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Drapal M, Enfissi EMA, Almeida J, Rapacz E, Nogueira M, Fraser PD. The potential of metabolomics in assessing global compositional changes resulting from the application of CRISPR/Cas9 technologies. Transgenic Res 2023; 32:265-278. [PMID: 37166587 DOI: 10.1007/s11248-023-00347-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/03/2023] [Indexed: 05/12/2023]
Abstract
Exhaustive analysis of genetically modified crops over multiple decades has increased societal confidence in the technology. New Plant Breeding Techniques are now emerging with improved precision and the ability to generate products containing no foreign DNA and mimic/replicate conventionally bred varieties. In the present study, metabolomic analysis was used to compare (i) tobacco genotypes with and without the CRISPR associated protein 9 (Cas9), (ii) tobacco lines with the edited and non-edited DE-ETIOLATED-1 gene without phenotype and (iii) leaf and fruit tissue from stable non-edited tomato progeny with and without the Cas9. In all cases, multivariate analysis based on the difference test using LC-HRMS/MS and GC-MS data indicated no significant difference in their metabolomes. The variations in metabolome composition that were evident could be associated with the processes of tissue culture regeneration and/or transformation (e.g. interaction with Agrobacterium). Metabolites responsible for the variance included quantitative changes of abundant, well characterised metabolites such as phenolics (e.g. chlorogenic acid) and several common sugars such as fructose. This study provides fundamental data on the characterisation of gene edited crops, that are important for the evaluation of the technology and its assessment. The approach also suggests that metabolomics could contribute to routine product-based analysis of crops/foods generated from New Plant Breeding approaches.
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Affiliation(s)
- Margit Drapal
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Eugenia M A Enfissi
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | | | - Elzbieta Rapacz
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Marilise Nogueira
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK.
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2
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Niñoles R, Arjona P, Azad SM, Hashim A, Casañ J, Bueso E, Serrano R, Espinosa A, Molina I, Gadea J. Kaempferol-3-rhamnoside overaccumulation in flavonoid 3'-hydroxylase tt7 mutants compromises seed coat outer integument differentiation and seed longevity. THE NEW PHYTOLOGIST 2023; 238:1461-1478. [PMID: 36829299 DOI: 10.1111/nph.18836] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Seeds slowly accumulate damage during storage, which ultimately results in germination failure. The seed coat protects the embryo from the external environment, and its composition is critical for seed longevity. Flavonols accumulate in the outer integument. The link between flavonol composition and outer integument development has not been explored. Genetic, molecular and ultrastructural assays on loss-of-function mutants of the flavonoid biosynthesis pathway were used to study the effect of altered flavonoid composition on seed coat development and seed longevity. Controlled deterioration assays indicate that loss of function of the flavonoid 3' hydroxylase gene TT7 dramatically affects seed longevity and seed coat development. Outer integument differentiation is compromised from 9 d after pollination in tt7 developing seeds, resulting in a defective suberin layer and incomplete degradation of seed coat starch. These distinctive phenotypes are not shared by other mutants showing abnormal flavonoid composition. Genetic analysis indicates that overaccumulation of kaempferol-3-rhamnoside is mainly responsible for the observed phenotypes. Expression profiling suggests that multiple cellular processes are altered in the tt7 mutant. Overaccumulation of kaempferol-3-rhamnoside in the seed coat compromises normal seed coat development. This observation positions TRANSPARENT TESTA 7 and the UGT78D1 glycosyltransferase, catalysing flavonol 3-O-rhamnosylation, as essential players in the modulation of seed longevity.
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Affiliation(s)
- Regina Niñoles
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Ed. 8E, C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | - Paloma Arjona
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Ed. 8E, C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | - Sepideh M Azad
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Ed. 8E, C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | - Aseel Hashim
- Department of Biology, Algoma University, 1520 Queen Street East, Sault Ste. Marie, ON, P6A 2G4, Canada
| | - Jose Casañ
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Ed. 8E, C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | - Eduardo Bueso
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Ed. 8E, C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | - Ramón Serrano
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Ed. 8E, C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | - Ana Espinosa
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Ed. 8E, C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | - Isabel Molina
- Department of Biology, Algoma University, 1520 Queen Street East, Sault Ste. Marie, ON, P6A 2G4, Canada
| | - Jose Gadea
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Ed. 8E, C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
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3
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Zhang M, Zeng Y, Peng R, Dong J, Lan Y, Duan S, Chang Z, Ren J, Luo G, Liu B, Růžička K, Zhao K, Wang HB, Jin HL. N 6-methyladenosine RNA modification regulates photosynthesis during photodamage in plants. Nat Commun 2022; 13:7441. [PMID: 36460653 PMCID: PMC9718803 DOI: 10.1038/s41467-022-35146-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 11/18/2022] [Indexed: 12/04/2022] Open
Abstract
N6-methyladenosine (m6A) modification of mRNAs affects many biological processes. However, the function of m6A in plant photosynthesis remains unknown. Here, we demonstrate that m6A modification is crucial for photosynthesis during photodamage caused by high light stress in plants. The m6A modification levels of numerous photosynthesis-related transcripts are changed after high light stress. We determine that the Arabidopsis m6A writer VIRILIZER (VIR) positively regulates photosynthesis, as its genetic inactivation drastically lowers photosynthetic activity and photosystem protein abundance under high light conditions. The m6A levels of numerous photosynthesis-related transcripts decrease in vir mutants, extensively reducing their transcript and translation levels, as revealed by multi-omics analyses. We demonstrate that VIR associates with the transcripts of genes encoding proteins with functions related to photoprotection (such as HHL1, MPH1, and STN8) and their regulatory proteins (such as regulators of transcript stability and translation), promoting their m6A modification and maintaining their stability and translation efficiency. This study thus reveals an important mechanism for m6A-dependent maintenance of photosynthetic efficiency in plants under high light stress conditions.
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Affiliation(s)
- Man Zhang
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China ,grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China ,grid.484195.5Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, 510640 Guangzhou, People’s Republic of China
| | - Yunping Zeng
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China
| | - Rong Peng
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China
| | - Jie Dong
- grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China
| | - Yelin Lan
- grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China
| | - Sujuan Duan
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China
| | - Zhenyi Chang
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China
| | - Jian Ren
- grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China
| | - Guanzheng Luo
- grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China
| | - Bing Liu
- grid.12981.330000 0001 2360 039XSchool of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People’s Republic of China
| | - Kamil Růžička
- grid.418095.10000 0001 1015 3316Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, 165 02 Prague 6, Czech Republic
| | - Kewei Zhao
- grid.411866.c0000 0000 8848 7685Guangzhou Key Laboratory of Chinese Medicine Research on Prevention and Treatment of Osteoporosis, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, No.263, Longxi Avenue, Guangzhou, People’s Republic of China
| | - Hong-Bin Wang
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China ,grid.419897.a0000 0004 0369 313XKey Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, People’s Republic of China ,grid.411866.c0000 0000 8848 7685State Key Laboratory of Dampness Syndrome of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Hong-Lei Jin
- grid.411866.c0000 0000 8848 7685Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People’s Republic of China ,grid.411866.c0000 0000 8848 7685Guangzhou Key Laboratory of Chinese Medicine Research on Prevention and Treatment of Osteoporosis, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, No.263, Longxi Avenue, Guangzhou, People’s Republic of China
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Anderson SA, Satyanarayan MB, Wessendorf RL, Lu Y, Fernandez DE. A homolog of GuidedEntry of Tail-anchored proteins3 functions in membrane-specific protein targeting in chloroplasts of Arabidopsis. THE PLANT CELL 2021; 33:2812-2833. [PMID: 34021351 PMCID: PMC8408437 DOI: 10.1093/plcell/koab145] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/18/2021] [Indexed: 05/12/2023]
Abstract
The chloroplasts and mitochondria of photosynthetic eukaryotes contain proteins that are closely related to cytosolic Guided Entry of Tail-anchored proteins3 (Get3). Get3 is a targeting factor that efficiently escorts tail-anchored (TA) proteins to the ER. Because other components of the cytosolic-targeting pathway appear to be absent in organelles, previous investigators have asserted that organellar Get3 homologs are unlikely to act as targeting factors. However, we show here both that the Arabidopsis thaliana chloroplast homolog designated as GET3B is structurally similar to cytosolic Get3 proteins and that it selectively binds a thylakoid-localized TA protein. Based on genetic interactions between a get3b mutation and mutations affecting the chloroplast signal recognition particle-targeting pathway, as well as changes in the abundance of photosynthesis-related proteins in mutant plants, we propose that GET3B acts primarily to direct proteins to the thylakoids. Furthermore, through molecular complementation experiments, we show that function of GET3B depends on its ability to hydrolyze ATP, and this is consistent with action as a targeting factor. We propose that GET3B and related organellar Get3 homologs play a role that is analogous to that of cytosolic Get3 proteins, and that GET3B acts as a targeting factor in the chloroplast stroma to deliver TA proteins in a membrane-specific manner.
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Affiliation(s)
- Stacy A. Anderson
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Manasa B. Satyanarayan
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008, USA
| | - Ryan L. Wessendorf
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008, USA
| | - Yan Lu
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008, USA
| | - Donna E. Fernandez
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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5
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Sanjaya A, Kazama Y, Ishii K, Muramatsu R, Kanamaru K, Ohbu S, Abe T, Fujiwara MT. An Argon-Ion-Induced Pale Green Mutant of Arabidopsis Exhibiting Rapid Disassembly of Mesophyll Chloroplast Grana. PLANTS (BASEL, SWITZERLAND) 2021; 10:848. [PMID: 33922223 PMCID: PMC8145761 DOI: 10.3390/plants10050848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/18/2021] [Accepted: 04/21/2021] [Indexed: 01/13/2023]
Abstract
Argon-ion beam is an effective mutagen capable of inducing a variety of mutation types. In this study, an argon ion-induced pale green mutant of Arabidopsis thaliana was isolated and characterized. The mutant, designated Ar50-33-pg1, exhibited moderate defects of growth and greening and exhibited rapid chlorosis in photosynthetic tissues. Fluorescence microscopy confirmed that mesophyll chloroplasts underwent substantial shrinkage during the chlorotic process. Genetic and whole-genome resequencing analyses revealed that Ar50-33-pg1 contained a large 940 kb deletion in chromosome V that encompassed more than 100 annotated genes, including 41 protein-coding genes such as TYRAAt1/TyrA1, EGY1, and MBD12. One of the deleted genes, EGY1, for a thylakoid membrane-localized metalloprotease, was the major contributory gene responsible for the pale mutant phenotype. Both an egy1 mutant and F1 progeny of an Ar50-33-pg1 × egy1 cross-exhibited chlorotic phenotypes similar to those of Ar50-33-pg1. Furthermore, ultrastructural analysis of mesophyll cells revealed that Ar50-33-pg1 and egy1 initially developed wild type-like chloroplasts, but these were rapidly disassembled, resulting in thylakoid disorganization and fragmentation, as well as plastoglobule accumulation, as terminal phenotypes. Together, these data support the utility of heavy-ion mutagenesis for plant genetic analysis and highlight the importance of EGY1 in the structural maintenance of grana in mesophyll chloroplasts.
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Affiliation(s)
- Alvin Sanjaya
- Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan; (A.S.); (R.M.)
| | - Yusuke Kazama
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjojima, Eiheiji, Yoshida, Fukui 910-1195, Japan
| | - Kotaro Ishii
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
| | - Ryohsuke Muramatsu
- Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan; (A.S.); (R.M.)
| | - Kengo Kanamaru
- Faculty of Agriculture, Kobe University, Nada, Kobe, Hyogo 657-8501, Japan;
| | - Sumie Ohbu
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
| | - Tomoko Abe
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
| | - Makoto T. Fujiwara
- Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan; (A.S.); (R.M.)
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
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6
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Fraser PD, Aharoni A, Hall RD, Huang S, Giovannoni JJ, Sonnewald U, Fernie AR. Metabolomics should be deployed in the identification and characterization of gene-edited crops. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:897-902. [PMID: 31923321 DOI: 10.1111/tpj.14679] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/17/2019] [Accepted: 01/07/2020] [Indexed: 05/23/2023]
Abstract
Gene-editing techniques are currently revolutionizing biology, allowing far greater precision than previous mutagenic and transgenic approaches. They are becoming applicable to a wide range of plant species and biological processes. Gene editing can rapidly improve a range of crop traits, including disease resistance, abiotic stress tolerance, yield, nutritional quality and additional consumer traits. Unlike transgenic approaches, however, it is not facile to forensically detect gene-editing events at the molecular level, as no foreign DNA exists in the elite line. These limitations in molecular detection approaches are likely to focus more attention on the products generated from the technology than on the process in itself. Rapid advances in sequencing and genome assembly increasingly facilitate genome sequencing as a means of characterizing new varieties generated by gene-editing techniques. Nevertheless, subtle edits such as single base changes or small deletions may be difficult to distinguish from normal variation within a genotype. Given these emerging scenarios, downstream 'omics' technologies reflective of edited affects, such as metabolomics, need to be used in a more prominent manner to fully assess compositional changes in novel foodstuffs. To achieve this goal, metabolomics or 'non-targeted metabolite analysis' needs to make significant advances to deliver greater representation across the metabolome. With the emergence of new edited crop varieties, we advocate: (i) concerted efforts in the advancement of 'omics' technologies, such as metabolomics, and (ii) an effort to redress the use of the technology in the regulatory assessment for metabolically engineered biotech crops.
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Affiliation(s)
- Paul D Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Robert D Hall
- Wageningen Research, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, the Netherlands
- Laboratory of Plant Physiology, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, the Netherlands
- Netherlands Metabolomics Centre, Einsteinweg 55, Leiden, the Netherlands
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100084, China
| | - James J Giovannoni
- USDA-ARS, Robert W. Holley Center and Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
| | - Uwe Sonnewald
- Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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Guan X, Okazaki Y, Zhang R, Saito K, Nikolau BJ. Dual-Localized Enzymatic Components Constitute the Fatty Acid Synthase Systems in Mitochondria and Plastids. PLANT PHYSIOLOGY 2020; 183:517-529. [PMID: 32245791 PMCID: PMC7271793 DOI: 10.1104/pp.19.01564] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/23/2020] [Indexed: 05/07/2023]
Abstract
Plant fatty acid biosynthesis occurs in both plastids and mitochondria. Here, we report the identification and characterization of Arabidopsis (Arabidopsis thaliana) genes encoding three enzymes shared between the mitochondria- and plastid-localized type II fatty acid synthase systems (mtFAS and ptFAS, respectively). Two of these enzymes, β-ketoacyl-acyl carrier protein (ACP) reductase and enoyl-ACP reductase, catalyze two of the reactions that constitute the core four-reaction cycle of the FAS system, which iteratively elongates the acyl chain by two carbon atoms per cycle. The third enzyme, malonyl-coenzyme A:ACP transacylase, catalyzes the reaction that loads the mtFAS system with substrate by malonylating the phosphopantetheinyl cofactor of ACP. GFP fusion experiments revealed that the these enzymes localize to both chloroplasts and mitochondria. This localization was validated by characterization of mutant alleles, which were rescued by transgenes expressing enzyme variants that were retargeted only to plastids or only to mitochondria. The singular retargeting of these proteins to plastids rescued the embryo lethality associated with disruption of the essential ptFAS system, but these rescued plants displayed phenotypes typical of the lack of mtFAS function, including reduced lipoylation of the H subunit of the glycine decarboxylase complex, hyperaccumulation of glycine, and reduced growth. However, these latter traits were reversible in an elevated-CO2 atmosphere, which suppresses mtFAS-associated photorespiration-dependent chemotypes. Sharing enzymatic components between mtFAS and ptFAS systems constrains the evolution of these nonredundant fatty acid biosynthetic machineries.
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Affiliation(s)
- Xin Guan
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011
| | - Yozo Okazaki
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Rwisdom Zhang
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011
- Department of Chemical Engineering, University of Southern California, Los Angeles, California 90007
| | - Kazuki Saito
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
| | - Basil J Nikolau
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
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8
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Fu X, Guan X, Garlock R, Nikolau BJ. Mitochondrial Fatty Acid Synthase Utilizes Multiple Acyl Carrier Protein Isoforms. PLANT PHYSIOLOGY 2020; 183:547-557. [PMID: 32094306 PMCID: PMC7271772 DOI: 10.1104/pp.19.01468] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/10/2020] [Indexed: 05/19/2023]
Abstract
Acyl carrier protein (ACP) is a highly conserved cofactor protein that is required by Type II fatty acid synthases (FASs). Here, we demonstrate that up to three mitochondrial ACP (mtACP) isoforms support the Arabidopsis (Arabidopsis thaliana) mitochondrially localized Type II FAS. The physiological importance of the three mtACPs was evaluated by characterizing the single, double, and triple mutants. The mtACP1 (At2g44620), mtACP2 (At1g65290), and mtACP3 (At5g47630) single mutants showed no discernible morphological growth phenotype. Functional redundancy among the three mtACPs was indicated by the embryo-lethal phenotype associated with simultaneous loss of all three mtACP genes. Characterization of all double mutant combinations revealed that although the mtacp1 mtacp3 and mtacp2 mtacp3 double mutant combinations showed no observable growth defect, the mtacp1 mtacp2 double mutant was viable but displayed delayed growth, reduced levels of posttranslationally lipoylated mitochondrial proteins, hyperaccumulation of photorespiratory Gly, and reduced accumulation of many intermediates in central metabolism. These alterations were partially reversed when the mtacp1 mtacp2 double mutant plants were grown in a nonphotorespiratory condition (i.e. 1% CO2 atmosphere) or in the presence of 2% Suc. In summary, mtACP, as a key component of mitochondrial fatty acid biosynthesis, is important in generating the fatty acid precursor of lipoic acid biosynthesis. Thus, the incomplete lipoylation of mitochondrial proteins in mtacp mutants, particularly Gly decarboxylase, affects the recovery of photorespiratory carbon, and this appears to be critical during embryogenesis.
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Affiliation(s)
- Xinyu Fu
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
| | - Xin Guan
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
| | - Rachel Garlock
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Basil J Nikolau
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
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9
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Fu X, Yang H, Pangestu F, Nikolau BJ. Failure to Maintain Acetate Homeostasis by Acetate-Activating Enzymes Impacts Plant Development. PLANT PHYSIOLOGY 2020; 182:1256-1271. [PMID: 31874860 PMCID: PMC7054878 DOI: 10.1104/pp.19.01162] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 12/12/2019] [Indexed: 05/09/2023]
Abstract
The metabolic intermediate acetyl-CoA links anabolic and catabolic processes and coordinates metabolism with cellular signaling by influencing protein acetylation. In this study we demonstrate that in Arabidopsis (Arabidopsis thaliana), two distinctly localized acetate-activating enzymes, ACETYL-COA SYNTHETASE (ACS) in plastids and ACETATE NON-UTILIZING1 (ACN1) in peroxisomes, function redundantly to prevent the accumulation of excess acetate. In contrast to the near wild-type morphological and metabolic phenotypes of acs or acn1 mutants, the acs acn1 double mutant is delayed in growth and sterile, which is associated with hyperaccumulation of cellular acetate and decreased accumulation of acetyl-CoA-derived intermediates of central metabolism. Using multiple mutant stocks and stable isotope-assisted metabolic analyses, we demonstrate the twin metabolic origins of acetate from the oxidation of ethanol and the nonoxidative decarboxylation of pyruvate, with acetaldehyde being the common intermediate precursor of acetate. Conversion from pyruvate to acetate is activated under hypoxic conditions, and ACS recovers carbon that would otherwise be lost from the plant as ethanol. Plastid-localized ACS metabolizes cellular acetate and contributes to the de novo biosynthesis of fatty acids and Leu; peroxisome-localized ACN1 enables the incorporation of acetate into organic acids and amino acids. Thus, the activation of acetate in distinct subcellular compartments provides plants with the metabolic flexibility to maintain physiological levels of acetate and a metabolic mechanism for the recovery of carbon that would otherwise be lost as ethanol, for example following hypoxia.
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Affiliation(s)
- Xinyu Fu
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
| | - Hannah Yang
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Febriana Pangestu
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Basil J Nikolau
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
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10
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Qi M, Zheng W, Zhao X, Hohenstein JD, Kandel Y, O'Conner S, Wang Y, Du C, Nettleton D, MacIntosh GC, Tylka GL, Wurtele ES, Whitham SA, Li L. QQS orphan gene and its interactor NF-YC4 reduce susceptibility to pathogens and pests. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:252-263. [PMID: 29878511 PMCID: PMC6330549 DOI: 10.1111/pbi.12961] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/04/2018] [Indexed: 05/19/2023]
Abstract
Enhancing the nutritional quality and disease resistance of crops without sacrificing productivity is a key issue for developing varieties that are valuable to farmers and for simultaneously improving food security and sustainability. Expression of the Arabidopsis thaliana species-specific AtQQS (Qua-Quine Starch) orphan gene or its interactor, NF-YC4 (Nuclear Factor Y, subunit C4), has been shown to increase levels of leaf/seed protein without affecting the growth and yield of agronomic species. Here, we demonstrate that overexpression of AtQQS and NF-YC4 in Arabidopsis and soybean enhances resistance/reduces susceptibility to viruses, bacteria, fungi, aphids and soybean cyst nematodes. A series of Arabidopsis mutants in starch metabolism were used to explore the relationships between QQS expression, carbon and nitrogen partitioning, and defense. The enhanced basal defenses mediated by QQS were independent of changes in protein/carbohydrate composition of the plants. We demonstrate that either AtQQS or NF-YC4 overexpression in Arabidopsis and in soybean reduces susceptibility of these plants to pathogens/pests. Transgenic soybean lines overexpressing NF-YC4 produce seeds with increased protein while maintaining healthy growth. Pull-down studies reveal that QQS interacts with human NF-YC, as well as with Arabidopsis NF-YC4, and indicate two QQS binding sites near the NF-YC-histone-binding domain. A new model for QQS interaction with NF-YC is speculated. Our findings illustrate the potential of QQS and NF-YC4 to increase protein and improve defensive traits in crops, overcoming the normal growth-defense trade-offs.
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Affiliation(s)
- Mingsheng Qi
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Wenguang Zheng
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIAUSA
| | - Xuefeng Zhao
- Laurence H. Baker Center for Bioinformatics and Biological StatisticsIowa State UniversityAmesIAUSA
| | - Jessica D. Hohenstein
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular BiologyIowa State UniversityAmesIAUSA
| | - Yuba Kandel
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Seth O'Conner
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIAUSA
- Department of Biological SciencesMississippi State UniversityStarkvilleMSUSA
| | - Yifan Wang
- Department of StatisticsIowa State UniversityAmesIAUSA
| | - Chuanlong Du
- Department of StatisticsIowa State UniversityAmesIAUSA
| | - Dan Nettleton
- Department of StatisticsIowa State UniversityAmesIAUSA
| | - Gustavo C. MacIntosh
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular BiologyIowa State UniversityAmesIAUSA
| | - Gregory L. Tylka
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Eve S. Wurtele
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIAUSA
- Center for Metabolic BiologyIowa State UniversityAmesIAUSA
| | - Steven A. Whitham
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Ling Li
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIAUSA
- Department of Biological SciencesMississippi State UniversityStarkvilleMSUSA
- Center for Metabolic BiologyIowa State UniversityAmesIAUSA
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11
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Oh S, Montgomery BL. Mesophyll-specific phytochromes impact chlorophyll light-harvesting complexes (LHCs) and non-photochemical quenching. PLANT SIGNALING & BEHAVIOR 2019; 14:1609857. [PMID: 31037997 PMCID: PMC6619949 DOI: 10.1080/15592324.2019.1609857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Phytochromes regulate light-dependent plastid development and plant growth and development. Prior analyses demonstrated that phytochromes regulate expression of Sigma factor 2 (SIG2), which is involved in plastid transcription and coordinates expression of plastid- and nuclear-encoded genes involved in plastid development, as well as plant growth and development. Mutation of SIG2 impacts distinct aspects of photosynthesis, resulting in elevated levels of cyclic electron flow and nonphotochemical quenching (NPQ). As we initially identified SIG2 expression as misregulated in a line lacking phytochromes in mesophyll tissues (i.e., CAB3::pBVR lines), here we report on an investigation of whether photosynthetic parameters such as NPQ are also disrupted in CAB3::pBVR lines. We determined that a specific parameter of NPQ, i.e., energy-dependent quenching (qE) which is a rapidly induced photoprotective mechanism that dissipates stressful absorption of excess light energy during photosynthesis, is disrupted when mesophyll phytochromes are significantly depleted. The observed reduction in NPQ levels in strong CAB3::pBVR lines is associated with a reduction in the accumulation of Lhcb1 proteins and assembly or stability of light-harvesting complexes (LHCs), especially trimeric LHC. These results implicate mesophyll-localized phytochromes in a specific aspect of phytochrome-mediated NPQ, likely through regulation of chlorophyll synthesis and accumulation and the associated impacts on chlorophyll-protein complexes. This role is distinct from the impact of mesophyll phytochrome-dependent control of SIG2 and associated NPQ regulation.
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Affiliation(s)
- Sookyung Oh
- Department of Energy — Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Beronda L. Montgomery
- Department of Energy — Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- CONTACT Beronda L. Montgomery Department of Energy — Plant Research Laboratory, Michigan State University, 612 Wilson Road, Room 106, East Lansing, MI 48824, USA
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12
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Wang K, Froehlich JE, Zienkiewicz A, Hersh HL, Benning C. A Plastid Phosphatidylglycerol Lipase Contributes to the Export of Acyl Groups from Plastids for Seed Oil Biosynthesis. THE PLANT CELL 2017; 29:1678-1696. [PMID: 28687655 PMCID: PMC5559756 DOI: 10.1105/tpc.17.00397] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/29/2017] [Accepted: 07/06/2017] [Indexed: 05/20/2023]
Abstract
The lipid composition of thylakoid membranes inside chloroplasts is conserved from leaves to developing embryos. A finely tuned lipid assembly machinery is required to build these membranes during Arabidopsis thaliana development. Contrary to thylakoid lipid biosynthetic enzymes, the functions of most predicted chloroplast lipid-degrading enzymes remain to be elucidated. Here, we explore the biochemistry and physiological function of an Arabidopsis thylakoid membrane-associated lipase, PLASTID LIPASE1 (PLIP1). PLIP1 is a phospholipase A1 In vivo, PLIP1 hydrolyzes polyunsaturated acyl groups from a unique chloroplast-specific phosphatidylglycerol that contains 16:1 Δ3trans as its second acyl group. Thus far, a specific function of this 16:1 Δ3trans -containing phosphatidylglycerol in chloroplasts has remained elusive. The PLIP1 gene is highly expressed in seeds, and plip1 mutant seeds contain less oil and exhibit delayed germination compared with the wild type. Acyl groups released by PLIP1 are exported from the chloroplast, reincorporated into phosphatidylcholine, and ultimately enter seed triacylglycerol. Thus, 16:1 Δ3trans uniquely labels a small but biochemically active plastid phosphatidylglycerol pool in developing Arabidopsis embryos, which is subject to PLIP1 activity, thereby contributing a small fraction of the polyunsaturated fatty acids present in seed oil. We propose that acyl exchange involving thylakoid lipids functions in acyl export from plastids and seed oil biosynthesis.
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Affiliation(s)
- Kun Wang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - John E Froehlich
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Agnieszka Zienkiewicz
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Great Lakes Bioenergy Research Center, East Lansing, Michigan 48823
| | - Hope Lynn Hersh
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Great Lakes Bioenergy Research Center, East Lansing, Michigan 48823
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
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13
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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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14
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Hackett JB, Shi X, Kobylarz AT, Lucas MK, Wessendorf RL, Hines KM, Bentolila S, Hanson MR, Lu Y. An Organelle RNA Recognition Motif Protein Is Required for Photosystem II Subunit psbF Transcript Editing. PLANT PHYSIOLOGY 2017; 173:2278-2293. [PMID: 28213559 PMCID: PMC5373051 DOI: 10.1104/pp.16.01623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 02/13/2017] [Indexed: 05/02/2023]
Abstract
Loss-of-function mutations in ORGANELLE RNA RECOGNITION MOTIF PROTEIN6 (ORRM6) result in the near absence of RNA editing of psbF-C77 and the reduction in accD-C794 editing in Arabidopsis (Arabidopsis thaliana). The orrm6 mutants have decreased levels of photosystem II (PSII) proteins, especially PsbF, lower PSII activity, pale green pigmentation, smaller leaf and plant sizes, and retarded growth. Stable expression of ORRM6 rescues the orrm6 editing defects and mutant phenotype. Unlike ORRM1, the other known ORRM plastid editing factor, ORRM6, does not contain RNA editing interacting protein/multiple organellar RNA editing factor (RIP/MORF) boxes, which are required for ORRM1 to interact with site-specific pentatricopeptide repeat protein editing factors. ORRM6 interacts with RIP1/MORF8, RIP2/MORF2, and RIP9/MORF9, known components of RNA editosomes. While some plastid RRM proteins are involved in other forms of RNA processing and translation, the primary function of ORRM6 is evidently to mediate psbF-C77 editing, like the essential site-specific pentatricopeptide repeat protein LOW PSII ACCUMULATION66. Stable expression in the orrm6 mutants of a nucleus-encoded, plastid-targeted PsbF protein from a psbF gene carrying a T at nucleotide 77 significantly increases leaf and plant sizes, chlorophyll content, and PSII activity. These transformants demonstrate that plastid RNA editing can be bypassed through the expression of nucleus-encoded, edited forms of plastid genes.
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Affiliation(s)
- Justin B Hackett
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
| | - Xiaowen Shi
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
| | - Amy T Kobylarz
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
| | - Meriah K Lucas
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
| | - Ryan L Wessendorf
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
| | - Kevin M Hines
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
| | - Stephane Bentolila
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
| | - Maureen R Hanson
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
| | - Yan Lu
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410 (J.B.H., A.T.K., M.K.L., R.L.W., Y.L.); and
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 (X.S., K.M.H., S.B., M.R.H.)
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15
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Guan X, Okazaki Y, Lithio A, Li L, Zhao X, Jin H, Nettleton D, Saito K, Nikolau BJ. Discovery and Characterization of the 3-Hydroxyacyl-ACP Dehydratase Component of the Plant Mitochondrial Fatty Acid Synthase System. PLANT PHYSIOLOGY 2017; 173:2010-2028. [PMID: 28202596 PMCID: PMC5373057 DOI: 10.1104/pp.16.01732] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/08/2017] [Indexed: 05/06/2023]
Abstract
We report the characterization of the Arabidopsis (Arabidopsis thaliana) 3-hydroxyacyl-acyl carrier protein dehydratase (mtHD) component of the mitochondrial fatty acid synthase (mtFAS) system, encoded by AT5G60335. The mitochondrial localization and catalytic capability of mtHD were demonstrated with a green fluorescent protein transgenesis experiment and by in vivo complementation and in vitro enzymatic assays. RNA interference (RNAi) knockdown lines with reduced mtHD expression exhibit traits typically associated with mtFAS mutants, namely a miniaturized morphological appearance, reduced lipoylation of lipoylated proteins, and altered metabolomes consistent with the reduced catalytic activity of lipoylated enzymes. These alterations are reversed when mthd-rnai mutant plants are grown in a 1% CO2 atmosphere, indicating the link between mtFAS and photorespiratory deficiency due to the reduced lipoylation of glycine decarboxylase. In vivo biochemical feeding experiments illustrate that sucrose and glycolate are the metabolic modulators that mediate the alterations in morphology and lipid accumulation. In addition, both mthd-rnai and mtkas mutants exhibit reduced accumulation of 3-hydroxytetradecanoic acid (i.e. a hallmark of lipid A-like molecules) and abnormal chloroplastic starch granules; these changes are not reversible by the 1% CO2 atmosphere, demonstrating two novel mtFAS functions that are independent of photorespiration. Finally, RNA sequencing analysis revealed that mthd-rnai and mtkas mutants are nearly equivalent to each other in altering the transcriptome, and these analyses further identified genes whose expression is affected by a functional mtFAS system but independent of photorespiratory deficiency. These data demonstrate the nonredundant nature of the mtFAS system, which contributes unique lipid components needed to support plant cell structure and metabolism.
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MESH Headings
- Amino Acid Sequence
- Arabidopsis/enzymology
- Arabidopsis/genetics
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Blotting, Western
- Carbon Dioxide/metabolism
- Fatty Acid Synthase, Type II/genetics
- Fatty Acid Synthase, Type II/metabolism
- Fatty Acid Synthases/genetics
- Fatty Acid Synthases/metabolism
- Gene Expression Regulation, Plant
- Glycolates/metabolism
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- Hydro-Lyases/genetics
- Hydro-Lyases/metabolism
- Metabolomics/methods
- Microscopy, Confocal
- Microscopy, Electron, Transmission
- Mitochondria/enzymology
- Mitochondria/ultrastructure
- Mutation
- Myristic Acids/metabolism
- Plants, Genetically Modified
- RNA Interference
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, RNA/methods
- Sequence Homology, Amino Acid
- Sucrose/metabolism
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Affiliation(s)
- Xin Guan
- Department of Biochemistry, Biophysics, and Molecular Biology (X.G., H.J., B.J.N.), National Science Foundation Engineering Research Center for Biorenewable Chemicals (X.G., B.J.N.), Department of Statistics (A.L., D.N.), Department of Genetics, Development, and Cellular Biology (L.L.), Laurence H. Baker Center for Bioinformatics and Biological Statistics (X.Z.), and Center for Metabolic Biology (B.J.N.), Iowa State University, Ames, Iowa 50011
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.O., K.S.); and
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
| | - Yozo Okazaki
- Department of Biochemistry, Biophysics, and Molecular Biology (X.G., H.J., B.J.N.), National Science Foundation Engineering Research Center for Biorenewable Chemicals (X.G., B.J.N.), Department of Statistics (A.L., D.N.), Department of Genetics, Development, and Cellular Biology (L.L.), Laurence H. Baker Center for Bioinformatics and Biological Statistics (X.Z.), and Center for Metabolic Biology (B.J.N.), Iowa State University, Ames, Iowa 50011
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.O., K.S.); and
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
| | - Andrew Lithio
- Department of Biochemistry, Biophysics, and Molecular Biology (X.G., H.J., B.J.N.), National Science Foundation Engineering Research Center for Biorenewable Chemicals (X.G., B.J.N.), Department of Statistics (A.L., D.N.), Department of Genetics, Development, and Cellular Biology (L.L.), Laurence H. Baker Center for Bioinformatics and Biological Statistics (X.Z.), and Center for Metabolic Biology (B.J.N.), Iowa State University, Ames, Iowa 50011
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.O., K.S.); and
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
| | - Ling Li
- Department of Biochemistry, Biophysics, and Molecular Biology (X.G., H.J., B.J.N.), National Science Foundation Engineering Research Center for Biorenewable Chemicals (X.G., B.J.N.), Department of Statistics (A.L., D.N.), Department of Genetics, Development, and Cellular Biology (L.L.), Laurence H. Baker Center for Bioinformatics and Biological Statistics (X.Z.), and Center for Metabolic Biology (B.J.N.), Iowa State University, Ames, Iowa 50011
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.O., K.S.); and
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
| | - Xuefeng Zhao
- Department of Biochemistry, Biophysics, and Molecular Biology (X.G., H.J., B.J.N.), National Science Foundation Engineering Research Center for Biorenewable Chemicals (X.G., B.J.N.), Department of Statistics (A.L., D.N.), Department of Genetics, Development, and Cellular Biology (L.L.), Laurence H. Baker Center for Bioinformatics and Biological Statistics (X.Z.), and Center for Metabolic Biology (B.J.N.), Iowa State University, Ames, Iowa 50011
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.O., K.S.); and
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
| | - Huanan Jin
- Department of Biochemistry, Biophysics, and Molecular Biology (X.G., H.J., B.J.N.), National Science Foundation Engineering Research Center for Biorenewable Chemicals (X.G., B.J.N.), Department of Statistics (A.L., D.N.), Department of Genetics, Development, and Cellular Biology (L.L.), Laurence H. Baker Center for Bioinformatics and Biological Statistics (X.Z.), and Center for Metabolic Biology (B.J.N.), Iowa State University, Ames, Iowa 50011
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.O., K.S.); and
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
| | - Dan Nettleton
- Department of Biochemistry, Biophysics, and Molecular Biology (X.G., H.J., B.J.N.), National Science Foundation Engineering Research Center for Biorenewable Chemicals (X.G., B.J.N.), Department of Statistics (A.L., D.N.), Department of Genetics, Development, and Cellular Biology (L.L.), Laurence H. Baker Center for Bioinformatics and Biological Statistics (X.Z.), and Center for Metabolic Biology (B.J.N.), Iowa State University, Ames, Iowa 50011
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.O., K.S.); and
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
| | - Kazuki Saito
- Department of Biochemistry, Biophysics, and Molecular Biology (X.G., H.J., B.J.N.), National Science Foundation Engineering Research Center for Biorenewable Chemicals (X.G., B.J.N.), Department of Statistics (A.L., D.N.), Department of Genetics, Development, and Cellular Biology (L.L.), Laurence H. Baker Center for Bioinformatics and Biological Statistics (X.Z.), and Center for Metabolic Biology (B.J.N.), Iowa State University, Ames, Iowa 50011
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.O., K.S.); and
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
| | - Basil J Nikolau
- Department of Biochemistry, Biophysics, and Molecular Biology (X.G., H.J., B.J.N.), National Science Foundation Engineering Research Center for Biorenewable Chemicals (X.G., B.J.N.), Department of Statistics (A.L., D.N.), Department of Genetics, Development, and Cellular Biology (L.L.), Laurence H. Baker Center for Bioinformatics and Biological Statistics (X.Z.), and Center for Metabolic Biology (B.J.N.), Iowa State University, Ames, Iowa 50011;
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan (Y.O., K.S.); and
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan (K.S.)
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16
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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: 24] [Impact Index Per Article: 3.4] [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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17
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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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18
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Guan X, Nikolau BJ. AAE13 encodes a dual-localized malonyl-CoA synthetase that is crucial for mitochondrial fatty acid biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:581-93. [PMID: 26836315 DOI: 10.1111/tpj.13130] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/12/2016] [Accepted: 01/18/2016] [Indexed: 05/19/2023]
Abstract
Malonyl-CoA is a key intermediate in a number of metabolic processes associated with its role as a substrate in acylation and condensation reactions. These types of reactions occur in plastids, the cytosol and mitochondria, and although carboxylation of acetyl-CoA is the known mechanism for generating the distinct plastidial and cytosolic pools, the metabolic origin of the mitochondrial malonyl-CoA pool is still unclear. In this study we demonstrate that malonyl-CoA synthetase encoded by the Arabidopsis AAE13 (AT3G16170) gene is localized in both the cytosol and the mitochondria. These isoforms are translated from two types of transcripts, one that contains and one that does not contain a mitochondrial-targeting pre-sequence. Whereas the cytosolic AAE13 protein is not essential, due to the presence of a redundant malonyl-CoA generating system provided by a cytosolic acetyl-CoA carboxylase, the mitochondrial AAE13 protein is essential for plant growth. Phenotypes of the aae13-1 mutant are transgenically reversed only if the mitochondrial pre-sequence is present in the ectopically expressed AAE13 proteins. The aae13-1 mutant exhibits typical metabolic phenotypes associated with a deficiency in the mitochondrial fatty acid synthase system, namely depleted lipoylation of the H subunit of the photorespiratory enzyme glycine decarboxylase, increased accumulation of glycine and glycolate and reduced levels of sucrose. Most of these metabolic alterations, and associated morphological changes, are reversed when the aae13-1 mutant is grown in a non-photorespiratory condition (i.e. a 1% CO2 atmosphere), demonstrating that they are a consequence of the deficiency in photorespiration due to the inability to generate lipoic acid from mitochondrially synthesized fatty acids.
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Affiliation(s)
- Xin Guan
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
- The NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, 50011, USA
| | - Basil J Nikolau
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
- The NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, IA, 50011, USA
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19
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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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20
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Guan X, Chen H, Abramson A, Man H, Wu J, Yu O, Nikolau BJ. A phosphopantetheinyl transferase that is essential for mitochondrial fatty acid biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:718-32. [PMID: 26402847 DOI: 10.1111/tpj.13034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 05/23/2023]
Abstract
In this study we report the molecular genetic characterization of the Arabidopsis mitochondrial phosphopantetheinyl transferase (mtPPT), which catalyzes the phosphopantetheinylation and thus activation of mitochondrial acyl carrier protein (mtACP) of mitochondrial fatty acid synthase (mtFAS). This catalytic capability of the purified mtPPT protein (encoded by AT3G11470) was directly demonstrated in an in vitro assay that phosphopantetheinylated mature Arabidopsis apo-mtACP isoforms. The mitochondrial localization of the AT3G11470-encoded proteins was validated by the ability of their N-terminal 80-residue leader sequence to guide a chimeric GFP protein to this organelle. A T-DNA-tagged null mutant mtppt-1 allele shows an embryo-lethal phenotype, illustrating a crucial role of mtPPT for embryogenesis. Arabidopsis RNAi transgenic lines with reduced mtPPT expression display typical phenotypes associated with a deficiency in the mtFAS system, namely miniaturized plant morphology, slow growth, reduced lipoylation of mitochondrial proteins, and the hyperaccumulation of photorespiratory intermediates, glycine and glycolate. These morphological and metabolic alterations are reversed when these plants are grown in a non-photorespiratory condition (i.e. 1% CO2 atmosphere), demonstrating that they are a consequence of a deficiency in photorespiration due to the reduced lipoylation of the photorespiratory glycine decarboxylase.
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Affiliation(s)
- Xin Guan
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
- The NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, 50011, USA
| | - Hui Chen
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
- Conagen Inc., Bedford, MA, 01730, USA
| | - Alex Abramson
- The NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, 50011, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Huimin Man
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
- Conagen Inc., Bedford, MA, 01730, USA
| | - Jinxia Wu
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Oliver Yu
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
- Wuxi NewWay Biotech Co., Ltd., Wuxi, Jiangsu, 214043, China
| | - Basil J Nikolau
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
- The NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, IA, 50011, USA
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21
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Clark TJ, Lu Y. Analysis of Loss-of-Function Mutants in Aspartate Kinase and Homoserine Dehydrogenase Genes Points to Complexity in the Regulation of Aspartate-Derived Amino Acid Contents. PLANT PHYSIOLOGY 2015; 168:1512-26. [PMID: 26063505 PMCID: PMC4528744 DOI: 10.1104/pp.15.00364] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/09/2015] [Indexed: 05/07/2023]
Abstract
Biosynthesis of aspartate (Asp)-derived amino acids lysine (Lys), methionine (Met), threonine (Thr), and isoleucine involves monofunctional Asp kinases (AKs) and dual-functional Asp kinase-homoserine dehydrogenases (AK-HSDHs). Four-week-old loss-of-function Arabidopsis (Arabidopsis thaliana) mutants in the AK-HSDH2 gene had increased amounts of Asp and Asp-derived amino acids, especially Thr, in leaves. To explore mechanisms behind this phenotype, we obtained single mutants for other AK and AK-HSDH genes, generated double mutants from ak-hsdh2 and ak mutants, and performed free and protein-bound amino acid profiling, transcript abundance, and activity assays. The increases of Asp, Lys, and Met in ak-hsdh2 were also observed in ak1-1, ak2-1, ak3-1, and ak-hsdh1-1. However, the Thr increase in ak-hsdh2 was observed in ak-hsdh1-1 but not in ak1-1, ak2-1, or ak3-1. Activity assays showed that AK2 and AK-HSDH1 are the major contributors to overall AK and HSDH activities, respectively. Pairwise correlation analysis revealed positive correlations between the amount of AK transcripts and Lys-sensitive AK activity and between the amount of AK-HSDH transcripts and both Thr-sensitive AK activity and total HSDH activity. In addition, the ratio of total AK activity to total HSDH activity negatively correlates with the ratio of Lys to the total amount of Met, Thr, and isoleucine. These data led to the hypothesis that the balance between Lys-sensitive AKs and Thr-sensitive AK-HSDHs is important for maintaining the amounts and ratios of Asp-derived amino acids.
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Affiliation(s)
- Teresa J Clark
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410
| | - Yan Lu
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008-5410
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22
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Liu J, Last RL. A land plant-specific thylakoid membrane protein contributes to photosystem II maintenance in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:731-43. [PMID: 25846821 DOI: 10.1111/tpj.12845] [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] [Received: 12/12/2014] [Revised: 03/04/2015] [Accepted: 03/31/2015] [Indexed: 05/24/2023]
Abstract
The structure and function of photosystem II (PSII) are highly susceptible to photo-oxidative damage induced by high-fluence or fluctuating light. However, many of the mechanistic details of how PSII homeostasis is maintained under photoinhibitory light remain to be determined. We describe an analysis of the Arabidopsis thaliana gene At5g07020, which encodes an unannotated integral thylakoid membrane protein. Loss of the protein causes altered PSII function under high-irradiance light, and hence it is named 'Maintenance of PSII under High light 1' (MPH1). The MPH1 protein co-purifies with PSII core complexes and co-immunoprecipitates core proteins. Consistent with a role in PSII structure, PSII complexes (supercomplexes, dimers and monomers) of the mph1 mutant are less stable in plants subjected to photoinhibitory light. Accumulation of PSII core proteins is compromised under these conditions in the presence of translational inhibitors. This is consistent with the hypothesis that the mutant has enhanced PSII protein damage rather than defective repair. These data are consistent with the distribution of the MPH1 protein in grana and stroma thylakoids, and its interaction with PSII core complexes. Taken together, these results strongly suggest a role for MPH1 in the protection and/or stabilization of PSII under high-light stress in land plants.
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Affiliation(s)
- Jun Liu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
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23
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Fristedt R, Herdean A, Blaby-Haas CE, Mamedov F, Merchant SS, Last RL, Lundin B. PHOTOSYSTEM II PROTEIN33, a protein conserved in the plastid lineage, is associated with the chloroplast thylakoid membrane and provides stability to photosystem II supercomplexes in Arabidopsis. PLANT PHYSIOLOGY 2015; 167:481-92. [PMID: 25511433 PMCID: PMC4326745 DOI: 10.1104/pp.114.253336] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Photosystem II (PSII) is a multiprotein complex that catalyzes the light-driven water-splitting reactions of oxygenic photosynthesis. Light absorption by PSII leads to the production of excited states and reactive oxygen species that can cause damage to this complex. Here, we describe Arabidopsis (Arabidopsis thaliana) At1g71500, which encodes a previously uncharacterized protein that is a PSII auxiliary core protein and hence is named PHOTOSYSTEM II PROTEIN33 (PSB33). We present evidence that PSB33 functions in the maintenance of PSII-light-harvesting complex II (LHCII) supercomplex organization. PSB33 encodes a protein with a chloroplast transit peptide and one transmembrane segment. In silico analysis of PSB33 revealed a light-harvesting complex-binding motif within the transmembrane segment and a large surface-exposed head domain. Biochemical analysis of PSII complexes further indicates that PSB33 is an integral membrane protein located in the vicinity of LHCII and the PSII CP43 reaction center protein. Phenotypic characterization of mutants lacking PSB33 revealed reduced amounts of PSII-LHCII supercomplexes, very low state transition, and a lower capacity for nonphotochemical quenching, leading to increased photosensitivity in the mutant plants under light stress. Taken together, these results suggest a role for PSB33 in regulating and optimizing photosynthesis in response to changing light levels.
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Affiliation(s)
- Rikard Fristedt
- Department of Chemistry and Biochemistry (R.F., C.E.B.-H., S.S.M.) and Institute for Genomics and Proteomics (S.S.M.), University of California, Los Angeles, California 90095;Department of Biological and Environmental Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden (A.H., B.L.);Department of Chemistry, Ångström Laboratory, Uppsala University, 751 20 Uppsala, Sweden (F.M.); andDepartment of Biochemistry and Molecular Biology and Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., B.L.)
| | - Andrei Herdean
- Department of Chemistry and Biochemistry (R.F., C.E.B.-H., S.S.M.) and Institute for Genomics and Proteomics (S.S.M.), University of California, Los Angeles, California 90095;Department of Biological and Environmental Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden (A.H., B.L.);Department of Chemistry, Ångström Laboratory, Uppsala University, 751 20 Uppsala, Sweden (F.M.); andDepartment of Biochemistry and Molecular Biology and Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., B.L.)
| | - Crysten E Blaby-Haas
- Department of Chemistry and Biochemistry (R.F., C.E.B.-H., S.S.M.) and Institute for Genomics and Proteomics (S.S.M.), University of California, Los Angeles, California 90095;Department of Biological and Environmental Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden (A.H., B.L.);Department of Chemistry, Ångström Laboratory, Uppsala University, 751 20 Uppsala, Sweden (F.M.); andDepartment of Biochemistry and Molecular Biology and Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., B.L.)
| | - Fikret Mamedov
- Department of Chemistry and Biochemistry (R.F., C.E.B.-H., S.S.M.) and Institute for Genomics and Proteomics (S.S.M.), University of California, Los Angeles, California 90095;Department of Biological and Environmental Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden (A.H., B.L.);Department of Chemistry, Ångström Laboratory, Uppsala University, 751 20 Uppsala, Sweden (F.M.); andDepartment of Biochemistry and Molecular Biology and Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., B.L.)
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry (R.F., C.E.B.-H., S.S.M.) and Institute for Genomics and Proteomics (S.S.M.), University of California, Los Angeles, California 90095;Department of Biological and Environmental Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden (A.H., B.L.);Department of Chemistry, Ångström Laboratory, Uppsala University, 751 20 Uppsala, Sweden (F.M.); andDepartment of Biochemistry and Molecular Biology and Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., B.L.)
| | - Robert L Last
- Department of Chemistry and Biochemistry (R.F., C.E.B.-H., S.S.M.) and Institute for Genomics and Proteomics (S.S.M.), University of California, Los Angeles, California 90095;Department of Biological and Environmental Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden (A.H., B.L.);Department of Chemistry, Ångström Laboratory, Uppsala University, 751 20 Uppsala, Sweden (F.M.); andDepartment of Biochemistry and Molecular Biology and Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., B.L.)
| | - Björn Lundin
- Department of Chemistry and Biochemistry (R.F., C.E.B.-H., S.S.M.) and Institute for Genomics and Proteomics (S.S.M.), University of California, Los Angeles, California 90095;Department of Biological and Environmental Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden (A.H., B.L.);Department of Chemistry, Ångström Laboratory, Uppsala University, 751 20 Uppsala, Sweden (F.M.); andDepartment of Biochemistry and Molecular Biology and Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., B.L.)
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Benstein RM, Ludewig K, Wulfert S, Wittek S, Gigolashvili T, Frerigmann H, Gierth M, Flügge UI, Krueger S. Arabidopsis phosphoglycerate dehydrogenase1 of the phosphoserine pathway is essential for development and required for ammonium assimilation and tryptophan biosynthesis. THE PLANT CELL 2013; 25:5011-29. [PMID: 24368794 PMCID: PMC3904002 DOI: 10.1105/tpc.113.118992] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/26/2013] [Accepted: 12/06/2013] [Indexed: 05/17/2023]
Abstract
In plants, two independent serine biosynthetic pathways, the photorespiratory and glycolytic phosphoserine (PS) pathways, have been postulated. Although the photorespiratory pathway is well characterized, little information is available on the function of the PS pathway in plants. Here, we present a detailed characterization of phosphoglycerate dehydrogenases (PGDHs) as components of the PS pathway in Arabidopsis thaliana. All PGDHs localize to plastids and possess similar kinetic properties, but they differ with respect to their sensitivity to serine feedback inhibition. Furthermore, analysis of pgdh1 and phosphoserine phosphatase mutants revealed an embryo-lethal phenotype and PGDH1-silenced lines were inhibited in growth. Metabolic analyses of PGDH1-silenced lines grown under ambient and high CO2 conditions indicate a direct link between PS biosynthesis and ammonium assimilation. In addition, we obtained several lines of evidence for an interconnection between PS and tryptophan biosynthesis, because the expression of PGDH1 and phosphoserine aminotransferase1 is regulated by MYB51 and MYB34, two activators of tryptophan biosynthesis. Moreover, the concentration of tryptophan-derived glucosinolates and auxin were reduced in PGDH1-silenced plants. In essence, our results provide evidence for a vital function of PS biosynthesis for plant development and metabolism.
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25
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Savage LJ, Imre KM, Hall DA, Last RL. Analysis of essential Arabidopsis nuclear genes encoding plastid-targeted proteins. PLoS One 2013; 8:e73291. [PMID: 24023856 PMCID: PMC3762728 DOI: 10.1371/journal.pone.0073291] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 07/18/2013] [Indexed: 11/26/2022] Open
Abstract
The Chloroplast 2010 Project (http://www.plastid.msu.edu/) identified and phenotypically characterized homozygous mutants in over three thousand genes, the majority of which encode plastid-targeted proteins. Despite extensive screening by the community, no homozygous mutant alleles were available for several hundred genes, suggesting that these might be enriched for genes of essential function. Attempts were made to generate homozygotes in ~1200 of these lines and 521 of the homozygous viable lines obtained were deposited in the Arabidopsis Biological Resource Center (http://abrc.osu.edu/). Lines that did not yield a homozygote in soil were tested as potentially homozygous lethal due to defects either in seed or seedling development. Mutants were characterized at four stages of development: developing seed, mature seed, at germination, and developing seedlings. To distinguish seed development or seed pigment-defective mutants from seedling development mutants, development of seeds was assayed in siliques from heterozygous plants. Segregating seeds from heterozygous parents were sown on supplemented media in an attempt to rescue homozygous seedlings that could not germinate or survive in soil. Growth of segregating seeds in air and air enriched to 0.3% carbon dioxide was compared to discover mutants potentially impaired in photorespiration or otherwise responsive to CO2 supplementation. Chlorophyll fluorescence measurements identified CO2-responsive mutants with altered photosynthetic parameters. Examples of genes with a viable mutant allele and one or more putative homozygous-lethal alleles were documented. RT-PCR of homozygotes for potentially weak alleles revealed that essential genes may remain undiscovered because of the lack of a true null mutant allele. This work revealed 33 genes with two or more lethal alleles and 73 genes whose essentiality was not confirmed with an independent lethal mutation, although in some cases second leaky alleles were identified.
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Affiliation(s)
- Linda J. Savage
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Kathleen M. Imre
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - David A. Hall
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Robert L. Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
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26
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Savage LJ, Imre KM, Hall DA, Last RL. Analysis of essential Arabidopsis nuclear genes encoding plastid-targeted proteins. PLoS One 2013; 8:e73291. [PMID: 24023856 DOI: 10.1371/journal.pone.0073291.s012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 07/18/2013] [Indexed: 05/25/2023] Open
Abstract
The Chloroplast 2010 Project (http://www.plastid.msu.edu/) identified and phenotypically characterized homozygous mutants in over three thousand genes, the majority of which encode plastid-targeted proteins. Despite extensive screening by the community, no homozygous mutant alleles were available for several hundred genes, suggesting that these might be enriched for genes of essential function. Attempts were made to generate homozygotes in ~1200 of these lines and 521 of the homozygous viable lines obtained were deposited in the Arabidopsis Biological Resource Center (http://abrc.osu.edu/). Lines that did not yield a homozygote in soil were tested as potentially homozygous lethal due to defects either in seed or seedling development. Mutants were characterized at four stages of development: developing seed, mature seed, at germination, and developing seedlings. To distinguish seed development or seed pigment-defective mutants from seedling development mutants, development of seeds was assayed in siliques from heterozygous plants. Segregating seeds from heterozygous parents were sown on supplemented media in an attempt to rescue homozygous seedlings that could not germinate or survive in soil. Growth of segregating seeds in air and air enriched to 0.3% carbon dioxide was compared to discover mutants potentially impaired in photorespiration or otherwise responsive to CO2 supplementation. Chlorophyll fluorescence measurements identified CO2-responsive mutants with altered photosynthetic parameters. Examples of genes with a viable mutant allele and one or more putative homozygous-lethal alleles were documented. RT-PCR of homozygotes for potentially weak alleles revealed that essential genes may remain undiscovered because of the lack of a true null mutant allele. This work revealed 33 genes with two or more lethal alleles and 73 genes whose essentiality was not confirmed with an independent lethal mutation, although in some cases second leaky alleles were identified.
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Affiliation(s)
- Linda J Savage
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
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27
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Abstract
With increasing demand to support and accelerate progress in breeding for novel traits, the plant research community faces the need to accurately measure increasingly large numbers of plants and plant parameters. The goal is to provide quantitative analyses of plant structure and function relevant for traits that help plants better adapt to low-input agriculture and resource-limited environments. We provide an overview of the inherently multidisciplinary research in plant phenotyping, focusing on traits that will assist in selecting genotypes with increased resource use efficiency. We highlight opportunities and challenges for integrating noninvasive or minimally invasive technologies into screening protocols to characterize plant responses to environmental challenges for both controlled and field experimentation. Although technology evolves rapidly, parallel efforts are still required because large-scale phenotyping demands accurate reporting of at least a minimum set of information concerning experimental protocols, data management schemas, and integration with modeling. The journey toward systematic plant phenotyping has only just begun.
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Affiliation(s)
- Fabio Fiorani
- IBG-2: Plant Sciences, Institute for Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany.
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28
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Wurtele ES, Chappell J, Jones AD, Celiz MD, Ransom N, Hur M, Rizshsky L, Crispin M, Dixon P, Liu J, P Widrlechner M, Nikolau BJ. Medicinal plants: a public resource for metabolomics and hypothesis development. Metabolites 2012; 2:1031-59. [PMID: 24957774 PMCID: PMC3901233 DOI: 10.3390/metabo2041031] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 10/30/2012] [Accepted: 10/31/2012] [Indexed: 11/16/2022] Open
Abstract
Specialized compounds from photosynthetic organisms serve as rich resources for drug development. From aspirin to atropine, plant-derived natural products have had a profound impact on human health. Technological advances provide new opportunities to access these natural products in a metabolic context. Here, we describe a database and platform for storing, visualizing and statistically analyzing metabolomics data from fourteen medicinal plant species. The metabolomes and associated transcriptomes (RNAseq) for each plant species, gathered from up to twenty tissue/organ samples that have experienced varied growth conditions and developmental histories, were analyzed in parallel. Three case studies illustrate different ways that the data can be integrally used to generate testable hypotheses concerning the biochemistry, phylogeny and natural product diversity of medicinal plants. Deep metabolomics analysis of Camptotheca acuminata exemplifies how such data can be used to inform metabolic understanding of natural product chemical diversity and begin to formulate hypotheses about their biogenesis. Metabolomics data from Prunella vulgaris, a species that contains a wide range ofantioxidant, antiviral, tumoricidal and anti-inflammatory constituents, provide a case study of obtaining biosystematic and developmental fingerprint information from metabolite accumulation data in a little studied species. Digitalis purpurea, well known as a source of cardiac glycosides, is used to illustrate how integrating metabolomics and transcriptomics data can lead to identification of candidate genes encoding biosynthetic enzymes in the cardiac glycoside pathway. Medicinal Plant Metabolomics Resource (MPM) [1] provides a framework for generating experimentally testable hypotheses about the metabolic networks that lead to the generation of specialized compounds, identifying genes that control their biosynthesis and establishing a basis for modeling metabolism in less studied species. The database is publicly available and can be used by researchers in medicine and plant biology.
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Affiliation(s)
- Eve Syrkin Wurtele
- Department of Genetics, Cell and Developmental Biology, Iowa State University, Ames, IA 50011, USA.
| | - Joe Chappell
- Department of Cellular and Molecular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA
| | - A Daniel Jones
- Department of Biochemistry & Molecular Biology and Deptment of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Mary Dawn Celiz
- Department of Biochemistry & Molecular Biology and Deptment of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Nick Ransom
- Department of Genetics, Cell and Developmental Biology, Iowa State University, Ames, IA 50011, USA
| | - Manhoi Hur
- Department of Genetics, Cell and Developmental Biology, Iowa State University, Ames, IA 50011, USA
| | - Ludmila Rizshsky
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA50011, USA
| | - Matthew Crispin
- Department of Genetics, Cell and Developmental Biology, Iowa State University, Ames, IA 50011, USA
| | - Philip Dixon
- Department of Statistics, Iowa State University, Ames, IA 50011, USA
| | - Jia Liu
- Department of Statistics, Iowa State University, Ames, IA 50011, USA
| | - Mark P Widrlechner
- Department of Ecology, Evolution, and Organismal Biology and Department of Horticulture, Iowa State University, Ames, IA 50011, USA
| | - Basil J Nikolau
- Center for Metabolic Biology, The Plant Science Institute, Iowa State University, Ames, IA 50011, USA
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Li X, Moellering ER, Liu B, Johnny C, Fedewa M, Sears BB, Kuo MH, Benning C. A galactoglycerolipid lipase is required for triacylglycerol accumulation and survival following nitrogen deprivation in Chlamydomonas reinhardtii. THE PLANT CELL 2012; 24:4670-86. [PMID: 23161887 PMCID: PMC3531859 DOI: 10.1105/tpc.112.105106] [Citation(s) in RCA: 212] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 10/16/2012] [Accepted: 10/27/2012] [Indexed: 05/17/2023]
Abstract
Following N deprivation, microalgae accumulate triacylglycerols (TAGs). To gain mechanistic insights into this phenomenon, we identified mutants with reduced TAG content following N deprivation in the model alga Chlamydomonas reinhardtii. In one of the mutants, the disruption of a galactoglycerolipid lipase-encoding gene, designated PLASTID GALACTOGLYCEROLIPID DEGRADATION1 (PGD1), was responsible for the primary phenotype: reduced TAG content, altered TAG composition, and reduced galactoglycerolipid turnover. The recombinant PGD1 protein, which was purified from Escherichia coli extracts, hydrolyzed monogalactosyldiacylglycerol into its lyso-lipid derivative. In vivo pulse-chase labeling identified galactoglycerolipid pools as a major source of fatty acids esterified in TAGs following N deprivation. Moreover, the fatty acid flux from plastid lipids to TAG was decreased in the pgd1 mutant. Apparently, de novo-synthesized fatty acids in Chlamydomonas reinhardtii are, at least partially, first incorporated into plastid lipids before they enter TAG synthesis. As a secondary effect, the pgd1 mutant exhibited a loss of viability following N deprivation, which could be avoided by blocking photosynthetic electron transport. Thus, the pgd1 mutant provides evidence for an important biological function of TAG synthesis following N deprivation, namely, relieving a detrimental overreduction of the photosynthetic electron transport chain.
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Affiliation(s)
- Xiaobo Li
- Department of Energy–Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Eric R. Moellering
- Department of Energy–Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Bensheng Liu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Cassandra Johnny
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Marie Fedewa
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Barbara B. Sears
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Min-Hao Kuo
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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30
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Kirma M, Araújo WL, Fernie AR, Galili G. The multifaceted role of aspartate-family amino acids in plant metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:4995-5001. [PMID: 22516796 DOI: 10.1093/jxb/ers119] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Plants represent the major sources of human foods and livestock feeds, worldwide. However, the limited content of the essential amino acid lysine in cereal grains represents a major nutritional problem for human and for livestock feeding in developed countries. Optimizing the level of lysine in cereal grains requires extensive knowledge on the biological processes regulating the homeostasis of this essential amino acid as well as the biological consequences of this homeostasis. Manipulating biosynthetic and catabolic enzymes of lysine metabolism enabled an enhanced accumulation of this essential amino acid in seeds. However, this approach had a major effect on the levels of various metabolites of the tricarboxylic acid (TCA) cycle, revealing a strong interaction between lysine metabolism and cellular energy metabolism. Recent studies discussed here have shed new light on the metabolic processes responsible for the catabolism of lysine, as well as isoleucine, another amino acid of the aspartate-family pathway, into the TCA cycle. Here we discuss progress being made to understand biological processes associated with the catabolism of amino acids of the aspartate-family pathway and its importance for optimal improvement of the nutritional quality of plants.
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Affiliation(s)
- Menny Kirma
- Department of Plant Science, The Weizmnn Institute of Science, Rehovot 76100, Israel
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31
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Tegeder M. Transporters for amino acids in plant cells: some functions and many unknowns. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:315-21. [PMID: 22366488 DOI: 10.1016/j.pbi.2012.02.001] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 01/31/2012] [Accepted: 02/01/2012] [Indexed: 05/18/2023]
Abstract
Membrane proteins are essential to move amino acids in or out of plant cells as well as between organelles. While many putative amino acid transporters have been identified, function in nitrogen movement in plants has only been shown for a few proteins. Those studies demonstrate that import systems are fundamental in partitioning of amino acids at cellular and whole plant level. Physiological data further suggest that amino acid transporters are key-regulators in plant metabolism and that their activities affect growth and development. By contrast, knowledge on the molecular mechanisms of cellular export processes as well as on intracellular transport of amino acids is scarce. Similarly, little is known about the regulation of amino acid transporter function and involvement of the transporters in amino acid signaling. Future studies need to identify the missing components to elucidate the importance of amino acid transport processes for whole plant physiology and productivity.
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Affiliation(s)
- Mechthild Tegeder
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA.
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32
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Wei Q, Li J, Zhang L, Wu P, Chen Y, Li M, Jiang H, Wu G. Cloning and characterization of a β-ketoacyl-acyl carrier protein synthase II from Jatropha curcas. JOURNAL OF PLANT PHYSIOLOGY 2012; 169:816-824. [PMID: 22424763 DOI: 10.1016/j.jplph.2012.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 01/12/2012] [Accepted: 02/06/2012] [Indexed: 05/31/2023]
Abstract
A cDNA clone encoding a putative β-ketoacyl-acyl carrier protein (ACP) synthase II (KASII), a key enzyme in fatty acid biosynthesis, was isolated from Jatropha curcas L., a woody oil plant. The isolated cDNA clone of JcKASII contained a 1722-bp open reading frame coding for 573 amino acids with a predicted molecular mass of about 60.98 kDa and the conserved Cys(324) residues that has been proposed as the active site of KASII proteins. The deduced amino acid sequence of the cDNA clone had about 70-84% identity with the KASII from other plants. The transcript of JcKASII was detected in all tissues examined and increased during seed maturation. Expression of JcKASII in the Arabidopsis KASII mutant (fab1) could complement the fatty acid composition of the mutant. Overexpression of JcKASII cDNA under the cauliflower mosaic virus 35S promoter in Arabidopsis resulted in decreasing 16-carbon fatty acids and increasing 18-carbon fatty acids in leaves and seeds. Taken together, these results show that JcKASII could function in 18-carbon fatty acids accumulation in plant and may be useful in the genetic engineering of J. curcas.
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Affiliation(s)
- Qian Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
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Kochevenko A, Araújo WL, Maloney GS, Tieman DM, Do PT, Taylor MG, Klee HJ, Fernie AR. Catabolism of branched chain amino acids supports respiration but not volatile synthesis in tomato fruits. MOLECULAR PLANT 2012; 5:366-75. [PMID: 22199237 DOI: 10.1093/mp/ssr108] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The branched-chain amino acid transaminases (BCATs) have a crucial role in metabolism of the branched-chain amino acids leucine, isoleucine, and valine. These enzymes catalyze the last step of synthesis and the initial step of degradation of these amino acids. Although the biosynthetic pathways of branched chain amino acids in plants have been extensively investigated and a number of genes have been characterized, their catabolism in plants is not yet completely understood. We previously characterized the branched chain amino acid transaminase gene family in tomato, revealing both the subcellular localization and kinetic properties of the enzymes encoded by six genes. Here, we examined possible functions of the enzymes during fruit development. We further characterized transgenic plants differing in the expression of branched chain amino acid transaminases 1 and 3, evaluating the rates of respiration in fruits deficient in BCAT1 and the levels of volatiles in lines overexpressing either BCAT1 or BCAT3. We quantitatively tested, via precursor and isotope feeding experiments, the importance of the branched chain amino acids and their corresponding keto acids in the formation of fruit volatiles. Our results not only demonstrate for the first time the importance of branched chain amino acids in fruit respiration, but also reveal that keto acids, rather than amino acids, are the likely precursors for the branched chain flavor volatiles.
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Affiliation(s)
- Andrej Kochevenko
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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34
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Bell SM, Burgoon LD, Last RL. MIPHENO: data normalization for high throughput metabolite analysis. BMC Bioinformatics 2012; 13:10. [PMID: 22244038 PMCID: PMC3278354 DOI: 10.1186/1471-2105-13-10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 01/13/2012] [Indexed: 01/27/2023] Open
Abstract
Background High throughput methodologies such as microarrays, mass spectrometry and plate-based small molecule screens are increasingly used to facilitate discoveries from gene function to drug candidate identification. These large-scale experiments are typically carried out over the course of months and years, often without the controls needed to compare directly across the dataset. Few methods are available to facilitate comparisons of high throughput metabolic data generated in batches where explicit in-group controls for normalization are lacking. Results Here we describe MIPHENO (Mutant Identification by Probabilistic High throughput-Enabled Normalization), an approach for post-hoc normalization of quantitative first-pass screening data in the absence of explicit in-group controls. This approach includes a quality control step and facilitates cross-experiment comparisons that decrease the false non-discovery rates, while maintaining the high accuracy needed to limit false positives in first-pass screening. Results from simulation show an improvement in both accuracy and false non-discovery rate over a range of population parameters (p < 2.2 × 10-16) and a modest but significant (p < 2.2 × 10-16) improvement in area under the receiver operator characteristic curve of 0.955 for MIPHENO vs 0.923 for a group-based statistic (z-score). Analysis of the high throughput phenotypic data from the Arabidopsis Chloroplast 2010 Project (http://www.plastid.msu.edu/) showed ~ 4-fold increase in the ability to detect previously described or expected phenotypes over the group based statistic. Conclusions Results demonstrate MIPHENO offers substantial benefit in improving the ability to detect putative mutant phenotypes from post-hoc analysis of large data sets. Additionally, it facilitates data interpretation and permits cross-dataset comparison where group-based controls are missing. MIPHENO is applicable to a wide range of high throughput screenings and the code is freely available as Additional file 1 as well as through an R package in CRAN.
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Affiliation(s)
- Shannon M Bell
- Quantitative Biology Program, Michigan State University, East Lansing, MI, USA
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35
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Bell SM, Burgoon LD, Last RL. MIPHENO: data normalization for high throughput metabolite analysis. BMC Bioinformatics 2012. [PMID: 22244038 DOI: 10.1186/1471-2105- 13-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
BACKGROUND High throughput methodologies such as microarrays, mass spectrometry and plate-based small molecule screens are increasingly used to facilitate discoveries from gene function to drug candidate identification. These large-scale experiments are typically carried out over the course of months and years, often without the controls needed to compare directly across the dataset. Few methods are available to facilitate comparisons of high throughput metabolic data generated in batches where explicit in-group controls for normalization are lacking. RESULTS Here we describe MIPHENO (Mutant Identification by Probabilistic High throughput-Enabled Normalization), an approach for post-hoc normalization of quantitative first-pass screening data in the absence of explicit in-group controls. This approach includes a quality control step and facilitates cross-experiment comparisons that decrease the false non-discovery rates, while maintaining the high accuracy needed to limit false positives in first-pass screening. Results from simulation show an improvement in both accuracy and false non-discovery rate over a range of population parameters (p < 2.2 × 10(-16)) and a modest but significant (p < 2.2 × 10(-16)) improvement in area under the receiver operator characteristic curve of 0.955 for MIPHENO vs 0.923 for a group-based statistic (z-score). Analysis of the high throughput phenotypic data from the Arabidopsis Chloroplast 2010 Project (http://www.plastid.msu.edu/) showed ~ 4-fold increase in the ability to detect previously described or expected phenotypes over the group based statistic. CONCLUSIONS Results demonstrate MIPHENO offers substantial benefit in improving the ability to detect putative mutant phenotypes from post-hoc analysis of large data sets. Additionally, it facilitates data interpretation and permits cross-dataset comparison where group-based controls are missing. MIPHENO is applicable to a wide range of high throughput screenings and the code is freely available as Additional file 1 as well as through an R package in CRAN.
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Affiliation(s)
- Shannon M Bell
- Quantitative Biology Program, Michigan State University, East Lansing, MI, USA
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36
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Quanbeck SM, Brachova L, Campbell AA, Guan X, Perera A, He K, Rhee SY, Bais P, Dickerson JA, Dixon P, Wohlgemuth G, Fiehn O, Barkan L, Lange I, Lange BM, Lee I, Cortes D, Salazar C, Shuman J, Shulaev V, Huhman DV, Sumner LW, Roth MR, Welti R, Ilarslan H, Wurtele ES, Nikolau BJ. Metabolomics as a Hypothesis-Generating Functional Genomics Tool for the Annotation of Arabidopsis thaliana Genes of "Unknown Function". FRONTIERS IN PLANT SCIENCE 2012; 3:15. [PMID: 22645570 PMCID: PMC3355754 DOI: 10.3389/fpls.2012.00015] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 01/17/2012] [Indexed: 05/19/2023]
Abstract
Metabolomics is the methodology that identifies and measures global pools of small molecules (of less than about 1,000 Da) of a biological sample, which are collectively called the metabolome. Metabolomics can therefore reveal the metabolic outcome of a genetic or environmental perturbation of a metabolic regulatory network, and thus provide insights into the structure and regulation of that network. Because of the chemical complexity of the metabolome and limitations associated with individual analytical platforms for determining the metabolome, it is currently difficult to capture the complete metabolome of an organism or tissue, which is in contrast to genomics and transcriptomics. This paper describes the analysis of Arabidopsis metabolomics data sets acquired by a consortium that includes five analytical laboratories, bioinformaticists, and biostatisticians, which aims to develop and validate metabolomics as a hypothesis-generating functional genomics tool. The consortium is determining the metabolomes of Arabidopsis T-DNA mutant stocks, grown in standardized controlled environment optimized to minimize environmental impacts on the metabolomes. Metabolomics data were generated with seven analytical platforms, and the combined data is being provided to the research community to formulate initial hypotheses about genes of unknown function (GUFs). A public database (www.PlantMetabolomics.org) has been developed to provide the scientific community with access to the data along with tools to allow for its interactive analysis. Exemplary datasets are discussed to validate the approach, which illustrate how initial hypotheses can be generated from the consortium-produced metabolomics data, integrated with prior knowledge to provide a testable hypothesis concerning the functionality of GUFs.
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Affiliation(s)
- Stephanie M. Quanbeck
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
| | - Libuse Brachova
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
| | - Alexis A. Campbell
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
| | - Xin Guan
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
| | - Ann Perera
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
| | - Kun He
- Department of Plant Biology, Carnegie Institution for ScienceStanford, CA, USA
| | - Seung Y. Rhee
- Department of Plant Biology, Carnegie Institution for ScienceStanford, CA, USA
| | - Preeti Bais
- Bioinformatics and Computational Biology Program, Iowa State UniversityAmes, IA, USA
| | - Julie A. Dickerson
- Bioinformatics and Computational Biology Program, Iowa State UniversityAmes, IA, USA
| | - Philip Dixon
- Department of Statistics, Iowa State UniversityAmes, IA, USA
| | | | - Oliver Fiehn
- Genome Center, University of CaliforniaDavis, CA, USA
| | - Lenore Barkan
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State UniversityPullman, WA, USA
| | - Iris Lange
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State UniversityPullman, WA, USA
| | - B. Markus Lange
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State UniversityPullman, WA, USA
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei UniversitySeoul, Korea
| | - Diego Cortes
- Anatomy and Neurobiology, Virginia Commonwealth UniversityRichmond, VA, USA
| | - Carolina Salazar
- Department of Biological Sciences, University of North TexasDenton, TX, USA
| | - Joel Shuman
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
| | - Vladimir Shulaev
- Department of Biological Sciences, University of North TexasDenton, TX, USA
| | - David V. Huhman
- Plant Biology Division, The Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Lloyd W. Sumner
- Plant Biology Division, The Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Mary R. Roth
- Division of Biology, Kansas State UniversityManhattan, KS, USA
| | - Ruth Welti
- Division of Biology, Kansas State UniversityManhattan, KS, USA
| | - Hilal Ilarslan
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmes, IA, USA
| | - Eve S. Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmes, IA, USA
| | - Basil J. Nikolau
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
- *Correspondence: Basil J. Nikolau, Iowa State University, 3254 Molecular Biology Building, Ames, IA 50011, USA. e-mail:
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Rapid LC-MS/MS profiling of protein amino acids and metabolically related compounds for large-scale assessment of metabolic phenotypes. Methods Mol Biol 2012; 828:1-11. [PMID: 22125131 DOI: 10.1007/978-1-61779-445-2_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Amino acids extracted from a biological matrix can be resolved and measured using a 6-min per sample method through high-performance liquid chromatography with a short C18 column and rapid gradient using the ion-pairing reagent perfluoroheptanoic acid. LC-tandem mass spectrometry with multiple reaction monitoring (MRM) transitions selective for each compound allows simultaneous quantification of the 20 proteinogenic amino acids and 5 metabolically related compounds. Distinct MRM transitions were also established for selective detection of the isomers leucine/isoleucine and threonine/homoserine.
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Lu Y, Savage LJ, Last RL. Chloroplast phenomics: systematic phenotypic screening of chloroplast protein mutants in Arabidopsis. Methods Mol Biol 2011; 775:161-85. [PMID: 21863443 DOI: 10.1007/978-1-61779-237-3_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
As part of a project to analyze chloroplast functional networks systematically, we have subjected mutants in >3,200 nuclear genes predicted to encode chloroplast-targeted proteins in Arabidopsis thaliana (http://www.plastid.msu.edu) to parallel phenotypic assays. Detailed methods are presented for the various assays being used in this project to study chloroplast biology. These include morphological analysis of plants, chloroplasts, and seeds using controlled vocabulary. Metabolites synthesized in the chloroplast such as starch, amino acids, and fatty acids are analyzed in groups according to their chemical properties. As an indicator for the relative composition of seed storage oil and proteins, the carbon and nitrogen contents are determined by an elemental analyzer. The methods in this chapter describe how the assays are configured to run in relatively high throughput, maximizing data quality.
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Affiliation(s)
- Yan Lu
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA.
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Lu Y. The occurrence of a thylakoid-localized small zinc finger protein in land plants. PLANT SIGNALING & BEHAVIOR 2011; 6:1881-5. [PMID: 22080791 PMCID: PMC3337170 DOI: 10.4161/psb.6.12.18022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Previous studies showed that LOW QUANTUM YIELD OF PHOTOSYSTEM II 1 (LQY1), a small thylakoid zinc finger protein was involved in maintenance and repair of Photosystem II (PSII). Here the author provide additional evidence for the role of LQY1 in PSII maintenance and repair and further commentary on the occurrence of LQY1 protein among land plants. After exposure to high light, Arabidopsis thaliana mutants lacking functional LQY1 gene (At1g75690) are more photoinhibited than wild-type control plants; display higher total non-photochemical quenching and photoinhibitory quenching. These results are consistent with the initial observation that lqy1 mutants have lower PSII efficiency than wild-type plants after high-light treatment. The low-PSII-efficiency phenotype can be suppressed upon complementation of lqy1 mutants with the LQY1 gene from wild-type plants. This further demonstrates that LQY1 is important in maintaining the activity of photosystem II in Arabidopsis. LQY1 homologs are present in land plants but are absent from sequenced genomes of green algae and cyanobacteria, which may reflect plant adaptation to excess light stress during the transition to land.
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Affiliation(s)
- Yan Lu
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA.
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40
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Furbank RT, Tester M. Phenomics--technologies to relieve the phenotyping bottleneck. TRENDS IN PLANT SCIENCE 2011; 16:635-44. [PMID: 22074787 DOI: 10.1016/j.tplants.2011.09.005] [Citation(s) in RCA: 675] [Impact Index Per Article: 51.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 09/19/2011] [Accepted: 09/27/2011] [Indexed: 05/18/2023]
Abstract
Global agriculture is facing major challenges to ensure global food security, such as the need to breed high-yielding crops adapted to future climates and the identification of dedicated feedstock crops for biofuel production (biofuel feedstocks). Plant phenomics offers a suite of new technologies to accelerate progress in understanding gene function and environmental responses. This will enable breeders to develop new agricultural germplasm to support future agricultural production. In this review we present plant physiology in an 'omics' perspective, review some of the new high-throughput and high-resolution phenotyping tools and discuss their application to plant biology, functional genomics and crop breeding.
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Affiliation(s)
- Robert T Furbank
- High Resolution Plant Phenomics Centre, Australian Plant Phenomics Facility, CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia.
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41
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Bolle C, Schneider A, Leister D. Perspectives on Systematic Analyses of Gene Function in Arabidopsis thaliana: New Tools, Topics and Trends. Curr Genomics 2011; 12:1-14. [PMID: 21886450 PMCID: PMC3129038 DOI: 10.2174/138920211794520187] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 10/28/2010] [Accepted: 11/23/2010] [Indexed: 11/22/2022] Open
Abstract
Since the sequencing of the nuclear genome of Arabidopsis thaliana ten years ago, various large-scale analyses of gene function have been performed in this model species. In particular, the availability of collections of lines harbouring random T-DNA or transposon insertions, which include mutants for almost all of the ~27,000 A. thaliana genes, has been crucial for the success of forward and reverse genetic approaches. In the foreseeable future, genome-wide phenotypic data from mutant analyses will become available for Arabidopsis, and will stimulate a flood of novel in-depth gene-function analyses. In this review, we consider the present status of resources and concepts for systematic studies of gene function in A. thaliana. Current perspectives on the utility of loss-of-function and gain-of-function mutants will be discussed in light of the genetic and functional redundancy of many A. thaliana genes.
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Affiliation(s)
- C Bolle
- Lehrstuhl für Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, D-82152 Planegg-Martinsried, Germany
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CLUMPED CHLOROPLASTS 1 is required for plastid separation in Arabidopsis. Proc Natl Acad Sci U S A 2011; 108:18530-5. [PMID: 22025705 DOI: 10.1073/pnas.1106706108] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We identified an Arabidopsis thaliana mutant, clumped chloroplasts 1 (clmp1), in which disruption of a gene of unknown function causes chloroplasts to cluster instead of being distributed throughout the cytoplasm. The phenotype affects chloroplasts and nongreen plastids in multiple organs and cell types, but is detectable only at certain developmental stages. In young leaf petioles of clmp1, where clustering is prevalent, cells lacking chloroplasts are detected, suggesting impaired chloroplast partitioning during mitosis. Although organelle distribution and partitioning are actin-dependent in plants, the actin cytoskeleton in clmp1 is indistinguishable from that in WT, and peroxisomes and mitochondria are distributed normally. A CLMP1-YFP fusion protein that complements clmp1 localizes to discrete foci in the cytoplasm, most of which colocalize with the cell periphery or with chloroplasts. Ultrastructural analysis revealed that chloroplasts within clmp1 clusters are held together by membranous connections, including thin isthmi characteristic of late-stage chloroplast division. This finding suggests that constriction of dividing chloroplasts proceeds normally in clmp1, but separation is impaired. Consistently, chloroplast size and number, as well as positioning of the plastid division proteins FtsZ and ARC5/DRP5B, are unaffected in clmp1, indicating that loss of CLMP1-mediated chloroplast separation does not prevent otherwise normal division. CLMP1-like sequences are unique to green algae and land plants, and the CLMP1 sequence suggests that it functions through protein-protein interactions. Our studies identify a unique class of proteins required for plastid separation after the constriction stage of plastid division and indicate that CLMP1 activity is also required for plastid distribution and partitioning during cell division.
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Ajjawi I, Coku A, Froehlich JE, Yang Y, Osteryoung KW, Benning C, Last RL. A J-like protein influences fatty acid composition of chloroplast lipids in Arabidopsis. PLoS One 2011; 6:e25368. [PMID: 22028775 PMCID: PMC3196505 DOI: 10.1371/journal.pone.0025368] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 09/01/2011] [Indexed: 12/26/2022] Open
Abstract
A comprehensive understanding of the lipid and fatty acid metabolic machinery is needed for optimizing production of oils and fatty acids for fuel, industrial feedstocks and nutritional improvement in plants. T-DNA mutants in the poorly annotated Arabidopsis thaliana gene At1g08640 were identified as containing moderately high levels (50–100%) of 16∶1Δ7 and 18∶1Δ9 leaf fatty acids and subtle decreases (5–30%) of 16∶3 and 18∶3 (http://www.plastid.msu.edu/). TLC separation of fatty acids in the leaf polar lipids revealed that the chloroplastic galactolipids monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) were the main lipid types affected by this mutation. Analysis of the inferred amino acid sequence of At1g08640 predicted the presence of a transit peptide, three transmembrane domains and an N-terminal J-like domain, and the gene was named CJD1 for Chloroplast J-like Domain 1. GFP reporter experiments and in vitro chloroplast import assays demonstrated CJD1 is a chloroplast membrane protein. Screening of an Arabidopsis cDNA library by yeast-2-hybrid (Y2H) using the J-like domain of CJD1 as bait identified a plastidial inner envelope protein (Accumulation and Replication of Chloroplasts 6, ARC6) as the primary interacting partner in the Y2H assay. ARC6 plays a central role in chloroplast division and binds CJD1 via its own J-like domain along with an adjacent conserved region whose function is not fully known. These results provide a starting point for future investigations of how mutations in CJD1 affect lipid composition.
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Affiliation(s)
- Imad Ajjawi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Ardian Coku
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - John E. Froehlich
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
- Michigan State University (MSU)–Department of Engineering (DOE) Plant Research Laboratories, Michigan State University, East Lansing, Michigan, United States of America
| | - Yue Yang
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Katherine W. Osteryoung
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Robert L. Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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Screening or selection for chloroplast biogenesis mutants of Arabidopsis, following chemical or insertional mutagenesis. Methods Mol Biol 2011; 774:3-18. [PMID: 21822829 DOI: 10.1007/978-1-61779-234-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
The power of Arabidopsis as a model organism lies in the depth and breadth of genetic tools available for its study. This also applies to the study of chloroplast biology. Although vast numbers of mutants have been identified in Arabidopsis, the continued use of forward-genetic screening approaches remains valuable for the isolation and study of previously overlooked mutants and novel mutations in sensitised backgrounds (i.e., suppressors or enhancers of previously known mutants). In addition, reverse-genetic collections of insertional mutants are now extensive and provide unique opportunities for gene function discovery. Here, we describe methods for the chemical mutagenesis of Arabidopsis, the screening of mutants visually, on the basis of gene-expression phenotypes (scored as reduced or enhanced activity of reporter genes), and the use of databases to select for existing mutations from historic collections or insertional mutagenesis programmes.
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45
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He D, Han C, Yao J, Shen S, Yang P. Constructing the metabolic and regulatory pathways in germinating rice seeds through proteomic approach. Proteomics 2011; 11:2693-713. [DOI: 10.1002/pmic.201000598] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 02/23/2011] [Accepted: 04/12/2011] [Indexed: 12/15/2022]
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46
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Lu Y, Hall DA, Last RL. A small zinc finger thylakoid protein plays a role in maintenance of photosystem II in Arabidopsis thaliana. THE PLANT CELL 2011; 23:1861-75. [PMID: 21586683 PMCID: PMC3123961 DOI: 10.1105/tpc.111.085456] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 03/22/2011] [Accepted: 04/25/2011] [Indexed: 05/18/2023]
Abstract
This work identifies LOW QUANTUM YIELD OF PHOTOSYSTEM II1 (LQY1), a Zn finger protein that shows disulfide isomerase activity, interacts with the photosystem II (PSII) core complex, and may act in repair of photodamaged PSII complexes. Two mutants of an unannotated small Zn finger containing a thylakoid membrane protein of Arabidopsis thaliana (At1g75690; LQY1) were found to have a lower quantum yield of PSII photochemistry and reduced PSII electron transport rate following high-light treatment. The mutants dissipate more excess excitation energy via nonphotochemical pathways than wild type, and they also display elevated accumulation of reactive oxygen species under high light. After high-light treatment, the mutants have less PSII-light-harvesting complex II supercomplex than wild-type plants. Analysis of thylakoid membrane protein complexes showed that wild-type LQY1 protein comigrates with the PSII core monomer and the CP43-less PSII monomer (a marker for ongoing PSII repair and reassembly). PSII repair and reassembly involve the breakage and formation of disulfide bonds among PSII proteins. Interestingly, the recombinant LQY1 protein demonstrates a protein disulfide isomerase activity. LQY1 is more abundant in stroma-exposed thylakoids, where key steps of PSII repair and reassembly take place. The absence of the LQY1 protein accelerates turnover and synthesis of PSII reaction center protein D1. These results suggest that the LQY1 protein may be involved in maintaining PSII activity under high light by regulating repair and reassembly of PSII complexes.
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Affiliation(s)
- Yan Lu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - David A. Hall
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Robert L. Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Address correspondence to
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Lu Y, Savage LJ, Larson MD, Wilkerson CG, Last RL. Chloroplast 2010: a database for large-scale phenotypic screening of Arabidopsis mutants. PLANT PHYSIOLOGY 2011; 155:1589-600. [PMID: 21224340 PMCID: PMC3091111 DOI: 10.1104/pp.110.170118] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Large-scale phenotypic screening presents challenges and opportunities not encountered in typical forward or reverse genetics projects. We describe a modular database and laboratory information management system that was implemented in support of the Chloroplast 2010 Project, an Arabidopsis (Arabidopsis thaliana) reverse genetics phenotypic screen of more than 5,000 mutants (http://bioinfo.bch.msu.edu/2010_LIMS; www.plastid.msu.edu). The software and laboratory work environment were designed to minimize operator error and detect systematic process errors. The database uses Ruby on Rails and Flash technologies to present complex quantitative and qualitative data and pedigree information in a flexible user interface. Examples are presented where the database was used to find opportunities for process changes that improved data quality. We also describe the use of the data-analysis tools to discover mutants defective in enzymes of leucine catabolism (heteromeric mitochondrial 3-methylcrotonyl-coenzyme A carboxylase [At1g03090 and At4g34030] and putative hydroxymethylglutaryl-coenzyme A lyase [At2g26800]) based upon a syndrome of pleiotropic seed amino acid phenotypes that resembles previously described isovaleryl coenzyme A dehydrogenase (At3g45300) mutants. In vitro assay results support the computational annotation of At2g26800 as hydroxymethylglutaryl-coenzyme A lyase.
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Wang X, Yang Y, Yu C, Zhou J, Cheng Y, Yan C, Chen J. A highly efficient method for construction of rice artificial MicroRNA vectors. Mol Biotechnol 2011; 46:211-8. [PMID: 20496050 DOI: 10.1007/s12033-010-9291-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Artificial microRNA (amiRNA) has become a powerful tool for gene silencing in plants. A new method for easy and rapid construction of rice artificial miRNA vector is described. The procedure involved modification of the pCAMBIA1300-UR vector by insertion of a 'vector modification fragment'. This was prepared from the precursor of Os-amiR528 by eliminating the central miRNA-containing region while simultaneously creating an AfeI restriction site. The fragment was then introduced to the destination vector to produce a multipurpose 'Highly Efficient gene Silencing Compatible vector' (HESC vector). AfeI was used to produce linearized HESC vectors, and a blunt end PCR product that included amiRNA sequence was cloned into this site by a single ligation reaction to create the completed amiRNA vector. Tests showed that the method was highly efficient, and greatly reduced the time needed for vector construction and resulted in a DNA sequence identical to that of the current method, making it particularly suitable for use in a systems biology approach to functional genomic research.
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Affiliation(s)
- Xuming Wang
- Institute of Virology and Biotechnology (MOA and Zhejiang Provincial Key Laboratory for Plant Virology), Zhejiang Academy of Agricultural Sciences, Shiqiao Road 198#, Hangzhou, 310021, Zhejiang, People's Republic of China.
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49
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Armbruster U, Pesaresi P, Pribil M, Hertle A, Leister D. Update on chloroplast research: new tools, new topics, and new trends. MOLECULAR PLANT 2011; 4:1-16. [PMID: 20924030 DOI: 10.1093/mp/ssq060] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Chloroplasts, the green differentiation form of plastids, are the sites of photosynthesis and other important plant functions. Genetic and genomic technologies have greatly boosted the rate of discovery and functional characterization of chloroplast proteins during the past decade. Indeed, data obtained using high-throughput methodologies, in particular proteomics and transcriptomics, are now routinely used to assign functions to chloroplast proteins. Our knowledge of many chloroplast processes, notably photosynthesis and photorespiration, has reached such an advanced state that biotechnological approaches to crop improvement now seem feasible. Meanwhile, efforts to identify the entire complement of chloroplast proteins and their interactions are progressing rapidly, making the organelle a prime target for systems biology research in plants.
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Affiliation(s)
- Ute Armbruster
- Lehrstuhl für Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, D-82152 Planegg-Martinsried, Germany
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50
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Codrea MC, Hakala-Yatkin M, Kårlund-Marttila A, Nedbal L, Aittokallio T, Nevalainen OS, Tyystjärvi E. Mahalanobis distance screening of Arabidopsis mutants with chlorophyll fluorescence. PHOTOSYNTHESIS RESEARCH 2010; 105:273-83. [PMID: 20730565 DOI: 10.1007/s11120-010-9578-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 06/21/2010] [Indexed: 05/08/2023]
Abstract
Rapid nondestructive screening of mutants is a common step in many research projects in plant biology. Here we report the development of a method that uses kinetic imaging of chlorophyll fluorescence to detect phenotypes that differ from wild-type plants. The method uses multiple fluorescence features simultaneously in order to catch different types of photosynthesis-related mutants with a single assay. The Mahalanobis distance was used to evaluate the degree of similarity in fluorescence features between the wild-type and test plants, and plants differing strongly from the wild-type were classified as mutants. The method was tested on a collection of photosynthesis-related mutants of Arabidopsis thaliana. The plants were evaluated from images in which the color of each pixel depended on the Mahalanobis distance of the fluorescence features. Two parameters of the color-coding procedure were used to adjust the trade-off between detection of true mutants and erratic classification of wild-type plants as mutants. We found that a large percentage of photosynthesis-related mutants can be detected with this method. Scripts for the free statistics software R are provided to facilitate the practical application of the method.
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Affiliation(s)
- Marius C Codrea
- Department of Information Technology, University of Turku, 20014 Turku, Finland
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