1
|
Zhang S, Chen Z, Zhao J, Diao S, Tian L, Zhao Y, Li F, Zhu GP. Interfamily Grafted Hybrids Vitis vinifera/ Schisandra chinensis Resulted in Transcriptomic, Phenotypic, and Metabolic Changes. PLANTS (BASEL, SWITZERLAND) 2024; 13:1676. [PMID: 38931108 PMCID: PMC11207768 DOI: 10.3390/plants13121676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/26/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Long-distance transfer of genetic material and metabolites between rootstock and scions is well documented in homo-grafted hybrids but has rarely been reported in genetically-distant grafts where the rootstock and scion belong to different families. In this study, we grafted Vitis vinifera scions onto Schisandra chinensis stocks and obtained 20 vegetative hybrids, Vitis vinifera/Schisandra chinensis (Vs). After 25 years of growth, we found that the phenotypes of the leaves, internodes, and fruits of the Vs hybrids above the graft union resembled an intermediate phenotype between V. vinifera and S. chinensis, and the new traits were stable when propagated vegetatively. We further analyzed genetic differences between Vv plants and Vs hybrids using high-throughput sequencing, while metabolomes were analyzed by liquid chromatography-mass spectrometry (LC-MS). We found a total of 2113 differentially expressed genes (DEGs). GO annotation and KEGG pathway enrichment analysis showed that these DEGs enriched mainly in oxidation-reduction and metabolic processes. Seventy-nine differentially expressed miRNAs (DEMs) containing 27 known miRNAs and 52 novel miRNAs were identified. A degradation analysis detected 840 target genes corresponding to 252 miRNAs, of which 12 DEMs and their corresponding target gene expression levels were mostly negatively correlated. Furthermore, 1188 differential metabolic compounds were identified. In particular, in Vs hybrids, the abundance of the metabolites schizandrin and gomisin as the main medicinal ingredients in S. chinensis were down-regulated and up-regulated, respectively. Our data demonstrated the effects of interfamily grafts on the phenotype, transcript profile and metabolites of the scion, and also provided new insight into the genetic, phenotypic, and metabolic plasticity associated with genetically distant grafted hybrids.
Collapse
Affiliation(s)
- Shulin Zhang
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China (Z.C.)
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China (F.L.)
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China;
| | - Zhuo Chen
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China (Z.C.)
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China (F.L.)
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China;
| | - Junhui Zhao
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China (Z.C.)
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming 650223, China
| | - Songfeng Diao
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China (F.L.)
| | - Li Tian
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China;
| | - Ying Zhao
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China;
| | - Fangdong Li
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China (F.L.)
| | - Gao-Pu Zhu
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China (Z.C.)
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China (F.L.)
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China;
| |
Collapse
|
2
|
da Fonseca-Pereira P, Monteiro-Batista RDC, Araújo WL, Nunes-Nesi A. Harnessing enzyme cofactors and plant metabolism: an essential partnership. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1014-1036. [PMID: 36861364 DOI: 10.1111/tpj.16167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/18/2023] [Accepted: 02/25/2023] [Indexed: 05/31/2023]
Abstract
Cofactors are fundamental to the catalytic activity of enzymes. Additionally, because plants are a critical source of several cofactors (i.e., including their vitamin precursors) within the context of human nutrition, there have been several studies aiming to understand the metabolism of coenzymes and vitamins in plants in detail. For example, compelling evidence has been brought forth regarding the role of cofactors in plants; specifically, it is becoming increasingly clear that an adequate supply of cofactors in plants directly affects their development, metabolism, and stress responses. Here, we review the state-of-the-art knowledge on the significance of coenzymes and their precursors with regard to general plant physiology and discuss the emerging functions attributed to them. Furthermore, we discuss how our understanding of the complex relationship between cofactors and plant metabolism can be used for crop improvement.
Collapse
Affiliation(s)
- Paula da Fonseca-Pereira
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Rita de Cássia Monteiro-Batista
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Wagner L Araújo
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Adriano Nunes-Nesi
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| |
Collapse
|
3
|
Moura Dias H, Vieira AP, de Jesus EM, de Setta N, Barros G, Van Sluys MA. Functional and comparative analysis of THI1 gene in grasses with a focus on sugarcane. PeerJ 2023; 11:e14973. [PMID: 37214086 PMCID: PMC10194071 DOI: 10.7717/peerj.14973] [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: 07/14/2022] [Accepted: 02/07/2023] [Indexed: 05/24/2023] Open
Abstract
De novo synthesis of thiamine (vitamin B1) in plants depends on the action of thiamine thiazole synthase, which synthesizes the thiazole ring, and is encoded by the THI1 gene. Here, we investigated the evolution and diversity of THI1 in Poaceae, where C4 and C3 photosynthetic plants co-evolved. An ancestral duplication of THI1 is observed in Panicoideae that remains in many modern monocots, including sugarcane. In addition to the two sugarcane copies (ScTHI1-1 and ScTHI1-2), we identified ScTHI1-2 alleles showing differences in their sequence, indicating divergence between ScTHI1-2a and ScTHI1-2b. Such variations are observed only in the Saccharum complex, corroborating the phylogeny. At least five THI1 genomic environments were found in Poaceae, two in sugarcane, M. sinensis, and S. bicolor. The THI1 promoter in Poaceae is highly conserved at 300 bp upstream of the start codon ATG and has cis-regulatory elements that putatively bind to transcription factors associated with development, growth, development and biological rhythms. An experiment set to compare gene expression levels in different tissues across the sugarcane R570 life cycle showed that ScTHI1-1 was expressed mainly in leaves regardless of age. Furthermore, ScTHI1 displayed relatively high expression levels in meristem and culm, which varied with the plant age. Finally, yeast complementation studies with THI4-defective strain demonstrate that only ScTHI1-1 and ScTHI1-2b isoforms can partially restore thiamine auxotrophy, albeit at a low frequency. Taken together, the present work supports the existence of multiple origins of THI1 harboring genomic regions in Poaceae with predicted functional redundancy. In addition, it questions the contribution of the levels of the thiazole ring in C4 photosynthetic plant tissues or potentially the relevance of the THI1 protein activity.
Collapse
Affiliation(s)
| | | | | | - Nathalia de Setta
- Botanica/IB, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
- Universidade Federal do ABC, Sao Bernardo do Campo, Sao Paulo, Brazil
| | - Gesiele Barros
- Botanica/IB, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | | |
Collapse
|
4
|
Md Ahaik FA, Mohd Taufik SH, Faiqah Johari NA, Zainal Abidin AA, Balia Yusof ZN. Optimization of nucleic acid extraction and amplification of a thiamine biosynthesis gene fragment from selected Malaysian seaweeds. Genes Genet Syst 2023; 97:247-256. [PMID: 36631109 DOI: 10.1266/ggs.22-00088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Obtaining high-quality nucleic acid extracted from seaweeds is notoriously difficult due to contamination with polysaccharides and polyphenolic compounds after cell disruption. Specific methods need to be employed for RNA isolation in different seaweed species, and therefore studies of the thiamine biosynthesis pathway have been limited. Two selected Malaysian species which are highly abundant and underutilized, namely Gracilaria sp. and Padina sp., representing the red and brown seaweeds, respectively, were collected to develop optimized total RNA extraction methods. Prior to that, DNA was extracted, and amplification of the 18S rRNA gene and the THIC gene (encoding the first enzyme in the pyrimidine branch of the thiamine biosynthesis pathway) from the DNA template was successful in Gracilaria sp. only. RNA was then extracted from both seaweeds using three different existing methods, with some modifications, using cetyltrimethylammonium bromide, guanidine thiocyanate and sodium dodecyl sulphate. Methods I and III proved to be efficient for Padina sp. and Gracilaria sp., respectively, for the extraction of highly purified RNA, with A260/A280 values of 2.0 and 1.8. However, amplification of the housekeeping gene glyceraldehyde-3-phosphate dehydrogenase and the THIC gene was successful in only Gracilaria sp. cDNA derived from extracted RNA. Further modifications are required to improve the exploitation of nucleic acids from brown seaweeds, which has been proven to be difficult. This work should pave the way for molecular studies of seaweeds generally and for the elucidation, specifically, of the thiamine biosynthesis pathway.
Collapse
Affiliation(s)
- Fatin Amira Md Ahaik
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia
| | - Siti Hajar Mohd Taufik
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia
| | - Nur Asna Faiqah Johari
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia
| | | | - Zetty Norhana Balia Yusof
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia.,Aquatic Animal Health and Therapeutics Laboratory (AquaHealth), Institute of Bioscience, Universiti Putra Malaysia.,Bioprocessing and Biomanufacturing Research Complex, Universiti Putra Malaysia
| |
Collapse
|
5
|
Niu R, Zhu X, Wang L, Zhang K, Li D, Ji J, Niu L, Gao X, Luo J, Cui J. Evaluation of Hamiltonella on Aphis gossypii fitness based on life table parameters and RNA sequencing. PEST MANAGEMENT SCIENCE 2023; 79:306-314. [PMID: 36151951 DOI: 10.1002/ps.7200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 08/31/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Insect endosymbionts are widespread in nature and known to play key roles in regulating host biology. As a secondary endosymbiont, bacteria in the genus Hamiltonella help cotton aphids (Aphis gossypii) defend against parasitism by parasitoid wasps, however, the potential negative impacts of these bacteria on cotton aphid biology remain largely unclear. RESULTS This study aims to evaluate the potential impacts of Hamiltonella on the growth and development of cotton aphids based on life table parameters and RNA sequencing. The results showed that infection with Hamiltonella resulted in smaller body type and lower body weight in aphids. Compared to the control group, there were significant differences in the finite and intrinsic rates of increase and mean generation time. Furthermore, the RNA sequencing data revealed that the genes related to energy synthesis and nutrient metabolism pathways were significantly downregulated and genes related to molting and nervous system pathways were significantly upregulated in the Hamiltonella population. CONCLUSION Our results confirm that Hamiltonella retarded the growth and development of cotton aphids accompanied by the downregulation of genes related to energy synthesis and nutrient metabolism, which provides new insights into aphid-symbiont interactions and may support the development of improved aphid management strategies. © 2022 Society of Chemical Industry.
Collapse
Affiliation(s)
- Ruichang Niu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiangzhen Zhu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Li Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Kaixin Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Dongyang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jichao Ji
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lin Niu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xueke Gao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Junyu Luo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jinjie Cui
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| |
Collapse
|
6
|
Li W, Mi X, Jin X, Zhang D, Zhu G, Shang X, Zhang D, Guo W. Thiamine functions as a key activator for modulating plant health and broad-spectrum tolerance in cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:374-390. [PMID: 35506325 DOI: 10.1111/tpj.15793] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 04/23/2022] [Accepted: 05/01/2022] [Indexed: 06/14/2023]
Abstract
Global climate changes cause an increase of abiotic and biotic stresses that tremendously threaten the world's crop security. However, studies on broad-spectrum response pathways involved in biotic and abiotic stresses are relatively rare. Here, by comparing the time-dependent transcriptional changes and co-expression analysis of cotton (Gossypium hirsutum) root tissues under abiotic and biotic stress conditions, we discovered the common stress-responsive genes and stress metabolism pathways under different stresses, which included the circadian rhythm, thiamine and galactose metabolism, carotenoid, phenylpropanoid, flavonoid, and zeatin biosynthesis, and the mitogen-activated protein kinase signaling pathway. We found that thiamine metabolism was an important intersection between abiotic and biotic stresses; the key thiamine synthesis genes, GhTHIC and GhTHI1, were highly induced at the early stage of stresses. We confirmed that thiamine was crucial and necessary for cotton growth and development, and its deficiency could be recovered by exogenous thiamine supplement. Furthermore, we revealed that exogenous thiamine enhanced stress tolerance in cotton via increasing calcium signal transduction and activating downstream stress-responsive genes. Overall, our studies demonstrated that thiamine played a crucial role in the tradeoff between plant health and stress resistance. The thiamine deficiency caused by stresses could transiently induce upregulation of thiamine biosynthetic genes in vivo, while it could be totally salvaged by exogenous thiamine application, which could significantly improve cotton broad-spectrum stress tolerance and enhance plant growth and development.
Collapse
Affiliation(s)
- Weixi Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinyue Mi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuanxiang Jin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China
| | - Daiwei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China
| | - Guozhong Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoguang Shang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China
| | - Dayong Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
7
|
Chen P, Liu P, Zhang Q, Zhao L, Hao X, Liu L, Bu C, Pan Y, Zhang D, Song Y. Dynamic physiological and transcriptome changes reveal a potential relationship between the circadian clock and salt stress response in Ulmus pumila. Mol Genet Genomics 2022; 297:303-317. [PMID: 35089426 DOI: 10.1007/s00438-021-01838-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 11/13/2021] [Indexed: 11/26/2022]
Abstract
Despite the important role the circadian clock plays in numerous critical physiological responses in plants, such as hypocotyl elongation, leaf movement, stomatal opening, flowering, and stress responses, there have been no investigations into the effect of the circadian clock on physiological and transcriptional networks under salt stress. Ulmus pumila L. has been reported to tolerate 100-150 mM NaCl treatment. We measured the diurnal variation in photosynthesis and chlorophyll fluorescence parameters and performed a time-course transcriptome analysis of 2-years-old U. pumila seedlings under salt treatment to dissect the physiological regulation and potential relationship between the circadian network and the salt stress response. Seedlings in 150 mM NaCl treatment exhibited salt-induced physiological enhancement compared to the control group. A total of 7009 differentially expressed unigenes (DEGs) were identified under salt stress, of which 16 DEGs were identified as circadian rhythm-related DEGs (crDEGs). Further analysis of dynamic expression changes revealed that DEGs involved in four crucial pathways-photosynthesis, thiamine metabolism, abscisic acid synthesis and metabolism, and the hormone-MAPK signal crosstalk pathway-are closely related to the circadian clock. Finally, we constructed a co-expression network between the circadian clock and these four crucial pathways. Our results help shed light on the molecular link between the circadian network and salt stress tolerance in U. pumila.
Collapse
Affiliation(s)
- Panfei Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing, 102300, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Peng Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Quanfeng Zhang
- Hebei Academy of Forestry Sciences, No. 75, Xuefu Road, Hebei, 050072, People's Republic of China
| | - Lei Zhao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Xuri Hao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Lei Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Chenhao Bu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Yanjun Pan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Yuepeng Song
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.
| |
Collapse
|
8
|
Bizzio LN, Tieman D, Munoz PR. Branched-Chain Volatiles in Fruit: A Molecular Perspective. FRONTIERS IN PLANT SCIENCE 2022; 12:814138. [PMID: 35154212 PMCID: PMC8829073 DOI: 10.3389/fpls.2021.814138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/23/2021] [Indexed: 05/03/2023]
Abstract
Branched-chain volatiles (BCVs) constitute an important family of fruit volatile metabolites essential to the characteristic flavor and aroma profiles of many edible fruits. Yet in contrast to other groups of volatile organic compounds important to fruit flavor such as terpenoids, phenylpropanoids, and oxylipins, the molecular biology underlying BCV biosynthesis remains poorly understood. This lack of knowledge is a barrier to efforts aimed at obtaining a more comprehensive understanding of fruit flavor and aroma and the biology underlying these complex phenomena. In this review, we discuss the current state of knowledge regarding fruit BCV biosynthesis from the perspective of molecular biology. We survey the diversity of BCV compounds identified in edible fruits as well as explore various hypotheses concerning their biosynthesis. Insights from branched-chain precursor compound metabolism obtained from non-plant organisms and how they may apply to fruit BCV production are also considered, along with potential avenues for future research that might clarify unresolved questions regarding BCV metabolism in fruits.
Collapse
Affiliation(s)
- Lorenzo N. Bizzio
- Blueberry Breeding and Genomics Lab, Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
| | - Denise Tieman
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Patricio R. Munoz
- Blueberry Breeding and Genomics Lab, Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
| |
Collapse
|
9
|
Osama SK, Kerr ED, Yousif AM, Phung TK, Kelly AM, Fox GP, Schulz BL. Proteomics reveals commitment to germination in barley seeds is marked by loss of stress response proteins and mobilisation of nutrient reservoirs. J Proteomics 2021; 242:104221. [PMID: 33866056 DOI: 10.1016/j.jprot.2021.104221] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 02/06/2023]
Abstract
Germination is a critical process in the reproduction and propagation of flowering plants, and is also the key stage of industrial grain malting. Germination commences when seeds are steeped in water, followed by degradation of the endosperm cell walls, enzymatic digestion of starch and proteins to provide nutrients for the growing plant, and emergence of the radicle from the seed. Dormancy is a state where seeds fail to germinate upon steeping, but which prevents inappropriate premature germination of the seeds before harvest from the field. This can result in inefficiencies in industrial malting. We used Sequential Window Acquisition of all THeoretical ions Mass Spectrometry (SWATH-MS) proteomics to measure changes in the barley seed proteome throughout germination. We found a large number of proteins involved in desiccation tolerance and germination inhibition rapidly decreased in abundance after imbibition. This was followed by a decrease in proteins involved in lipid, protein and nutrient reservoir storage, consistent with induction and activation of systems for nutrient mobilisation to provide nutrients to the growing embryo. Dormant seeds that failed to germinate showed substantial biochemical activity distinct from that of seeds undergoing germination, with differences in sulfur metabolic enzymes, endogenous alpha-amylase/trypsin inhibitors, and histone proteins. We verified our findings with analysis of germinating barley seeds from two commercial malting facilities, demonstrating that key features of the dynamic proteome of germinating barley seeds were conserved between laboratory and industrial scales. The results provide a more detailed understanding of the changes in the barley proteome during germination and give possible target proteins for testing or to inform selective breeding to enhance germination or control dormancy. SIGNIFICANCE: Germination is critical to the reproduction and propagation of flowering plants, and in industrial malting. Dormancy, where seeds fail to germinate upon steeping, can result in inefficiencies in industrial malting. Our DIA/SWATH-MS proteomics analyses identified key changes during germination, including an initial loss of proteins involved in desiccation tolerance and germination inhibition, followed by decreases in lipid, protein and nutrient reservoir storage. These changes were consistent between laboratory and industrial malting scales, and therefore demonstrate the utility of laboratory-scale barley germination as a model system for industrial malt house processes. We also showed that dormant seeds that failed to germinate showed substantial biochemical activity distinct from that of seeds undergoing germination, consistent with dormancy being an actively regulated state. Our results provide a more detailed understanding of the changes in the barley proteome during germination and give possible target proteins for testing or to inform selective breeding to enhance germination or control dormancy.
Collapse
Affiliation(s)
- Sarah K Osama
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, Qld 4350, Australia
| | - Edward D Kerr
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia
| | - Adel M Yousif
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Sandy Bay Campus, TAS, 7005, Australia
| | - Toan K Phung
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia
| | - Alison M Kelly
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, Qld 4350, Australia; Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, Qld 4350, Australia
| | - Glen P Fox
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, Qld 4350, Australia; Department of Food Science and Technology, University of California Davis, CA 95616, USA.
| | - Benjamin L Schulz
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia.
| |
Collapse
|
10
|
Bioinformatic and experimental evidence for suicidal and catalytic plant THI4s. Biochem J 2020; 477:2055-2069. [PMID: 32441748 DOI: 10.1042/bcj20200297] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/14/2022]
Abstract
Like fungi and some prokaryotes, plants use a thiazole synthase (THI4) to make the thiazole precursor of thiamin. Fungal THI4s are suicide enzymes that destroy an essential active-site Cys residue to obtain the sulfur atom needed for thiazole formation. In contrast, certain prokaryotic THI4s have no active-site Cys, use sulfide as sulfur donor, and are truly catalytic. The presence of a conserved active-site Cys in plant THI4s and other indirect evidence implies that they are suicidal. To confirm this, we complemented the Arabidopsistz-1 mutant, which lacks THI4 activity, with a His-tagged Arabidopsis THI4 construct. LC-MS analysis of tryptic peptides of the THI4 extracted from leaves showed that the active-site Cys was predominantly in desulfurated form, consistent with THI4 having a suicide mechanism in planta. Unexpectedly, transcriptome data mining and deep proteome profiling showed that barley, wheat, and oat have both a widely expressed canonical THI4 with an active-site Cys, and a THI4-like paralog (non-Cys THI4) that has no active-site Cys and is the major type of THI4 in developing grains. Transcriptomic evidence also indicated that barley, wheat, and oat grains synthesize thiamin de novo, implying that their non-Cys THI4s synthesize thiazole. Structure modeling supported this inference, as did demonstration that non-Cys THI4s have significant capacity to complement thiazole auxotrophy in Escherichia coli. There is thus a prima facie case that non-Cys cereal THI4s, like their prokaryotic counterparts, are catalytic thiazole synthases. Bioenergetic calculations show that, relative to suicide THI4s, such enzymes could save substantial energy during the grain-filling period.
Collapse
|
11
|
Zhang S, Sun F, Wang W, Yang G, Zhang C, Wang Y, Liu S, Xi Y. Comparative transcriptome analysis provides key insights into seedling development in switchgrass ( Panicum virgatum L.). BIOTECHNOLOGY FOR BIOFUELS 2019; 12:193. [PMID: 31402932 PMCID: PMC6683553 DOI: 10.1186/s13068-019-1534-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.), a warm-season perennial C4 plant, can be used as a forage plant, a soil and water conservation plant, a windbreak plant, and as a good source of biofuels and alternative energy with low planting costs. However, switchgrass exhibits low rates of seedling development compared to other crops, which means it is typically out-competed by weeds. There is a large variation in seedling development rates among different plantlets in switchgrass, which limits its usefulness for large-scale cultivation. Little is currently known about the molecular reasons for slow seedling growth. RESULTS Characterization of the seedling development process via growth indices indicated a relatively stagnant growth stage in switchgrass. A total of 678 differentially expressed genes (DEGs) were identified from the comparison of transcriptomes from slowly developed (sd) and rapidly developed (rd) switchgrass seedlings. Gene ontology and pathway enrichment analysis showed that DEGs were enriched in diterpenoid biosynthesis, thiamine metabolism, and circadian rhythm. Transcription factor enrichment and expression analyses showed MYB-related, bHLH and NAC family genes were essential for seedling growth. The transcriptome results were consistent with those of quantitative real-time polymerase chain reaction. Then, the expression profiles of maize and switchgrass were compared during seedling leaf development. A total of 128 DEGs that play key roles in seedling growth were aligned to maize genes. Transcriptional information and physiological indices suggested that several genes involved in the circadian rhythm, thiamine metabolism, energy metabolism, gibberellic acid biosynthesis, and signal transduction played important roles in seedling development. CONCLUSIONS The seedling development process of switchgrass was characterized, and the molecular differences between slowly developed and rapidly developed seedlings were discussed. This study provides new insights into the reasons for slow seedling development in switchgrass and will be useful for the genetic improvement of switchgrass and other crops.
Collapse
Affiliation(s)
- Shumeng Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Fengli Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Weiwei Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Guoyu Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Chao Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yongfeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Shudong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yajun Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| |
Collapse
|
12
|
Yin Y, Tian L, Li X, Huang M, Liu L, Wu P, Li M, Jiang H, Wu G, Chen Y. The role of endogenous thiamine produced via THIC in root nodule symbiosis in Lotus japonicus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:311-320. [PMID: 31128701 DOI: 10.1016/j.plantsci.2019.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/11/2019] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
Thiamine is a pivotal primary metabolite which is indispensable to all organisms. Although its biosynthetic pathway has been well documented, the mechanism by which thiamine influences the legume-rhizobium symbiosis remains uncertain. Here, we used overexpressing transgenic plants, mutants and grafting experiments to investigate the roles played by thiamine in Lotus japonicus nodulation. ljthic mutants displayed lethal phenotypes and the defect could be overcome by supplementation of thiamine or by overexpression of LjTHIC. Reciprocal grafting between L. japonicus wild-type Gifu B-129 and ljthic showed that the photosynthetic products of the aerial part made a major contribution to overcoming the nodulation defect in ljthic. Overexpression of LjTHIC in Lotus japonicus (OE-LjTHIC) decreased shoot growth and increased the activity of the enzymes 2-oxoglutarate dehydrogenase and pyruvate dehydrogenase. OE-LjTHIC plants exhibited an increase in the number of infection threads and also developed more nodules, which were of smaller size but unchanged nitrogenase activity compared to the wildtype. Taken together, our results suggest that endogenous thiamine produced via LjTHIC acts as an essential nutrient provided by the host plant for rhizobial infection and nodule growth in the Lotus japonicus - rhizobium interaction.
Collapse
Affiliation(s)
- Yehu Yin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Lu Tian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xueliu Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Mingchao Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Leru Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Pingzhi Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Meiru Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Huawu Jiang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Guojiang Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Yaping Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China.
| |
Collapse
|
13
|
Feng X, Yang S, Tang K, Zhang Y, Leng J, Ma J, Wang Q, Feng X. GmPGL1, a Thiamine Thiazole Synthase, Is Required for the Biosynthesis of Thiamine in Soybean. FRONTIERS IN PLANT SCIENCE 2019; 10:1546. [PMID: 31824549 PMCID: PMC6883718 DOI: 10.3389/fpls.2019.01546] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/05/2019] [Indexed: 05/21/2023]
Abstract
Thiamine is an essential cofactor in several enzymatic reactions for all living organisms. Animals cannot synthesize thiamine and depend on their diet. Enhancing the content of thiamine is one of the most important goals of plant breeding to solve the thiamine deficiency associated with the low-thiamin staple crops. In this study, a Glycine max pale green leaf 1 (Gmpgl1) mutant was isolated from the EMS mutagenized population of soybean cultivar, Williams 82. Map-based cloning of the GmPGL1 locus revealed a single nucleotide deletion at the 292th nucleotide residue of the first exon of Glyma.10g251500 gene in Gmpgl1 mutant plant, encoding a thiamine thiazole synthase. Total thiamine contents decreased in both seedlings and seeds of the Gmpgl1 mutant. Exogenous application of thiazole restored the pale green leaf phenotype of the mutant. The deficiency of thiamine in Gmpgl1 mutant led to reduced activities of the pyruvate dehydrogenase (PDH) and pyruvate decarboxylase (PDC), and decreased contents of six amino acids as compared to that in the wild type plants. These results revealed that GmPGL1 played an essential role in thiamine thiazole biosynthesis.
Collapse
Affiliation(s)
- Xingxing Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of eography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Suxin Yang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of eography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
- *Correspondence: Suxin Yang,
| | - Kuanqiang Tang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of eography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yaohua Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of eography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Jiantian Leng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of eography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| | - Jingjing Ma
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of eography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Quan Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of eography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of eography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun, China
| |
Collapse
|
14
|
Guan Z, Wang W, Yu X, Lin W, Miao Y. Comparative Proteomic Analysis of Coregulation of CIPK14 and WHIRLY1/3 Mediated Pale Yellowing of Leaves in Arabidopsis. Int J Mol Sci 2018; 19:E2231. [PMID: 30065159 PMCID: PMC6121582 DOI: 10.3390/ijms19082231] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 07/27/2018] [Accepted: 07/27/2018] [Indexed: 01/08/2023] Open
Abstract
Pale yellowing of leaf variegation is observed in the mutant Arabidopsis lines Calcineurin B-Like-Interacting Protein Kinase14 (CIPK14) overexpression (oeCIPK14) and double-knockout WHIRLY1/WHIRLY3 (why1/3). Further, the relative distribution of WHIRLY1 (WHY1) protein between plastids and the nucleus is affected by the phosphorylation of WHY1 by CIPK14. To elucidate the coregulation of CIPK14 and WHIRLY1/WHIRLY3-mediated pale yellowing of leaves, a differential proteomic analysis was conducted between the oeCIPK14 variegated (oeCIPK14-var) line, why1/3 variegated (why1/3-var) line, and wild type (WT). More than 800 protein spots were resolved on each gel, and 67 differentially abundant proteins (DAPs) were identified by matrix-assisted laser desorption ionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF-MS). Of these 67 proteins, 34 DAPs were in the oeCIPK14-var line and 33 DAPs were in the why1/3-var line compared to the WT. Five overlapping proteins were differentially expressed in both the oeCIPK14-var and why1/3-var lines: ATP-dependent Clp protease proteolytic subunit-related protein 3 (ClpR3), Ribulose bisphosphate carboxylase large chain (RBCL), Beta-amylase 3 (BAM3), Ribosome-recycling factor (RRF), and Ribulose bisphosphate carboxylase small chain (RBCS). Bioinformatics analysis showed that most of the DAPs are involved in photosynthesis, defense and antioxidation pathways, protein metabolism, amino acid metabolism, energy metabolism, malate biosynthesis, lipid metabolism, and transcription. Thus, in the why1/3-var and oeCIPK14-var lines, there was a decrease in the photosystem parameters, including the content of chlorophyll, the photochemical efficiency of photosystem (PS II) (Fv/Fm), and electron transport rates (ETRs), but there was an increase in non-photochemical quenching (NPQ). Both mutants showed high sensitivity to intense light. Based on the annotation of the DAPs from both why1/3-var and oeCIPK14-var lines, we conclude that the CIPK14 phosphorylation-mediated WHY1 deficiency in plastids is related to the impairment of protein metabolism, leading to chloroplast dysfunction.
Collapse
Affiliation(s)
- Zhe Guan
- Center for Molecular Cell and Systems Biology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Wanzhen Wang
- Center for Molecular Cell and Systems Biology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Xingle Yu
- Center for Molecular Cell and Systems Biology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Wenfang Lin
- Center for Molecular Cell and Systems Biology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ying Miao
- Center for Molecular Cell and Systems Biology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| |
Collapse
|
15
|
Hu C, Quan C, Zhou J, Yu Q, Bai Z, Xu Z, Gao X, Li L, Zhu J, Chen R. Identification and characterization of a novel abiotic stress responsive OsTHIC gene from rice. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1457984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Changqiong Hu
- Key Laboratory of Crop Genetic Resources and Improvement, Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Changqian Quan
- Key Laboratory of Crop Genetic Resources and Improvement, Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Jingmin Zhou
- Key Laboratory of Crop Genetic Resources and Improvement, Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Qiang Yu
- Key Laboratory of Crop Genetic Resources and Improvement, Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Zhigang Bai
- Key Laboratory of Crop Genetic Resources and Improvement, Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Zhengjun Xu
- Key Laboratory of Crop Genetic Resources and Improvement, Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Xiaoling Gao
- Key Laboratory of Crop Genetic Resources and Improvement, Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Lihua Li
- Key Laboratory of Crop Genetic Resources and Improvement, Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Jianqing Zhu
- Key Laboratory of Crop Genetic Resources and Improvement, Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Rongjun Chen
- Key Laboratory of Crop Genetic Resources and Improvement, Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| |
Collapse
|
16
|
Minhas AP, Tuli R, Puri S. Pathway Editing Targets for Thiamine Biofortification in Rice Grains. FRONTIERS IN PLANT SCIENCE 2018; 9:975. [PMID: 30042775 PMCID: PMC6048418 DOI: 10.3389/fpls.2018.00975] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 06/15/2018] [Indexed: 05/21/2023]
Abstract
Thiamine deficiency is common in populations consuming polished rice as a major source of carbohydrates. Thiamine is required to synthesize thiamine pyrophosphate (TPP), an essential cofactor of enzymes of central metabolism. Its biosynthesis pathway has been partially elucidated and the effect of overexpression of a few genes such as thi1 and thiC, on thiamine accumulation in rice has been reported. Based on current knowledge, this review focuses on the potential of gene editing in metabolic engineering of thiamine biosynthesis pathway to improve thiamine in rice grains. Candidate genes, suitable for modification of the structural part to evolve more efficient versions of enzymes in the pathway, are discussed. For example, adjacent cysteine residues may be introduced in the catalytic domain of thi4 to improve the turn over activity of thiamine thiazole synthase 2. Motif specific editing to modify promoter regulatory regions of genes is discussed to modulate gene expression. Editing cis acting regulatory elements in promoter region can shift the expression of transporters and thiamine binding proteins to endosperm. This can enhance dietary availability of thiamine from rice grains. Differential transcriptomics on rice varieties with contrasting grain thiamine and functional genomic studies will identify more strategic targets for editing in future. Developing functionally enhanced foods by biofortification is a sustainable approach to make diets wholesome.
Collapse
|
17
|
Proteomics reveals key proteins participating in growth difference between fall dormant and non-dormant alfalfa in terminal buds. J Proteomics 2017; 173:126-138. [PMID: 29229487 DOI: 10.1016/j.jprot.2017.11.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/18/2017] [Accepted: 11/30/2017] [Indexed: 12/14/2022]
Abstract
To explore the molecular mechanism of growth differences between fall dormant (FD) and non-FD alfalfa, we conducted iTRAQ-based quantitative proteomics on terminal buds of Maverick (FD) and Cuf101 (non-FD) cultivars, identified differential abundance protein species (DAPS) and verified expression profiling of certain corresponding mRNA by qRT-PCR. A total of 3872 protein species were annotated. Of the 90 DAPS, 56 and 34 were respectively up- and down-accumulated in Maverick, compared to Cuf101. They were grouped into 35 functional categories and enriched in seven pathways. Of which, auxin polar transport was up-regulated, while phenylpropanoid biosynthesis, pyruvate metabolism and transportation, vitamin B1 synthesis process and flavonoid biosynthesis were down-regulated in Maverick, comparing with Cuf101. In Maverick, mRNA abundances of l-asparaginase, chalcone and stilbene synthase family protein, cinnamyl alcohol dehydrogenase-like protein, thiazole biosynthetic enzyme, pyruvate dehydrogenase E1 beta subunit, and aldo/keto reductase family oxidoreductase were significantly lower at FD than at other stages, and lower than in Cuf101. We also observed opposite mRNA profiles of thiazole biosynthetic enzyme, chalcone and stilbene synthase family protein, pyruvate dehydrogenase E1 beta subunit in both cultivars from summer to autumn. Our results suggest that these DAPS could play important roles in growth difference between FD and non-FD alfalfa. BIOLOGICAL SIGNIFICANCE Up to now, as far as we know, currently the proteins related with the growth differences between FD and non-FD alfalfa cultivars in autumn have not yet been identified in terminal buds. This study identified the protein species expressed in alfalfa terminal buds, selected differentially abundant protein species in terminal buds between Maverick (FD) and Cuf101 (non-FD) cultivars in autumn and identified the important protein species participated in the growth differences. This study lays a foundation for further investigation of the molecular mechanism of the growth differences between FD and non-FD alfalfa and the cultivation of advanced alfalfa cultivars.
Collapse
|
18
|
Hsieh WY, Liao JC, Wang HT, Hung TH, Tseng CC, Chung TY, Hsieh MH. The Arabidopsis thiamin-deficient mutant pale green1 lacks thiamin monophosphate phosphatase of the vitamin B 1 biosynthesis pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:145-157. [PMID: 28346710 DOI: 10.1111/tpj.13552] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/20/2017] [Accepted: 03/21/2017] [Indexed: 05/24/2023]
Abstract
Thiamin diphosphate (TPP, vitamin B1 ) is an essential coenzyme present in all organisms. Animals obtain TPP from their diets, but plants synthesize TPPde novo. We isolated and characterized an Arabidopsis pale green1 (pale1) mutant that contained higher concentrations of thiamin monophosphate (TMP) and less thiamin and TPP than the wild type. Supplementation with thiamin, but not the thiazole and pyrimidine precursors, rescued the mutant phenotype, indicating that the pale1 mutant is a thiamin-deficient mutant. Map-based cloning and whole-genome sequencing revealed that the pale1 mutant has a mutation in At5g32470 encoding a TMP phosphatase of the TPP biosynthesis pathway. We further confirmed that the mutation of At5g32470 is responsible for the mutant phenotypes by complementing the pale1 mutant with constructs overexpressing full-length At5g32470. Most plant TPP biosynthetic enzymes are located in the chloroplasts and cytosol, but At5g32470-GFP localized to the mitochondrion of the root, hypocotyl, mesophyll and guard cells of the 35S:At5g32470-GFP complemented plants. The subcellular localization of a functional TMP phosphatase suggests that the complete vitamin B1 biosynthesis pathway may involve the chloroplasts, mitochondria and cytosol in plants. Analysis of PALE1 promoter-uidA activity revealed that PALE1 is mainly expressed in vascular tissues of Arabidopsis seedlings. Quantitative RT-PCR analysis of TPP biosynthesis genes and genes encoding the TPP-dependent enzymes pyruvate dehydrogenase, α-ketoglutarate dehydrogenase and transketolase revealed that the transcript levels of these genes were upregulated in the pale1 mutant. These results suggest that endogenous levels of TPP may affect the expression of genes involved in TPP biosynthesis and TPP-dependent enzymes.
Collapse
Affiliation(s)
- Wei-Yu Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Jo-Chien Liao
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Hsin-Tzu Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Tzu-Huan Hung
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung, 41362, Taiwan
| | - Ching-Chih Tseng
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Tsui-Yun Chung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Ming-Hsiun Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| |
Collapse
|
19
|
Mangel N, Fudge JB, Fitzpatrick TB, Gruissem W, Vanderschuren H. Vitamin B1 diversity and characterization of biosynthesis genes in cassava. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3351-3363. [PMID: 28859374 PMCID: PMC5853225 DOI: 10.1093/jxb/erx196] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 05/22/2017] [Indexed: 05/06/2023]
Abstract
Vitamin B1, which consists of the vitamers thiamin and its phosphorylated derivatives, is an essential micronutrient for all living organisms because it is required as a metabolic cofactor in several enzymatic reactions. Genetic diversity of vitamin B1 biosynthesis and accumulation has not been investigated in major crop species other than rice and potato. We analyzed cassava germplasm for accumulation of B1 vitamers. Vitamin B1 content in leaves and roots of 41 cassava accessions showed significant variation between accessions. HPLC analyses of B1 vitamers revealed distinct profiles in cassava leaves and storage roots, with nearly equal relative levels of thiamin pyrophosphate and thiamin monophosphate in leaves, but mostly thiamin pyrophosphate in storage roots. Unusually, the cassava genome has two genes encoding the 4-amino-2-methyl-5-hydroxymethylpyrimidine phosphate synthase, THIC (MeTHIC1 and MeTHIC2), both of which carry a riboswitch in the 3'-UTR, as well as the adenylated thiazole synthase, THI1 (MeTHI1a and MeTHI1b). The THIC and THI1 genes are expressed at very low levels in storage roots compared with the accumulation of vitamin B1, indicating only limited biosynthesis de novo therein. In leaves, vitamin B1 content is negatively correlated with THIC and THI1 expression levels, suggesting post-transcriptional regulation of THIC by the riboswitch present in the 3'-UTR of the THIC mRNA and regulation of THI1 by promoter activity or alternative post-transcriptional mechanisms.
Collapse
Affiliation(s)
| | - Jared B Fudge
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | | | - Hervé Vanderschuren
- Department of Biology, ETH Zurich, Zurich, Switzerland
- AgroBioChem Department, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| |
Collapse
|
20
|
Vigna BBZ, de Oliveira FA, de Toledo-Silva G, da Silva CC, do Valle CB, de Souza AP. Leaf transcriptome of two highly divergent genotypes of Urochloa humidicola (Poaceae), a tropical polyploid forage grass adapted to acidic soils and temporary flooding areas. BMC Genomics 2016; 17:910. [PMID: 27835957 PMCID: PMC5106776 DOI: 10.1186/s12864-016-3270-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 11/05/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Urochloa humidicola (Koronivia grass) is a polyploid (6x to 9x) species that is used as forage in the tropics. Facultative apospory apomixis is present in most of the genotypes of this species, although one individual has been described as sexual. Molecular studies have been restricted to molecular marker approaches for genetic diversity estimations and linkage map construction. The objectives of the present study were to describe and compare the leaf transcriptome of two important genotypes that are highly divergent in terms of their phenotypes and reproduction modes: the sexual BH031 and the aposporous apomictic cultivar BRS Tupi. RESULTS We sequenced the leaf transcriptome of Koronivia grass using an Illumina GAIIx system, which produced 13.09 Gb of data that consisted of 163,575,526 paired-end reads between the two libraries. We de novo-assembled 76,196 transcripts with an average length of 1,152 bp and filtered 35,093 non-redundant unigenes. A similarity search against the non-redundant National Center of Biotechnology Information (NCBI) protein database returned 65 % hits. We annotated 24,133 unigenes in the Phytozome database and 14,082 unigenes in the UniProtKB/Swiss-Prot database, assigned 108,334 gene ontology terms to 17,255 unigenes and identified 5,324 unigenes in 327 known metabolic pathways. Comparisons with other grasses via a reciprocal BLAST search revealed a larger number of orthologous genes for the Panicum species. The unigenes were involved in C4 photosynthesis, lignocellulose biosynthesis and flooding stress responses. A search for functional molecular markers revealed 4,489 microsatellites and 560,298 single nucleotide polymorphisms (SNPs). A quantitative real-time PCR analysis validated the RNA-seq expression analysis and allowed for the identification of transcriptomic differences between the two evaluated genotypes. Moreover, 192 unannotated sequences were classified as containing complete open reading frames, suggesting that the new, potentially exclusive genes should be further investigated. CONCLUSION The present study represents the first whole-transcriptome sequencing of U. humidicola leaves, providing an important public information source of transcripts and functional molecular markers. The qPCR analysis indicated that the expression of certain transcripts confirmed the differential expression observed in silico, which demonstrated that RNA-seq is useful for identifying differentially expressed and unique genes. These results corroborate the findings from previous studies and suggest a hybrid origin for BH031.
Collapse
Affiliation(s)
| | - Fernanda Ancelmo de Oliveira
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Guilherme de Toledo-Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Present Address: Department of Biochemistry, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, SC Brazil
| | - Carla Cristina da Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Department of Plant Biology, Biology Institute, UNICAMP, Campinas, SP Brazil
| |
Collapse
|
21
|
Wang L, Ye, Liu H, Liu X, Wei C, Huang Y, Liu Y, Tu J. Both overexpression and suppression of an Oryza sativa NB-LRR-like gene OsLSR result in autoactivation of immune response and thiamine accumulation. Sci Rep 2016; 6:24079. [PMID: 27052628 PMCID: PMC4823736 DOI: 10.1038/srep24079] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/18/2016] [Indexed: 01/27/2023] Open
Abstract
Tight and accurate regulation of immunity and thiamine biosynthesis is critical for proper defence mechanisms and several primary metabolic cycles in plants. Although thiamine is known to enhance plant defence by priming, the mechanism by which thiamine biosynthesis responds to immune signals remains poorly understood. Here we identified a novel rice (Oryza sativa L.) NB-LRR gene via an insertion mutation, this mutant confesses a low seed setting phenotype and the corresponding genetic locus was named OsLSR (Low seed setting related). Comparing with wildtype plant, both overexpression and suppression of OsLSR lead to the autoactivation of the rice immune system and accumulation of thiamine, which result in a great fitness cost and yield penalty. Moreover, when fused with eGFP at their C terminus, two fragments, OsLSR1-178 and OsLSR464-546, localized to chloroplasts where thiamine is produced. Our result suggests that OsLSR differs from traditional NB-LRR genes. Its expression is closely related to the immune status and thiamine level in plant cells and should be maintained within a narrow range for rice growth.
Collapse
Affiliation(s)
- Liangchao Wang
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road No 866, Hangzhou, 310058, China
| | - Ye
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road No 866, Hangzhou, 310058, China
| | - Huachun Liu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road No 866, Hangzhou, 310058, China
| | - Xuejiao Liu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road No 866, Hangzhou, 310058, China
| | - Chuchu Wei
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road No 866, Hangzhou, 310058, China
| | - Yuqing Huang
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road No 866, Hangzhou, 310058, China
| | - Yujun Liu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road No 866, Hangzhou, 310058, China
| | - Jumin Tu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road No 866, Hangzhou, 310058, China
| |
Collapse
|
22
|
Li CL, Wang M, Wu XM, Chen DH, Lv HJ, Shen JL, Qiao Z, Zhang W. THI1, a Thiamine Thiazole Synthase, Interacts with Ca2+-Dependent Protein Kinase CPK33 and Modulates the S-Type Anion Channels and Stomatal Closure in Arabidopsis. PLANT PHYSIOLOGY 2016; 170:1090-104. [PMID: 26662273 PMCID: PMC4734576 DOI: 10.1104/pp.15.01649] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 12/09/2015] [Indexed: 05/06/2023]
Abstract
Thiamine is required for both plant growth and development. Here, the involvement of a thiamine thiazole synthase, THI1, has been demonstrated in both guard cell abscisic acid (ABA) signaling and the drought response in Arabidopsis (Arabidopsis thaliana). THI1 overexpressors proved to be more sensitive to ABA than the wild type with respect to both the activation of guard cell slow type anion channels and stomatal closure; this effectively reduced the rate of water loss from the plant and thereby enhanced its level of drought tolerance. A yeast two-hybrid strategy was used to screen a cDNA library from epidermal strips of leaves for THI1 regulatory factors, and identified CPK33, a Ca(2+)-dependent protein kinase, as interactor with THI1 in a plasma membrane-delimited manner. Loss-of-function cpk33 mutants were hypersensitive to ABA activation of slow type anion channels and ABA-induced stomatal closure, while the CPK33 overexpression lines showed opposite phenotypes. CPK33 kinase activity was essential for ABA-induced stomatal closure. Consistent with their contrasting regulatory role over stomatal closure, THI1 suppressed CPK33 kinase activity in vitro. Together, our data reveal a novel regulatory role of thiamine thiazole synthase to kinase activity in guard cell signaling.
Collapse
Affiliation(s)
- Chun-Long Li
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100, China
| | - Mei Wang
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100, China
| | - Xiao-Meng Wu
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100, China
| | - Dong-Hua Chen
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100, China
| | - Hong-Jun Lv
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100, China
| | - Jian-Lin Shen
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100, China
| | - Zhu Qiao
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100, China
| | - Wei Zhang
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100, China
| |
Collapse
|
23
|
Dong W, Thomas N, Ronald PC, Goyer A. Overexpression of Thiamin Biosynthesis Genes in Rice Increases Leaf and Unpolished Grain Thiamin Content But Not Resistance to Xanthomonas oryzae pv. oryzae. FRONTIERS IN PLANT SCIENCE 2016; 7:616. [PMID: 27242822 PMCID: PMC4861732 DOI: 10.3389/fpls.2016.00616] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/22/2016] [Indexed: 05/06/2023]
Abstract
Thiamin diphosphate (ThDP), also known as vitamin B1, serves as an enzymatic cofactor in glucose metabolism, the Krebs cycle, and branched-chain amino acid biosynthesis in all living organisms. Unlike plants and microorganisms, humans are not able to synthesize ThDP de novo and must obtain it from their diet. Staple crops such as rice are poor sources of thiamin. Hence, populations that mainly consume rice commonly suffer thiamin deficiency. In addition to thiamin's nutritional function, studies in rice have shown that some thiamin biosynthesis genes are involved in resistance to Xanthomonas oryzae, which causes a serious disease in rice fields. This study shows that overexpression of two thiamin biosynthesis genes, 4-methyl-5-β-hydroxyethylthiazole phosphate synthase and 4-amino-2-methyl-5-hydroxymethylpyrimidine phosphate synthase, involved in the first steps of the thiazole and pyrimidine synthesis branches, respectively, increased thiamin content up to fivefold in unpolished seeds that retain the bran. However, thiamin levels in polished seeds with removed bran were similar to those found in polished control seeds. Plants with higher accumulation of thiamin did not show enhanced resistance to X. oryzae. These results indicate that stacking of two traits can enhance thiamin accumulation in rice unpolished grain. We discuss potential roadblocks that prevent thiamin accumulation in the endosperm.
Collapse
Affiliation(s)
- Wei Dong
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
- Hermiston Agricultural Research and Extension Center, Oregon State UniversityHermiston, OR, USA
| | - Nicholas Thomas
- Department of Plant Pathology, University of California, DavisDavis, CA, USA
| | - Pamela C. Ronald
- Department of Plant Pathology, University of California, DavisDavis, CA, USA
| | - Aymeric Goyer
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
- Hermiston Agricultural Research and Extension Center, Oregon State UniversityHermiston, OR, USA
- *Correspondence: Aymeric Goyer,
| |
Collapse
|
24
|
Dong W, Stockwell VO, Goyer A. Enhancement of Thiamin Content in Arabidopsis thaliana by Metabolic Engineering. PLANT & CELL PHYSIOLOGY 2015; 56:2285-96. [PMID: 26454882 DOI: 10.1093/pcp/pcv148] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 10/02/2015] [Indexed: 05/06/2023]
Abstract
Thiamin is an essential nutrient in the human diet. Severe thiamin deficiency leads to beriberi, a lethal disease which is common in developing countries. Thiamin biofortification of staple food crops is a possible strategy to alleviate thiamin deficiency-related diseases. In plants, thiamin plays a role in the response to abiotic and biotic stresses, and data from the literature suggest that boosting thiamin content could increase resistance to stresses. Here, we tested an engineering strategy to increase thiamin content in Arabidopsis. Thiamin is composed of a thiazole ring linked to a pyrimidine ring by a methylene bridge. THI1 and THIC are the first committed steps in the synthesis of the thiazole and pyrimidine moieties, respectively. Arabidopsis plants were transformed with a vector containing the THI1-coding sequence under the control of a constitutive promoter. Total thiamin leaf content in THI1 plants was up approximately 2-fold compared with the wild type. THI1-overexpressing lines were then crossed with pre-existing THIC-overexpressing lines. Resulting THI1 × THIC plants accumulated up to 3.4- and 2.6-fold more total thiamin than wild-type plants in leaf and seeds, respectively. After inoculation with Pseudomonas syringae, THI1 × THIC plants had lower populations than the wild-type control. However, THI1 × THIC plants subjected to various abiotic stresses did not show any visible or biochemical changes compared with the wild type. We discuss the impact of engineering thiamin biosynthesis on the nutritional value of plants and their resistance to biotic and abiotic stresses.
Collapse
Affiliation(s)
- Wei Dong
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330, USA Hermiston Agricultural Research and Extension Center, Oregon State University, 2121 S First Street, Hermiston, OR 97838, USA Present address: Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Virginia O Stockwell
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330, USA
| | - Aymeric Goyer
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330, USA Hermiston Agricultural Research and Extension Center, Oregon State University, 2121 S First Street, Hermiston, OR 97838, USA
| |
Collapse
|
25
|
Schmidt R, Waschina S, Boettger-Schmidt D, Kost C, Kaleta C. Computing autocatalytic sets to unravel inconsistencies in metabolic network reconstructions. ACTA ACUST UNITED AC 2014; 31:373-81. [PMID: 25286919 DOI: 10.1093/bioinformatics/btu658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
MOTIVATION Genome-scale metabolic network reconstructions have been established as a powerful tool for the prediction of cellular phenotypes and metabolic capabilities of organisms. In recent years, the number of network reconstructions has been constantly increasing, mostly because of the availability of novel (semi-)automated procedures, which enabled the reconstruction of metabolic models based on individual genomes and their annotation. The resulting models are widely used in numerous applications. However, the accuracy and predictive power of network reconstructions are commonly limited by inherent inconsistencies and gaps. RESULTS Here we present a novel method to validate metabolic network reconstructions based on the concept of autocatalytic sets. Autocatalytic sets correspond to collections of metabolites that, besides enzymes and a growth medium, are required to produce all biomass components in a metabolic model. These autocatalytic sets are well-conserved across all domains of life, and their identification in specific genome-scale reconstructions allows us to draw conclusions about potential inconsistencies in these models. The method is capable of detecting inconsistencies, which are neglected by other gap-finding methods. We tested our method on the Model SEED, which is the largest repository for automatically generated genome-scale network reconstructions. In this way, we were able to identify a significant number of missing pathways in several of these reconstructions. Hence, the method we report represents a powerful tool to identify inconsistencies in large-scale metabolic networks. AVAILABILITY AND IMPLEMENTATION The method is available as source code on http://users.minet.uni-jena.de/∼m3kach/ASBIG/ASBIG.zip. CONTACT christoph.kaleta@uni-jena.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Ralf Schmidt
- Research Group Theoretical Systems Biology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, 07743 Jena, Department of Bioorganic Chemistry, Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology, 07745 Jena, Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, 07745 Jena and Department of Computational Biology, Institute for Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Silvio Waschina
- Research Group Theoretical Systems Biology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, 07743 Jena, Department of Bioorganic Chemistry, Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology, 07745 Jena, Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, 07745 Jena and Department of Computational Biology, Institute for Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark Research Group Theoretical Systems Biology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, 07743 Jena, Department of Bioorganic Chemistry, Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology, 07745 Jena, Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, 07745 Jena and Department of Computational Biology, Institute for Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Daniela Boettger-Schmidt
- Research Group Theoretical Systems Biology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, 07743 Jena, Department of Bioorganic Chemistry, Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology, 07745 Jena, Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, 07745 Jena and Department of Computational Biology, Institute for Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Christian Kost
- Research Group Theoretical Systems Biology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, 07743 Jena, Department of Bioorganic Chemistry, Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology, 07745 Jena, Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, 07745 Jena and Department of Computational Biology, Institute for Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Christoph Kaleta
- Research Group Theoretical Systems Biology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, 07743 Jena, Department of Bioorganic Chemistry, Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology, 07745 Jena, Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, 07745 Jena and Department of Computational Biology, Institute for Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark Research Group Theoretical Systems Biology, Faculty of Biology and Pharmacy, Friedrich Schiller University Jena, 07743 Jena, Department of Bioorganic Chemistry, Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology, 07745 Jena, Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, 07745 Jena and Department of Computational Biology, Institute for Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| |
Collapse
|
26
|
Manzetti S, Zhang J, van der Spoel D. Thiamin Function, Metabolism, Uptake, and Transport. Biochemistry 2014; 53:821-35. [DOI: 10.1021/bi401618y] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sergio Manzetti
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
for Cell and Molecular Biology, University of Uppsala, Box 596, 751
24 Uppsala, Sweden
- Fjordforsk A.S., Fresvik 6896, Norway
| | - Jin Zhang
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
for Cell and Molecular Biology, University of Uppsala, Box 596, 751
24 Uppsala, Sweden
- Department
of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - David van der Spoel
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
for Cell and Molecular Biology, University of Uppsala, Box 596, 751
24 Uppsala, Sweden
| |
Collapse
|
27
|
Guan JC, Hasnain G, Garrett TJ, Chase CD, Gregory J, Hanson AD, McCarty DR. Divisions of labor in the thiamin biosynthetic pathway among organs of maize. FRONTIERS IN PLANT SCIENCE 2014; 5:370. [PMID: 25136345 PMCID: PMC4120688 DOI: 10.3389/fpls.2014.00370] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/11/2014] [Indexed: 05/06/2023]
Abstract
The B vitamin thiamin is essential for central metabolism in all cellular organisms including plants. While plants synthesize thiamin de novo, organs vary widely in their capacities for thiamin synthesis. We use a transcriptomics approach to appraise the distribution of de novo synthesis and thiamin salvage pathways among organs of maize. We identify at least six developmental contexts in which metabolically active, non-photosynthetic organs exhibit low expression of one or both branches of the de novo thiamin biosynthetic pathway indicating a dependence on inter-cellular transport of thiamin and/or thiamin precursors. Neither the thiazole (THI4) nor pyrimidine (THIC) branches of the pathway are expressed in developing pollen implying a dependence on import of thiamin from surrounding floral and inflorescence organs. Consistent with that hypothesis, organs of the male inflorescence and flowers are shown to have high relative expression of the thiamin biosynthetic pathway and comparatively high thiamin contents. By contrast, divergent patterns of THIC and THI4 expression occur in the shoot apical meristem, embyro sac, embryo, endosperm, and root-tips suggesting that these sink organs acquire significant amounts of thiamin via salvage pathways. In the root and shoot meristems, expression of THIC in the absence of THI4 indicates a capacity for thiamin synthesis via salvage of thiazole, whereas the opposite pattern obtains in embryo and endosperm implying that seed storage organs are poised for pyrimidine salvage. Finally, stable isotope labeling experiments set an upper limit on the rate of de novo thiamin biosynthesis in maize leaf explants. Overall, the observed patterns of thiamin biosynthetic gene expression mirror the strategies for thiamin acquisition that have evolved in bacteria.
Collapse
Affiliation(s)
- Jiahn-Chou Guan
- Genetics Institute and Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of FloridaGainesville, FL, USA
| | - Ghulam Hasnain
- Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of FloridaGainesville, FL, USA
| | - Timothy J. Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of FloridaGainesville, FL, USA
| | - Christine D. Chase
- Genetics Institute and Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of FloridaGainesville, FL, USA
| | - Jesse Gregory
- Department of Food Science and Human Nutrition, Institute of Food and Agricultural Sciences, University of FloridaGainesville, FL, USA
| | - Andrew D. Hanson
- Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of FloridaGainesville, FL, USA
| | - Donald R. McCarty
- Genetics Institute and Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of FloridaGainesville, FL, USA
- *Correspondence: Donald R. McCarty, Genetics Institute and Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, PO 110690, Gainesville, FL 32611, USA e-mail:
| |
Collapse
|
28
|
Sun C, Wang L, Hu D, Riquicho ARM, Liu T, Hou X, Li Y. Proteomic analysis of non-heading Chinese cabbage infected with Hyaloperonospora parasitica. J Proteomics 2013; 98:15-30. [PMID: 24334100 DOI: 10.1016/j.jprot.2013.11.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 11/24/2013] [Accepted: 11/29/2013] [Indexed: 12/29/2022]
Abstract
UNLABELLED Downy mildew is a serious fungal disease in non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino) that is caused by Hyaloperonospora parasitica, which infects members of the Brassicaceae family. For breeding improvement, researchers must understand the defence mechanisms employed by non-heading Chinese cabbage to combat H. parasitica infection. Using 2-DE protein analysis, we compared the proteomes from leaves of non-heading Chinese cabbage seedlings that were infected with H. parasitica or that were only treated with water at different time points post-infection. By MS analysis, 91 protein spots with significant differences in abundance (>2-fold, p<0.05) were identified in mock- and H. parasitica-inoculated leaves. Next, a resistance strategy for incompatible interactions was proposed. This network consisted of several functional components, including enhanced ethylene biosynthesis and energy supply, balanced ROS production and scavenging, accelerated protein metabolism and photorespiratory, reduced photosynthesis, and induced photosystem repair. These findings increase our knowledge of incompatible interactions between plants and pathogens and also provide new insight regarding the function of plant molecular processes, which should assist in the discovery of new strategies for pathogen control. BIOLOGICAL SIGNIFICANCE This study reported the proteomic analysis of the incompatible interactions between non-heading Chinese cabbage and downy mildew using 2-DE and MS. In total, 91 protein spots that were related to the resistance response were identified. These proteins were assigned to different functional categories, such as amino acid and carbohydrate metabolism, photosynthesis and photorespiration, protein metabolism, signal transduction, redox homeostasis, and ethylene biosynthesis. Meanwhile, several key proteins were determined to be associated with ethylene signalling, ROS scavenging and resistance-related proteins. Consistent with these results, the expression of ethylene biosynthesis genes and response genes, as well as the activity of antioxidant enzymes, increased after inoculation. These findings provide new insight for further understanding the molecular mechanisms of plant resistance.
Collapse
Affiliation(s)
- Chengzhen Sun
- Horticultural Department, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing 210095, China; Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing 210095, China
| | - Li Wang
- Horticultural Department, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing 210095, China; Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing 210095, China
| | - Die Hu
- Horticultural Department, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing 210095, China; Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing 210095, China
| | - Ali Ramuli Maquina Riquicho
- Horticultural Department, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing 210095, China; Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing 210095, China
| | - Tongkun Liu
- Horticultural Department, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing 210095, China; Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing 210095, China
| | - Xilin Hou
- Horticultural Department, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing 210095, China; Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing 210095, China
| | - Ying Li
- Horticultural Department, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing 210095, China; Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing 210095, China.
| |
Collapse
|
29
|
Downs GS, Bi YM, Colasanti J, Wu W, Chen X, Zhu T, Rothstein SJ, Lukens LN. A developmental transcriptional network for maize defines coexpression modules. PLANT PHYSIOLOGY 2013; 161:1830-43. [PMID: 23388120 PMCID: PMC3613459 DOI: 10.1104/pp.112.213231] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Here, we present a genome-wide overview of transcriptional circuits in the agriculturally significant crop species maize (Zea mays). We examined transcript abundance data at 50 developmental stages, from embryogenesis to senescence, for 34,876 gene models and classified genes into 24 robust coexpression modules. Modules were strongly associated with tissue types and related biological processes. Sixteen of the 24 modules (67%) have preferential transcript abundance within specific tissues. One-third of modules had an absence of gene expression in specific tissues. Genes within a number of modules also correlated with the developmental age of tissues. Coexpression of genes is likely due to transcriptional control. For a number of modules, key genes involved in transcriptional control have expression profiles that mimic the expression profiles of module genes, although the expression of transcriptional control genes is not unusually representative of module gene expression. Known regulatory motifs are enriched in several modules. Finally, of the 13 network modules with more than 200 genes, three contain genes that are notably clustered (P < 0.05) within the genome. This work, based on a carefully selected set of major tissues representing diverse stages of maize development, demonstrates the remarkable power of transcript-level coexpression networks to identify underlying biological processes and their molecular components.
Collapse
|
30
|
Bocobza SE, Malitsky S, Araújo WL, Nunes-Nesi A, Meir S, Shapira M, Fernie AR, Aharoni A. Orchestration of thiamin biosynthesis and central metabolism by combined action of the thiamin pyrophosphate riboswitch and the circadian clock in Arabidopsis. THE PLANT CELL 2013; 25:288-307. [PMID: 23341335 PMCID: PMC3584542 DOI: 10.1105/tpc.112.106385] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 12/13/2012] [Accepted: 12/30/2012] [Indexed: 05/18/2023]
Abstract
Riboswitches are natural RNA elements that posttranscriptionally regulate gene expression by binding small molecules and thereby autonomously control intracellular levels of these metabolites. Although riboswitch-based mechanisms have been examined extensively, the integration of their activity with global physiology and metabolism has been largely overlooked. Here, we explored the regulation of thiamin biosynthesis and the consequences of thiamin pyrophosphate riboswitch deficiency on metabolism in Arabidopsis thaliana. Our results show that thiamin biosynthesis is largely regulated by the circadian clock via the activity of the THIAMIN C SYNTHASE (THIC) promoter, while the riboswitch located at the 3' untranslated region of this gene controls overall thiamin biosynthesis. Surprisingly, the results also indicate that the rate of thiamin biosynthesis directs the activity of thiamin-requiring enzymes and consecutively determines the rate of carbohydrate oxidation via the tricarboxylic acid cycle and pentose-phosphate pathway. Our model suggests that in Arabidopsis, the THIC promoter and the thiamin-pyrophosphate riboswitch act simultaneously to tightly regulate thiamin biosynthesis in a circadian manner and consequently sense and control vital points of core cellular metabolism.
Collapse
Affiliation(s)
- Samuel E. Bocobza
- Department of Plant Sciences, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Sergey Malitsky
- Department of Plant Sciences, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Wagner L. Araújo
- Max-Planck-Institut fur Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
| | - Adriano Nunes-Nesi
- Max-Planck-Institut fur Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
| | - Sagit Meir
- Department of Plant Sciences, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Michal Shapira
- Department of Life Sciences, Ben Gurion University at the Negev, 84105 Beer Sheva, Israel
| | - Alisdair R. Fernie
- Max-Planck-Institut fur Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, 76100 Rehovot, Israel
- Address correspondence to
| |
Collapse
|
31
|
|
32
|
Frelin O, Agrimi G, Laera VL, Castegna A, Richardson LGL, Mullen RT, Lerma-Ortiz C, Palmieri F, Hanson AD. Identification of mitochondrial thiamin diphosphate carriers from Arabidopsis and maize. Funct Integr Genomics 2012; 12:317-26. [DOI: 10.1007/s10142-012-0273-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 02/17/2012] [Accepted: 03/02/2012] [Indexed: 10/28/2022]
|
33
|
Rapala-Kozik M, Wolak N, Kujda M, Banas AK. The upregulation of thiamine (vitamin B1) biosynthesis in Arabidopsis thaliana seedlings under salt and osmotic stress conditions is mediated by abscisic acid at the early stages of this stress response. BMC PLANT BIOLOGY 2012; 12:2. [PMID: 22214485 PMCID: PMC3261115 DOI: 10.1186/1471-2229-12-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Accepted: 01/03/2012] [Indexed: 05/04/2023]
Abstract
BACKGROUND Recent reports suggest that vitamin B1 (thiamine) participates in the processes underlying plant adaptations to certain types of abiotic and biotic stress, mainly oxidative stress. Most of the genes coding for enzymes involved in thiamine biosynthesis in Arabidopsis thaliana have been identified. In our present study, we examined the expression of thiamine biosynthetic genes, of genes encoding thiamine diphosphate-dependent enzymes and the levels of thiamine compounds during the early (sensing) and late (adaptation) responses of Arabidopsis seedlings to oxidative, salinity and osmotic stress. The possible roles of plant hormones in the regulation of the thiamine contribution to stress responses were also explored. RESULTS The expression of Arabidopsis genes involved in the thiamine diphosphate biosynthesis pathway, including that of THI1, THIC, TH1 and TPK, was analyzed for 48 h in seedlings subjected to NaCl or sorbitol treatment. These genes were found to be predominantly up-regulated in the early phase (2-6 h) of the stress response. The changes in these gene transcript levels were further found to correlate with increases in thiamine and its diphosphate ester content in seedlings, as well as with the enhancement of gene expression for enzymes which require thiamine diphosphate as a cofactor, mainly α-ketoglutarate dehydrogenase, pyruvate dehydrogenase and transketolase. In the case of the phytohormones including the salicylic, jasmonic and abscisic acids which are known to be involved in plant stress responses, only abscisic acid was found to significantly influence the expression of thiamine biosynthetic genes, the thiamine diphosphate levels, as well as the expression of genes coding for main thiamine diphosphate-dependent enzymes. Using Arabidopsis mutant plants defective in abscisic acid production, we demonstrate that this phytohormone is important in the regulation of THI1 and THIC gene expression during salt stress but that the regulatory mechanisms underlying the osmotic stress response are more complex. CONCLUSIONS On the basis of the obtained results and earlier reported data, a general model is proposed for the involvement of the biosynthesis of thiamine compounds and thiamine diphosphate-dependent enzymes in abiotic stress sensing and adaptation processes in plants. A possible regulatory role of abscisic acid in the stress sensing phase is also suggested by these data.
Collapse
Affiliation(s)
- Maria Rapala-Kozik
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, Poland
| | - Natalia Wolak
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, Poland
| | - Marta Kujda
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, Poland
| | - Agnieszka K Banas
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, Poland
| |
Collapse
|
34
|
Kolesiński P, Piechota J, Szczepaniak A. Initial characteristics of RbcX proteins from Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2011; 77:447-59. [PMID: 21922322 PMCID: PMC3195260 DOI: 10.1007/s11103-011-9823-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 08/24/2011] [Indexed: 05/03/2023]
Abstract
Form I of Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) is composed of eight large (RbcL) and eight small (RbcS) subunits. Assembly of these subunits into a functional holoenzyme requires the assistance of additional assembly factors. One such factor is RbcX, which has been demonstrated to act as a chaperone in the assembly of most cyanobacterial Rubisco complexes expressed in heterologous system established in Escherichia coli cells. Analysis of Arabidopsis thaliana genomic sequence revealed the presence of two genes encoding putative homologues of cyanobacterial RbcX protein: AtRbcX1 (At4G04330) and AtRbcX2 (At5G19855). In general, both RbcX homologues seem to have the same function which is chaperone activity during Rubisco biogenesis. However, detailed analysis revealed slight differences between them. AtRbcX2 is localized in the stromal fraction of chloroplasts whereas AtRbcX1 was found in the insoluble fraction corresponding with thylakoid membranes. Search for putative "partners" using mass spectrometry analysis suggested that apart from binding to RbcL, AtRbcX1 may also interact with β subunit of chloroplast ATP synthase. Quantitative RT-PCR analysis of AtRbcX1 and AtRbcX2 expression under various stress conditions indicated that AtRbcX2 is transcribed at a relatively stable level, while the transcription level of AtRbcX1 varies significantly. In addition, we present the attempts to elucidate the secondary structure of AtRbcX proteins using CD spectroscopy. Presented results are the first known approach to elucidate the role of RbcX proteins in Rubisco assembly in higher plants.
Collapse
Affiliation(s)
- Piotr Kolesiński
- Laboratory of Biophysics, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - Janusz Piechota
- Laboratory of Cellular Molecular Biology, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - Andrzej Szczepaniak
- Laboratory of Biophysics, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| |
Collapse
|
35
|
Zhao W, Cheng X, Huang Z, Fan H, Wu H, Ling HQ. Tomato LeTHIC is an Fe-Requiring HMP-P Synthase Involved in Thiamine Synthesis and Regulated by Multiple Factors. ACTA ACUST UNITED AC 2011; 52:967-82. [DOI: 10.1093/pcp/pcr048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
36
|
Woodward JB, Abeydeera ND, Paul D, Phillips K, Rapala-Kozik M, Freeling M, Begley TP, Ealick SE, McSteen P, Scanlon MJ. A maize thiamine auxotroph is defective in shoot meristem maintenance. THE PLANT CELL 2010; 22:3305-17. [PMID: 20971897 PMCID: PMC2990124 DOI: 10.1105/tpc.110.077776] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 08/27/2010] [Accepted: 09/25/2010] [Indexed: 05/18/2023]
Abstract
Plant shoots undergo organogenesis throughout their life cycle via the perpetuation of stem cell pools called shoot apical meristems (SAMs). SAM maintenance requires the coordinated equilibrium between stem cell division and differentiation and is regulated by integrated networks of gene expression, hormonal signaling, and metabolite sensing. Here, we show that the maize (Zea mays) mutant bladekiller1-R (blk1-R) is defective in leaf blade development and meristem maintenance and exhibits a progressive reduction in SAM size that results in premature shoot abortion. Molecular markers for stem cell maintenance and organ initiation reveal that both of these meristematic functions are progressively compromised in blk1-R mutants, especially in the inflorescence and floral meristems. Positional cloning of blk1-R identified a predicted missense mutation in a highly conserved amino acid encoded by thiamine biosynthesis2 (thi2). Consistent with chromosome dosage studies suggesting that blk1-R is a null mutation, biochemical analyses confirm that the wild-type THI2 enzyme copurifies with a thiazole precursor to thiamine, whereas the mutant enzyme does not. Heterologous expression studies confirm that THI2 is targeted to chloroplasts. All blk1-R mutant phenotypes are rescued by exogenous thiamine supplementation, suggesting that blk1-R is a thiamine auxotroph. These results provide insight into the role of metabolic cofactors, such as thiamine, during the proliferation of stem and initial cell populations.
Collapse
Affiliation(s)
- John B. Woodward
- Department of Plant Biology, Cornell University, Ithaca, New York 14853
| | | | - Debamita Paul
- Department of Chemistry, Cornell University, Ithaca, New York 14853
| | - Kimberly Phillips
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Maria Rapala-Kozik
- Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow 30-387, Poland
| | - Michael Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94704
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77842
| | - Steven E. Ealick
- Department of Chemistry, Cornell University, Ithaca, New York 14853
| | - Paula McSteen
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Michael J. Scanlon
- Department of Plant Biology, Cornell University, Ithaca, New York 14853
- Address correspondence to
| |
Collapse
|
37
|
Abstract
Germinated brown rice (GBR) of two popular Thailand varieties, Khao Dawk Mali 105 (KDML 105) and Chainat 1, with improved nutritional composition, was obtained by optimizing water soaking conditions. Different water pH (3, 4, 6 and 8), temperatures (25 °C, 35 °C and 45 °C), and soaking times (12 and 24 h) were tested. Using the response surface methodology (RSM), the best condition for producing GBR of both varieties was soaking in water with pH 6 and temperature of 35 °C for 24 h. It caused a 4- to 5-fold increase in gamma-amino butyric acid (GABA) content which, together with protein and lipid contents, were highest among treatments. Intermediate levels of thiamine (vitamin B1) and phytic acid (IP6) were obtained. In GBR of KDML 105 variety, GABA, vitamin B1 and IP6 contents were 16.48, 0.526 and 501.06 mg/100 g, respectively, while protein and lipid contents were 10.50% and 4.00%, respectively. For Chainat 1 variety, GABA, vitamin B1 and IP6 contents were 14.50, 0.436 and 486.03 mg/100 g, respectively, while protein and lipid contents were 9.80% and 3.99%, respectively. Carbohydrate and amylose contents differed by only less than 1-2% among treatments. Supplemental aeration during water soaking decreased GABA, protein and lipid contents, but increased vitamin B1 and IP6 contents in both varieties. Furthermore, cooked GBR of both varieties had softer texture than cooked ordinary brown rice.
Collapse
|
38
|
Rodriguez MCS, Edsgärd D, Hussain SS, Alquezar D, Rasmussen M, Gilbert T, Nielsen BH, Bartels D, Mundy J. Transcriptomes of the desiccation-tolerant resurrection plant Craterostigma plantagineum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 63:212-228. [PMID: 20444235 DOI: 10.1111/j.1365-313x.2010.04243.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Studies of the resurrection plant Craterostigma plantagineum have revealed some of the mechanisms which these desiccation-tolerant plants use to survive environments with extreme dehydration and restricted seasonal water. Most resurrection plants are polyploid with large genomes, which has hindered efforts to obtain whole genome sequences and perform mutational analysis. However, the application of deep sequencing technologies to transcriptomics now permits large-scale analyses of gene expression patterns despite the lack of a reference genome. Here we use pyro-sequencing to characterize the transcriptomes of C. plantagineum leaves at four stages of dehydration and rehydration. This reveals that genes involved in several pathways, such as those required for vitamin K and thiamin biosynthesis, are tightly regulated at the level of gene expression. Our analysis also provides a comprehensive picture of the array of cellular responses controlled by gene expression that allow resurrection plants to survive desiccation.
Collapse
Affiliation(s)
| | - Daniel Edsgärd
- Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, 2800 Lyngby, Denmark
| | - Syed S Hussain
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee 1, D-53115 Bonn, Germany
| | - David Alquezar
- Department of Biology, University of Copenhagen, Ole Maaloes vej. 5, 2200, Copenhagen, Denmark
| | - Morten Rasmussen
- Department of Biology, University of Copenhagen, Ole Maaloes vej. 5, 2200, Copenhagen, Denmark
| | - Thomas Gilbert
- Department of Biology, University of Copenhagen, Ole Maaloes vej. 5, 2200, Copenhagen, Denmark
| | - Bjørn H Nielsen
- Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, 2800 Lyngby, Denmark
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee 1, D-53115 Bonn, Germany
| | - John Mundy
- Department of Biology, University of Copenhagen, Ole Maaloes vej. 5, 2200, Copenhagen, Denmark
| |
Collapse
|
39
|
Huang S, Taylor NL, Narsai R, Eubel H, Whelan J, Millar AH. Experimental analysis of the rice mitochondrial proteome, its biogenesis, and heterogeneity. PLANT PHYSIOLOGY 2009; 149:719-34. [PMID: 19010998 PMCID: PMC2633852 DOI: 10.1104/pp.108.131300] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Accepted: 11/12/2008] [Indexed: 05/19/2023]
Abstract
Mitochondria in rice (Oryza sativa) are vital in expanding our understanding of the cellular response to reoxygenation of tissues after anaerobiosis, the crossroads of carbon and nitrogen metabolism, and the role of respiratory energy generation in cytoplasmic male sterility. We have combined density gradient and surface charge purification techniques with proteomics to provide an in-depth proteome of rice shoot mitochondria covering both soluble and integral membrane proteins. Quantitative comparisons of mitochondria purified by density gradients and after further surface charge purification have been used to ensure that the proteins identified copurify with mitochondria and to remove contaminants from the analysis. This rigorous approach to defining a subcellular proteome has yielded 322 nonredundant rice proteins and highlighted contaminants in previously reported rice mitochondrial proteomes. Comparative analysis with the Arabidopsis (Arabidopsis thaliana) mitochondrial proteome reveals conservation of a broad range of known and unknown function proteins in plant mitochondria, with only approximately 20% not having a clear homolog in the Arabidopsis mitochondrial proteome. As in Arabidopsis, only approximately 60% of the rice mitochondrial proteome is predictable using current organelle-targeting prediction tools. Use of the rice protein data set to explore rice transcript data provided insights into rice mitochondrial biogenesis during seed germination, leaf development, and heterogeneity in the expression of nucleus-encoded mitochondrial components in different rice tissues. Highlights include the identification of components involved in thiamine synthesis, evidence for coexpressed and unregulated expression of specific components of protein complexes, a selective anther-enhanced subclass of the decarboxylating segment of the tricarboxylic acid cycle, the differential expression of DNA and RNA replication components, and enhanced expression of specific metabolic components in photosynthetic tissues.
Collapse
Affiliation(s)
- Shaobai Huang
- Australian Research Council Centre of Excellence in Plant Energy Biology, M316, University of Western Australia, Crawley, 6009 Western Australia, Australia
| | | | | | | | | | | |
Collapse
|
40
|
Case study in systematic modelling: thiamine uptake in the yeast Saccharomyces cerevisiae. Essays Biochem 2008; 45:135-46. [PMID: 18793129 DOI: 10.1042/bse0450135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In recent years, with important advances in molecular biology, experimental and measurement technologies, it has become possible to generate the quantitative data that are needed for building mathematical models of complex biochemical processes. Cartoon-like diagrams of biological pathways can be turned into dynamical models, allowing simulation and analysis to gain an insight into the underlying control mechanisms and the behaviour of the overall system. This kind of system-level understanding has not been reachable from the study of the components of pathways in isolation. However, mathematical modelling does not only integrate the available knowledge about a certain system with newly generated experimental results. During the process of modelling, questions need to be addressed that lead to an increased quantitative understanding of the system. Models can be used to optimize experimental approaches and protocols and to test different hypotheses about the underlying biological mechanisms. Finally, a validated mathematical model can be used to perform in silico experiments that might be hard or impossible to do in the laboratory. In this chapter we present a case study of a systematic modelling approach applied to the thiamine uptake system of the yeast Saccharomyces cerevisiae. This example is part of our broader effort to model the whole of thiamine metabolism in yeast, which involves several additional processes such as thiamine utilization, biosynthesis and gene regulation. Our main goal is to describe how systematic modelling has improved the knowledge about the system under study.
Collapse
|
41
|
Abstract
Thiamine (vitamin B(1)) is an essential compound for organisms. It contains a pyrimidine ring structure and a thiazole ring structure. These two moieties of thiamine are synthesized independently and then coupled together. Here we report the molecular characterization of AtTHIC, which is involved in thiamine biosynthesis in Arabidopsis. AtTHIC is similar to Escherichia coli ThiC, which is involved in pyrimidine biosynthesis in prokaryotes. Heterologous expression of AtTHIC could functionally complement the thiC knock-out mutant of E. coli. Downregulation of AtTHIC expression by T-DNA insertion at its promoter region resulted in a drastic reduction of thiamine content in plants and the knock-down mutant thic1 showed albino (white leaves) and lethal phenotypes under the normal culture conditions. The thic1 mutant could be rescued by supplementation of thiamine and its defect functions could be complemented by expression of AtTHIC cDNA. Transient expression analysis revealed that the AtTHIC protein targets plastids and chloroplasts. AtTHIC was strongly expressed in leaves, flowers and siliques and the transcription of AtTHIC was downregulated by extrinsic thiamine. In conclusion, AtTHIC is a gene involved in pyrimidine synthesis in the thiamine biosynthesis pathway of Arabidopsis, and our results provide some new clues for elucidating the pathway of thiamine biosynthesis in plants.
Collapse
|
42
|
Dupont FM. Metabolic pathways of the wheat (Triticum aestivum) endosperm amyloplast revealed by proteomics. BMC PLANT BIOLOGY 2008; 8:39. [PMID: 18419817 PMCID: PMC2383896 DOI: 10.1186/1471-2229-8-39] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Accepted: 04/17/2008] [Indexed: 05/20/2023]
Abstract
BACKGROUND By definition, amyloplasts are plastids specialized for starch production. However, a proteomic study of amyloplasts isolated from wheat (Triticum aestivum Butte 86) endosperm at 10 days after anthesis (DPA) detected enzymes from many other metabolic and biosynthetic pathways. To better understand the role of amyloplasts in food production, the data from that study were evaluated in detail and an amyloplast metabolic map was outlined. RESULTS Analysis of 288 proteins detected in an amyloplast preparation predicted that 178 were amyloplast proteins. Criteria included homology with known plastid proteins, prediction of a plastid transit peptide for the wheat gene product or a close homolog, known plastid location of the pathway, and predicted plastid location for other members of the same pathway. Of these, 135 enzymes were arranged into 18 pathways for carbohydrate, lipid, amino acid, nucleic acid and other biosynthetic processes that are critical for grain-fill. Functions of the other proteins are also discussed. CONCLUSION The pathways outlined in this paper suggest that amyloplasts play a central role in endosperm metabolism. The interacting effects of genetics and environment on starch and protein production may be mediated in part by regulatory mechanisms within this organelle.
Collapse
Affiliation(s)
- Frances M Dupont
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, 800 Buchanan Street, Albany, CA 94710K, USA.
| |
Collapse
|
43
|
Ruiz-Roldán C, Puerto-Galán L, Roa J, Castro A, Di Pietro A, Roncero MIG, Hera C. The Fusarium oxysporum sti35 gene functions in thiamine biosynthesis and oxidative stress response. Fungal Genet Biol 2008; 45:6-16. [DOI: 10.1016/j.fgb.2007.09.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Revised: 06/27/2007] [Accepted: 09/12/2007] [Indexed: 01/07/2023]
|
44
|
Rapala-Kozik M, Kowalska E, Ostrowska K. Modulation of thiamine metabolism in Zea mays seedlings under conditions of abiotic stress. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:4133-43. [PMID: 18940932 DOI: 10.1093/jxb/ern253] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The responses of plants to abiotic stress involve the up-regulation of numerous metabolic pathways, including several major routes that engage thiamine diphosphate (TDP)-dependent enzymes. This suggests that the metabolism of thiamine (vitamin B1) and its phosphate esters in plants may be modulated under various stress conditions. In the present study, Zea mays seedlings were used as a model system to analyse for any relation between the plant response to abiotic stress and the properties of thiamine biosynthesis and activation. Conditions of drought, high salt, and oxidative stress were induced by polyethylene glycol, sodium chloride, and hydrogen peroxide, respectively. The expected increases in the abscisic acid levels and in the activities of antioxidant enzymes including catalase, ascorbate peroxidase, and glutathione reductase were found under each stress condition. The total thiamine compound content in the maize seedling leaves increased under each stress condition applied, with the strongest effects on these levels observed under the oxidative stress treatment. This increase was also found to be associated with changes in the relative distribution of free thiamine, thiamine monophosphate (TMP), and TDP. Surprisingly, the activity of the thiamine synthesizing enzyme, TMP synthase, responded poorly to abiotic stress, in contrast to the significant enhancement found for the activities of the TDP synthesizing enzyme, thiamine pyrophosphokinase, and a number of the TDP/TMP phosphatases. Finally, a moderate increase in the activity of transketolase, one of the major TDP-dependent enzymes, was detectable under conditions of salt and oxidative stress. These findings suggest a role of thiamine metabolism in the plant response to environmental stress.
Collapse
Affiliation(s)
- Maria Rapala-Kozik
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
| | | | | |
Collapse
|
45
|
Rapala-Kozik M, Olczak M, Ostrowska K, Starosta A, Kozik A. Molecular characterization of the thi3 gene involved in thiamine biosynthesis in Zea mays: cDNA sequence and enzymatic and structural properties of the recombinant bifunctional protein with 4-amino-5-hydroxymethyl-2-methylpyrimidine (phosphate) kinase and thiamine monophosphate synthase activities. Biochem J 2007; 408:149-59. [PMID: 17696876 PMCID: PMC2267346 DOI: 10.1042/bj20070677] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A thiamine biosynthesis gene, thi3, from maize Zea mays has been identified through cloning and sequencing of cDNA and heterologous overexpression of the encoded protein, THI3, in Escherichia coli. The recombinant THI3 protein was purified to homogeneity and shown to possess two essentially different enzymatic activities of HMP(-P) [4-amino-5-hydroxymethyl-2-methylpyrimidine (phosphate)] kinase and TMP (thiamine monophosphate) synthase. Both activities were characterized in terms of basic kinetic constants, with interesting findings that TMP synthase is uncompetitively inhibited by excess of one of the substrates [HMP-PP (HMP diphosphate)] and ATP. A bioinformatic analysis of the THI3 sequence suggested that these activities were located in two distinct, N-terminal kinase and C-terminal synthase, domains. Models of the overall folds of THI3 domains and the arrangements of active centre residues were obtained with the SWISS-MODEL protein modelling server, on the basis of the known three-dimensional structures of Salmonella enterica serotype Typhimurium HMP(-P) kinase and Bacillus subtilis TMP synthase. The essential roles of Gln98 and Met134 residues for HMP kinase activity and of Ser444 for TMP synthase activity were experimentally confirmed by site-directed mutagenesis.
Collapse
Affiliation(s)
- Maria Rapala-Kozik
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
| | | | | | | | | |
Collapse
|
46
|
Vitamin B1 biosynthesis in plants requires the essential iron sulfur cluster protein, THIC. Proc Natl Acad Sci U S A 2007; 104:19637-42. [PMID: 18048325 DOI: 10.1073/pnas.0709597104] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Vitamin B1 (thiamin) is an essential compound in all organisms acting as a cofactor in key metabolic reactions and has furthermore been implicated in responses to DNA damage and pathogen attack in plants. Despite the fact that it was discovered almost a century ago and deficiency is a widespread health problem, much remains to be deciphered about its biosynthesis. The vitamin is composed of a thiazole and pyrimidine heterocycle, which can be synthesized by prokaryotes, fungi, and plants. Plants are the major source of the vitamin in the human diet, yet little is known about the biosynthesis of the compound therein. In particular, it has never been verified whether the pyrimidine heterocycle is derived from purine biosynthesis through the action of the THIC protein as in bacteria, rather than vitamin B6 and histidine as demonstrated for fungi. Here, we identify a homolog of THIC in Arabidopsis and demonstrate its essentiality not only for vitamin B1 biosynthesis, but also plant viability. This step takes place in the chloroplast and appears to be regulated at several levels, including through the presence of a riboswitch in the 3'-untranslated region of THIC. Strong evidence is provided for the involvement of an iron-sulfur cluster in the remarkable chemical rearrangement reaction catalyzed by the THIC protein for which there is no chemical precedent. The results suggest that vitamin B1 biosynthesis in plants is in fact more similar to prokaryotic counterparts and that the THIC protein is likely to be the key regulatory protein in the pathway.
Collapse
|
47
|
Smith AG, Croft MT, Moulin M, Webb ME. Plants need their vitamins too. CURRENT OPINION IN PLANT BIOLOGY 2007; 10:266-75. [PMID: 17434786 DOI: 10.1016/j.pbi.2007.04.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 04/04/2007] [Indexed: 05/14/2023]
Abstract
Over recent years, the pathways for the biosynthesis of many vitamins have been elucidated at the molecular level in plants, and several unique features are emerging. One is that the mitochondrion plays an important role in the synthesis of folate (vitamin B9), biotin (B7), pantothenate (B5), ascorbate (C), and possibly thiamin (B1). Second, the production of some of these cofactors is regulated by developmental cues, and perhaps more surprisingly, by environmental signals such as high light and salinity. Moreover, the biosynthesis of thiamin in Arabidopsis may be negatively regulated by a riboswitch, a novel method of gene regulation that is characteristic of cofactor biosynthesis in bacteria. Vitamin B12 is unique in that it is not found in vascular plants, but is abundant in algae; recent molecular work has revealed that algae do not synthesise the vitamin but instead obtain it from bacteria.
Collapse
Affiliation(s)
- Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.
| | | | | | | |
Collapse
|
48
|
Ajjawi I, Tsegaye Y, Shintani D. Determination of the genetic, molecular, and biochemical basis of the Arabidopsis thaliana thiamin auxotroph th1. Arch Biochem Biophys 2006; 459:107-14. [PMID: 17174261 DOI: 10.1016/j.abb.2006.11.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2006] [Revised: 11/10/2006] [Accepted: 11/11/2006] [Indexed: 10/23/2022]
Abstract
2-methyl-4-amino-5-hydroxymethylpyrimidine phosphate kinase/thiamin monophosphate pyrophosphorylase (HMPPK/TMPPase) is a key enzyme involved in thiamin biosynthesis. A candidate HMPPK/TMPPase gene identified in the Arabidopsis genome complemented the thiamin auxotrophy of the th1 mutant, thus proving that the th1 locus corresponds to the structural gene for the HMPPK/TMPPase. Sequence comparisons between the wild-type HMPPK/TMPPase gene and the th1-201 mutant allele identified a single point mutation that caused the substitution of a phenylalanine for a conserved serine residue in the HMPPK domain. Functional analyses of the mutant HMPPK/TMPPase in Escherichia coli revealed that the amino acid substitution in the HMPPK domain of mutant enzyme resulted in a conformational change that severely compromised both activities of the bifunctional enzyme. Studies were also performed to identify the chloroplast as the specific subcellular locale of the Arabidopsis HMPPK/TMPPase.
Collapse
Affiliation(s)
- Imad Ajjawi
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | | | | |
Collapse
|
49
|
Ferreira S, Hjernø K, Larsen M, Wingsle G, Larsen P, Fey S, Roepstorff P, Salomé Pais M. Proteome profiling of Populus euphratica Oliv. upon heat stress. ANNALS OF BOTANY 2006; 98:361-77. [PMID: 16740589 PMCID: PMC2803470 DOI: 10.1093/aob/mcl106] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Populus euphratica is a light-demanding species ecologically characterized as a pioneer. It grows in shelter belts along riversides, being part of the natural desert forest ecosystems in China and Middle Eastern countries. It is able to survive extreme temperatures, drought and salt stress, marking itself out as an important plant species to study the mechanisms responsible for survival of woody plants under heat stress. METHODS Heat effects were evaluated through electrolyte leakage on leaf discs, and LT(50) was determined to occur above 50 degrees C. Protein accumulation profiles of leaves from young plants submitted to 42/37 degrees C for 3 d in a phytotron were determined through 2D-PAGE, and a total of 45 % of up- and downregulated proteins were detected. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF)/TOF analysis, combined with searches in different databases, enabled the identification of 82 % of the selected spots. KEY RESULTS Short-term upregulated proteins are related to membrane destabilization and cytoskeleton restructuring, sulfur assimilation, thiamine and hydrophobic amino acid biosynthesis, and protein stability. Long-term upregulated proteins are involved in redox homeostasis and photosynthesis. Late downregulated proteins are involved mainly in carbon metabolism. CONCLUSIONS Moderate heat response involves proteins related to lipid biogenesis, cytoskeleton structure, sulfate assimilation, thiamine and hydrophobic amino acid biosynthesis, and nuclear transport. Photostasis is achieved through carbon metabolism adjustment, a decrease of photosystem II (PSII) abundance and an increase of PSI contribution to photosynthetic linear electron flow. Thioredoxin h may have a special role in this process in P. euphratica upon moderate heat exposure.
Collapse
Affiliation(s)
- Sílvia Ferreira
- Unit of Molecular Biology and Plant Biotechnology, Institute of Applied Science and Technology, Science Faculty of Lisbon University, Campo Grande, 1749-016 Lisbon, Portugal.
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Medina-Silva R, Barros MP, Galhardo RS, Netto LES, Colepicolo P, Menck CFM. Heat stress promotes mitochondrial instability and oxidative responses in yeast deficient in thiazole biosynthesis. Res Microbiol 2006; 157:275-81. [PMID: 16171982 DOI: 10.1016/j.resmic.2005.07.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2005] [Revised: 07/07/2005] [Accepted: 07/07/2005] [Indexed: 11/24/2022]
Abstract
The Thi4 protein from Saccharomyces cerevisiae plays a pivotal role in the biosynthesis of thiazole, a precursor of thiamine (vitamin B1). In addition, the thi4-disrupted strain has shown increased frequencies of mitochondrial mutants (petite colonies) upon treatment with DNA damaging agents. In this work, we show that the thi4 strain presents significant induction of petites and reduced oxygen consumption when grown at 37 degrees C, a condition that induces high levels of reactive oxygen species in yeast. Oxidative stress parameters were thus measured in thi4 cells. The activities of superoxide dismutase and phospholipid hydroperoxide glutathione peroxidase were significantly increased when these mutants were grown at 37 degrees C compared to the wild-type strain (W303). The levels of carbonyl protein groups were also significantly higher for the thi4 strain than for W303. Still, significant reductions in protein thiols and reduced glutathione were observed for the mutated strain. Therefore, the Thi4 protein appears to play an important protective role during heat stress in yeast cells, a feature probably related to the mitochondrial instability and altered oxidative status observed in thi4 mutants.
Collapse
Affiliation(s)
- Renata Medina-Silva
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, Cidade Universitária, Brazil
| | | | | | | | | | | |
Collapse
|