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Amjadi Z, Hamzehzarghani H, Rodriguez VM, Huang YJ, Farahbakhsh F. Studying temperature's impact on Brassica napus resistance to identify key regulatory mechanisms using comparative metabolomics. Sci Rep 2024; 14:19865. [PMID: 39191882 DOI: 10.1038/s41598-024-68345-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/22/2024] [Indexed: 08/29/2024] Open
Abstract
To investigate the effects of temperature on Brassica napus (canola) resistance to Leptosphaeria maculans (LM), the causal agent of blackleg disease, metabolic profiles of LM infected resistant (R) and susceptible (S) canola cultivars at 21 °C and 28 °C were analyzed. Metabolites were detected in cotyledons of R and S plants at 48- and 120-h post-inoculation with LM using UPLC-QTOF/MS. The mock-inoculated plants were used as controls. Some of the resistance-related specific pathways, including lipid metabolism, amino acid metabolism, carbohydrate metabolism, and aminoacyl-tRNA biosynthesis, were down-regulated in S plants but up-regulated in R plants at 21 °C. However, some of these pathways were down-regulated in R plants at 28 °C. Amino acid metabolism, lipid metabolism, alkaloid biosynthesis, phenylpropanoid biosynthesis, and flavonoid biosynthesis were the pathways linked to combined heat and pathogen stresses. By using network analysis and enrichment analysis, these pathways were identified as important. The pathways of carotenoid biosynthesis, pyrimidine metabolism, and lysine biosynthesis were identified as unique mechanisms related to heat stress and may be associated with the breakdown of resistance against the pathogen. The increased susceptibility of R plants at 28 °C resulted in the down-regulation of signal transduction pathway components and compromised signaling, particularly during the later stages of infection. Deactivating LM-specific signaling networks in R plants under heat stress may result in compatible responses and deduction in signaling metabolites, highlighting global warming challenges in crop disease control.
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Affiliation(s)
- Zahra Amjadi
- Plant Protection Department, Shiraz University, Shiraz, Iran
| | | | - Víctor Manuel Rodriguez
- Group of Genetics, Breeding and Biochemistry of Brassicas, Misión Biológica de Galicia (MBG-CSIC), Apartado 28, 36080, Pontevedra, Spain
| | - Yong-Ju Huang
- Centre for Agriculture, Food and Environmental Management, University of Hertfordshire, Hatfield, Hertfordshire, AL10 9AB, UK
| | - Farideh Farahbakhsh
- Plant Protection Research Department, Fars Agricultural and Natural Resources and Education Center, Agricultural Research, Education, and Extension Organization (AREEO), Darab, Iran
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Ma X, Qin Z, Johnson KB, Sweat LH, Dai S, Li G, Li C. Transcriptomic responses to shifts in light and nitrogen in two congeneric diatom species. Front Microbiol 2024; 15:1437274. [PMID: 39206371 PMCID: PMC11349689 DOI: 10.3389/fmicb.2024.1437274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
Light and nitrogen availability are basic requirements for photosynthesis. Changing in light intensity and nitrogen concentration may require adaptive physiological and life process changes in phytoplankton cells. Our previous study demonstrated that two Thalassiosira species exhibited, respectively, distinctive physiological responses to light and nitrogen stresses. Transcriptomic analyses were employed to investigate the mechanisms behind the different physiological responses observed in two diatom species of the genus Thalassiosira. The results indicate that the congeneric species are different in their cellular responses to the same shifting light and nitrogen conditions. When conditions changed to high light with low nitrate (HLLN), the large-celled T. punctigera was photodamaged. Thus, the photosynthesis pathway and carbon fixation related genes were significantly down-regulated. In contrast, the small-celled T. pseudonana sacrificed cellular processes, especially amino acid metabolisms, to overcome the photodamage. When changing to high light with high nitrate (HLHN) conditions, the additional nitrogen appeared to compensate for the photodamage in the large-celled T. punctigera, with the tricarboxylic acid cycle (TCA cycle) and carbon fixation significantly boosted. Consequently, the growth rate of T. punctigera increased, which suggest that the larger-celled species is adapted for forming post-storm algal blooms. The impact of high light stress on the small-celled T. pseudonana was not mitigated by elevated nitrate levels, and photodamage persisted.
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Affiliation(s)
- Xiao Ma
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Province Key Laboratory of Applied Marine Biology, Guangzhou, China
| | - Zhen Qin
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Kevin B. Johnson
- Department of Biological Sciences, College of Science and Mathematics, Tarleton State University, Stephenville, TX, United States
| | - L. Holly Sweat
- Smithsonian Marine Station, Fort Pierce, FL, United States
| | - Sheng Dai
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Province Key Laboratory of Applied Marine Biology, Guangzhou, China
| | - Gang Li
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Province Key Laboratory of Applied Marine Biology, Guangzhou, China
- Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen, China
| | - Chaolun Li
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Province Key Laboratory of Applied Marine Biology, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
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Parveen K, Saddique MAB, Ali Z, Ur Rehman S, Zaib-Un-Nisa, Khan Z, Waqas M, Munir MZ, Hussain N, Muneer MA. Genome-wide analysis of Glutathione peroxidase (GPX) gene family in Chickpea (Cicer arietinum L.) under salinity stress. Gene 2024; 898:148088. [PMID: 38104951 DOI: 10.1016/j.gene.2023.148088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/23/2023] [Accepted: 12/13/2023] [Indexed: 12/19/2023]
Abstract
Chickpea is the second most widely grown legume in the world. Its cultivation is highly affected by saline soils. Salt stress damages its all growth stages from germination to maturity. It has a huge genetic diversity containing adaptation loci that can help produce salt-tolerant cultivars. The glutathione peroxidase (GPX) gene family plays an important role in regulating plant response to abiotic stimuli and protects cells from oxidative damage. In current research, the role of GPX genes is studied for inducing salt tolerance in chickpea. This study identifies the GPX gene family in Cicer arietinum. In response to the NaCl stress, the gene expression profiles of CaGPX3 were examined using real-time qRT-PCR. The results of phylogenetic analysis show that CaGPX genes have an evolutionary relationship with monocots, dicots, chlorophytes, and angiosperms. Gene structure analysis showed that CaGPX3, CaGPX4, and CaGPX5 have six, CaGPX2 has five, and CaGPX1 contains 9 exons. According to the Ka and Ks analysis chickpea has one pair of duplicated genes of GPX and the duplication was tandem with negative (purifying) selection Ka < Ks (<1). In-silico gene expression analysis revealed that CaGPX3 is a salt stress-responsive gene among all other five GPX members in chickpea. The qRT-PCR results showed that the CaGPX3 gene expression was co-ordinately regulated under salt stress conditions, confirming CaGPX3's key involvement in salt tolerance.
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Affiliation(s)
- Kauser Parveen
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture Multan, Pakistan
| | | | - Zulfiqar Ali
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan; Programs and Projects Department, Islamic Organization for Food Security, Astana, Kazakhstan
| | - Shoaib Ur Rehman
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture Multan, Pakistan; SINO-PAK Joint Research Laboratory, Institute of Plant Breeding and Biotechnology, MNS University of Agriculture Multan, Pakistan.
| | - Zaib-Un-Nisa
- Cotton Research Institute, Multan, Punjab, Pakistan
| | - Zulqurnain Khan
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture Multan, Pakistan
| | - Muhammad Waqas
- Pakistan Agricultural Research Council, Arid Zone Research Center, Pakistan Agricultural Research Council, Dera Ismail Khan, Pakistan
| | - Muhammad Zeeshan Munir
- School of Environment and Energy, Peking University Shenzhen Graduate School, 2199 Lishui Rd., Shenzhen 518055, China
| | - Niaz Hussain
- Arid Zone Research Institute Bhakkar, Punjab, Pakistan
| | - Muhammad Atif Muneer
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Suen PK, Zheng L, Yang QQ, Mak WS, Pak WY, Mo KY, Chan ML, Liu QQ, Qin L, Sun SSM. Lysine-rich rice partially enhanced the growth and development of skeletal system with better skeletal microarchitecture in young rats. Nutr Res 2024; 121:67-81. [PMID: 38043437 DOI: 10.1016/j.nutres.2023.11.005] [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: 08/14/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 12/05/2023]
Abstract
Rice is the primary staple food for half of the world's population but is low in lysine content. Previously, we developed transgenic rice with enhanced free lysine content in rice seeds (lysine-rich rice), which was shown safe for consumption and improved the growth in rats. However, the effects of lysine-rich rice on skeletal growth and development remained unknown. In this study, we hypothesized that lysine-rich rice improved skeletal growth and development in weaning rats. Male weaning Sprague-Dawley rats received lysine-rich rice (HFL) diet, wild-type rice (WT) diet, or wild-type rice with various contents of lysine supplementation diet for 70 days. Bone microarchitectures were examined by microcomputed tomography, bone strength was investigated by mechanical test, and dynamics of bone growth were examined by histomorphometric analysis. In addition, we explored the molecular mechanism of lysine and skeletal growth through biochemical testing of growth hormone, bone turnover marker, and amino acid content of rat serum analysis, as well as in a cell culture system. Results indicated that the HFL diet improved rats' bone growth, strength, and microarchitecture compared with the WT diet group. In addition, the HFL diet increased the serum essential amino acids, growth hormone (insulin-like growth factor-1), and bone formation marker concentrations. The cell culture model showed that lysine deficiency reduced insulin-like growth factor-1 and Osterix expression, Akt/mammalian target of rapamycin signaling, and matrix mineralization, and inhibited osteoblast differentiation associated with bone growth. Our findings showed that lysine-rich rice improved skeletal growth and development in weaning rats. A further increase of rice lysine content is highly desirable to fully optimize bone growth and development.
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Affiliation(s)
- Pui Kit Suen
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China; Institute of Plant Molecular Biology and Agriculture Biotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lizhen Zheng
- Musculoskeletal Research Laboratory of Department of Orthopaedics & Traumatology and Innovative Orthopaedic Biomaterial and Drug Translational Research Laboratory, Li Ka Shing Institute of Health, The Chinese University of Hong Kong, Hong Kong SAR, China; Center for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Science, China
| | - Qing-Qing Yang
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China; China Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Wan Sheung Mak
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wan Yu Pak
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kit Ying Mo
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Man-Ling Chan
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qiao-Quan Liu
- China Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Ling Qin
- Musculoskeletal Research Laboratory of Department of Orthopaedics & Traumatology and Innovative Orthopaedic Biomaterial and Drug Translational Research Laboratory, Li Ka Shing Institute of Health, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Samuel Sai-Ming Sun
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China; Institute of Plant Molecular Biology and Agriculture Biotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Baiyin B, Xiang Y, Hu J, Tagawa K, Son JE, Yamada S, Yang Q. Nutrient Solution Flowing Environment Affects Metabolite Synthesis Inducing Root Thigmomorphogenesis of Lettuce ( Lactuca sativa L.) in Hydroponics. Int J Mol Sci 2023; 24:16616. [PMID: 38068940 PMCID: PMC10706437 DOI: 10.3390/ijms242316616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
The principal difference between hydroponics and other substrate cultivation methods is the flowing liquid hydroponic cultivation substrate. Our previous studies have revealed that a suitable flowing environment of nutrient solution promoted root development and plant growth, while an excess flow environment was unfavorable for plants. To explain the thigmomorphogenetic response of excess flow-induced metabolic changes, six groups of lettuce (Lactuca sativa L.), including two flow conditions and three time periods, were grown. Compared with the plants without flow, the plants with flow showed decreased root fresh weight, total root length, root surface area, and root volume but increased average root diameter and root density. The roots with flow had more upregulated metabolites than those without flow, suggesting that the flow may trigger metabolic synthesis and activity. Seventy-nine common differential metabolites among six groups were screened, and enrichment analysis showed the most significant enrichment in the arginine biosynthesis pathway. Arginine was present in all the groups and exhibited greater concentrations in roots with flow than without flow. It can be speculated from the results that a high-flowing environment of nutrient solution promotes arginine synthesis, resulting in changes in root morphology. The findings provide insights on root thigmomorphogenesis affected by its growing conditions and help understand how plants respond to environmental mechanical forces.
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Affiliation(s)
- Bateer Baiyin
- Research Center for Smart Horticulture Engineering, Chengdu National Agricultural Science & Technology Center, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China; (B.B.); (Y.X.); (J.H.)
| | - Yue Xiang
- Research Center for Smart Horticulture Engineering, Chengdu National Agricultural Science & Technology Center, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China; (B.B.); (Y.X.); (J.H.)
| | - Jiangtao Hu
- Research Center for Smart Horticulture Engineering, Chengdu National Agricultural Science & Technology Center, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China; (B.B.); (Y.X.); (J.H.)
| | - Kotaro Tagawa
- Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan; (K.T.); (S.Y.)
| | - Jung Eek Son
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul 08826, Republic of Korea;
| | - Satoshi Yamada
- Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan; (K.T.); (S.Y.)
| | - Qichang Yang
- Research Center for Smart Horticulture Engineering, Chengdu National Agricultural Science & Technology Center, Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China; (B.B.); (Y.X.); (J.H.)
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D'Isita I, Di Palma AM, De Vita P, Germinara GS. Acceptance and utilization efficiency of a purple durum wheat genotype by Sitophilus granarius (L.). Sci Rep 2023; 13:14246. [PMID: 37648729 PMCID: PMC10468511 DOI: 10.1038/s41598-023-41384-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 08/25/2023] [Indexed: 09/01/2023] Open
Abstract
The granary weevil (Sitophilus granarius L.) is a major primary pest of stored cereals throughout the world. Among the major classes of plant secondary metabolites, flavonoids can affect insect feeding behaviour and their growth rate. In this study, the susceptibility of an anthocyanin-rich purple durum wheat genotype (T1303) to the granary weevil was evaluated in comparison with two yellow durum (Ofanto) and bread (Mec) wheat varieties. The feeding response and food utilisation efficiency by adult insects was also investigated by calculating nutritional indices in whole flour disk bioassays. Different levels of susceptibility to granary weevil emerged among genotypes tested. The mean food consumption by an insect, F1 progeny, and female parental offspring calculated for the T1303 genotype were significantly lower than those of yellow kernel wheat varieties. Moreover, T1303 genotype induced deterrence in the adult insects as demonstrated by the positive values of the food deterrence index. Besides, relative grow rate and efficiency conversion of ingested food indices were negative for T1303 and positive for both yellow wheat varieties indicating respectively a decrease and an increase of insect body weight during the bioassays. Finally, a higher mortality rate was recorded for insects fed on T1303 flour disks compared to disks obtained from yellow wheat varieties. These results provide evidence for the antifeedant and toxic effects of anthocyanins present in the T1303 pericarp against the granary weevil. Overall, this study contributes new insights into the mechanisms of host acceptance and food utilization by S. granarius and would be useful to identify antifeedant flavonoids as well as to develop varietal resistance-based strategies against this pest.
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Affiliation(s)
- Ilaria D'Isita
- Department of Agricultural Sciences, Food, Natural Resources and Engineering (DAFNE), University of Foggia, Via Napoli 25, 71122, Foggia, Italy
| | - Antonella Marta Di Palma
- Department of Agricultural Sciences, Food, Natural Resources and Engineering (DAFNE), University of Foggia, Via Napoli 25, 71122, Foggia, Italy
| | - Pasquale De Vita
- CREA Research Centre for Cereal and Industrial Crops, 71122, Foggia, Italy
| | - Giacinto Salvatore Germinara
- Department of Agricultural Sciences, Food, Natural Resources and Engineering (DAFNE), University of Foggia, Via Napoli 25, 71122, Foggia, Italy.
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Rodrigues V, Deusdado S. Meta-learning approach for bacteria classification and identification of informative genes of the Bacillus megaterium: tomato roots tissue interaction. 3 Biotech 2023; 13:271. [PMID: 37449251 PMCID: PMC10335980 DOI: 10.1007/s13205-023-03690-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 06/26/2023] [Indexed: 07/18/2023] Open
Abstract
Plant growth-promoting rhizobacteria (PGPRs) are bacteria that colonize the plant roots. These beneficial bacteria have an influence on plant development through multiple mechanisms, such as nutrient availability, alleviating biotic and abiotic stress, and secrete phytohormones. Therefore, their inoculation constitutes a powerful tool towards sustainable agriculture and crop production. To understand plant-PGPRs interaction we present the classification of PGPR using machine learning and meta-learning classifiers namely Support Vector Machine (SVM), Kernel Logistic Regression (KLR), meta-SVM and meta-KLR to predict the presence of Bacillus megaterium inoculated in tomato root tissues using publicly available transcriptomic data. The original dataset presents 36 significantly differentially expressed genes. As the meta-KLR achieved near-optimal performance considering all the relevant metrics, this meta learner was afterwards used to identify the informative genes (IGs). The outcomes showed 157 IGs, being present all significantly differentially expressed genes previously identified. Among the IGs, 113 were identified as tomato genes, 5 as Bacillus subtilis proteins, 1 as Escherichia coli protein and 6 were unidentified. Then, a functional enrichment analysis of the tomato IGs showed 175 biological processes, 22 molecular functions and 20 KEGG pathways involved in B. megaterium-tomato interaction. Furthermore, the biological networks study of their Arabidopsis thaliana orthologous genes identified the co-expression, predicted interaction, shared protein domains and co-localization networks. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03690-0.
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Affiliation(s)
| | - Sérgio Deusdado
- Instituto Politécnico de Bragança, CIMO—Centro de Investigação de Montanha, 5301-855 Bragança, Portugal
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Jabeen S, Saif R, Haq R, Hayat A, Naz S. Whole-genome sequencing and variant discovery of Citrus reticulata "Kinnow" from Pakistan. Funct Integr Genomics 2023; 23:227. [PMID: 37422603 DOI: 10.1007/s10142-023-01153-6] [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: 02/17/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/10/2023]
Abstract
Citrus is a source of nutritional and medicinal advantages, cultivated worldwide with major groups of sweet oranges, mandarins, grapefruits, kumquats, lemons and limes. Pakistan produces all major citrus groups with mandarin (Citrus reticulata) being the prominent group that includes local commercial cultivars Feutral's Early, Dancy, Honey, and Kinnow. The present study designed to understand the genetic architecture of this unique variety of Citrus reticulata 'Kinnow.' The whole-genome resequencing and variant calling was performed to map the genomic variability that might be responsible for its particular characteristics like taste, seedlessness, juice content, thickness of peel, and shelf-life. A total of 139,436,350 raw sequence reads were generated with 20.9 Gb data in Fastq format having 98% effectiveness and 0.2% base call error rate. Overall, 3,503,033 SNPs, 176,949 MNPs, 323,287 INS, and 333,083 DEL were identified using the GATK4 variant calling pipeline against Citrus clementina. Furthermore, g:Profiler was applied for annotating the newly found variants, harbor genes/transcripts and their involved pathways. A total of 73,864 transcripts harbors 4,336,352 variants, most of the observed variants were predicted in non-coding regions and 1009 transcripts were found well annotated by different databases. Out of total aforementioned transcripts, 588 involved in biological processes, 234 in molecular functions and 167 transcripts in cellular components. In a nutshell, 18,153 high impact variants and 216 genic variants found in the current study, which may be used after its functional validation for marker-assisted breeding programs of "Kinnow" to propagate its valued traits for the improvement of contemporary citrus varieties in the region.
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Affiliation(s)
- Sadia Jabeen
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Rashid Saif
- Department of Biotechnology, Qarshi University, Lahore, Pakistan
- Decode Genomics, Punjab University Employees Housing Scheme, Lahore, Pakistan
| | - Rukhama Haq
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Akbar Hayat
- Citrus Research Institute, Sargodha, Pakistan
| | - Shagufta Naz
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan.
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Yang Y, Shi L, Xu X, Wen J, Xie T, Li H, Li X, Chen M, Dou X, Yuan C, Song H, Xie B, Tao Y. Spermidine Synthase and Saccharopine Reductase Have Co-Expression Patterns Both in Basidiomycetes with Fusion Form and Ascomycetes with Separate Form. J Fungi (Basel) 2023; 9:jof9030352. [PMID: 36983520 PMCID: PMC10051792 DOI: 10.3390/jof9030352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/15/2023] Open
Abstract
Gene fusion is a process through which two or more distinct genes are fused into a single chimeric gene. Unlike most harmful fusion genes in cancer cells, in this study, we first found that spermidine synthetase- (SPDS, catalyst of spermidine biosynthesis) and saccharopine reductase- (SR, catalyst of the penultimate step of lysine biosynthesis) encoding genes form a natural chimeric gene, FfSpdsSr, in Flammulina filiformis. Through the cloning of full-length ORFs in different strains and the analysis of alternative splicing in developmental stages, FfSpdsSr has only one copy and unique transcript encoding chimeric SPDS-SR in F. filiformis. By an orthologous gene search of SpdsSr in more than 80 fungi, we found that the chimeric SpdsSr exists in basidiomycetes, while the two separate Spds and Sr independently exist in ascomycetes, chytridiomycetes, and oomycetes. Further, the transcript level of FfSpdsSr was investigated in different developmental stages and under some common environmental factors and stresses by RT-qPCR. The results showed that FfSpdsSr mainly up-regulated in the elongation stage and pileus development of F. filiformis, as well as under blue light, high temperature, H2O2, and MeJA treatments. Moreover, a total of 15 sets of RNA-Seq data, including 218 samples of Neurospora crassa, were downloaded from the GEO database and used to analyze the expression correlation of NcSpds and NcSr. The results showed that the separate NcSpds and NcSr shared highly similar co-expression patterns in the samples with different strains and different nutritional and environmental condition treatments. The chimeric SpdsSr in basidiomycetes and the co-expression pattern of the Spds and Sr in N. crassa indicate the special link of spermidine and lysine in fungi, which may play an important role in the growth and development of fruiting body and in response to the multiple environmental factors and abiotic stresses.
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Affiliation(s)
- Yayong Yang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lei Shi
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinyu Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jin Wen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tianyue Xie
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hui Li
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Xiaoyu Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengyu Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinyi Dou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chengjin Yuan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hanbing Song
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baogui Xie
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongxin Tao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: ; Tel.: +86-0591-83789281
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McNeil CJ, Araujo K, Godfrey K, Slupsky CM. Metabolite Signature and Differential Expression of Genes in Washington Navel Oranges ( Citrus sinensis) Infected by Spiroplasma citri. PHYTOPATHOLOGY 2023; 113:299-308. [PMID: 35984373 DOI: 10.1094/phyto-05-22-0177-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Spiroplasma citri is the pathogen that causes citrus stubborn disease (CSD). Infection of citrus with S. citri has been shown to cause leaf mottling, reduce fruit yield, and stunt tree growth. Fruit from trees exhibiting symptoms of CSD are misshapen and discolored. The symptoms of CSD are easily confused with nutrient deficiencies or symptoms of citrus greening disease. In this study, young Washington navel oranges (Citrus sinensis) were graft-inoculated with budwood originating from trees confirmed to be infected with S. citri. Leaf samples were collected monthly for 10 months for metabolomics and differential gene expression analyses. Significant differences in the concentration of metabolites and expressed genes were observed between control and S. citri-infected trees throughout the experiment. Metabolites and genes associated with important defense and stress pathways, including jasmonic acid signaling, cell wall modification, amino acid biosynthesis, and the production of antioxidant and antimicrobial secondary metabolites, were impacted by S. citri throughout the study, and even prior to symptom development. This work fills a current gap in knowledge surrounding the pathogenicity of S. citri and provides an updated mechanistic explanation for the development of CSD symptoms in S. citri-infected plants.
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Affiliation(s)
- Christopher J McNeil
- Department of Food Science & Technology, University of California-Davis, Davis, CA 95616
| | - Karla Araujo
- Contained Research Facility, University of California-Davis, Davis, CA 95616
| | - Kristine Godfrey
- Contained Research Facility, University of California-Davis, Davis, CA 95616
| | - Carolyn M Slupsky
- Department of Food Science & Technology, University of California-Davis, Davis, CA 95616
- Department of Nutrition, University of California-Davis, Davis, CA 95616
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11
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Yaghoubi Khanghahi M, AbdElgawad H, Verbruggen E, Korany SM, Alsherif EA, Beemster GTS, Crecchio C. Biofertilisation with a consortium of growth-promoting bacterial strains improves the nutritional status of wheat grain under control, drought, and salinity stress conditions. PHYSIOLOGIA PLANTARUM 2022; 174:e13800. [PMID: 36250979 DOI: 10.1111/ppl.13800] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/22/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
We investigated the effect of plant growth-promoting bacterial strains (PGPB) as biofertilisers on the grain metabolic composition of durum wheat (Triticum durum Desf.). To this aim, we conducted a greenhouse experiment where we grew durum wheat plants supplied with a biofertiliser consortium of four PGPB and/or chemical fertiliser (containing nitrogen, phosphorus, potassium, and zinc), under non-stress, drought (at 40% field capacity), or salinity (150 mM NaCl) conditions. Nutrient accumulations in the grain were increased in plants treated with the biofertiliser consortium, alone or with a half dose of chemical fertilisers, compared to those in no fertilisation treatment. A clear benefit of biofertiliser application in the improvement of protein, soluble sugar, starch, and lipid contents in the grains was observed in comparison with untreated controls, especially under stress conditions. The most striking observation was the absence of significant differences between biofertiliser and chemical fertiliser treatments for most parameters. Moreover, the overall response to the biofertiliser consortium was accompanied by greater changes in amino acids, organic acids, and fatty acid profiles. In conclusion, PGPB improved the metabolic and nutrient status of durum wheat grains to a similar extent as chemical fertilisers, particularly under stress conditions, demonstrating the value of PGPB as a sustainable fertilisation treatment.
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Affiliation(s)
| | - Hamada AbdElgawad
- Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, Belgium
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Erik Verbruggen
- Plants and Ecosystems Research Group, Department of Biology, University of Antwerp, Universiteitsplein 1C, Wilrijk, Belgium
| | - Shereen Magdy Korany
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Emad A Alsherif
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
- Biology Department, College of Science and Arts at Khulis, University of Jeddah, Jeddah, Saudi Arabia
| | - Gerrit T S Beemster
- Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Carmine Crecchio
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
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12
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Priyanka, Srivastava S, Sharma S. Metabolomic insight into the synergistic mechanism of action of a bacterial consortium in plant growth promotion. J Biosci Bioeng 2022; 134:399-406. [PMID: 36088211 DOI: 10.1016/j.jbiosc.2022.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/04/2022] [Accepted: 07/24/2022] [Indexed: 10/14/2022]
Abstract
It has been established that a consortium consisting of compatible plant growth promoting rhizobacterial strains outperforms their individual impacts on plant attributes. While the phenomenon of synergism is extensively reported, the mechanism that underpins it is yet to be elucidated. In the present study the impact of three plant growth promoting bacteria, Azotobacter chroococcum (A), Priestia megaterium (formerly Bacillus megaterium) (B), and Pseudomonas sp. SK3 (P) was studied as a consortium on the growth attributes of pigeonpea. In addition, microbe-microbe interactions were investigated through metabolomic profiling to understand the mechanism of synergism. Plant growth experiments revealed that bacterial consortium A + B + P showed a significant increase in plant attributes such as shoot length, root length, fresh weight, and dry weight as compared to monocultures and two-membered consortia. Metabolomic profiling through high resolution liquid chromatograph mass spectrometer revealed the presence of a few bioactive compounds in the consortium that might play a potential role in the enhancement of biometric parameters of the plant. Several compounds, such as antipyrine, 6,6-dimethoxy-2,5,5-trimethyl-2-hexene, N-methyltryptamine, 2,2-dimethyl-3,4-bis(4-methoxyphenyl)-2H-1-benzopyran-7-ol acetate, N6-hydroxy-l-lysine, and l-furosin, were detected in the metabolome of the consortium, which was unique among all the treatments. The study also detected a few metabolites involved in sphingolipid biosynthesis (ketosphinganine and sphinganine) known for cell signaling in the consortium. This unravels the possible mechanism of synergism between bacterial strains in a consortium. The metabolomic profile would be helpful to strategically develop unique and more effective consortia that are tailored to the soil type.
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Affiliation(s)
- Priyanka
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Sonal Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India.
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13
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Kiekens R, de Koning R, Toili MEM, Angenon G. The Hidden Potential of High-Throughput RNA-Seq Re-Analysis, a Case Study for DHDPS, Key Enzyme of the Aspartate-Derived Lysine Biosynthesis Pathway and Its Role in Abiotic and Biotic Stress Responses in Soybean. PLANTS 2022; 11:plants11131762. [PMID: 35807714 PMCID: PMC9269547 DOI: 10.3390/plants11131762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022]
Abstract
DHDPS is a key enzyme in the aspartate-derived lysine biosynthesis pathway and an evident object of study for biofortification strategies in plants. DHDPS isoforms with novel regulatory properties in Medicago truncatula were demonstrated earlier and hypothesized to be involved in abiotic and biotic stress responses. Here, we present a phylogenetic analysis of the DHPDS gene family in land plants which establishes the existence of a legume-specific class of DHDPS, termed DHDPS B-type, distinguishable from the DHDPS A-type commonly present in all land plants. The G. max genome comprises two A-type DHDPS genes (Gm.DHDPS-A1; Glyma.09G268200, Gm.DHDPS-A2; Glyma.18G221700) and one B-type (Gm.DHDPS-B; Glyma.03G022300). To further investigate the expression pattern of the G. max DHDPS isozymes in different plant tissues and under various stress conditions, 461 RNA-seq experiments were exploited and re-analyzed covering two expression atlases, 13 abiotic and 5 biotic stress studies. Gm.DHDPS-B is seen almost exclusively expressed in roots and nodules in addition to old cotyledons or senescent leaves while both DHDPS A-types are expressed constitutively in all tissues analyzed with the highest expression in mature seeds. Furthermore, Gm.DHDPS-B expression is significantly upregulated in some but not all stress responses including salt stress, flooding, ethylene or infection with Phytophthora sojae and coincides with downregulation of DHDPS A-types. In conclusion, we demonstrate the potential of an in-depth RNA-seq re-analysis for the guidance of future experiments and to expand on current knowledge.
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Affiliation(s)
- Raphaël Kiekens
- Research Group Plant Genetics, Vrije Universiteit Brussel, 1050 Brussels, Belgium; (R.K.); (R.d.K.); (M.E.M.T.)
| | - Ramon de Koning
- Research Group Plant Genetics, Vrije Universiteit Brussel, 1050 Brussels, Belgium; (R.K.); (R.d.K.); (M.E.M.T.)
| | - Mary Esther Muyoka Toili
- Research Group Plant Genetics, Vrije Universiteit Brussel, 1050 Brussels, Belgium; (R.K.); (R.d.K.); (M.E.M.T.)
- Department of Horticulture and Food Security, School of Agriculture and Environmental Sciences, College of Agriculture and Natural Resources, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya
| | - Geert Angenon
- Research Group Plant Genetics, Vrije Universiteit Brussel, 1050 Brussels, Belgium; (R.K.); (R.d.K.); (M.E.M.T.)
- Correspondence: ; Tel.: +32-2-629-1935
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14
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Roles of AGD2a in Plant Development and Microbial Interactions of Lotus japonicus. Int J Mol Sci 2022; 23:ijms23126863. [PMID: 35743304 PMCID: PMC9224730 DOI: 10.3390/ijms23126863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022] Open
Abstract
Arabidopsis AGD2 (Aberrant Growth and Death2) and its close homolog ALD1 (AGD2-like defense response protein 1) have divergent roles in plant defense. We previously reported that modulation of salicylic acid (SA) contents by ALD1 affects numbers of nodules produced by Lotus japonicus, but AGD2's role in leguminous plants remains unclear. A combination of enzymatic analysis and biological characterization of genetic materials was used to study the function of AGD2 (LjAGD2a and LjAGD2b) in L. japonicus. Both LjAGD2a and LjAGD2b could complement dapD and dapE mutants of Escherichia coli and had aminotransferase activity in vitro. ljagd2 plants, with insertional mutations of LjAGD2, had delayed flowering times and reduced seed weights. In contrast, overexpression of LjAGD2a in L. japonicus induced early flowering, with increases in seed and flower sizes, but reductions in pollen fertility and seed setting rates. Additionally, ljagd2a mutation resulted in increased expression of nodulin genes and corresponding increases in infection threads and nodule numbers following inoculation with Rhizobium. Changes in expression of LjAGD2a in L. japonicus also affected endogenous SA contents and hence resistance to pathogens. Our results indicate that LjAGD2a functions as an LL-DAP aminotransferase and plays important roles in plant development. Moreover, LjAGD2a activates defense signaling via the Lys synthesis pathway, thereby participating in legume-microbe interaction.
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15
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Weyandt N, Aghdam SA, Brown AMV. Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes. Front Microbiol 2022; 13:867392. [PMID: 35547116 PMCID: PMC9084900 DOI: 10.3389/fmicb.2022.867392] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
Wolbachia is a widespread endosymbiont of insects and filarial nematodes that profoundly influences host biology. Wolbachia has also been reported in rhizosphere hosts, where its diversity and function remain poorly characterized. The discovery that plant-parasitic nematodes (PPNs) host Wolbachia strains with unknown roles is of interest evolutionarily, ecologically, and for agriculture as a potential target for developing new biological controls. The goal of this study was to screen communities for PPN endosymbionts and analyze genes and genomic patterns that might indicate their role. Genome assemblies revealed 1 out of 16 sampled sites had nematode communities hosting a Wolbachia strain, designated wTex, that has highly diverged as one of the early supergroup L strains. Genome features, gene repertoires, and absence of known genes for cytoplasmic incompatibility, riboflavin, biotin, and other biosynthetic functions placed wTex between mutualist C + D strains and reproductive parasite A + B strains. Functional terms enriched in group L included protoporphyrinogen IX, thiamine, lysine, fatty acid, and cellular amino acid biosynthesis, while dN/dS analysis suggested the strongest purifying selection on arginine and lysine metabolism, and vitamin B6, heme, and zinc ion binding, suggesting these as candidate roles in PPN Wolbachia. Higher dN/dS pathways between group L, wPni from aphids, wFol from springtails, and wCfeT from cat fleas suggested distinct functional changes characterizing these early Wolbachia host transitions. PPN Wolbachia had several putative horizontally transferred genes, including a lysine biosynthesis operon like that of the mitochondrial symbiont Midichloria, a spirochete-like thiamine synthesis operon shared only with wCfeT, an ATP/ADP carrier important in Rickettsia, and a eukaryote-like gene that may mediate plant systemic acquired resistance through the lysine-to-pipecolic acid system. The Discovery of group L-like variants from global rhizosphere databases suggests diverse PPN Wolbachia strains remain to be discovered. These findings support the hypothesis of plant-specialization as key to shaping early Wolbachia evolution and present new functional hypotheses, demonstrating promise for future genomics-based rhizosphere screens.
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Affiliation(s)
- Nicholas Weyandt
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Shiva A Aghdam
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Amanda M V Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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16
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Yang Q, Zhao D, Zhang C, Sreenivasulu N, Sun SSM, Liu Q. Lysine biofortification of crops to promote sustained human health in the 21st century. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1258-1267. [PMID: 34723338 DOI: 10.1093/jxb/erab482] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/31/2021] [Indexed: 06/13/2023]
Abstract
Crop biofortification is pivotal in preventing malnutrition, with lysine considered the main limiting essential amino acid (EAA) required to maintain human health. Lysine deficiency is predominant in developing countries where cereal crops are the staple food, highlighting the need for efforts aimed at enriching the staple diet through lysine biofortification. Successful modification of aspartate kinase (AK) and dihydrodipicolinate synthase (DHDPS) feedback inhibition has been used to enrich lysine in transgenic rice plants without yield penalty, while increases in the lysine content of quality protein maize have been achieved via marker-assisted selection. Here, we reviewed the lysine metabolic pathway and proposed the use of metabolic engineering targets as the preferred option for fortification of lysine in crops. Use of gene editing technologies to translate the findings and engineer lysine catabolism is thus a pioneering step forward.
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Affiliation(s)
- Qingqing Yang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Dongsheng Zhao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Chuangquan Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Nese Sreenivasulu
- Consumer Driven Grain Quality and Nutrition Unit, Rice Breeding Innovation Platform, International Rice Research Institute, Los Banos, Philippines
| | - Samuel Sai-Ming Sun
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
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17
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Decouard B, Bailly M, Rigault M, Marmagne A, Arkoun M, Soulay F, Caïus J, Paysant-Le Roux C, Louahlia S, Jacquard C, Esmaeel Q, Chardon F, Masclaux-Daubresse C, Dellagi A. Genotypic Variation of Nitrogen Use Efficiency and Amino Acid Metabolism in Barley. FRONTIERS IN PLANT SCIENCE 2022; 12:807798. [PMID: 35185958 PMCID: PMC8854266 DOI: 10.3389/fpls.2021.807798] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/02/2021] [Indexed: 06/01/2023]
Abstract
Owing to the large genetic diversity of barley and its resilience under harsh environments, this crop is of great value for agroecological transition and the need for reduction of nitrogen (N) fertilizers inputs. In the present work, we investigated the diversity of a North African barley genotype collection in terms of growth under limiting N (LN) or ample N (HN) supply and in terms of physiological traits including amino acid content in young seedlings. We identified a Moroccan variety, Laanaceur, accumulating five times more lysine in its leaves than the others under both N nutritional regimes. Physiological characterization of the barley collection showed the genetic diversity of barley adaptation strategies to LN and highlighted a genotype x environment interaction. In all genotypes, N limitation resulted in global biomass reduction, an increase in C concentration, and a higher resource allocation to the roots, indicating that this organ undergoes important adaptive metabolic activity. The most important diversity concerned leaf nitrogen use efficiency (LNUE), root nitrogen use efficiency (RNUE), root nitrogen uptake efficiency (RNUpE), and leaf nitrogen uptake efficiency (LNUpE). Using LNUE as a target trait reflecting barley capacity to deal with N limitation, this trait was positively correlated with plant nitrogen uptake efficiency (PNUpE) and RNUpE. Based on the LNUE trait, we determined three classes showing high, moderate, or low tolerance to N limitation. The transcriptomic approach showed that signaling, ionic transport, immunity, and stress response were the major functions affected by N supply. A candidate gene encoding the HvNRT2.10 transporter was commonly up-regulated under LN in the three barley genotypes investigated. Genes encoding key enzymes required for lysine biosynthesis in plants, dihydrodipicolinate synthase (DHPS) and the catabolic enzyme, the bifunctional Lys-ketoglutarate reductase/saccharopine dehydrogenase are up-regulated in Laanaceur and likely account for a hyperaccumulation of lysine in this genotype. Our work provides key physiological markers of North African barley response to low N availability in the early developmental stages.
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Affiliation(s)
- Bérengère Decouard
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Marlène Bailly
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Martine Rigault
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Anne Marmagne
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Mustapha Arkoun
- Agro Innovation International - Laboratoire Nutrition Végétale, TIMAC AGRO International SAS, Saint Malo, France
| | - Fabienne Soulay
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - José Caïus
- Université Paris-Saclay, CNRS, INRAE, University of Évry Val d′Essonne, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Christine Paysant-Le Roux
- Université Paris-Saclay, CNRS, INRAE, University of Évry Val d′Essonne, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Said Louahlia
- Natural Resources and Environment Lab, Faculté Polydiscipliniare de Taza, Université Sidi Mohamed Ben Abdellah, Taza, Morocco
| | - Cédric Jacquard
- Université de Reims Champagne Ardenne, RIBP EA 4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Qassim Esmaeel
- Université de Reims Champagne Ardenne, RIBP EA 4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Fabien Chardon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Céline Masclaux-Daubresse
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Alia Dellagi
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
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18
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Bao XY, Yan JY, Yao YL, Wang YB, Visendi P, Seal S, Luan JB. Lysine provisioning by horizontally acquired genes promotes mutual dependence between whitefly and two intracellular symbionts. PLoS Pathog 2021; 17:e1010120. [PMID: 34843593 PMCID: PMC8659303 DOI: 10.1371/journal.ppat.1010120] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 12/09/2021] [Accepted: 11/16/2021] [Indexed: 11/18/2022] Open
Abstract
Horizontal gene transfer is widespread in insects bearing intracellular symbionts. Horizontally transferred genes (HTGs) are presumably involved in amino acid synthesis in sternorrhynchan insects. However, their role in insect-symbiont interactions remains largely unknown. We found symbionts Portiera, Hamiltonella and Rickettsia possess most genes involved in lysine synthesis in the whitefly Bemisia tabaci MEAM1 although their genomes are reduced. Hamiltonella maintains a nearly complete lysine synthesis pathway. In contrast, Portiera and Rickettsia require the complementation of whitefly HTGs for lysine synthesis and have lysE, encoding a lysine exporter. Furthermore, each horizontally transferred lysine gene of ten B. tabaci cryptic species shares an evolutionary origin. We demonstrated that Hamiltonella did not alter the titers of Portiera and Rickettsia or lysine gene expression of Portiera, Rickettsia and whiteflies. Hamiltonella also did not impact on lysine levels or protein localization in bacteriocytes harboring Portiera and ovaries infected with Rickettsia. Complementation with whitefly lysine synthesis HTGs rescued E. coli lysine gene knockout mutants. Silencing whitefly lysA in whiteflies harboring Hamiltonella reduced lysine levels, adult fecundity and titers of Portiera and Rickettsia without influencing the expression of Hamiltonella lysA. Furthermore, silencing whitefly lysA in whiteflies lacking Hamiltonella reduced lysine levels, adult fecundity and titers of Portiera and Rickettsia in ovarioles. Therefore, we, for the first time, demonstrated an essential amino acid lysine synthesized through HTGs is important for whitefly reproduction and fitness of both obligate and facultative symbionts, and it illustrates the mutual dependence between whitefly and its two symbionts. Collectively, this study reveals that acquisition of horizontally transferred lysine genes contributes to coadaptation and coevolution between B. tabaci and its symbionts.
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Affiliation(s)
- Xi-Yu Bao
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Jin-Yang Yan
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Ya-Lin Yao
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Yan-Bin Wang
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Paul Visendi
- Centre for Agriculture and the Bioeconomy, Institute for Future Environments, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Susan Seal
- Agriculture, Health and Environment Department, Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, United Kingdom
| | - Jun-Bo Luan
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
- * E-mail:
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19
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Li C, Ji Y, Li E. Understanding the Influences of Rice Starch Fine Structure and Protein Content on Cooked Rice Texture. STARCH-STARKE 2021. [DOI: 10.1002/star.202100253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Changfeng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture Yangzhou University Yangzhou 225009 China
- Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou 225009 China
| | - Yi Ji
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture Yangzhou University Yangzhou 225009 China
- Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou 225009 China
| | - Enpeng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture Yangzhou University Yangzhou 225009 China
- Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou 225009 China
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20
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Huang A, Coutu C, Harrington M, Rozwadowski K, Hegedus DD. Engineering a feedback inhibition-insensitive plant dihydrodipicolinate synthase to increase lysine content in Camelina sativa seeds. Transgenic Res 2021; 31:131-148. [PMID: 34802109 PMCID: PMC8821502 DOI: 10.1007/s11248-021-00291-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/11/2021] [Indexed: 11/28/2022]
Abstract
Camelina sativa (camelina) is emerging as an alternative oilseed crop due to its short growing cycle, low input requirements, adaptability to less favorable growing environments and a seed oil profile suitable for biofuel and industrial applications. Camelina meal and oil are also registered for use in animal and fish feeds; however, like meals derived from most cereals and oilseeds, it is deficient in certain essential amino acids, such as lysine. In higher plants, the reaction catalyzed by dihydrodipicolinate synthase (DHDPS) is the first committed step in the biosynthesis of lysine and is subject to regulation by lysine through feedback inhibition. Here, we report enhancement of lysine content in C. sativa seed via expression of a feedback inhibition-insensitive form of DHDPS from Corynebacterium glutamicums (CgDHDPS). Two genes encoding C. sativa DHDPS were identified and the endogenous enzyme is partially insensitive to lysine inhibition. Site-directed mutagenesis was used to examine the impact of alterations, alone and in combination, present in lysine-desensitized DHDPS isoforms from Arabidopsis thaliana DHDPS (W53R), Nicotiana tabacum (N80I) and Zea mays (E84K) on C. sativa DHDPS lysine sensitivity. When introduced alone, each of the alterations decreased sensitivity to lysine; however, enzyme specific activity was also affected. There was evidence of molecular or structural interplay between residues within the C. sativa DHDPS allosteric site as coupling of the W53R mutation with the N80V mutation decreased lysine sensitivity of the latter, but not to the level with the W53R mutation alone. Furthermore, the activity and lysine sensitivity of the triple mutant (W53R/N80V/E84T) was similar to the W53R mutation alone or the C. glutamicum DHDPS. The most active and most lysine-insensitive C. sativa DHDPS variant (W53R) was not inhibited by free lysine up to 1 mM, comparable to the C. glutamicums enzyme. Seed lysine content increased 13.6 -22.6% in CgDHDPS transgenic lines and 7.6–13.2% in the mCsDHDPS lines. The high lysine-accumulating lines from this work may be used to produce superior quality animal feed with improved essential amino acid profile.
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Affiliation(s)
- Alex Huang
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Cathy Coutu
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Myrtle Harrington
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Kevin Rozwadowski
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Dwayne D Hegedus
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada. .,Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada.
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21
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Amino Acid Transport and Metabolism Regulate Early Embryo Development: Species Differences, Clinical Significance, and Evolutionary Implications. Cells 2021; 10:cells10113154. [PMID: 34831375 PMCID: PMC8618253 DOI: 10.3390/cells10113154] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/05/2021] [Accepted: 11/11/2021] [Indexed: 12/11/2022] Open
Abstract
In this review we discuss the beneficial effects of amino acid transport and metabolism on pre- and peri-implantation embryo development, and we consider how disturbances in these processes lead to undesirable health outcomes in adults. Proline, glutamine, glycine, and methionine transport each foster cleavage-stage development, whereas leucine uptake by blastocysts via transport system B0,+ promotes the development of trophoblast motility and the penetration of the uterine epithelium in mammalian species exhibiting invasive implantation. (Amino acid transport systems and transporters, such as B0,+, are often oddly named. The reader is urged to focus on the transporters’ functions, not their names.) B0,+ also accumulates leucine and other amino acids in oocytes of species with noninvasive implantation, thus helping them to produce proteins to support later development. This difference in the timing of the expression of system B0,+ is termed heterochrony—a process employed in evolution. Disturbances in leucine uptake via system B0,+ in blastocysts appear to alter the subsequent development of embryos, fetuses, and placentae, with undesirable consequences for offspring. These consequences may include greater adiposity, cardiovascular dysfunction, hypertension, neural abnormalities, and altered bone growth in adults. Similarly, alterations in amino acid transport and metabolism in pluripotent cells in the blastocyst inner cell mass likely lead to epigenetic DNA and histone modifications that produce unwanted transgenerational health outcomes. Such outcomes might be avoided if we learn more about the mechanisms of these effects.
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22
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Wang Y, Huang L, Du F, Wang J, Zhao X, Li Z, Wang W, Xu J, Fu B. Comparative transcriptome and metabolome profiling reveal molecular mechanisms underlying OsDRAP1-mediated salt tolerance in rice. Sci Rep 2021; 11:5166. [PMID: 33664392 PMCID: PMC7933422 DOI: 10.1038/s41598-021-84638-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 02/18/2021] [Indexed: 11/09/2022] Open
Abstract
Integration of transcriptomics and metabolomics data can provide detailed information for better understanding the molecular mechanisms underlying salt tolerance in rice. In the present study, we report a comprehensive analysis of the transcriptome and metabolome of rice overexpressing the OsDRAP1 gene, which encodes an ERF transcription factor and was previously identified to be conferring drought tolerance. Phenotypic analysis showed that OsDRAP1 overexpression (OE) improved salt tolerance by increasing the survival rate under salt stress. OsDRAP1 affected the physiological indices such as superoxide dismutase (SOD), catalase (CAT) and malondialdehyde (MDA) to enhance redox homeostasis and membrane stability in response to salt stress. Higher basal expression of OsDRAP1 resulted in differential expression of genes that potentially function in intrinsic salt tolerance. A core set of genes with distinct functions in transcriptional regulation, organelle gene expression and ion transport were substantially up-regulated in the OE line in response to salt stress, implying their important role in OsDRAP1-mediated salt tolerance. Correspondingly, metabolome profiling detected a number of differentially metabolites in the OE line relative to the wild type under salt stress. These metabolites, including amino acids (proline, valine), organic acids (glyceric acid, phosphoenolpyruvic acid and ascorbic acid) and many secondary metabolites, accumulated to higher levels in the OE line, demonstrating their role in salt tolerance. Integration of transcriptome and metabolome analysis highlights the crucial role of amino acids and carbohydrate metabolism pathways in OsDRAP1-mediated salt tolerance.
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Affiliation(s)
- Yinxiao Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China
| | - Liyu Huang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China.,School of Agriculture, Yunnan University, Kunming, Yunnan, China.,Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, 650091, Yunnan, China
| | - Fengping Du
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China
| | - Juan Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China
| | - Xiuqin Zhao
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China.,School of Agronomy, Anhui Agricultural University, Hefei, China
| | - Wensheng Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China. .,School of Agronomy, Anhui Agricultural University, Hefei, China.
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China.
| | - Binying Fu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, South Zhong-Guan-Cun Street 12#, Beijing, 100081, China.
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23
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Yang Q, Yu W, Wu H, Zhang C, Sun SS, Liu Q. Lysine biofortification in rice by modulating feedback inhibition of aspartate kinase and dihydrodipicolinate synthase. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:490-501. [PMID: 32945115 PMCID: PMC7955878 DOI: 10.1111/pbi.13478] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/21/2020] [Accepted: 09/01/2020] [Indexed: 05/27/2023]
Abstract
Lysine is the main limiting essential amino acid (EAA) in the rice seeds, which is a major energy and nutrition source for humans and livestock. In higher plants, the rate-limiting steps in lysine biosynthesis pathway are catalysed by two key enzymes, aspartate kinase (AK) and dihydrodipicolinate synthase (DHDPS), and both are extremely sensitive to feedback inhibition by lysine. In this study, two rice AK mutants (AK1 and AK2) and five DHDPS mutants (DHDPS1-DHDPS5), all single amino acid substitution, were constructed. Their protein sequences passed an allergic sequence-based homology alignment. Mutant proteins were recombinantly expressed in Escherichia coli, and all were insensitive to the lysine analog S-(2-aminoethyl)-l-cysteine (AEC) at concentrations up to 12 mm. The AK and DHDPS mutants were transformed into rice, and free lysine was elevated in mature seeds of transgenic plants, especially those expressing AK2 or DHDPS1, 6.6-fold and 21.7-fold higher than the wild-type (WT) rice, respectively. We then engineered 35A2D1L plants by simultaneously expressing modified AK2 and DHDPS1, and inhibiting rice LKR/SDH (lysine ketoglutaric acid reductase/saccharopine dehydropine dehydrogenase). Free lysine levels in two 35A2D1L transgenic lines were 58.5-fold and 39.2-fold higher than in WT and transgenic rice containing native AK and DHDPS, respectively. Total free amino acid and total protein content were also elevated in 35A2D1L transgenic rice. Additionally, agronomic performance analysis indicated that transgenic lines exhibited normal plant growth, development and seed appearance comparable to WT plants. Thus, AK and DHDPS mutants may be used to improve the nutritional quality of rice and other cereal grains.
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Affiliation(s)
- Qing‐Qing Yang
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouChina
- State Key Laboratory of AgrobiotechnologySchool of Life SciencesThe Chinese University of Hong KongHong KongChina
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri‐Product Safety of the Ministry of EducationYangzhou UniversityYangzhouChina
| | - Wai‐Han Yu
- State Key Laboratory of AgrobiotechnologySchool of Life SciencesThe Chinese University of Hong KongHong KongChina
| | - Hong‐Yu Wu
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouChina
| | - Chang‐Quan Zhang
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouChina
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri‐Product Safety of the Ministry of EducationYangzhou UniversityYangzhouChina
| | - Samuel Sai‐Ming Sun
- State Key Laboratory of AgrobiotechnologySchool of Life SciencesThe Chinese University of Hong KongHong KongChina
| | - Qiao‐Quan Liu
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouChina
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri‐Product Safety of the Ministry of EducationYangzhou UniversityYangzhouChina
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24
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Hasan MM, Rima R. Genetic engineering to improve essential and conditionally essential amino acids in maize: transporter engineering as a reference. Transgenic Res 2021; 30:207-220. [PMID: 33583006 DOI: 10.1007/s11248-021-00235-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/21/2021] [Indexed: 11/27/2022]
Abstract
Ruminants and humans are unable to synthesize essential amino acids (EAAs) and conditionally essential amino acids (CEAAs) under normal conditions and need to acquire them from plant sources. Maize plays, as a major crop, a central role in global food security. However, maize is deficient in several EAAs and CEAAs. Genetic engineering has been successfully used to enrich the EAA content of maize to some extent, including the content of Lys, Trp, and Met. However, research on other EAAs is lacking. Genetic engineering provides several viable approaches for increasing the EAA content in maize, including transformation of a single gene, transformation of multiple genes in a single cassette, overexpression of putative amino acid transporters, engineering the amino acid biosynthesis pathway including silencing of feedback inhibition enzymes, and overexpression of major enzymes in this pathway. These challenging processes require a deep understanding of the biosynthetic and metabolic pathways of individual amino acids, and the interaction of individual amino acids with other metabolic pathways.
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Affiliation(s)
- Md Mahmudul Hasan
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
- The Key Laboratory of Plant-Soil Interactions, Ministry of Education, Center for Resources, Environment and Food Security, Department of Plant Nutrition, China Agricultural University, Beijing, 100193, China.
| | - Rima Rima
- Faculty of Food Science and Nutrition, Poznan University of Life Sciences, Poznan, Poland
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25
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Van Winkle LJ, Galat V, Iannaccone PM. Lysine Deprivation during Maternal Consumption of Low-Protein Diets Could Adversely Affect Early Embryo Development and Health in Adulthood. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17155462. [PMID: 32751190 PMCID: PMC7432313 DOI: 10.3390/ijerph17155462] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023]
Abstract
The conversion of lysine to glutamate is needed for signaling in all plants and animals. In mouse embryonic stem (mES) cells, and probably their progenitors, endogenous glutamate production and signaling help maintain cellular pluripotency and proliferation, although the source of glutamate is yet to be determined. If the source of glutamate is lysine, then lysine deprivation caused by maternal low-protein diets could alter early embryo development and, consequently, the health of the offspring in adulthood. For these reasons, we measured three pertinent variables in human embryonic stem (hES) cells as a model for the inner cell masses of human blastocysts. We found that RNA encoding the alpha-aminoadipic semialdehyde synthase enzyme, which regulates glutamate production from lysine, was highly expressed in hES cells. Moreover, the mean amount of lysine consumed by hES cells was 50% greater than the mean amount of glutamate they produced, indicating that lysine is likely converted to glutamate in these cells. Finally, hES cells expressed RNA encoding at least two glutamate receptors. Since this may also be the case for hES progenitor cells in blastocysts, further studies are warranted to verify the presence of this signaling process in hES cells and to determine whether lysine deprivation alters early mammalian embryo development.
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Affiliation(s)
- Lon J. Van Winkle
- Department of Biochemistry, Midwestern University, Downers Grove, IL 60515, USA
- Department of Medical Humanities, Rocky Vista University, 8401 S. Chambers Road, Parker, CO 80134, USA
- Correspondence:
| | - Vasiliy Galat
- Department of Pathology, Northwestern University Feinberg School of Medicine, Stanley Manne Children’s Research Institute and the Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60209, USA;
| | - Philip M. Iannaccone
- Departments of Pediatrics and Pathology, Northwestern University Feinberg School of Medicine and the Lurie Children’s Hospital of Chicago, Chicago, IL 60209, USA;
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26
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Das P, Adak S, Lahiri Majumder A. Genetic Manipulation for Improved Nutritional Quality in Rice. Front Genet 2020; 11:776. [PMID: 32793287 PMCID: PMC7393646 DOI: 10.3389/fgene.2020.00776] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/30/2020] [Indexed: 01/10/2023] Open
Abstract
Food with higher nutritional value is always desired for human health. Rice is the prime staple food in more than thirty developing countries, providing at least 20% of dietary protein, 3% of dietary fat and other essential nutrients. Several factors influence the nutrient content of rice which includes agricultural practices, post-harvest processing, cultivar type as well as manipulations followed by selection through breeding and genetic means. In addition to mutation breeding, genetic engineering approach also contributed significantly for the generation of nutrition added varieties of rice in the last decade or so. In the present review, we summarize the research update on improving the nutritional characteristics of rice by using genetic engineering and mutation breeding approach. We also compare the conventional breeding techniques of rice with modern molecular breeding techniques toward the generation of nutritionally improved rice variety as compared to other cereals in areas of micronutrients and availability of essential nutrients such as folate and iron. In addition to biofortification, our focus will be on the efforts to generate low phytate in seeds, increase in essential fatty acids or addition of vitamins (as in golden rice) all leading to the achievements in rice nutrition science. The superiority of biotechnology over conventional breeding being already established, it is essential to ascertain that there are no serious negative agronomic consequences for consumers with any difference in grain size or color or texture, when a nutritionally improved variety of rice is generated through genetic engineering technology.
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27
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Sarkar D, Maranas CD. SNPeffect: identifying functional roles of SNPs using metabolic networks. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:512-531. [PMID: 32167625 PMCID: PMC9328443 DOI: 10.1111/tpj.14746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/20/2020] [Indexed: 05/04/2023]
Abstract
Genetic sources of phenotypic variation have been a focus of plant studies aimed at improving agricultural yield and understanding adaptive processes. Genome-wide association studies identify the genetic background behind a trait by examining associations between phenotypes and single-nucleotide polymorphisms (SNPs). Although such studies are common, biological interpretation of the results remains a challenge; especially due to the confounding nature of population structure and the systematic biases thus introduced. Here, we propose a complementary analysis (SNPeffect) that offers putative genotype-to-phenotype mechanistic interpretations by integrating biochemical knowledge encoded in metabolic models. SNPeffect is used to explain differential growth rate and metabolite accumulation in A. thaliana and P. trichocarpa accessions as the outcome of SNPs in enzyme-coding genes. To this end, we also constructed a genome-scale metabolic model for Populus trichocarpa, the first for a perennial woody tree. As expected, our results indicate that growth is a complex polygenic trait governed by carbon and energy partitioning. The predicted set of functional SNPs in both species are associated with experimentally characterized growth-determining genes and also suggest putative ones. Functional SNPs were found in pathways such as amino acid metabolism, nucleotide biosynthesis, and cellulose and lignin biosynthesis, in line with breeding strategies that target pathways governing carbon and energy partition.
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Affiliation(s)
- Debolina Sarkar
- Department of Chemical EngineeringPennsylvania State UniversityUniversity ParkPAUSA
| | - Costas D. Maranas
- Department of Chemical EngineeringPennsylvania State UniversityUniversity ParkPAUSA
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28
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An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism. Nat Commun 2020; 11:2931. [PMID: 32523014 PMCID: PMC7286885 DOI: 10.1038/s41467-020-16815-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/21/2020] [Indexed: 11/08/2022] Open
Abstract
Despite intensive study, plant lysine catabolism beyond the 2-oxoadipate (2OA) intermediate remains unvalidated. Recently we described a missing step in the D-lysine catabolism of Pseudomonas putida in which 2OA is converted to D-2-hydroxyglutarate (2HG) via hydroxyglutarate synthase (HglS), a DUF1338 family protein. Here we solve the structure of HglS to 1.1 Å resolution in substrate-free form and in complex with 2OA. We propose a successive decarboxylation and intramolecular hydroxylation mechanism forming 2HG in a Fe(II)- and O2-dependent manner. Specificity is mediated by a single arginine, highly conserved across most DUF1338 proteins. An Arabidopsis thaliana HglS homolog coexpresses with known lysine catabolism enzymes, and mutants show phenotypes consistent with disrupted lysine catabolism. Structural and biochemical analysis of Oryza sativa homolog FLO7 reveals identical activity to HglS despite low sequence identity. Our results suggest DUF1338-containing enzymes catalyze the same biochemical reaction, exerting the same physiological function across bacteria and eukaryotes. Hydroxyglutarate synthase (HglS) converts 2-oxoadipate to D-2- hydroxyglutarate during lysine catabolism in bacteria. Here the authors use structural and biochemical approaches to show that HglS acts via successive decarboxylation and intramolecular hydroxylation and that homologous enzymes catalyze the final step of lysine catabolism in plants.
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29
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Zhao M, Lin Y, Chen H. Improving nutritional quality of rice for human health. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1397-1413. [PMID: 31915876 DOI: 10.1007/s00122-019-03530-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 12/30/2019] [Indexed: 05/27/2023]
Abstract
This review surveys rice nutritional value, mainly focusing on breeding achievements via adoption of both genetic engineering and non-transgenic strategies to improve key nutrients associated with human health. Rice (Oryza sativa) is an essential component of the diets and livelihoods of over 3.5 billion people. Polished rice is mostly consumed as staple food, fulfilling daily energy demands and part of the protein requirement. Brown rice is comparatively more nutritious, containing more lipids, minerals, vitamins, dietary fiber, micronutrients, and bioactive compounds. In this article, we review the nutritional facts about rice including the level of γ-aminobutyric acid, resistant starch, lysine, iron, zinc, β-carotene, folate, anthocyanin, various carotenoids, and flavonoids, focusing on their synthesis and metabolism and the advances in their biofortification via adoption of both conventional and genetic engineering strategies. We conclude that besides representing a staple food, rice has the potential to become a source of various essential nutrients or bioactive compounds through appropriate genetic improvements to benefit human health and prevent certain chronic diseases. Finally, we discuss the available, non-genetically engineering strategies for the nutritional improvement of rice, including their main strengths and constraints.
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Affiliation(s)
- Mingchao Zhao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
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30
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Soba D, Ben Mariem S, Fuertes-Mendizábal T, Méndez-Espinoza AM, Gilard F, González-Murua C, Irigoyen JJ, Tcherkez G, Aranjuelo I. Metabolic Effects of Elevated CO 2 on Wheat Grain Development and Composition. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:8441-8451. [PMID: 31339045 DOI: 10.1021/acs.jafc.9b01594] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The increase in the atmospheric CO2 concentration is predicted to influence wheat production and grain quality and nutritional properties. In the present study, durum wheat (Triticum durum Desf. cv. Sula) was grown under two different CO2 (400 versus 700 μmol mol-1) concentrations to examine effects on the crop yield and grain quality at different phenological stages (from grain filling to maturity). Exposure to elevated CO2 significantly increased aboveground biomass and grain yield components. Growth at elevated CO2 diminished the elemental N content as well as protein and free amino acids, with a typical decrease in glutamine, which is the most represented amino acid in grain proteins. Such a general decrease in nitrogenous compounds was associated with altered kinetics of protein accumulation, N remobilization, and N partitioning. Our results highlight important modifications of grain metabolism that have implications for its nutritional quality.
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Affiliation(s)
- David Soba
- Instituto de Agrobiotecnología (IdAB) , Consejo Superior de Investigaciones Científicas-Gobierno de Navarra , Avenida Pamplona 123 , 31006 Mutilva , Spain
| | - Sinda Ben Mariem
- Instituto de Agrobiotecnología (IdAB) , Consejo Superior de Investigaciones Científicas-Gobierno de Navarra , Avenida Pamplona 123 , 31006 Mutilva , Spain
| | - Teresa Fuertes-Mendizábal
- Department of Plant Biology and Ecology , University of the Basque Country (UPV/EHU) , 48940 Bilbao , Spain
| | - Ana María Méndez-Espinoza
- Plant Breeding and Phenomic Center, Faculty of Agricultural Sciences , Universidad de Talca , Talca 3460000 , Chile
| | - Françoise Gilard
- Plateforme Métabolisme-Métabolome, Institut de Biologie des Plantes, CNRS UMR 8618 , Université Paris-Sud , Bâtiment 630, 91405 Orsay Cedex, France
- INRA, UMR INRA/UCBN 950 Ecophysiologie Végétale, Agronomie et Nutritions NCS, IFR 146 ICORE, Institut de Biologie Fondamentale et Appliquée , Université de Caen Basse-Normandie , 14032 Caen , France
| | - Carmen González-Murua
- Department of Plant Biology and Ecology , University of the Basque Country (UPV/EHU) , 48940 Bilbao , Spain
| | - Juan J Irigoyen
- Grupo de Fisiología del Estrés en Plantas (Departamento de Biología Ambiental), Unidad Asociada al CSIC, EEAD, Zaragoza e ICVV, Logroño, Facultades de Ciencias y Farmacia , Universidad de Navarra , Irunlarrea 1 , 31008 Pamplona , Spain
| | - Guillaume Tcherkez
- Research School of Biology, Joint College of Sciences , Australian National University , 2601 Canberra , Australian Capital Territory , Australia
| | - Iker Aranjuelo
- Instituto de Agrobiotecnología (IdAB) , Consejo Superior de Investigaciones Científicas-Gobierno de Navarra , Avenida Pamplona 123 , 31006 Mutilva , Spain
- Department of Plant Biology and Ecology , University of the Basque Country (UPV/EHU) , 48940 Bilbao , Spain
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31
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Hartmann M, Zeier J. l-lysine metabolism to N-hydroxypipecolic acid: an integral immune-activating pathway in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:5-21. [PMID: 30035374 DOI: 10.1111/tpj.14037] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/22/2018] [Accepted: 07/03/2018] [Indexed: 05/03/2023]
Abstract
l-lysine catabolic routes in plants include the saccharopine pathway to α-aminoadipate and decarboxylation of lysine to cadaverine. The current review will cover a third l-lysine metabolic pathway having a major role in plant systemic acquired resistance (SAR) to pathogen infection that was recently discovered in Arabidopsis thaliana. In this pathway, the aminotransferase AGD2-like defense response protein (ALD1) α-transaminates l-lysine and generates cyclic dehydropipecolic (DP) intermediates that are subsequently reduced to pipecolic acid (Pip) by the reductase SAR-deficient 4 (SARD4). l-pipecolic acid, which occurs ubiquitously in the plant kingdom, is further N-hydroxylated to the systemic acquired resistance (SAR)-activating metabolite N-hydroxypipecolic acid (NHP) by flavin-dependent monooxygenase1 (FMO1). N-hydroxypipecolic acid induces the expression of a set of major plant immune genes to enhance defense readiness, amplifies resistance responses, acts synergistically with the defense hormone salicylic acid, promotes the hypersensitive cell death response and primes plants for effective immune mobilization in cases of future pathogen challenge. This pathogen-inducible NHP biosynthetic pathway is activated at the transcriptional level and involves feedback amplification. Apart from FMO1, some cytochrome P450 monooxygenases involved in secondary metabolism catalyze N-hydroxylation reactions in plants. In specific taxa, pipecolic acid might also serve as a precursor in the biosynthesis of specialized natural products, leading to C-hydroxylated and otherwise modified piperidine derivatives, including indolizidine alkaloids. Finally, we show that NHP is glycosylated in Arabidopsis to form a hexose-conjugate, and then discuss open questions in Pip/NHP-related research.
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Affiliation(s)
- Michael Hartmann
- Department of Biology, Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Universitätsstraße 1, D-40225, Düsseldorf, Germany
| | - Jürgen Zeier
- Department of Biology, Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Universitätsstraße 1, D-40225, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, D-40225, Düsseldorf, Germany
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Wen W, Jin M, Li K, Liu H, Xiao Y, Zhao M, Alseekh S, Li W, de Abreu E Lima F, Brotman Y, Willmitzer L, Fernie AR, Yan J. An integrated multi-layered analysis of the metabolic networks of different tissues uncovers key genetic components of primary metabolism in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:1116-1128. [PMID: 29381266 DOI: 10.1111/tpj.13835] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 12/20/2017] [Accepted: 01/08/2018] [Indexed: 06/07/2023]
Abstract
Primary metabolism plays a pivotal role in normal plant growth, development and reproduction. As maize is a major crop worldwide, the primary metabolites produced by maize plants are of immense importance from both calorific and nutritional perspectives. Here a genome-wide association study (GWAS) of 61 primary metabolites using a maize association panel containing 513 inbred lines identified 153 significant loci associated with the level of these metabolites in four independent tissues. The genome-wide expression level of 760 genes was also linked with metabolite levels within the same tissue. On average, the genetic variants at each locus or transcriptional variance of each gene identified here were estimated to have a minor effect (4.4-7.8%) on primary metabolic variation. Thirty-six loci or genes were prioritized as being worthy of future investigation, either with regard to functional characterization or for their utility for genetic improvement. This target list includes the well-known opaque 2 (O2) and lkr/sdh genes as well as many less well-characterized genes. During our investigation of these 36 loci, we analyzed the genetic components and variations underlying the trehalose, aspartate and aromatic amino acid pathways, thereby functionally characterizing four genes involved in primary metabolism in maize.
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Affiliation(s)
- Weiwei Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
| | - Min Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kun Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingchao Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Yariv Brotman
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Lothar Willmitzer
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Blümel RC, Fischer DF, Grundler FM. Effects of exogenous amino acid applications on the plant-parasitic nematode Heterodera schachtii. NEMATOLOGY 2018. [DOI: 10.1163/15685411-00003169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
Amino acid (AA) applications have been reported to affect plant-parasitic nematodes. Here, we analysed the effects of methionine (Met), lysine (Lys), threonine (Thr), isoleucine (Ile), homoserine (Hom) and tryptophan (Trp) on the sedentary plant-parasitic nematode, Heterodera schachtii, under in vitro conditions. No AA showed direct effects on the activity of infective second-stage juveniles (J2) of H. schachtii. Soaking J2 in Lys for 24 h increased the number of developing females and reduced the number of males. Thr treatments reduced the total number of nematodes developing in the host plant. The strongest effects were observed when AA were added to the nutrient medium in a monoxenic Arabidopsis thaliana culture. Ile, Met or Thr clearly reduced the number of female nematodes developing in the host plant. These AA are direct metabolic derivatives of Hom. Direct effects on pre-infective J2 can be differentiated from effects that may involve the host plant.
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Affiliation(s)
- Roman Christopher Blümel
- 1Institute of Crop Science and Resource Conservation (INRES), Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, D-53115 Bonn, Germany
- 2Current address: Bayer Crop Science, Alfred-Nobel-Str. 50, 40789 Monheim, Germany
| | - Daniel F. Fischer
- 3Evonik Nutrition & Care GmbH, Rodenbacher Chaussee 4, 63457 Hanau-Wolfgang, Germany
| | - Florian M.W. Grundler
- 1Institute of Crop Science and Resource Conservation (INRES), Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, D-53115 Bonn, Germany
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Das A, Rushton PJ, Rohila JS. Metabolomic Profiling of Soybeans (Glycine max L.) Reveals the Importance of Sugar and Nitrogen Metabolism under Drought and Heat Stress. PLANTS (BASEL, SWITZERLAND) 2017; 6:E21. [PMID: 28587097 PMCID: PMC5489793 DOI: 10.3390/plants6020021] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/15/2017] [Accepted: 05/22/2017] [Indexed: 02/01/2023]
Abstract
Soybean is an important crop that is continually threatened by abiotic stresses, especially drought and heat stress. At molecular levels, reduced yields due to drought and heat stress can be seen as a result of alterations in metabolic homeostasis of vegetative tissues. At present an incomplete understanding of abiotic stress-associated metabolism and identification of associated metabolites remains a major gap in soybean stress research. A study with a goal to profile leaf metabolites under control conditions (28/24 °C), drought [28/24 °C, 10% volumetric water content (VWC)], and heat stress (43/35 °C) was conducted in a controlled environment. Analyses of non-targeted metabolomic data showed that in response to drought and heat stress, key metabolites (carbohydrates, amino acids, lipids, cofactors, nucleotides, peptides and secondary metabolites) were differentially accumulated in soybean leaves. The metabolites for various cellular processes, such as glycolysis, the tricarboxylic acid (TCA) cycle, the pentose phosphate pathway, and starch biosynthesis, that regulate carbohydrate metabolism, amino acid metabolism, peptide metabolism, and purine and pyrimidine biosynthesis, were found to be affected by drought as well as heat stress. Computationally based regulatory networks predicted additional compounds that address the possibility of other metabolites and metabolic pathways that could also be important for soybean under drought and heat stress conditions. Metabolomic profiling demonstrated that in soybeans, keeping up with sugar and nitrogen metabolism is of prime significance, along with phytochemical metabolism under drought and heat stress conditions.
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Affiliation(s)
- Aayudh Das
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, USA.
| | - Paul J Rushton
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
- 22nd Century Group Inc., Clarence, NY 14031, USA.
| | - Jai S Rohila
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR 72160, USA.
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Sougrakpam Y, Deswal R. Hippophae rhamnoides N-glycoproteome analysis: a small step towards sea buckthorn proteome mining. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2016; 22:473-484. [PMID: 27924120 PMCID: PMC5120047 DOI: 10.1007/s12298-016-0390-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 05/09/2023]
Abstract
Hippophae rhamnoides is a hardy shrub capable of growing under extreme environmental conditions namely, high salt, drought and cold. Its ability to grow under extreme conditions and its wide application in pharmaceutical and nutraceutical industry calls for its in-depth analysis. N-glycoproteome mining by con A affinity chromatography from seedling was attempted. The glycoproteome was resolved on first and second dimension gel electrophoresis. A total of 48 spots were detected and 10 non-redundant proteins were identified by MALDI-TOF/TOF. Arabidopsis thaliana protein disulfide isomerase-like 1-4 (ATPDIL1-4) electron transporter, protein disulphide isomerase, calreticulin 1 (CRT1), glycosyl hydrolase family 38 (GH 38) protein, phantastica, maturase k, Arabidopsis trithorax related protein 6 (ATXR 6), cysteine protease inhibitor were identified out of which ATXR 6, phantastica and putative ATPDIL1-4 electron transporter are novel glycoproteins. Calcium binding protein CRT1 was validated for its calcium binding by stains all staining. GO analysis showed involvement of GH 38 and ATXR 6 in glycan and lysine degradation pathways. This is to our knowledge the first report of glycoproteome analysis for any Elaeagnaceae member.
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Affiliation(s)
- Yaiphabi Sougrakpam
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, New Delhi, India
| | - Renu Deswal
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, New Delhi, India
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Jiang SY, Ma A, Xie L, Ramachandran S. Improving protein content and quality by over-expressing artificially synthetic fusion proteins with high lysine and threonine constituent in rice plants. Sci Rep 2016; 6:34427. [PMID: 27677708 PMCID: PMC5039639 DOI: 10.1038/srep34427] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/13/2016] [Indexed: 12/19/2022] Open
Abstract
Rice grains are rich in starch but low in protein with very low level of both lysine and threonine. Thus, it is important to further improve protein quality and quantity, especially to increase lysine and threonine content in rice grains. We artificially synthesized two new genes by fusing endogenous rice genes with lysine (K)/threonine (T) motif (TKTKK) coding sequences. They were designated as TKTKK1 and TKTKK2 and their encoded proteins consist of 73.1% and 83.5% of lysine/threonine, respectively. These two genes were under the control of 35S promoter and were independently introduced into the rice genome to generate transgenic plants. Our data showed that overexpression of TKTKK1 generated stable proteins with expected molecular weight and the transgenic rice seeds significantly increased lysine, threonine, total amino acids and crude protein content by 33.87%, 21.21%, 19.43% and 20.45%, respectively when compared with wild type control; significant improvement was also observed in transgenic rice seeds overexpressing TKTKK2. However, limited improvement in protein quality and quantity was observed in transgenic seeds carrying tandom array of these two new genes. Our data provide the basis and alternative strategy on further improving protein quality and quantity in other crops or vegetable plants by synthetic biology.
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Affiliation(s)
- Shu-Ye Jiang
- Rice Functional Genomics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore 117604, Singapore
| | - Ali Ma
- Rice Functional Genomics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore 117604, Singapore
| | - Lifen Xie
- Rice Functional Genomics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore 117604, Singapore
| | - Srinivasan Ramachandran
- Rice Functional Genomics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore 117604, Singapore
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Yang QQ, Zhang CQ, Chan ML, Zhao DS, Chen JZ, Wang Q, Li QF, Yu HX, Gu MH, Sun SSM, Liu QQ. Biofortification of rice with the essential amino acid lysine: molecular characterization, nutritional evaluation, and field performance. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4285-96. [PMID: 27252467 PMCID: PMC5301931 DOI: 10.1093/jxb/erw209] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Rice (Oryza sativa L.), a major staple crop worldwide, has limited levels of the essential amino acid lysine. We previously produced engineered rice with increased lysine content by expressing bacterial aspartate kinase and dihydrodipicolinate synthase and inhibiting rice lysine ketoglutarate reductase/saccharopine dehydrogenase activity. However, the grain quality, field performance, and integration patterns of the transgenes in these lysine-enriched lines remain unclear. In the present study, we selected several elite transgenic lines with endosperm-specific or constitutive regulation of the above key enzymes but lacking the selectable marker gene. All target transgenes were integrated into the intragenic region in the rice genome. Two pyramid transgenic lines (High Free Lysine; HFL1 and HFL2) with free lysine levels in seeds up to 25-fold that of wild type were obtained via a combination of the above two transgenic events. We observed a dramatic increase in total free amino acids and a slight increase in total protein content in both pyramid lines. Moreover, the general physicochemical properties were improved in pyramid transgenic rice, but the starch composition was not affected. Field trials indicated that the growth of HFL transgenic rice was normal, except for a slight difference in plant height and grain colour. Taken together, these findings will be useful for the potential commercialization of high-lysine transgenic rice.
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Affiliation(s)
- Qing-Qing Yang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province / Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Chang-Quan Zhang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province / Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province / Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Man-Ling Chan
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Dong-Sheng Zhao
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province / Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Jin-Zhu Chen
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province / Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Qing Wang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province / Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Qian-Feng Li
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province / Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province / Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Heng-Xiu Yu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province / Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province / Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Ming-Hong Gu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province / Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Samuel Sai-Ming Sun
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Qiao-Quan Liu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province / Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province / Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
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Galili G, Amir R, Fernie AR. The Regulation of Essential Amino Acid Synthesis and Accumulation in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:153-78. [PMID: 26735064 DOI: 10.1146/annurev-arplant-043015-112213] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Although amino acids are critical for all forms of life, only proteogenic amino acids that humans and animals cannot synthesize de novo and therefore must acquire in their diets are classified as essential. Nine amino acids-lysine, methionine, threonine, phenylalanine, tryptophan, valine, isoleucine, leucine, and histidine-fit this definition. Despite their nutritional importance, several of these amino acids are present in limiting quantities in many of the world's major crops. In recent years, a combination of reverse genetic and biochemical approaches has been used to define the genes encoding the enzymes responsible for synthesizing, degrading, and regulating these amino acids. In this review, we describe recent advances in our understanding of the metabolism of the essential amino acids, discuss approaches for enhancing their levels in plants, and appraise efforts toward their biofortification in crop plants.
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Affiliation(s)
- Gad Galili
- Department of Plant Science, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Rachel Amir
- Laboratory of Plant Science, MIGAL-Galilee Research Institute, Kiryat Shmona 11016, Israel;
| | - Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
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Domingos S, Fino J, Cardoso V, Sánchez C, Ramalho JC, Larcher R, Paulo OS, Oliveira CM, Goulao LF. Shared and divergent pathways for flower abscission are triggered by gibberellic acid and carbon starvation in seedless Vitis vinifera L. BMC PLANT BIOLOGY 2016; 16:38. [PMID: 26832927 PMCID: PMC4736245 DOI: 10.1186/s12870-016-0722-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/21/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Abscission is a highly coordinated developmental process by which plants control vegetative and reproductive organs load. Aiming at get new insights on flower abscission regulation, changes in the global transcriptome, metabolome and physiology were analyzed in 'Thompson Seedless' grapevine (Vitis vinifera L.) inflorescences, using gibberellic acid (GAc) spraying and shading as abscission stimuli, applied at bloom. RESULTS Natural flower drop rates increased from 63.1% in non-treated vines to 83% and 99% in response to GAc and shade treatments, respectively. Both treatments had a broad effect on inflorescences metabolism. Specific impacts from shade included photosynthesis inhibition, associated nutritional stress, carbon/nitrogen imbalance and cell division repression, whereas GAc spraying induced energetic metabolism simultaneously with induction of nucleotide biosynthesis and carbon metabolism, therefore, disclosing alternative mechanisms to regulate abscission. Regarding secondary metabolism, changes in flavonoid metabolism were the most represented metabolic pathways in the samples collected following GAc treatment while phenylpropanoid and stilbenoid related pathways were predominantly affected in the inflorescences by the shade treatment. However, both GAc and shade treated inflorescences revealed also shared pathways, that involved the regulation of putrescine catabolism, the repression of gibberellin biosynthesis, the induction of auxin biosynthesis and the activation of ethylene signaling pathways and antioxidant mechanisms, although often the quantitative changes occurred on specific transcripts and metabolites of the pathways. CONCLUSIONS Globally, the results suggest that chemical and environmental cues induced contrasting effects on inflorescence metabolism, triggering flower abscission by different mechanisms and pinpointing the participation of novel abscission regulators. Grapevine showed to be considered a valid model to study molecular pathways of flower abscission competence acquisition, noticeably responding to independent stimuli.
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Affiliation(s)
- Sara Domingos
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal.
- Instituto de Investigação Científica Tropical, I.P. (IICT), Lisbon, Portugal.
| | - Joana Fino
- Instituto de Investigação Científica Tropical, I.P. (IICT), Lisbon, Portugal.
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.
| | - Vânia Cardoso
- Instituto de Investigação Científica Tropical, I.P. (IICT), Lisbon, Portugal.
| | - Claudia Sánchez
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Oeiras, Portugal.
| | - José C Ramalho
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal.
- Instituto de Investigação Científica Tropical, I.P. (IICT), Lisbon, Portugal.
- GeoBioTec, Faculdade de Ciências e Tecnolgia (FCT), Universidade Nova de Lisboa (UNL), Caparica, Portugal.
| | - Roberto Larcher
- FEM-IASMA, Fondazione Edmund Mach, Istituto Agrario di San Michele all'Adige, San Michele all'Adige, TN, Italy.
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.
| | - Cristina M Oliveira
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal.
| | - Luis F Goulao
- Instituto de Investigação Científica Tropical, I.P. (IICT), Lisbon, Portugal.
- Present address: Colégio Food, Farming and Forestry, Universidade de Lisboa (ULisboa), Lisbon, Portugal.
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Chamoun R, Aliferis KA, Jabaji S. Identification of signatory secondary metabolites during mycoparasitism of Rhizoctonia solani by Stachybotrys elegans. Front Microbiol 2015; 6:353. [PMID: 25972848 PMCID: PMC4413796 DOI: 10.3389/fmicb.2015.00353] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/08/2015] [Indexed: 11/24/2022] Open
Abstract
Stachybotrys elegans is able to parasitize the fungal plant pathogen Rhizoctonia solani AG-3 following a complex and intimate interaction, which, among others, includes the production of cell wall-degrading enzymes, intracellular colonization, and expression of pathogenic process encoding genes. However, information on the metabolome level is non-existent during mycoparasitism. Here, we performed a direct-infusion mass spectrometry (DIMS) metabolomics analysis using an LTQ Orbitrap analyzer in order to detect changes in the profiles of induced secondary metabolites of both partners during this mycoparasitic interaction 4 and 5 days following its establishment. The diketopiperazine(s) (DKPs) cyclo(S-Pro-S-Leu)/cyclo(S-Pro-S-Ile), ethyl 2-phenylacetate, and 3-nitro-4-hydroxybenzoic acid were detected as the primary response of Rhizoctonia 4 days following dual-culturing with Stachybotrys, whereas only the latter metabolite was up-regulated 1 day later. On the other hand, trichothecenes and atranones were mycoparasite-derived metabolites identified during mycoparasitism 4 and 5 days following dual-culturing. All the above secondary metabolites are known to exhibit bioactivity, including fungitoxicity, and represent key elements that determine the outcome of the interaction being studied. Results could be further exploited in programs for the evaluation of the bioactivity of these metabolites per se or their chemical analogs, and/or genetic engineering programs to obtain more efficient mycoparasite strains with improved efficacy and toxicological profiles.
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Affiliation(s)
- Rony Chamoun
- Department of Plant Science, McGill University Sainte-Anne-de-Bellevue, QC, Canada
| | | | - Suha Jabaji
- Department of Plant Science, McGill University Sainte-Anne-de-Bellevue, QC, Canada
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41
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Schmidt D, Rizzi V, Gaziola SA, Medici LO, Vincze E, Kozak M, Lea PJ, Azevedo RA. Lysine metabolism in antisense C-hordein barley grains. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 87:73-83. [PMID: 25559386 DOI: 10.1016/j.plaphy.2014.12.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/23/2014] [Indexed: 06/04/2023]
Abstract
The grain proteins of barley are deficient in lysine and threonine due to their low concentrations in the major storage protein class, the hordeins, especially in the C-hordein subgroup. Previously produced antisense C-hordein transgenic barley lines have an improved amino acid composition, with increased lysine, methionine and threonine contents. The objective of the study was to investigate the possible changes in the regulation of key enzymes of the aspartate metabolic pathway and the contents of aspartate-derived amino acids in the nontransgenic line (Hordeum vulgare L. cv. Golden Promise) and five antisense C-hordein transgenic barley lines. Considering the amounts of soluble and protein-bound aspartate-derived amino acids together with the analysis of key enzymes of aspartate metabolic pathway, we suggest that the C-hordein suppression did not only alter the metabolism of at least one aspartate-derived amino acid (threonine), but major changes were also detected in the metabolism of lysine and methionine. Modifications in the activities and regulation of aspartate kinase, dihydrodipicolinate synthase and homoserine dehydrogenase were observed in most transgenic lines. Furthermore the activities of lysine α-ketoglutarate reductase and saccharopine dehydrogenase were also altered, although the extent varied among the transgenic lines.
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Affiliation(s)
- Daiana Schmidt
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba CEP 13418-900, Brazil
| | - Vanessa Rizzi
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba CEP 13418-900, Brazil
| | - Salete A Gaziola
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba CEP 13418-900, Brazil
| | - Leonardo O Medici
- Departamento de Ciências Fisiológicas, Universidade Federal Rural do Rio de Janeiro, Seropédica CEP 23890-000, Brazil
| | - Eva Vincze
- Faculty of Agricultural Sciences, Department of Genetics and Biotechnology, Research Centre Flakkebjerg, University of Aarhus, Forsoegsvej 1, DK-4200 Slagelse, Denmark
| | - Marcin Kozak
- Department of Botany, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-766 Warsaw, Poland
| | - Peter J Lea
- Lancaster Environment Centre, University of Lancaster, Lancaster LA1 4YQ, United Kingdom
| | - Ricardo A Azevedo
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba CEP 13418-900, Brazil.
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Kumar A, Dwivedi S, Singh RP, Chakrabarty D, Mallick S, Trivedi PK, Adhikari B, Tripathi RD. Evaluation of amino acid profile in contrasting arsenic accumulating rice genotypes under arsenic stress. BIOLOGIA PLANTARUM 2014; 58:733-742. [DOI: 10.1007/s10535-014-0435-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
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Pratelli R, Pilot G. Regulation of amino acid metabolic enzymes and transporters in plants. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5535-56. [PMID: 25114014 DOI: 10.1093/jxb/eru320] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Amino acids play several critical roles in plants, from providing the building blocks of proteins to being essential metabolites interacting with many branches of metabolism. They are also important molecules that shuttle organic nitrogen through the plant. Because of this central role in nitrogen metabolism, amino acid biosynthesis, degradation, and transport are tightly regulated to meet demand in response to nitrogen and carbon availability. While much is known about the feedback regulation of the branched biosynthesis pathways by the amino acids themselves, the regulation mechanisms at the transcriptional, post-transcriptional, and protein levels remain to be identified. This review focuses mainly on the current state of our understanding of the regulation of the enzymes and transporters at the transcript level. Current results describing the effect of transcription factors and protein modifications lead to a fragmental picture that hints at multiple, complex levels of regulation that control and coordinate transport and enzyme activities. It also appears that amino acid metabolism, amino acid transport, and stress signal integration can influence each other in a so-far unpredictable fashion.
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Affiliation(s)
- Réjane Pratelli
- Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24060, USA
| | - Guillaume Pilot
- Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24060, USA
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Boex-Fontvieille ERA, Gauthier PPG, Gilard F, Hodges M, Tcherkez GGB. A new anaplerotic respiratory pathway involving lysine biosynthesis in isocitrate dehydrogenase-deficient Arabidopsis mutants. THE NEW PHYTOLOGIST 2013; 199:673-82. [PMID: 23718121 DOI: 10.1111/nph.12319] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 04/07/2013] [Indexed: 05/11/2023]
Abstract
The cornerstone of carbon (C) and nitrogen (N) metabolic interactions - respiration - is presently not well understood in plant cells: the source of the key intermediate 2-oxoglutarate (2OG), to which reduced N is combined to yield glutamate and glutamine, remains somewhat unclear. We took advantage of combined mutations of NAD- and NADP-dependent isocitrate dehydrogenase activity and investigated the associated metabolic effects in Arabidopsis leaves (the major site of N assimilation in this genus), using metabolomics and (13)C-labelling techniques. We show that a substantial reduction in leaf isocitrate dehydrogenase activity did not lead to changes in the respiration efflux rate but respiratory metabolism was reorchestrated: 2OG production was supplemented by a metabolic bypass involving both lysine synthesis and degradation. Although the recycling of lysine has long been considered important in sustaining respiration, we show here that lysine neosynthesis itself participates in an alternative respiratory pathway. Lys metabolism thus contributes to explaining the metabolic flexibility of plant leaves and the effect (or the lack thereof) of respiratory mutations.
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Long X, Liu Q, Chan M, Wang Q, Sun SSM. Metabolic engineering and profiling of rice with increased lysine. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:490-501. [PMID: 23279104 DOI: 10.1111/pbi.12037] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 11/07/2012] [Accepted: 11/26/2012] [Indexed: 05/07/2023]
Abstract
Lysine (Lys) is the first limiting essential amino acid in rice, a stable food for half of the world population. Efforts, including genetic engineering, have not achieved a desirable level of Lys in rice. Here, we genetically engineered rice to increase Lys levels by expressing bacterial lysine feedback-insensitive aspartate kinase (AK) and dihydrodipicolinate synthase (DHPS) to enhance Lys biosynthesis; through RNA interference of rice lysine ketoglutaric acid reductase/saccharopine dehydropine dehydrogenase (LKR/SDH) to down-regulate its catabolism; and by combined expression of AK and DHPS and interference of LKR/SDH to achieve both metabolic effects. In these transgenic plants, free Lys levels increased up to ~12-fold in leaves and ~60-fold in seeds, substantially greater than the 2.5-fold increase in transgenic rice seeds reported by the only previous related study. To better understand the metabolic regulation of Lys accumulation in rice, metabolomic methods were employed to analyse the changes in metabolites of the Lys biosynthesis and catabolism pathways in leaves and seeds at different stages. Free Lys accumulation was mainly regulated by its biosynthesis in leaves and to a greater extent by catabolism in seeds. The transgenic plants did not show observable changes in plant growth and seed germination nor large changes in levels of asparagine (Asn) and glutamine (Gln) in leaves, which are the major amino acids transported into seeds. Although Lys was highly accumulated in leaves of certain transgenic lines, a corresponding higher Lys accumulation was not observed in seeds, suggesting that free Lys transport from leaves into seeds did not occur.
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Affiliation(s)
- Xiaohang Long
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
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Erzeel E, Van Bochaute P, Thu TT, Angenon G. Medicago truncatula dihydrodipicolinate synthase (DHDPS) enzymes display novel regulatory properties. PLANT MOLECULAR BIOLOGY 2013; 81:401-415. [PMID: 23329373 DOI: 10.1007/s11103-013-0008-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 01/04/2013] [Indexed: 06/01/2023]
Abstract
Lysine biosynthesis in plants is tightly regulated by feedback inhibition of the end product on the first enzyme of the lysine-specific branch, dihydrodipicolinate synthase (DHDPS). Three complete DHDPS coding sequences and one partial sequence were obtained in Medicago truncatula via inverse PCR. Analysis of the MtDHDPS sequences indicated the presence of isozymes (MtDHDPS2 and MtDHDPS3) with multiple amino acid substitutions on positions previously shown to be involved in feedback inhibition and of residues important for catalytic activity, possibly affecting the enzymatic properties of these isoforms. Sequences similar to MtDHDPS2 and 3 are present in Lotus japonicus and Glycine max, suggesting the existence of a specific conserved class of DHDPS genes within the Fabaceae family. The MtDHDPS genes were found by quantitative RT-PCR analysis to be expressed in an organ-specific manner in M. truncatula. All four MtDHDPS enzymes were expressed separately in Escherichia coli, revealing a strongly reduced sensitivity of the MtDHDPS2 protein to lysine feedback inhibition and a severely reduced activity of the MtDHDPS3 protein. Remarkably, MtDHDPS3 expression in Arabidopsis thaliana produced transgenic plants with a significantly increased threonine level, suggesting a dominant DHDPS inhibiting role of this isoform. This is supported by co-expression experiments in E. coli which indicate that AtDHDPS and MtDHDPS3 interact and may form hetero-oligomers with strongly reduced enzymatic activity. In conclusion, analysis of DHDPS in M. truncatula revealed the presence of unique isozymes displaying novel regulatory properties.
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Affiliation(s)
- Ellen Erzeel
- Laboratory of Plant Genetics, Institute for Molecular Biology and Biotechnology, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050, Brussels, Belgium
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Galili G, Amir R. Fortifying plants with the essential amino acids lysine and methionine to improve nutritional quality. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:211-22. [PMID: 23279001 DOI: 10.1111/pbi.12025] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/27/2012] [Accepted: 10/12/2012] [Indexed: 05/03/2023]
Abstract
Humans, as well as farm animals, cannot synthesize a number of essential amino acids, which are critical for their survival. Hence, these organisms must obtain these essential amino acids from their diets. Cereal and legume crops, which represent the major food and feed sources for humans and livestock worldwide, possess limiting levels of some of these essential amino acids, particularly Lys and Met. Extensive efforts were made to fortify crop plants with these essential amino acids using traditional breeding and mutagenesis. However, aside from some results obtained with maize, none of these approaches was successful. Therefore, additional efforts using genetic engineering approaches concentrated on increasing the synthesis and reducing the catabolism of these essential amino acids and also on the expression of recombinant proteins enriched in them. In the present review, we discuss the basic biological aspects associated with the synthesis and accumulation of these amino acids in plants and also describe recent developments associated with the fortification of crop plants with essential amino acids by genetic engineering approaches.
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Affiliation(s)
- Gad Galili
- Department of Plant Science, The Weizmann Institute of Science, Rehovot, Israel.
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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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Griffin MDW, Billakanti JM, Wason A, Keller S, Mertens HDT, Atkinson SC, Dobson RCJ, Perugini MA, Gerrard JA, Pearce FG. Characterisation of the first enzymes committed to lysine biosynthesis in Arabidopsis thaliana. PLoS One 2012; 7:e40318. [PMID: 22792278 PMCID: PMC3390394 DOI: 10.1371/journal.pone.0040318] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 06/04/2012] [Indexed: 11/19/2022] Open
Abstract
In plants, the lysine biosynthetic pathway is an attractive target for both the development of herbicides and increasing the nutritional value of crops given that lysine is a limiting amino acid in cereals. Dihydrodipicolinate synthase (DHDPS) and dihydrodipicolinate reductase (DHDPR) catalyse the first two committed steps of lysine biosynthesis. Here, we carry out for the first time a comprehensive characterisation of the structure and activity of both DHDPS and DHDPR from Arabidopsis thaliana. The A. thaliana DHDPS enzyme (At-DHDPS2) has similar activity to the bacterial form of the enzyme, but is more strongly allosterically inhibited by (S)-lysine. Structural studies of At-DHDPS2 show (S)-lysine bound at a cleft between two monomers, highlighting the allosteric site; however, unlike previous studies, binding is not accompanied by conformational changes, suggesting that binding may cause changes in protein dynamics rather than large conformation changes. DHDPR from A. thaliana (At-DHDPR2) has similar specificity for both NADH and NADPH during catalysis, and has tighter binding of substrate than has previously been reported. While all known bacterial DHDPR enzymes have a tetrameric structure, analytical ultracentrifugation, and scattering data unequivocally show that At-DHDPR2 exists as a dimer in solution. The exact arrangement of the dimeric protein is as yet unknown, but ab initio modelling of x-ray scattering data is consistent with an elongated structure in solution, which does not correspond to any of the possible dimeric pairings observed in the X-ray crystal structure of DHDPR from other organisms. This increased knowledge of the structure and function of plant lysine biosynthetic enzymes will aid future work aimed at improving primary production.
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Affiliation(s)
- Michael D. W. Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Jagan M. Billakanti
- Biomolecular Interactions Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Industrial Research Limited, Lower Hutt, New Zealand
| | - Akshita Wason
- Biomolecular Interactions Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Sabrina Keller
- Biomolecular Interactions Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Sarah C. Atkinson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Renwick C. J. Dobson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
- Biomolecular Interactions Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Matthew A. Perugini
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Juliet A. Gerrard
- Biomolecular Interactions Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Industrial Research Limited, Lower Hutt, New Zealand
| | - Frederick Grant Pearce
- Biomolecular Interactions Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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