandeep Sharma
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - M Nagaraj Kumar
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
| | - David L Des Marais
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Paul E Verslues
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
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Liang Y, Kong F, Torres-Romero I, Burlacot A, Cuine S, Légeret B, Billon E, Brotman Y, Alseekh S, Fernie AR, Beisson F, Peltier G, Li-Beisson Y. Branched-Chain Amino Acid Catabolism Impacts Triacylglycerol Homeostasis in Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2019; 179:1502-1514. [PMID: 30728273 PMCID: PMC6446750 DOI: 10.1104/pp.18.01584] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 01/30/2019] [Indexed: 05/05/2023]
Abstract
Nitrogen (N) starvation-induced triacylglycerol (TAG) synthesis, and its complex relationship with starch metabolism in algal cells, has been intensively studied; however, few studies have examined the interaction between amino acid metabolism and TAG biosynthesis. Here, via a forward genetic screen for TAG homeostasis, we isolated a Chlamydomonas (Chlamydomonas reinhardtii) mutant (bkdE1α) that is deficient in the E1α subunit of the branched-chain ketoacid dehydrogenase (BCKDH) complex. Metabolomics analysis revealed a defect in the catabolism of branched-chain amino acids in bkdE1α Furthermore, this mutant accumulated 30% less TAG than the parental strain during N starvation and was compromised in TAG remobilization upon N resupply. Intriguingly, the rate of mitochondrial respiration was 20% to 35% lower in bkdE1α compared with the parental strains. Three additional knockout mutants of the other components of the BCKDH complex exhibited phenotypes similar to that of bkdE1α Transcriptional responses of BCKDH to different N status were consistent with its role in TAG homeostasis. Collectively, these results indicate that branched-chain amino acid catabolism contributes to TAG metabolism by providing carbon precursors and ATP, thus highlighting the complex interplay between distinct subcellular metabolisms for oil storage in green microalgae.
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Affiliation(s)
- Yuanxue Liang
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Fantao Kong
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Ismael Torres-Romero
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Adrien Burlacot
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Stéphan Cuine
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Bertrand Légeret
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Emmanuelle Billon
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Yariv Brotman
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Fred Beisson
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Gilles Peltier
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
| | - Yonghua Li-Beisson
- Aix-Marseille University, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique Cadarache, Saint-Paul-lez Durance F-13108, France
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de Oliveira MVV, Jin X, Chen X, Griffith D, Batchu S, Maeda HA. Imbalance of tyrosine by modulating TyrA arogenate dehydrogenases impacts growth and development of Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:901-922. [PMID: 30457178 DOI: 10.1111/tpj.14169] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/09/2018] [Accepted: 11/13/2018] [Indexed: 06/09/2023]
Abstract
l-Tyrosine is an essential aromatic amino acid required for the synthesis of proteins and a diverse array of plant natural products; however, little is known on how the levels of tyrosine are controlled in planta and linked to overall growth and development. Most plants synthesize tyrosine by TyrA arogenate dehydrogenases, which are strongly feedback-inhibited by tyrosine and encoded by TyrA1 and TyrA2 genes in Arabidopsis thaliana. While TyrA enzymes have been extensively characterized at biochemical levels, their in planta functions remain uncertain. Here we found that TyrA1 suppression reduces seed yield due to impaired anther dehiscence, whereas TyrA2 knockout leads to slow growth with reticulate leaves. The tyra2 mutant phenotypes were exacerbated by TyrA1 suppression and rescued by the expression of TyrA2, TyrA1 or tyrosine feeding. Low-light conditions synchronized the tyra2 and wild-type growth, and ameliorated the tyra2 leaf reticulation. After shifting to normal light, tyra2 transiently decreased tyrosine and subsequently increased aspartate before the appearance of the leaf phenotypes. Overexpression of the deregulated TyrA enzymes led to hyper-accumulation of tyrosine, which was also accompanied by elevated aspartate and reticulate leaves. These results revealed that TyrA1 and TyrA2 have distinct and overlapping functions in flower and leaf development, respectively, and that imbalance of tyrosine, caused by altered TyrA activity and regulation, impacts growth and development of Arabidopsis. The findings provide critical bases for improving the production of tyrosine and its derived natural products, and further elucidating the coordinated metabolic and physiological processes to maintain tyrosine levels in plants.
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Affiliation(s)
- Marcos V V de Oliveira
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Xing Jin
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Xuan Chen
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Daniel Griffith
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Sai Batchu
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
- Department of Biology, The College of New Jersey, Biology Building, 2000 Pennington Road, Ewing, NJ, 08628, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
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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
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Fang C, Luo J, Wang S. The Diversity of Nutritional Metabolites: Origin, Dissection, and Application in Crop Breeding. FRONTIERS IN PLANT SCIENCE 2019; 10:1028. [PMID: 31475024 PMCID: PMC6706459 DOI: 10.3389/fpls.2019.01028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/23/2019] [Indexed: 05/21/2023]
Abstract
The chemical diversity of plants is very high, and plant-based foods provide almost all the nutrients necessary for human health, either directly or indirectly. With advancements in plant metabolomics studies, the concept of nutritional metabolites has been expanded and updated. Because the concentration of many nutrients is usually low in plant-based foods, especially those from crops, metabolome-assisted breeding techniques using molecular markers associated with the synthesis of nutritional metabolites have been developed and used to improve nutritional quality of crops. Here, we review the origins of the diversity of nutrient metabolites from a genomic perspective and the role of gene duplication and divergence. In addition, we systematically review recent advances in the metabolomic and genetic basis of metabolite production in major crops. With the development of genome sequencing and metabolic detection technologies, multi-omic integrative analysis of genomes, transcriptomes, and metabolomes has greatly facilitated the deciphering of the genetic basis of metabolic pathways and the diversity of nutrient metabolites. Finally, we summarize the application of nutrient diversity in crop breeding and discuss the future development of a viable alternative to metabolome-assisted breeding techniques that can be used to improve crop nutrient quality.
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Affiliation(s)
- Chuanying Fang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shouchuang Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- *Correspondence: Shouchuang Wang,
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Ren Y, Yobi A, Marshall L, Angelovici R, Rodriguez O, Holding DR. Generation and Evaluation of Modified Opaque-2 Popcorn Suggests a Route to Quality Protein Popcorn. FRONTIERS IN PLANT SCIENCE 2018; 9:1803. [PMID: 30574157 PMCID: PMC6291453 DOI: 10.3389/fpls.2018.01803] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/20/2018] [Indexed: 06/01/2023]
Abstract
Introducing traits from dent corn to popcorn is challenging because it is difficult to recover adequate popping characteristics. QPM (Quality Protein Maize) is a dent corn variety carrying the opaque-2 (o2) mutation, specifying increased amounts of normally limiting essential amino acids, and modifier genes which restore the wild type vitreous kernel phenotype. In this study, we introgressed o2 and selected for endosperm modification using vitreousness and high 27-kD gamma zein content. In this way, we recovered high-lysine, fully poppable Quality Protein Popcorn (QPP). BC2F4 individuals with vitreous kernels were confirmed to be o2 mutants by both genotyping and SDS-PAGE. Amino acid profiling of BC2F4 individuals showed that they all have significantly increased lysine compared with popcorn parental lines. Principal Component Analysis of the amino acid profiles showed that all introgressions were grouped with corresponding QPM parental lines. Popping analysis of the BC2F5 individuals showed that while there is variability in popping volume between lines, some lines show equivalent popping to the popcorn parent. In this proof-of-concept study for QPP, we have shown that it is possible to rapidly recover sufficient popcorn characteristics in a modified o2 background using simple phenotypic, biochemical and genetic selection. Furthermore, this shows increased γ-zein is an acceptable substitute for α-zein for full poppability. Since we have developed multiple QPP introgressions, this gives good scope for ongoing hybrid production and future evaluation of agronomic performance and selection of elite hybrids. In a wider context, this study shows the potential for breeding beneficial traits into popcorn for agronomic improvement.
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Affiliation(s)
- Ying Ren
- Department of Agronomy and Horticulture, University of Nebraska – Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation – Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, United States
| | - Abou Yobi
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Leandra Marshall
- Department of Agronomy and Horticulture, University of Nebraska – Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation – Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, United States
| | - Ruthie Angelovici
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Oscar Rodriguez
- Department of Agronomy and Horticulture, University of Nebraska – Lincoln, Lincoln, NE, United States
| | - David R. Holding
- Department of Agronomy and Horticulture, University of Nebraska – Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation – Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, United States
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Zhang Z, Dunwell JM, Zhang YM. An integrated omics analysis reveals molecular mechanisms that are associated with differences in seed oil content between Glycine max and Brassica napus. BMC PLANT BIOLOGY 2018; 18:328. [PMID: 30514240 PMCID: PMC6280547 DOI: 10.1186/s12870-018-1542-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 11/20/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND Rapeseed (Brassica napus L.) and soybean (Glycine max L.) seeds are rich in both protein and oil, which are major sources of biofuels and nutrition. Although the difference in seed oil content between soybean (~ 20%) and rapeseed (~ 40%) exists, little is known about its underlying molecular mechanism. RESULTS An integrated omics analysis was performed in soybean, rapeseed, Arabidopsis (Arabidopsis thaliana L. Heynh), and sesame (Sesamum indicum L.), based on Arabidopsis acyl-lipid metabolism- and carbon metabolism-related genes. As a result, candidate genes and their transcription factors and microRNAs, along with phylogenetic analysis and co-expression network analysis of the PEPC gene family, were found to be largely associated with the difference between the two species. First, three soybean genes (Glyma.13G148600, Glyma.13G207900 and Glyma.12G122900) co-expressed with GmPEPC1 are specifically enriched during seed storage protein accumulation stages, while the expression of BnPEPC1 is putatively inhibited by bna-miR169, and two genes BnSTKA and BnCKII are co-expressed with BnPEPC1 and are specifically associated with plant circadian rhythm, which are related to seed oil biosynthesis. Then, in de novo fatty acid synthesis there are rapeseed-specific genes encoding subunits β-CT (BnaC05g37990D) and BCCP1 (BnaA03g06000D) of heterogeneous ACCase, which could interfere with synthesis rate, and β-CT is positively regulated by four transcription factors (BnaA01g37250D, BnaA02g26190D, BnaC01g01040D and BnaC07g21470D). In triglyceride synthesis, GmLPAAT2 is putatively inhibited by three miRNAs (gma-miR171, gma-miR1516 and gma-miR5775). Finally, in rapeseed there was evidence for the expansion of gene families, CALO, OBO and STERO, related to lipid storage, and the contraction of gene families, LOX, LAH and HSI2, related to oil degradation. CONCLUSIONS The molecular mechanisms associated with differences in seed oil content provide the basis for future breeding efforts to improve seed oil content.
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Affiliation(s)
- Zhibin Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000 China
| | - Jim M. Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AS UK
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
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Yobi A, Angelovici R. A High-Throughput Absolute-Level Quantification of Protein-Bound Amino Acids in Seeds. ACTA ACUST UNITED AC 2018; 3:e20084. [PMID: 30408333 DOI: 10.1002/cppb.20084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this unit, we describe a high-throughput absolute quantification protocol for 16 protein-bound amino acids (PBAAs) that combines a microscale protein hydrolysis step and an absolute quantification step using multiple reaction monitoring-based liquid chromatography-tandem mass spectrometry detection. The approach facilitates analysis of a few hundred samples per week by using a 96-well-plate extraction setup and avoiding use of additives. Importantly, the method uses only ∼3 mg of tissue per sample and includes 12 heavy-amino-acid internal standards to enable quantification of the absolute levels of PBAAs with high precision, accuracy, and reproducibility. The protocol described herein has been optimized for seed samples but is applicable to other plant tissues. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Abou Yobi
- Bond Life Sciences Center, Division of Biological Sciences, Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri
| | - Ruthie Angelovici
- Bond Life Sciences Center, Division of Biological Sciences, Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri
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Amir R, Galili G, Cohen H. The metabolic roles of free amino acids during seed development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 275:11-18. [PMID: 30107877 DOI: 10.1016/j.plantsci.2018.06.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/07/2018] [Accepted: 06/13/2018] [Indexed: 05/03/2023]
Abstract
Amino acids play vital roles in the central metabolism of seeds. They are primarily utilized for the synthesis of seed-storage proteins, but also serve as precursors for the biosynthesis of secondary metabolites and as a source of energy. Here, we aimed at describing the knowledge accumulated in recent years describing the changes occurring in the contents of free amino acids (FAAs) during seed development. Since several essential amino acids are found in low levels in seeds (e.g., Lys, Met, Thr, Val, Leu, Ile and His), or play unique functional roles in seed development (e.g., Pro and the non-proteinogenic γ-aminobutyrate [GABA]), we also briefly describe studies carried out in order to alter their levels in seeds and determine the effects of the manipulation on seed biology. The lion share of these studies highlights strong positive correlations between the biosynthetic pathways of FAAs, meaning that when the levels of a certain amino acid change in seeds, the contents of other FAAs tend to elevate as well. These observations infer a tight regulatory network operating in the biosynthesis of FAAs during seed development.
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Affiliation(s)
- Rachel Amir
- Laboratory of Plant Science, Migal - Galilee Technology Center, Kiryat Shmona 12100, Israel; Tel-Hai College, Upper Galilee 11016, Israel.
| | - Gad Galili
- Department of Plant & Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hagai Cohen
- Department of Plant & Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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Chen J, Wang J, Chen W, Sun W, Peng M, Yuan Z, Shen S, Xie K, Jin C, Sun Y, Liu X, Fernie AR, Yu S, Luo J. Metabolome Analysis of Multi-Connected Biparental Chromosome Segment Substitution Line Populations. PLANT PHYSIOLOGY 2018; 178:612-625. [PMID: 30139795 PMCID: PMC6181037 DOI: 10.1104/pp.18.00490] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/14/2018] [Indexed: 05/05/2023]
Abstract
Metabolomic analysis coupled with advanced genetic populations represents a powerful tool with which to investigate the plant metabolome. However, genetic analyses of the rice (Oryza sativa) metabolome have been conducted mainly using natural accessions or a single biparental population. Here, the flag leaves from three interconnected chromosome segment substitution line populations with a common recurrent genetic background were used to dissect rice metabolic diversity. We effectively used multiple interconnected biparental populations, constructed by introducing genomic segments into Zhenshan 97 from ACC10 (A/Z), Minghui 63 (M/Z), and Nipponbare (N/Z), to map metabolic quantitative trait loci (mQTL). A total of 1,587 mQTL were generated, of which 684, 479, and 722 were obtained from the A/Z, M/Z, and N/Z chromosome segment substitution line populations, respectively, and we designated 99 candidate genes for 367 mQTL. In addition, 1,001 mQTL were generated specifically from joint linkage analysis with 25 candidate genes assigned. Several of these candidates were validated, such as LOC_Os07g01020 for the in vivo content of pyridoxine and its derivative and LOC_Os04g25980 for cis-zeatin glucosyltransferase activity. We propose a novel biosynthetic pathway for O-methylapigenin C-pentoside and demonstrated that LOC_Os04g11970 encodes a component of this pathway through fine-mapping. We postulate that the methylated apigenin may confer plant disease resistance. This study demonstrates the power of using multiple interconnected populations to generate a large number of veritable mQTL. The combined results are discussed in the context of functional metabolomics and the possible features of assigned candidates underlying respective metabolites.
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Affiliation(s)
- Jie Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jilin Wang
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Wei Chen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Peng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiyang Yuan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangqian Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Kun Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng Jin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yangyang Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xianqing Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 144776, Germany
- Center of Plant System Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Institute of Tropical Agriculture and Forestry of Hainan University, Haikou, Hainan 572208, China
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63
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Hildebrandt TM. Synthesis versus degradation: directions of amino acid metabolism during Arabidopsis abiotic stress response. PLANT MOLECULAR BIOLOGY 2018; 98:121-135. [PMID: 30143990 DOI: 10.1007/s11103-018-0767-0] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/15/2018] [Indexed: 05/19/2023]
Abstract
During abiotic stress low abundant amino acids are not synthesized but they accumulate due to increased protein turnover under conditions inducing carbohydrate starvation (dehydration, salt stress, darkness) and are degraded. Metabolic adaptation is crucial for abiotic stress resistance in plants, and accumulation of specific amino acids as well as secondary metabolites derived from amino acid metabolism has been implicated in increased tolerance to adverse environmental conditions. The role of proline, which is synthesized during Arabidopsis stress response to act as a compatible osmolyte, has been well established. However, conclusions drawn about potential functions of other amino acids such as leucine, valine, and isoleucine are not entirely consistent. This study reevaluates published datasets with a special emphasis on changes in the free amino acid pool and transcriptional regulation of the associated anabolic and catabolic pathways. In order to gain a comprehensive overview about the general direction of amino acid metabolism under abiotic stress conditions a complete map of all currently known enzymatic steps involved in amino acid synthesis and degradation was assembled including also the initial steps leading to the synthesis of secondary metabolites. Microarray datasets and amino acid profiles of Arabidopsis plants exposed to dehydration, high salinity, extended darkness, cold, and heat were systematically analyzed to identify trends in fluxes of amino acid metabolism. Some high abundant amino acids such as proline, arginine, asparagine, glutamine, and GABA are synthesized during abiotic stress to act as compatible osmolytes, precursors for secondary metabolites, or storage forms of organic nitrogen. In contrast, most of the low abundant amino acids are not synthesized but they accumulate due to increased protein turnover under conditions inducing carbohydrate starvation (dehydration, salt stress, extended darkness) and are degraded.
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Affiliation(s)
- Tatjana M Hildebrandt
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany.
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64
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Peng Y, Liu H, Chen J, Shi T, Zhang C, Sun D, He Z, Hao Y, Chen W. Genome-Wide Association Studies of Free Amino Acid Levels by Six Multi-Locus Models in Bread Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:1196. [PMID: 30154817 PMCID: PMC6103272 DOI: 10.3389/fpls.2018.01196] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 07/26/2018] [Indexed: 05/02/2023]
Abstract
Genome-wide association studies (GWAS) have been widely used to dissect the complex biosynthetic processes of plant metabolome. Most studies have used single-locus GWAS approaches, such as mixed linear model (MLM), and little is known about more efficient algorithms to implement multi-locus GWAS. Here, we report a comprehensive GWAS of 20 free amino acid (FAA) levels in kernels of bread wheat (Triticumaestivum L.) based on 14,646 SNPs by six multi-locus models (FASTmrEMMA, FASTmrMLM, ISISEM-BLASSO, mrMLM, pKWmEB, and pLARmEB). Our results showed that 328 significant quantitative trait nucleotides (QTNs) were identified in total (38, 8, 92, 45, 117, and 28, respectively, for the above six models). Among them, 66 were repeatedly detected by more than two models, and 155 QTNs appeared only in one model, indicating the reliability and complementarity of these models. We also found that the number of significant QTNs for different FAAs varied from 8 to 41, which revealed the complexity of the genetic regulation of metabolism, and further demonstrated the necessity of the multi-locus GWAS. Around these significant QTNs, 15 candidate genes were found to be involved in FAA biosynthesis, and one candidate gene (TraesCS1D01G052500, annotated as tryptophan decarboxylase) was functionally identified to influence the content of tryptamine in vitro. Our study demonstrated the power and efficiency of multi-locus GWAS models in crop metabolome research and provided new insights into understanding FAA biosynthesis in wheat.
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Affiliation(s)
- Yanchun Peng
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Jie Chen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Taotao Shi
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chi Zhang
- School of Chemical Science and Engineering, Royal Institute of Technology, Stockholm, Sweden
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanfeng Hao
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Chen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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65
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Li A, Jia S, Yobi A, Ge Z, Sato SJ, Zhang C, Angelovici R, Clemente TE, Holding DR. Editing of an Alpha-Kafirin Gene Family Increases, Digestibility and Protein Quality in Sorghum. PLANT PHYSIOLOGY 2018; 177:1425-1438. [PMID: 29925584 PMCID: PMC6084649 DOI: 10.1104/pp.18.00200] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/02/2018] [Indexed: 05/24/2023]
Abstract
Kafirins are the major storage proteins in sorghum (Sorghum bicolor) grains and form protein bodies with poor digestibility. Since kafirins are devoid of the essential amino acid lysine, they also impart poor protein quality to the kernel. The α-kafirins, which make up most of the total kafirins, are largely encoded by the k1C family of highly similar genes. We used a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing approach to target the k1C genes to create variants with reduced kafirin levels and improved protein quality and digestibility. A single guide RNA was designed to introduce mutations in a conserved region encoding the endoplasmic reticulum signal peptide of α-kafirins. Sequencing of kafirin PCR products revealed extensive edits in 25 of 26 events in one or multiple k1C family members. T1 and T2 seeds showed reduced α-kafirin levels, and selected T2 events showed significantly increased grain protein digestibility and lysine content. Thus, a single consensus single guide RNA carrying target sequence mismatches is sufficient for extensive editing of all k1C genes. The resulting quality improvements can be deployed rapidly for breeding and the generation of transgene-free, improved cultivars of sorghum, a major crop worldwide.
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Affiliation(s)
- Aixia Li
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Shangang Jia
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Abou Yobi
- Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65201
| | - Zhengxiang Ge
- Center for Biotechnology, University of Nebraska, Lincoln, Nebraska 68588
| | - Shirley J Sato
- Center for Biotechnology, University of Nebraska, Lincoln, Nebraska 68588
| | - Chi Zhang
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Ruthie Angelovici
- Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65201
| | - Thomas E Clemente
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - David R Holding
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
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66
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Latimer S, Li Y, Nguyen TTH, Soubeyrand E, Fatihi A, Elowsky CG, Block A, Pichersky E, Basset GJ. Metabolic reconstructions identify plant 3-methylglutaconyl-CoA hydratase that is crucial for branched-chain amino acid catabolism in mitochondria. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:358-370. [PMID: 29742810 DOI: 10.1111/tpj.13955] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 04/19/2018] [Accepted: 04/24/2018] [Indexed: 06/08/2023]
Abstract
The proteinogenic branched-chain amino acids (BCAAs) leucine, isoleucine and valine are essential nutrients for mammals. In plants, BCAAs double as alternative energy sources when carbohydrates become limiting, the catabolism of BCAAs providing electrons to the respiratory chain and intermediates to the tricarboxylic acid cycle. Yet, the actual architecture of the degradation pathways of BCAAs is not well understood. In this study, gene network modeling in Arabidopsis and rice, and plant-prokaryote comparative genomics detected candidates for 3-methylglutaconyl-CoA hydratase (4.2.1.18), one of the missing plant enzymes of leucine catabolism. Alignments of these protein candidates sampled from various spermatophytes revealed non-homologous N-terminal extensions that are lacking in their bacterial counterparts, and green fluorescent protein-fusion experiments demonstrated that the Arabidopsis protein, product of gene At4g16800, is targeted to mitochondria. Recombinant At4g16800 catalyzed the dehydration of 3-hydroxymethylglutaryl-CoA into 3-methylglutaconyl-CoA, and displayed kinetic features similar to those of its prokaryotic homolog. When at4g16800 knockout plants were subjected to dark-induced carbon starvation, their rosette leaves displayed accelerated senescence as compared with control plants, and this phenotype was paralleled by a marked increase in the accumulation of free and total leucine, isoleucine and valine. The seeds of the at4g16800 mutant showed a similar accumulation of free BCAAs. These data suggest that 3-methylglutaconyl-CoA hydratase is not solely involved in the degradation of leucine, but is also a significant contributor to that of isoleucine and valine. Furthermore, evidence is shown that unlike the situation observed in Trypanosomatidae, leucine catabolism does not contribute to the formation of the terpenoid precursor mevalonate.
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Affiliation(s)
- Scott Latimer
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida, 32611, USA
| | - Yubing Li
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida, 32611, USA
| | - Thuong T H Nguyen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Eric Soubeyrand
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida, 32611, USA
| | - Abdelhak Fatihi
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Christian G Elowsky
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Anna Block
- Center for Medical, Agricultural and Veterinary Entomology, ARS, USDA, Gainesville, Florida, 32608, USA
| | - Eran Pichersky
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Gilles J Basset
- Department of Horticultural Sciences, University of Florida, Gainesville, Florida, 32611, USA
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67
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Hirota T, Izumi M, Wada S, Makino A, Ishida H. Vacuolar Protein Degradation via Autophagy Provides Substrates to Amino Acid Catabolic Pathways as an Adaptive Response to Sugar Starvation in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2018; 59:1363-1376. [PMID: 29390157 DOI: 10.1093/pcp/pcy005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/04/2018] [Indexed: 05/28/2023]
Abstract
The vacuolar lytic degradation of proteins releases free amino acids that plants can use instead of sugars for respiratory energy production. Autophagy is a major cellular process leading to the transport of proteins into the vacuole for degradation. Here, we examine the contribution of autophagy to the amino acid metabolism response to sugar starvation in mature leaves of Arabidopsis thaliana. During sugar starvation arising from the exposure of wild-type (WT) plants to darkness, autophagic transport of chloroplast stroma, which contains most of the proteins in a leaf, into the vacuolar lumen was induced within 2 d. During this time, the level of soluble proteins, primarily Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase), decreased and the amount of free amino acid increased. In dark-treated autophagy-defective (atg) mutants, the decrease of soluble proteins was suppressed, which resulted in the compromised release of basic amino acids, branched-chain amino acids (BCAAs) and aromatic amino acids. The impairment of BCAA catabolic pathways in the knockout mutants of the electron transfer flavoprotein (ETF)/ETF:ubiquinone oxidoreductase (etfqo) complex and the electron donor protein isovaleryl-CoA dehydrogenase (ivdh) caused a reduced tolerance to dark treatment similar to that in the atg mutants. The enhanced accumulation of BCAAs in the ivdh and etfqo mutants during the dark treatment was reduced by additional autophagy deficiency. These results indicate that vacuolar protein degradation via autophagy serves as an adaptive response to disrupted photosynthesis by providing substrates to amino acid catabolic pathways, including BCAA catabolism mediated by IVDH and ETFQO.
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Affiliation(s)
- Takaaki Hirota
- Department of Applied Plant Science, Graduate School of Agricultural Science, Tohoku University, Aramaki Aza Aoba, Sendai, Japan
| | - Masanori Izumi
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aramaki Aza Aoba, Sendai, Japan
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Katahira, Sendai, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Shinya Wada
- Department of Applied Plant Science, Graduate School of Agricultural Science, Tohoku University, Aramaki Aza Aoba, Sendai, Japan
| | - Amane Makino
- Department of Applied Plant Science, Graduate School of Agricultural Science, Tohoku University, Aramaki Aza Aoba, Sendai, Japan
| | - Hiroyuki Ishida
- Department of Applied Plant Science, Graduate School of Agricultural Science, Tohoku University, Aramaki Aza Aoba, Sendai, Japan
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68
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Wen W, Jin M, Li K, Liu H, Xiao Y, Zhao M, Alseekh S, Li W, de Abreu E Lima F, Brotman Y, Willmitzer L, Fernie AR, Yan J. An integrated multi-layered analysis of the metabolic networks of different tissues uncovers key genetic components of primary metabolism in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:1116-1128. [PMID: 29381266 DOI: 10.1111/tpj.13835] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 12/20/2017] [Accepted: 01/08/2018] [Indexed: 06/07/2023]
Abstract
Primary metabolism plays a pivotal role in normal plant growth, development and reproduction. As maize is a major crop worldwide, the primary metabolites produced by maize plants are of immense importance from both calorific and nutritional perspectives. Here a genome-wide association study (GWAS) of 61 primary metabolites using a maize association panel containing 513 inbred lines identified 153 significant loci associated with the level of these metabolites in four independent tissues. The genome-wide expression level of 760 genes was also linked with metabolite levels within the same tissue. On average, the genetic variants at each locus or transcriptional variance of each gene identified here were estimated to have a minor effect (4.4-7.8%) on primary metabolic variation. Thirty-six loci or genes were prioritized as being worthy of future investigation, either with regard to functional characterization or for their utility for genetic improvement. This target list includes the well-known opaque 2 (O2) and lkr/sdh genes as well as many less well-characterized genes. During our investigation of these 36 loci, we analyzed the genetic components and variations underlying the trehalose, aspartate and aromatic amino acid pathways, thereby functionally characterizing four genes involved in primary metabolism in maize.
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Affiliation(s)
- Weiwei Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
| | - Min Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kun Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingchao Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Yariv Brotman
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Lothar Willmitzer
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Zhao L, Deng L, Zhang Q, Jing X, Ma M, Yi B, Wen J, Ma C, Tu J, Fu T, Shen J. Autophagy contributes to sulfonylurea herbicide tolerance via GCN2-independent regulation of amino acid homeostasis. Autophagy 2018; 14:702-714. [PMID: 29377765 DOI: 10.1080/15548627.2017.1407888] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Sulfonylurea (SU) herbicides inhibit branched-chain amino acid (BCAA) biosynthesis by targeting acetolactate synthase. Plants have evolved target-site resistance and metabolic tolerance to SU herbicides; the GCN2 (general control non-repressible 2) pathway is also involved in SU tolerance. Here, we report a novel SU tolerance mechanism, autophagy, which we call 'homeostatic tolerance,' is involved in amino acid signaling in Arabidopsis. The activation and reversion of autophagy and GCN2 by the SU herbicide tribenuron-methyl (TM) and exogenous BCAA, respectively, confirmed that TM-induced BCAA starvation is responsible for the activation of autophagy and GCN2. Genetic and biochemical analyses revealed a lower proportion of free BCAA and more sensitive phenotypes in atg5, atg7, and gcn2 single mutants than in wild-type seedlings after TM treatment; the lowest proportion of free BCAA and the most sensitive phenotypes were found in atg5 gcn2 and atg7 gcn2 double mutants. Immunoblotting and microscopy revealed that TM-induced activation of autophagy and GCN2 signaling do not depend on the presence of each other, and these 2 pathways may serve as mutually compensatory mechanisms against TM. TM inhibited the TOR (target of rapamycin), and activated autophagy in an estradiol-induced TOR RNAi line, suggesting that TM-induced BCAA starvation activates autophagy, probably via TOR inactivation. Autophagy and GCN2 were also activated, and independently contributed to TM tolerance in plants conferring metabolic tolerance. Together, these data suggest that autophagy is a proteolytic process for amino acid recycling and contributes to GCN2-independent SU tolerance, probably by its ability to replenish fresh BCAA.
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Affiliation(s)
- Lun Zhao
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Li Deng
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Qing Zhang
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Xue Jing
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Meng Ma
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Bin Yi
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Jing Wen
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Chaozhi Ma
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Jinxing Tu
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Tingdong Fu
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Jinxiong Shen
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
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70
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Wu S, Tohge T, Cuadros-Inostroza Á, Tong H, Tenenboim H, Kooke R, Méret M, Keurentjes JB, Nikoloski Z, Fernie AR, Willmitzer L, Brotman Y. Mapping the Arabidopsis Metabolic Landscape by Untargeted Metabolomics at Different Environmental Conditions. MOLECULAR PLANT 2018; 11:118-134. [PMID: 28866081 DOI: 10.1016/j.molp.2017.08.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 08/16/2017] [Accepted: 08/23/2017] [Indexed: 05/07/2023]
Abstract
Metabolic genome-wide association studies (mGWAS), whereupon metabolite levels are regarded as traits, can help unravel the genetic basis of metabolic networks. A total of 309 Arabidopsis accessions were grown under two independent environmental conditions (control and stress) and subjected to untargeted LC-MS-based metabolomic profiling; levels of the obtained hydrophilic metabolites were used in GWAS. Our two-condition-based GWAS for more than 3000 semi-polar metabolites resulted in the detection of 123 highly resolved metabolite quantitative trait loci (p ≤ 1.0E-08), 24.39% of which were environment-specific. Interestingly, differently from natural variation in Arabidopsis primary metabolites, which tends to be controlled by a large number of small-effect loci, we found several major large-effect loci alongside a vast number of small-effect loci controlling variation of secondary metabolites. The two-condition-based GWAS was followed by integration with network-derived metabolite-transcript correlations using a time-course stress experiment. Through this integrative approach, we selected 70 key candidate associations between structural genes and metabolites, and experimentally validated eight novel associations, two of them showing differential genetic regulation in the two environments studied. We demonstrate the power of combining large-scale untargeted metabolomics-based GWAS with time-course-derived networks both performed under different abiotic environments for identifying metabolite-gene associations, providing novel global insights into the metabolic landscape of Arabidopsis.
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Affiliation(s)
- Si Wu
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Álvaro Cuadros-Inostroza
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; MetaSysX GmbH, Am Mühlenberg 11, 14476 Potsdam-Golm, Germany
| | - Hao Tong
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Hezi Tenenboim
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; MetaSysX GmbH, Am Mühlenberg 11, 14476 Potsdam-Golm, Germany
| | - Rik Kooke
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Michaël Méret
- MetaSysX GmbH, Am Mühlenberg 11, 14476 Potsdam-Golm, Germany
| | - Joost B Keurentjes
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Lothar Willmitzer
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Yariv Brotman
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel.
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71
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Zhao L, Deng L, Zhang Q, Jing X, Ma M, Yi B, Wen J, Ma C, Tu J, Fu T, Shen J. Autophagy contributes to sulfonylurea herbicide tolerance via GCN2-independent regulation of amino acid homeostasis. Autophagy 2018. [PMID: 29377765 DOI: 10.1080/15548627] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Sulfonylurea (SU) herbicides inhibit branched-chain amino acid (BCAA) biosynthesis by targeting acetolactate synthase. Plants have evolved target-site resistance and metabolic tolerance to SU herbicides; the GCN2 (general control non-repressible 2) pathway is also involved in SU tolerance. Here, we report a novel SU tolerance mechanism, autophagy, which we call 'homeostatic tolerance,' is involved in amino acid signaling in Arabidopsis. The activation and reversion of autophagy and GCN2 by the SU herbicide tribenuron-methyl (TM) and exogenous BCAA, respectively, confirmed that TM-induced BCAA starvation is responsible for the activation of autophagy and GCN2. Genetic and biochemical analyses revealed a lower proportion of free BCAA and more sensitive phenotypes in atg5, atg7, and gcn2 single mutants than in wild-type seedlings after TM treatment; the lowest proportion of free BCAA and the most sensitive phenotypes were found in atg5 gcn2 and atg7 gcn2 double mutants. Immunoblotting and microscopy revealed that TM-induced activation of autophagy and GCN2 signaling do not depend on the presence of each other, and these 2 pathways may serve as mutually compensatory mechanisms against TM. TM inhibited the TOR (target of rapamycin), and activated autophagy in an estradiol-induced TOR RNAi line, suggesting that TM-induced BCAA starvation activates autophagy, probably via TOR inactivation. Autophagy and GCN2 were also activated, and independently contributed to TM tolerance in plants conferring metabolic tolerance. Together, these data suggest that autophagy is a proteolytic process for amino acid recycling and contributes to GCN2-independent SU tolerance, probably by its ability to replenish fresh BCAA.
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Affiliation(s)
- Lun Zhao
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Li Deng
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Qing Zhang
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Xue Jing
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Meng Ma
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Bin Yi
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Jing Wen
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Chaozhi Ma
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Jinxing Tu
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Tingdong Fu
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
| | - Jinxiong Shen
- a National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed , Huazhong Agricultural University , Wuhan , China
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72
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Peng M, Shahzad R, Gul A, Subthain H, Shen S, Lei L, Zheng Z, Zhou J, Lu D, Wang S, Nishawy E, Liu X, Tohge T, Fernie AR, Luo J. Differentially evolved glucosyltransferases determine natural variation of rice flavone accumulation and UV-tolerance. Nat Commun 2017; 8:1975. [PMID: 29213047 PMCID: PMC5719032 DOI: 10.1038/s41467-017-02168-x] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/10/2017] [Indexed: 01/08/2023] Open
Abstract
Decoration of phytochemicals contributes to the majority of metabolic diversity in nature, whereas how this process alters the biological functions of their precursor molecules remains to be investigated. Flavones, an important yet overlooked subclass of flavonoids, are most commonly conjugated with sugar moieties by UDP-dependent glycosyltransferases (UGTs). Here, we report that the natural variation of rice flavones is mainly determined by OsUGT706D1 (flavone 7-O-glucosyltransferase) and OsUGT707A2 (flavone 5-O-glucosyltransferase). UV-B exposure and transgenic evaluation demonstrate that their allelic variation contributes to UV-B tolerance in nature. Biochemical characterization of over 40 flavonoid UGTs reveals their differential evolution in angiosperms. These combined data provide biochemical insight and genetic regulation into flavone biosynthesis and additionally suggest that adoption of the positive alleles of these genes into breeding programs will likely represent a potential strategy aimed at producing stress-tolerant plants.
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Affiliation(s)
- Meng Peng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Raheel Shahzad
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Ambreen Gul
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Hizar Subthain
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangqian Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Long Lei
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhigang Zheng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Junjie Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Dandan Lu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Shouchuang Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Elsayed Nishawy
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Desert Research Center, Genetics Resource Department, Egyptian Deserts Gene Bank, Cairo, 11735, Egypt
| | - Xianqing Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Takayuki Tohge
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, 572208, China.
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73
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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: 53] [Impact Index Per Article: 7.6] [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.
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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
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74
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Huang T, Jander G. Abscisic acid-regulated protein degradation causes osmotic stress-induced accumulation of branched-chain amino acids in Arabidopsis thaliana. PLANTA 2017; 246:737-747. [PMID: 28668976 DOI: 10.1007/s00425-017-2727-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 06/21/2017] [Indexed: 05/22/2023]
Abstract
Whereas proline accumulates through de novo biosynthesis in plants subjected to osmotic stress, leucine, isoleucine, and valine accumulation in drought-stressed Arabidopsis thaliana is caused by abscisic acid-regulated protein degradation. In response to several kinds of abiotic stress, plants greatly increase their accumulation of free amino acids. Although stress-induced proline increases have been studied the most extensively, the fold-increase of other amino acids, in particular branched-chain amino acids (BCAAs; leucine, isoleucine, and valine), is often higher than that of proline. In Arabidopsis thaliana (Arabidopsis), BCAAs accumulate in response to drought, salt, mannitol, polyethylene glycol, herbicide treatment, and nitrogen starvation. Plants that are deficient in abscisic acid signaling accumulate lower amounts of BCAAs, but not proline and most other amino acids. Previous bioinformatic studies had suggested that amino acid synthesis, rather than protein degradation, is responsible for the observed BCAA increase in osmotically stressed Arabidopsis. However, whereas treatment with the protease inhibitor MG132 decreased drought-induced BCAA accumulation, inhibition of BCAA biosynthesis with the acetolactate synthase inhibitors chlorsulfuron and imazapyr did not. Additionally, overexpression of BRANCHED-CHAIN AMINO ACID TRANSFERASE2 (BCAT2), which is upregulated in response to osmotic stress and functions in BCAA degradation, decreased drought-induced BCAA accumulation. Together, these results demonstrate that BCAA accumulation in osmotically stressed Arabidopsis is primarily the result of protein degradation. After relief of the osmotic stress, BCAA homeostasis is restored over time by amino acid degradation involving BCAT2. Thus, drought-induced BCAA accumulation is different from that of proline, which is accumulated due to de novo synthesis in an abscisic acid-independent manner and remains elevated for a more prolonged period of time after removal of the osmotic stress.
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Affiliation(s)
- Tengfang Huang
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
- Keygene Inc, Rockville, MD, 20850, USA
| | - Georg Jander
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA.
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75
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Abstract
Plant metabolic studies have traditionally focused on the role and regulation of the enzymes catalyzing key reactions within specific pathways. Within the past 20 years, reverse genetic approaches have allowed direct determination of the effects of the deficiency, or surplus, of a given protein on the biochemistry of a plant. In parallel, top-down approaches have also been taken, which rely on screening broad, natural genetic diversity for metabolic diversity. Here, we compare and contrast the various strategies that have been adopted to enhance our understanding of the natural diversity of metabolism. We also detail how these approaches have enhanced our understanding of both specific and global aspects of the genetic regulation of metabolism. Finally, we discuss how such approaches are providing important insights into the evolution of plant secondary metabolism.
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Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
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76
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Schertl P, Danne L, Braun HP. 3-Hydroxyisobutyrate Dehydrogenase Is Involved in Both, Valine and Isoleucine Degradation in Arabidopsis thaliana. PLANT PHYSIOLOGY 2017; 175:51-61. [PMID: 28705827 PMCID: PMC5580760 DOI: 10.1104/pp.17.00649] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/11/2017] [Indexed: 05/29/2023]
Abstract
In plants, amino acid catabolism is especially relevant in metabolic stress situations (e.g. limited carbohydrate availability during extended darkness). Under these conditions, amino acids are used as alternative substrates for respiration. Complete oxidation of the branched-chain amino acids (BCAAs) leucine, isoleucine (Ile), and valine (Val) in the mitochondria efficiently allows the formation of ATP by oxidative phosphorylation. However, the metabolic pathways for BCAA breakdown are largely unknown so far in plants. A systematic search for Arabidopsis (Arabidopsis thaliana) genes encoding proteins resembling enzymes involved in BCAA catabolism in animals, fungi, and bacteria as well as proteomic analyses of mitochondrial fractions from Arabidopsis allowed the identification of a putative 3-hydroxyisobutyrate dehydrogenase, AtHDH1 (At4g20930), involved in Val degradation. Systematic substrate screening analyses revealed that the protein uses 3-hydroxyisobutyrate but additionally 3-hydroxypropionate as substrates. This points to a role of the enzyme not only in Val but possibly also in Ile metabolism. At4g20930 knockdown plants were characterized to test this conclusion. Root toxicity assays revealed increased root growth inhibition of the mutants if cultivated in the presence of Val or Ile but not in the presence of leucine. We conclude that AtHDH1 has a dual role in BCAA metabolism in plants.
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Affiliation(s)
- Peter Schertl
- Institut für Pflanzengenetik, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Lennart Danne
- Institut für Pflanzengenetik, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, 30419 Hannover, Germany
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77
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Xing A, Last RL. A Regulatory Hierarchy of the Arabidopsis Branched-Chain Amino Acid Metabolic Network. THE PLANT CELL 2017; 29:1480-1499. [PMID: 28522547 PMCID: PMC5502462 DOI: 10.1105/tpc.17.00186] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/12/2017] [Accepted: 05/11/2017] [Indexed: 05/18/2023]
Abstract
The branched-chain amino acids (BCAAs) Ile, Val, and Leu are essential nutrients that humans and other animals obtain from plants. However, total and relative amounts of plant BCAAs rarely match animal nutritional needs, and improvement requires a better understanding of the mechanistic basis for BCAA homeostasis. We present an in vivo regulatory model of BCAA homeostasis derived from analysis of feedback-resistant Arabidopsis thaliana mutants for the three allosteric committed enzymes in the biosynthetic network: threonine deaminase (also named l-O-methylthreonine resistant 1 [OMR1]), acetohydroxyacid synthase small subunit 2 (AHASS2), and isopropylmalate synthase 1 (IPMS1). In this model, OMR1 exerts primary control on Ile accumulation and functions independently of AHAS and IPMS AHAS and IPMS regulate Val and Leu homeostasis, where AHAS affects total Val+Leu and IPMS controls partitioning between these amino acids. In addition, analysis of feedback-resistant and loss-of-function single and double mutants revealed that each AHAS and IPMS isoenzyme contributes to homeostasis rather than being functionally redundant. The characterized feedback resistance mutations caused increased free BCAA levels in both seedlings and seeds. These results add to our understanding of the basis of in vivo BCAA homeostasis and inform approaches to improve the amount and balance of these essential nutrients in crops.
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Affiliation(s)
- Anqi Xing
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824-1319
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78
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Gipson AB, Morton KJ, Rhee RJ, Simo S, Clayton JA, Perrett ME, Binkley CG, Jensen EL, Oakes DL, Rouhier MF, Rouhier KA. Disruptions in valine degradation affect seed development and germination in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:1029-1039. [PMID: 28321931 PMCID: PMC5461199 DOI: 10.1111/tpj.13538] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 03/07/2017] [Accepted: 03/10/2017] [Indexed: 05/20/2023]
Abstract
We have functionally characterized the role of two putative mitochondrial enzymes in valine degradation using insertional mutants. Prior to this study, the relationship between branched-chain amino acid degradation (named for leucine, valine and isoleucine) and seed development was limited to leucine catabolism. Using a reverse genetics approach, we show that disruptions in the mitochondrial valine degradation pathway affect seed development and germination in Arabidopsis thaliana. A null mutant of 3-hydroxyisobutyryl-CoA hydrolase (CHY4, At4g31810) resulted in an embryo lethal phenotype, while a null mutant of methylmalonate semialdehyde dehydrogenase (MMSD, At2g14170) resulted in seeds with wrinkled coats, decreased storage reserves, elevated valine and leucine, and reduced germination rates. These data highlight the unique contributions CHY4 and MMSD make to the overall growth and viability of plants. It also increases our knowledge of the role branched-chain amino acid catabolism plays in seed development and amino acid homeostasis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Kerry A. Rouhier
- Kenyon College 200 N. College Rd, Gambier, OH 43022
- Doan University 1014 Boswell Ave, Crete, NE 68333
- Corresponding author: Kerry A. Rouhier, 200 N. College Rd, Gambier, OH 43022, USA tel: (740) 427-5359, fax: (740) 427-5731,
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79
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Knoch D, Riewe D, Meyer RC, Boudichevskaia A, Schmidt R, Altmann T. Genetic dissection of metabolite variation in Arabidopsis seeds: evidence for mQTL hotspots and a master regulatory locus of seed metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1655-1667. [PMID: 28338798 PMCID: PMC5444479 DOI: 10.1093/jxb/erx049] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
To gain insight into genetic factors controlling seed metabolic composition and its relationship to major seed properties, an Arabidopsis recombinant inbred line (RIL) population, derived from accessions Col-0 and C24, was studied using an MS-based metabolic profiling approach. Relative intensities of 311 polar primary metabolites were used to identify associated genomic loci and to elucidate their interactions by quantitative trait locus (QTL) mapping. A total of 786 metabolic QTLs (mQTLs) were unequally distributed across the genome, forming several hotspots. For the branched-chain amino acid leucine, mQTLs and candidate genes were elucidated in detail. Correlation studies displayed links between metabolite levels, seed protein content, and seed weight. Principal component analysis revealed a clustering of samples, with PC1 mapping to a region on the short arm of chromosome IV. The overlap of this region with mQTL hotspots indicates the presence of a potential master regulatory locus of seed metabolism. As a result of database queries, a series of candidate regulatory genes, including bZIP10, were identified within this region. Depending on the search conditions, metabolic pathway-derived candidate genes for 40-61% of tested mQTLs could be determined, providing an extensive basis for further identification and characterization of hitherto unknown genes causal for natural variation of Arabidopsis seed metabolism.
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Affiliation(s)
- Dominic Knoch
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - David Riewe
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Rhonda Christiane Meyer
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Anastassia Boudichevskaia
- Department of Breeding Research/Genome Plasticity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Renate Schmidt
- Department of Breeding Research/Genome Plasticity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Thomas Altmann
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
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80
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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.
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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.)
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Lee EJ, Oh M, Hwang JU, Li-Beisson Y, Nishida I, Lee Y. Seed-Specific Overexpression of the Pyruvate Transporter BASS2 Increases Oil Content in Arabidopsis Seeds. FRONTIERS IN PLANT SCIENCE 2017; 8:194. [PMID: 28265278 PMCID: PMC5316546 DOI: 10.3389/fpls.2017.00194] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 01/31/2017] [Indexed: 05/11/2023]
Abstract
Seed oil is important not only for human and animal nutrition, but also for various industrial applications. Numerous genetic engineering strategies have been attempted to increase the oil content per seed, but few of these strategies have involved manipulating the transporters. Pyruvate is a major source of carbon for de novo fatty acid biosynthesis in plastids, and the embryo's demand for pyruvate is reported to increase during active oil accumulation. In this study, we tested our hypothesis that oil biosynthesis could be boosted by increasing pyruvate flux into plastids. We expressed the known plastid-localized pyruvate transporter BILE ACID:SODIUM SYMPORTER FAMILY PROTEIN 2 (BASS2) under the control of a seed-specific soybean (Glycine max) glycinin-1 promoter in Arabidopsis thaliana. The resultant transgenic Arabidopsis plants (OEs), which expressed high levels of BASS2, produced seeds that were larger and heavier and contained 10-37% more oil than those of the wild type (WT), but were comparable to the WT seeds in terms of protein and carbohydrate contents. The total seed number did not differ significantly between the WT and OEs. Therefore, oil yield per plant was increased by 24-43% in the OE lines compared to WT. Taken together, our results demonstrate that seed-specific overexpression of the pyruvate transporter BASS2 promotes oil production in Arabidopsis seeds. Thus, manipulating the level of specific transporters is a feasible approach for increasing the seed oil content.
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Affiliation(s)
- Eun-Jung Lee
- Division of Integrative Biosciences and Biotechnology, Plant Cell Biology Laboratory, Pohang University of Science and TechnologyPohang, South Korea
| | - Minwoo Oh
- Division of Integrative Biosciences and Biotechnology, Plant Cell Biology Laboratory, Pohang University of Science and TechnologyPohang, South Korea
| | - Jae-Ung Hwang
- Division of Integrative Biosciences and Biotechnology, Plant Cell Biology Laboratory, Pohang University of Science and TechnologyPohang, South Korea
| | - Yonghua Li-Beisson
- Department of Plant Biology and Environmental Microbiology, CEA/Centre National de la Recherche Scientifique/Aix-Marseille University, CEA CadaracheMarseille, France
| | - Ikuo Nishida
- Division of Life Science, Graduate School of Science and Engineering, Saitama UniversitySaitama, Japan
| | - Youngsook Lee
- Division of Integrative Biosciences and Biotechnology, Plant Cell Biology Laboratory, Pohang University of Science and TechnologyPohang, South Korea
- *Correspondence: Youngsook Lee
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82
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Riewe D, Jeon HJ, Lisec J, Heuermann MC, Schmeichel J, Seyfarth M, Meyer RC, Willmitzer L, Altmann T. A naturally occurring promoter polymorphism of the Arabidopsis FUM2 gene causes expression variation, and is associated with metabolic and growth traits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:826-838. [PMID: 27520391 DOI: 10.1111/tpj.13303] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 07/13/2016] [Accepted: 08/05/2016] [Indexed: 05/05/2023]
Abstract
Fumarate and malate are known intermediates of the TCA cycle, a mitochondrial metabolic pathway generating NADH for respiration. Arabidopsis thaliana and other Brassicaceae contain an additional cytosolic fumarase (FUM2) that functions in carbon assimilation and nitrogen use. Here, we report the identification of a hitherto unknown FUM2 promoter insertion/deletion (InDel) polymorphism found between the Col-0 and C24 accessions, which also divides a large number of Arabidopsis accessions carrying either the Col-0 or the C24 allele. The polymorphism consists of two stretches of 2.1 and 3.8 kb, which are both absent from the promotor region of Col-0 FUM2. By analysing mutants as well as mapping and natural populations with contrasting FUM2 alleles, the promotor insertion was linked to reduced FUM2 mRNA expression, reduced fumarase activity and reduced fumarate/malate ratio in leaves. In a large population of 174 natural accessions, the polymorphism was also found to be associated with the fumarate/malate ratio, malate and fumarate levels, and with dry weight at 15 days after sowing (DAS). The association with biomass production was confirmed in an even larger (251) accession population for dry weight at 22 DAS. The dominant Col-0 allele that results in increased fumarate/malate ratios and enhanced biomass production is predominantly found in central/eastern European accessions, whereas the C24 type allele is prevalent on the Iberian Peninsula, west of the Rhine and in the British Isles. Our findings support the role of FUM2 in diurnal carbon storage, and point to a growth advantage of accessions carrying the FUM2 Col-0 allele.
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Affiliation(s)
- David Riewe
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Hea-Jung Jeon
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Jan Lisec
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam-Golm, Germany
| | - Marc C Heuermann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Judith Schmeichel
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Monique Seyfarth
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Rhonda C Meyer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Lothar Willmitzer
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam-Golm, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
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83
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Wu S, Alseekh S, Cuadros-Inostroza Á, Fusari CM, Mutwil M, Kooke R, Keurentjes JB, Fernie AR, Willmitzer L, Brotman Y. Combined Use of Genome-Wide Association Data and Correlation Networks Unravels Key Regulators of Primary Metabolism in Arabidopsis thaliana. PLoS Genet 2016; 12:e1006363. [PMID: 27760136 PMCID: PMC5070769 DOI: 10.1371/journal.pgen.1006363] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/13/2016] [Indexed: 01/12/2023] Open
Abstract
Plant primary metabolism is a highly coordinated, central, and complex network of biochemical processes regulated at both the genetic and post-translational levels. The genetic basis of this network can be explored by analyzing the metabolic composition of genetically diverse genotypes in a given plant species. Here, we report an integrative strategy combining quantitative genetic mapping and metabolite‒transcript correlation networks to identify functional associations between genes and primary metabolites in Arabidopsis thaliana. Genome-wide association study (GWAS) was used to identify metabolic quantitative trait loci (mQTL). Correlation networks built using metabolite and transcript data derived from a previously published time-course stress study yielded metabolite‒transcript correlations identified by covariation. Finally, results obtained in this study were compared with mQTL previously described. We applied a statistical framework to test and compare the performance of different single methods (network approach and quantitative genetics methods, representing the two orthogonal approaches combined in our strategy) with that of the combined strategy. We show that the combined strategy has improved performance manifested by increased sensitivity and accuracy. This combined strategy allowed the identification of 92 candidate associations between structural genes and primary metabolites, which not only included previously well-characterized gene‒metabolite associations, but also revealed novel associations. Using loss-of-function mutants, we validated two of the novel associations with genes involved in tyrosine degradation and in β-alanine metabolism. In conclusion, we demonstrate that applying our integrative strategy to the largely untapped resource of metabolite-transcript associations can facilitate the discovery of novel metabolite-related genes. This integrative strategy is not limited to A. thaliana, but generally applicable to other plant species.
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Affiliation(s)
- Si Wu
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Álvaro Cuadros-Inostroza
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- MetaSysX GmbH, Potsdam-Golm, Germany
| | - Corina M. Fusari
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Marek Mutwil
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Rik Kooke
- Laboratory of Genetics, Wageningen University, Wageningen, the Netherlands
| | | | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Lothar Willmitzer
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Yariv Brotman
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
- * E-mail:
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84
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Gonzalez-Jorge S, Mehrshahi P, Magallanes-Lundback M, Lipka AE, Angelovici R, Gore MA, DellaPenna D. ZEAXANTHIN EPOXIDASE Activity Potentiates Carotenoid Degradation in Maturing Seed. PLANT PHYSIOLOGY 2016; 171:1837-51. [PMID: 27208224 PMCID: PMC4936585 DOI: 10.1104/pp.16.00604] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 05/03/2016] [Indexed: 05/19/2023]
Abstract
Elucidation of the carotenoid biosynthetic pathway has enabled altering the composition and content of carotenoids in various plants, but to achieve desired nutritional impacts, the genetic components regulating carotenoid homeostasis in seed, the plant organ consumed in greatest abundance, must be elucidated. We used a combination of linkage mapping, genome-wide association studies (GWAS), and pathway-level analysis to identify nine loci that impact the natural variation of seed carotenoids in Arabidopsis (Arabidopsis thaliana). ZEAXANTHIN EPOXIDASE (ZEP) was the major contributor to carotenoid composition, with mutants lacking ZEP activity showing a remarkable 6-fold increase in total seed carotenoids relative to the wild type. Natural variation in ZEP gene expression during seed development was identified as the underlying mechanism for fine-tuning carotenoid composition, stability, and ultimately content in Arabidopsis seed. We previously showed that two CAROTENOID CLEAVAGE DIOXYGENASE enzymes, CCD1 and CCD4, are the primary mediators of seed carotenoid degradation, and here we demonstrate that ZEP acts as an upstream control point of carotenoid homeostasis, with ZEP-mediated epoxidation targeting carotenoids for degradation by CCD enzymes. Finally, four of the nine loci/enzymatic activities identified as underlying natural variation in Arabidopsis seed carotenoids also were identified in a recent GWAS of maize (Zea mays) kernel carotenoid variation. This first comparison of the natural variation in seed carotenoids in monocots and dicots suggests a surprising overlap in the genetic architecture of these traits between the two lineages and provides a list of likely candidates to target for selecting seed carotenoid variation in other species.
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Affiliation(s)
- Sabrina Gonzalez-Jorge
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.G.-J., P.M., M.M.-L., R.A., D.D.P.);Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA United Kingdom (S.G.-J., P.M.);Department of Crop Sciences, College of Agricultural, Consumer, and Environmental Sciences, University of Illinois, Urbana-Champaign, Illinois 61801 (A.E.L.);Division of Biological Sciences, University of Missouri, Columbia, Missouri 65201 (R.A.); andPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (M.A.G.)
| | - Payam Mehrshahi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.G.-J., P.M., M.M.-L., R.A., D.D.P.);Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA United Kingdom (S.G.-J., P.M.);Department of Crop Sciences, College of Agricultural, Consumer, and Environmental Sciences, University of Illinois, Urbana-Champaign, Illinois 61801 (A.E.L.);Division of Biological Sciences, University of Missouri, Columbia, Missouri 65201 (R.A.); andPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (M.A.G.)
| | - Maria Magallanes-Lundback
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.G.-J., P.M., M.M.-L., R.A., D.D.P.);Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA United Kingdom (S.G.-J., P.M.);Department of Crop Sciences, College of Agricultural, Consumer, and Environmental Sciences, University of Illinois, Urbana-Champaign, Illinois 61801 (A.E.L.);Division of Biological Sciences, University of Missouri, Columbia, Missouri 65201 (R.A.); andPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (M.A.G.)
| | - Alexander E Lipka
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.G.-J., P.M., M.M.-L., R.A., D.D.P.);Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA United Kingdom (S.G.-J., P.M.);Department of Crop Sciences, College of Agricultural, Consumer, and Environmental Sciences, University of Illinois, Urbana-Champaign, Illinois 61801 (A.E.L.);Division of Biological Sciences, University of Missouri, Columbia, Missouri 65201 (R.A.); andPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (M.A.G.)
| | - Ruthie Angelovici
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.G.-J., P.M., M.M.-L., R.A., D.D.P.);Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA United Kingdom (S.G.-J., P.M.);Department of Crop Sciences, College of Agricultural, Consumer, and Environmental Sciences, University of Illinois, Urbana-Champaign, Illinois 61801 (A.E.L.);Division of Biological Sciences, University of Missouri, Columbia, Missouri 65201 (R.A.); andPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (M.A.G.)
| | - Michael A Gore
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.G.-J., P.M., M.M.-L., R.A., D.D.P.);Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA United Kingdom (S.G.-J., P.M.);Department of Crop Sciences, College of Agricultural, Consumer, and Environmental Sciences, University of Illinois, Urbana-Champaign, Illinois 61801 (A.E.L.);Division of Biological Sciences, University of Missouri, Columbia, Missouri 65201 (R.A.); andPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (M.A.G.)
| | - Dean DellaPenna
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (S.G.-J., P.M., M.M.-L., R.A., D.D.P.);Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA United Kingdom (S.G.-J., P.M.);Department of Crop Sciences, College of Agricultural, Consumer, and Environmental Sciences, University of Illinois, Urbana-Champaign, Illinois 61801 (A.E.L.);Division of Biological Sciences, University of Missouri, Columbia, Missouri 65201 (R.A.); andPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (M.A.G.)
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85
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Pires MV, Pereira Júnior AA, Medeiros DB, Daloso DM, Pham PA, Barros KA, Engqvist MKM, Florian A, Krahnert I, Maurino VG, Araújo WL, Fernie AR. The influence of alternative pathways of respiration that utilize branched-chain amino acids following water shortage in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:1304-19. [PMID: 26616144 DOI: 10.1111/pce.12682] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 11/13/2015] [Accepted: 11/15/2015] [Indexed: 05/23/2023]
Abstract
During dark-induced senescence isovaleryl-CoA dehydrogenase (IVDH) and D-2-hydroxyglutarate dehydrogenase (D-2HGDH) act as alternate electron donors to the ubiquinol pool via the electron-transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase (ETF/ETFQO) pathway. However, the role of this pathway in response to other stresses still remains unclear. Here, we demonstrated that this alternative pathway is associated with tolerance to drought in Arabidopsis. In comparison with wild type (WT) and lines overexpressing D-2GHDH, loss-of-function etfqo-1, d2hgdh-2 and ivdh-1 mutants displayed compromised respiration rates and were more sensitive to drought. Our results demonstrated that an operational ETF/ETFQO pathway is associated with plants' ability to withstand drought and to recover growth once water becomes replete. Drought-induced metabolic reprogramming resulted in an increase in tricarboxylic acid (TCA) cycle intermediates and total amino acid levels, as well as decreases in protein, starch and nitrate contents. The enhanced levels of the branched-chain amino acids in loss-of-function mutants appear to be related to their increased utilization as substrates for the TCA cycle under water stress. Our results thus show that mitochondrial metabolism is highly active during drought stress responses and provide support for a role of alternative respiratory pathways within this response.
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Affiliation(s)
- Marcel V Pires
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Max-Planck Partner Group, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Adilson A Pereira Júnior
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - David B Medeiros
- Max-Planck Partner Group, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Danilo M Daloso
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Max-Planck Partner Group, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Phuong Anh Pham
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Kallyne A Barros
- Max-Planck Partner Group, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Martin K M Engqvist
- Plant Molecular Physiology and Biotechnology, Institute of Plant Developmental and Molecular Biology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstr 1, D-40225, Düsseldorf, Germany
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Göterborg, Sweden
| | - Alexandra Florian
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Ina Krahnert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Veronica G Maurino
- Plant Molecular Physiology and Biotechnology, Institute of Plant Developmental and Molecular Biology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstr 1, D-40225, Düsseldorf, Germany
| | - Wagner L Araújo
- Max-Planck Partner Group, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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86
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Hong J, Yang L, Zhang D, Shi J. Plant Metabolomics: An Indispensable System Biology Tool for Plant Science. Int J Mol Sci 2016; 17:ijms17060767. [PMID: 27258266 PMCID: PMC4926328 DOI: 10.3390/ijms17060767] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/04/2016] [Accepted: 05/06/2016] [Indexed: 11/16/2022] Open
Abstract
As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plant behavior under both normal and stressed conditions. Hereby, we summarize the current knowledge on the genetic and biochemical mechanisms underlying plant growth, development, and stress responses, focusing further on the contributions of metabolomics to practical applications in crop quality improvement and food safety assessment, as well as plant metabolic engineering. We also highlight the current challenges and future perspectives in this inspiring area, with the aim to stimulate further studies leading to better crop improvement of yield and quality.
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Affiliation(s)
- Jun Hong
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Litao Yang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
- Plant Genomics Center, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia.
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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87
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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.
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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;
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88
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Kobayashi Y, Sadhukhan A, Tazib T, Nakano Y, Kusunoki K, Kamara M, Chaffai R, Iuchi S, Sahoo L, Kobayashi M, Hoekenga OA, Koyama H. Joint genetic and network analyses identify loci associated with root growth under NaCl stress in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2016; 39:918-34. [PMID: 26667381 DOI: 10.1111/pce.12691] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 12/04/2015] [Accepted: 12/06/2015] [Indexed: 05/19/2023]
Abstract
Plants have evolved a series of tolerance mechanisms to saline stress, which perturbs physiological processes throughout the plant. To identify genetic mechanisms associated with salinity tolerance, we performed linkage analysis and genome-wide association study (GWAS) on maintenance of root growth of Arabidopsis thaliana in hydroponic culture with weak and severe NaCl toxicity. The top 200 single-nucleotide polymorphisms (SNPs) determined by GWAS could cumulatively explain approximately 70% of the variation observed at each stress level. The most significant SNPs were linked to the genes of ATP-binding cassette B10 and vacuolar proton ATPase A2. Several known salinity tolerance genes such as potassium channel KAT1 and calcium sensor SOS3 were also linked to SNPs in the top 200. In parallel, we constructed a gene co-expression network to independently verify that particular groups of genes work together to a common purpose. We identify molecular mechanisms to confer salt tolerance from both predictable and novel physiological sources and validate the utility of combined genetic and network analysis. Additionally, our study indicates that the genetic architecture of salt tolerance is responsive to the severity of stress. These gene datasets are a significant information resource for a following exploration of gene function.
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Affiliation(s)
- Yuriko Kobayashi
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
| | - Ayan Sadhukhan
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Tanveer Tazib
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
| | - Yuki Nakano
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
| | - Kazutaka Kusunoki
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
| | - Mohamed Kamara
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
- Agronomy Department, Faculty of Agriculture, Kafrelsheikh University, Kafr el-Sheikh, 33516, Egypt
| | - Radhouane Chaffai
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
- Laboratory of Biotechnology and Bio-Geo Resources Valorization, Higher Institute of Biotechnology, University of Manouba BiotechPole, Sidi Thabet, Ariana, 2020, Tunisia
| | - Satoshi Iuchi
- Experimental Plant Division, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Lingaraj Sahoo
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Masatomo Kobayashi
- Experimental Plant Division, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | | | - Hiroyuki Koyama
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
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89
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Guo R, Huang Z, Deng Y, Chen X, XuHan X, Lai Z. Comparative Transcriptome Analyses Reveal a Special Glucosinolate Metabolism Mechanism in Brassica alboglabra Sprouts. FRONTIERS IN PLANT SCIENCE 2016; 7:1497. [PMID: 27757119 PMCID: PMC5047911 DOI: 10.3389/fpls.2016.01497] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/20/2016] [Indexed: 05/20/2023]
Abstract
Brassica sprouts contain abundant phytochemicals, especially glucosinolates (GSs). Various methods have been used to enhance GS content in sprouts. However, the molecular basis of GS metabolism in sprouts remains an open question. Here we employed RNA-seq analysis to compare the transcriptomes of high-GS (JL-08) and low-GS (JL-09) Brassica alboglabra sprouts. Paired-end Illumina RNA-seq reads were generated and mapped to the Brassica oleracea reference genome. The differentially expressed genes were analyzed between JL-08 and JL-09. Among these, 1477 genes were up-regulated and 1239 down-regulated in JL-09 compared with JL-08. Enrichment analysis of these differentially expressed genes showed that the GS biosynthesis had the smallest enrichment factor and the highest Q-value of all metabolic pathways in Kyoto Encyclopedia of Genes and Genomes database, indicating the main metabolic difference between JL-08 and JL-09 is the GS biosynthetic pathway. Thirty-seven genes of the sequenced data were annotated as putatively involved in GS biosynthesis, degradation, and regulation, of which 11 were differentially expressed in JL-08 and JL-09. The expression level of GS degradation enzyme myrosinase in high-GS JL-08 was lower compared with low-GS JL-09. Surprisingly, in high-GS JL-08, the expression levels of GS biosynthesis genes were also lower than those in low-GS JL-09. As the GS contents in sprouts are determined by dynamic equilibrium of seed stored GS mobilization, de novo synthesis, degradation, and extra transport, the result of this study leads us to suggest that efforts to increase GS content should focus on either raising GS content in seeds or decreasing myrosinase activity, rather than improving the expression level of GS biosynthesis genes in sprouts.
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Affiliation(s)
- Rongfang Guo
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Zhongkai Huang
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Yanping Deng
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Xiaodong Chen
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Xu XuHan
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institut de la Recherche Interdisciplinaire de ToulouseToulouse, France
- *Correspondence: Xu XuHan
| | - Zhongxiong Lai
- Department of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Zhongxiong Lai
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90
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Scossa F, Brotman Y, de Abreu E Lima F, Willmitzer L, Nikoloski Z, Tohge T, Fernie AR. Genomics-based strategies for the use of natural variation in the improvement of crop metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:47-64. [PMID: 26566824 DOI: 10.1016/j.plantsci.2015.05.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/29/2015] [Accepted: 05/31/2015] [Indexed: 05/08/2023]
Abstract
Next-generation genomics holds great potential in the study of plant phenotypic variation. With several crop reference genomes now available, the affordable costs of de novo genome assembly or target resequencing offer the opportunity to mine the enormous amount of genetic diversity hidden in crop wild relatives. Wide introgressions from these wild ancestors species or land races represent a possible strategy to improve cultivated varieties. In this review, we discuss the mechanisms underlying metabolic diversity within plant species and the possible strategies (and barriers) to introgress novel metabolic traits into cultivated varieties. We show how deep genomic surveys uncover various types of structural variants from extended gene pools of major crops and highlight how this variation may be used for the improvement of crop metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany; Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Frutticoltura, Via di Fioranello 52, 00134 Rome, Italy.
| | - Yariv Brotman
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | | | - Lothar Willmitzer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Zoran Nikoloski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
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91
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Genome-Wide Analysis of Seed Acid Detergent Lignin (ADL) and Hull Content in Rapeseed (Brassica napus L.). PLoS One 2015; 10:e0145045. [PMID: 26673885 PMCID: PMC4684223 DOI: 10.1371/journal.pone.0145045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/29/2015] [Indexed: 11/19/2022] Open
Abstract
A stable yellow-seeded variety is the breeding goal for obtaining the ideal rapeseed (Brassica napus L.) plant, and the amount of acid detergent lignin (ADL) in the seeds and the hull content (HC) are often used as yellow-seeded rapeseed screening indices. In this study, a genome-wide association analysis of 520 accessions was performed using the Q + K model with a total of 31,839 single-nucleotide polymorphism (SNP) sites. As a result, three significant associations on the B. napus chromosomes A05, A09, and C05 were detected for seed ADL content. The peak SNPs were within 9.27, 14.22, and 20.86 kb of the key genes BnaA.PAL4, BnaA.CAD2/BnaA.CAD3, and BnaC.CCR1, respectively. Further analyses were performed on the major locus of A05, which was also detected in the seed HC examination. A comparison of our genome-wide association study (GWAS) results and previous linkage mappings revealed a common chromosomal region on A09, which indicates that GWAS can be used as a powerful complementary strategy for dissecting complex traits in B. napus. Genomic selection (GS) utilizing the significant SNP markers based on the GWAS results exhibited increased predictive ability, indicating that the predictive ability of a given model can be substantially improved by using GWAS and GS.
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92
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Hildebrandt TM, Nunes Nesi A, Araújo WL, Braun HP. Amino Acid Catabolism in Plants. MOLECULAR PLANT 2015; 8:1563-79. [PMID: 26384576 DOI: 10.1016/j.molp.2015.09.005] [Citation(s) in RCA: 572] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 05/19/2023]
Abstract
Amino acids have various prominent functions in plants. Besides their usage during protein biosynthesis, they also represent building blocks for several other biosynthesis pathways and play pivotal roles during signaling processes as well as in plant stress response. In general, pool sizes of the 20 amino acids differ strongly and change dynamically depending on the developmental and physiological state of the plant cell. Besides amino acid biosynthesis, which has already been investigated in great detail, the catabolism of amino acids is of central importance for adjusting their pool sizes but so far has drawn much less attention. The degradation of amino acids can also contribute substantially to the energy state of plant cells under certain physiological conditions, e.g. carbon starvation. In this review, we discuss the biological role of amino acid catabolism and summarize current knowledge on amino acid degradation pathways and their regulation in the context of plant cell physiology.
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Affiliation(s)
- Tatjana M Hildebrandt
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany.
| | - Adriano Nunes Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil.
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
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93
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Peng C, Uygun S, Shiu SH, Last RL. The Impact of the Branched-Chain Ketoacid Dehydrogenase Complex on Amino Acid Homeostasis in Arabidopsis. PLANT PHYSIOLOGY 2015; 169:1807-20. [PMID: 25986129 PMCID: PMC4634046 DOI: 10.1104/pp.15.00461] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/15/2015] [Indexed: 05/05/2023]
Abstract
The branched-chain amino acids (BCAAs) Leu, Ile, and Val are among nine essential amino acids that must be obtained from the diet of humans and other animals, and can be nutritionally limiting in plant foods. Despite genetic evidence of its importance in regulating seed amino acid levels, the full BCAA catabolic network is not completely understood in plants, and limited information is available regarding its regulation. In this study, transcript coexpression analyses revealed positive correlations among BCAA catabolism genes in stress, development, diurnal/circadian, and light data sets. A core subset of BCAA catabolism genes, including those encoding putative branched-chain ketoacid dehydrogenase subunits, is highly expressed during the night in plants on a diel cycle and in prolonged darkness. Mutants defective in these subunits accumulate higher levels of BCAAs in mature seeds, providing genetic evidence for their function in BCAA catabolism. In addition, prolonged dark treatment caused the mutants to undergo senescence early and overaccumulate leaf BCAAs. These results extend the previous evidence that BCAAs can be catabolized and serve as respiratory substrates at multiple steps. Moreover, comparison of amino acid profiles between mature seeds and dark-treated leaves revealed differences in amino acid accumulation when BCAA catabolism is perturbed. Together, these results demonstrate the consequences of blocking BCAA catabolism during both normal growth conditions and under energy-limited conditions.
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Affiliation(s)
- Cheng Peng
- Department of Plant Biology (C.P., S.-H.S., R.L.L.), Department of Energy Plant Research Laboratory (C.P., S.U.), Genetics Program (S.U., S.-H.S.), and Department of Biochemistry and Molecular Biology (R.L.L.), Michigan State University, East Lansing, Michigan 48824
| | - Sahra Uygun
- Department of Plant Biology (C.P., S.-H.S., R.L.L.), Department of Energy Plant Research Laboratory (C.P., S.U.), Genetics Program (S.U., S.-H.S.), and Department of Biochemistry and Molecular Biology (R.L.L.), Michigan State University, East Lansing, Michigan 48824
| | - Shin-Han Shiu
- Department of Plant Biology (C.P., S.-H.S., R.L.L.), Department of Energy Plant Research Laboratory (C.P., S.U.), Genetics Program (S.U., S.-H.S.), and Department of Biochemistry and Molecular Biology (R.L.L.), Michigan State University, East Lansing, Michigan 48824
| | - Robert L Last
- Department of Plant Biology (C.P., S.-H.S., R.L.L.), Department of Energy Plant Research Laboratory (C.P., S.U.), Genetics Program (S.U., S.-H.S.), and Department of Biochemistry and Molecular Biology (R.L.L.), Michigan State University, East Lansing, Michigan 48824
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94
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Soltis NE, Kliebenstein DJ. Natural Variation of Plant Metabolism: Genetic Mechanisms, Interpretive Caveats, and Evolutionary and Mechanistic Insights. PLANT PHYSIOLOGY 2015; 169:1456-68. [PMID: 26272883 PMCID: PMC4634085 DOI: 10.1104/pp.15.01108] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/12/2015] [Indexed: 05/06/2023]
Abstract
Combining quantitative genetics studies with metabolomics/metabolic profiling platforms, genomics, and transcriptomics is creating significant progress in identifying the causal genes controlling natural variation in metabolite accumulations and profiles. In this review, we discuss key mechanistic and evolutionary insights that are arising from these studies. This includes the potential role of transport and other processes in leading to a separation of the site of mechanistic causation and metabolic consequence. A reilluminated observation is the potential for genomic variation in the organelle to alter phenotypic variation alone and in epistatic interaction with the nuclear genetic variation. These studies are also highlighting new aspects of metabolic pleiotropy both in terms of the breadth of loci altering metabolic variation as well as the potential for broader effects on plant defense regulation of the metabolic variation than has previously been predicted. We also illustrate caveats that can be overlooked when translating quantitative genetics descriptors such as heritability and per-locus r(2) to mechanistic or evolutionary interpretations.
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Affiliation(s)
- Nicole E Soltis
- Department of Plant Sciences, University of California, Davis, California 95616 (N.E.S., D.J.K.); andDynaMo Center of Excellence, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (D.J.K.)
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, California 95616 (N.E.S., D.J.K.); andDynaMo Center of Excellence, University of Copenhagen, DK-1871 Frederiksberg C, Denmark (D.J.K.)
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95
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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.
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Affiliation(s)
- Kurt Lächler
- Institut Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany
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96
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Luo J. Metabolite-based genome-wide association studies in plants. CURRENT OPINION IN PLANT BIOLOGY 2015; 24:31-8. [PMID: 25637954 DOI: 10.1016/j.pbi.2015.01.006] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/13/2015] [Accepted: 01/14/2015] [Indexed: 05/18/2023]
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97
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Gene expression profiling for seed protein and oil synthesis during early seed development in soybean. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0269-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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98
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Ogura T, Busch W. From phenotypes to causal sequences: using genome wide association studies to dissect the sequence basis for variation of plant development. CURRENT OPINION IN PLANT BIOLOGY 2015; 23:98-108. [PMID: 25449733 DOI: 10.1016/j.pbi.2014.11.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 11/04/2014] [Accepted: 11/05/2014] [Indexed: 05/20/2023]
Abstract
Tremendous natural variation of growth and development exists within species. Uncovering the molecular mechanisms that tune growth and development promises to shed light on a broad set of biological issues including genotype to phenotype relations, regulatory mechanisms of biological processes and evolutionary questions. Recent progress in sequencing and data processing capabilities has enabled Genome Wide Association Studies (GWASs) to identify DNA sequence polymorphisms that underlie the variation of biological traits. In the last years, GWASs have proven powerful in revealing the complex genetic bases of many phenotypes in various plant species. Here we highlight successful recent GWASs that uncovered mechanistic and sequence bases of trait variation related to plant growth and development and discuss important considerations for conducting successful GWASs.
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Affiliation(s)
- Takehiko Ogura
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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99
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Xue M, Long J, Jiang Q, Wang M, Chen S, Pang Q, He Y. Distinct patterns of the histone marks associated with recruitment of the methionine chain-elongation pathway from leucine biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:805-12. [PMID: 25428994 PMCID: PMC4321544 DOI: 10.1093/jxb/eru440] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Aliphatic glucosinolates (GLSs) are derived from chain-elongated methionine produced by an iterative three-step process, known to be evolutionarily recruited from leucine biosynthesis. The divergence of homologous genes between two pathways is mainly linked to the alterations in biochemical features. In this study, it was discovered that a distinct pattern of histone modifications is associated with and/or contributes to the divergence of the two pathways. In general, genes involved in leucine biosynthesis were robustly associated with H3k4me2 and H3K4me3. In contrast, despite the considerable abundances of H3K4me2 observed in some of genes involved in methionine chain elongation, H3K4me3 was completely missing. This H3K4m3-depleted pattern had no effect on gene transcription, whereas it seemingly co-evolved with the entire pathway of aliphatic GLS biosynthesis. The results reveal a novel association of the epigenetic marks with plant secondary metabolism, and may help to understand the recruitment of the methionine chain-elongation pathway from leucine biosynthesis.
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Affiliation(s)
- Ming Xue
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jingcheng Long
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qinlong Jiang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Minghui Wang
- Computational Biology Service Unit, Cornell University, Ithaca, NY14853, USA
| | - Sixue Chen
- Department of Biology, Genetics Institute, and Plant Molecular & Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA
| | - Qiuying Pang
- Alkali Soil Natural Environmental Science Center, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Northeast Forestry University, Harbin, Heilongjiang 14850, China
| | - Yan He
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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100
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Toubiana D, Batushansky A, Tzfadia O, Scossa F, Khan A, Barak S, Zamir D, Fernie AR, Nikoloski Z, Fait A. Combined correlation-based network and mQTL analyses efficiently identified loci for branched-chain amino acid, serine to threonine, and proline metabolism in tomato seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:121-33. [PMID: 25359542 DOI: 10.1111/tpj.12717] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 10/22/2014] [Indexed: 05/20/2023]
Abstract
Correlation-based network analysis (CNA) of the metabolic profiles of seeds of a tomato introgression line mapping population revealed a clique of proteinogenic amino acids: Gly, Ile, Pro, Ser, Thr, and Val. Correlations between profiles of these amino acids exhibited a statistically significant average correlation coefficient of 0.84 as compared with an average correlation coefficient of 0.39 over the 16 119 other metabolite cliques containing six metabolites. In silico removal of cliques was used to quantify their importance in determining seminal network properties, highlighting the strong effects of the amino acid clique. Quantitative trait locus analysis revealed co-localization for the six amino acids on chromosome 2, 4 and 10. Sequence analysis identified a unique set of 10 genes on chromosome 2 only, which were associated with amino acid metabolism and specifically the metabolism of Ser-Gly and their conversion into branched-chain amino acids. Metabolite profiling of a set of sublines, with introgressions on chromosome 2, identified a significant change in the abundance of the six amino acids in comparison with M82. Expression analysis of candidate genes affecting Ser metabolism matched the observation from the metabolite data, suggesting a coordinated behavior of the level of these amino acids at the genetic level. Analysis of transcription factor binding sites in the promoter regions of the identified genes suggested combinatorial response to light and the circadian clock.
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Affiliation(s)
- David Toubiana
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Midreshet Ben-Gurion, Israel
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