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Qu L, Huang X, Su X, Zhu G, Zheng L, Lin J, Wang J, Xue H. Potato: from functional genomics to genetic improvement. MOLECULAR HORTICULTURE 2024; 4:34. [PMID: 39160633 PMCID: PMC11331666 DOI: 10.1186/s43897-024-00105-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/17/2024] [Indexed: 08/21/2024]
Abstract
Potato is the most widely grown non-grain crop and ranks as the third most significant global food crop following rice and wheat. Despite its long history of cultivation over vast areas, slow breeding progress and environmental stress have led to a scarcity of high-yielding potato varieties. Enhancing the quality and yield of potato tubers remains the ultimate objective of potato breeding. However, conventional breeding has faced challenges due to tetrasomic inheritance, high genomic heterozygosity, and inbreeding depression. Recent advancements in molecular biology and functional genomic studies of potato have provided valuable insights into the regulatory network of physiological processes and facilitated trait improvement. In this review, we present a summary of identified factors and genes governing potato growth and development, along with progress in potato genomics and the adoption of new breeding technologies for improvement. Additionally, we explore the opportunities and challenges in potato improvement, offering insights into future avenues for potato research.
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Affiliation(s)
- Li Qu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xueqing Huang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xin Su
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guoqing Zhu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lingli Zheng
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jing Lin
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiawen Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongwei Xue
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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Kaur G, Jain S, Bhushan S, Das N, Sharma M, Sharma D. Role of microRNAs and their putative mechanism in regulating potato (Solanum tuberosum L.) life cycle and response to various environmental stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108334. [PMID: 38219424 DOI: 10.1016/j.plaphy.2024.108334] [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: 02/26/2023] [Revised: 10/31/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024]
Abstract
The exponentially increasing population and the demand for food is inextricably linked. This has shifted global attention to improving crop plant traits to meet global food demands. Potato (Solanum tuberosum L.) is a major non-grain food crop that is grown all over the world. Currently, some of the major global potato research work focuses on the significance of microRNAs (miRNAs) in potato. miRNAs are a type of non-coding RNAs that regulate the gene expression of their target mRNA genes by cleavage and/or their translational inhibition. This suggests an essential role of miRNAs in a multitude of plant biological processes, including maintenance of genome integrity, plant growth, development and maturation, and initiation of responses to various stress conditions. Therefore, engineering miRNAs to generate stress-resistant varieties of potato may result in high yield and improved nutritional qualities. In this review, we discuss the potato miRNAs specifically known to play an essential role in the various stages of the potato life cycle, conferring stress-resistant characteristics, and modifying gene expression. This review highlights the significance of the miRNA machinery in plants, especially potato, encouraging further research into engineering miRNAs to boost crop yields and tolerance towards stress.
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Affiliation(s)
- Gurpreet Kaur
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004, Punjab, India
| | - Sahil Jain
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Sakshi Bhushan
- Department of Botany, Central University of Jammu, Jammu and Kashmir (UT), India
| | - Niranjan Das
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004, Punjab, India
| | - Munish Sharma
- Department of Plant Science, Central University of Himachal Pradesh, Shahpur Parisar, Kangra, Himachal Pradesh, India.
| | - Deepak Sharma
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada.
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Zounková A, Konečný J, Lipavská H, Mašková P. BEL transcription factors in prominent Solanaceae crops: the missing pieces of the jigsaw in plant development. PLANTA 2023; 259:14. [PMID: 38070043 DOI: 10.1007/s00425-023-04289-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023]
Abstract
MAIN CONCLUSION Understanding BEL transcription factors roles in potato and tomato varies considerably with little overlap. The review suggests reciprocal use of gained results to proceed with the knowledge in both crops The proper development of organs that plants use for reproduction, like fruits or tubers, is crucial for the survival and competitiveness of the species and thus subject to strict regulations. Interestingly, the controls of potato (Solanum tuberosum) tuber and tomato (S. lycopersicum) fruit development use common mechanisms, including the action of the BEL transcription factors (TFs). Although more than ten BEL genes have been identified in either genome, only a few of them have been characterized. The review summarizes knowledge of BEL TFs' roles in these closely related Solanaceae species, focusing on those that are essential for tuberization in potato, namely StBEL5, StBEL11 and StBEL29, and for fruit development in tomato - SlBEL11, SlBL2 and SIBL4. Comprehension of the roles of individual BEL TFs, however, is not yet sufficient. Different levels of understanding of important characteristics are described, such as BEL transcript accumulation patterns, their mobility, BEL protein interaction with KNOX partners, subcellular localisation, and their target genes during initiation and development of the organs in question. A comparison of the knowledge on BEL TFs and their mechanisms of action in potato and tomato may provide inspiration for faster progress in the study of both models through the exchange of information and ideas. Both crops are extremely important for human nutrition. In addition, their production is likely to be threatened by the upcoming climate change, so there is a particular need for breeding using a deep knowledge of control mechanisms.
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Affiliation(s)
- Andrea Zounková
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 12800, Prague 2, Czech Republic
| | - Jan Konečný
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 12800, Prague 2, Czech Republic
| | - Helena Lipavská
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 12800, Prague 2, Czech Republic
| | - Petra Mašková
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 12800, Prague 2, Czech Republic.
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Yuan J, Cheng L, Li H, An C, Wang Y, Zhang F. Physiological and protein profiling analysis provides insight into the underlying molecular mechanism of potato tuber development regulated by jasmonic acid in vitro. BMC PLANT BIOLOGY 2022; 22:481. [PMID: 36210448 PMCID: PMC9549635 DOI: 10.1186/s12870-022-03852-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/19/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND Jasmonates (JAs) are one of important phytohormones regulating potato tuber development. It is a complex process and the underlying molecular mechanism regulating tuber development by JAs is still limited. This study attempted to illuminate it through the potential proteomic dynamics information about tuber development in vitro regulated by exogenous JA. RESULTS A combined analysis of physiological and iTRAQ (isobaric tags for relative and absolute quantification)-based proteomic approach was performed in tuber development in vitro under exogenous JA treatments (0, 0.5, 5 and 50 μΜ). Physiological results indicated that low JA concentration (especially 5 μM) promoted tuber development, whereas higher JA concentration (50 μM) showed inhibition effect. A total of 257 differentially expressed proteins (DEPs) were identified by iTRAQ, which provided a comprehensive overview on the functional protein profile changes of tuber development regulated by JA. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that low JA concentration (especially 5 μM) exhibited the promotion effects on tuber development in various cellular processes. Some cell wall polysaccharide synthesis and cytoskeleton formation-related proteins were up-regulated by JA to promote tuber cell expansion. Some primary carbon metabolism-related enzymes were up-regulated by JA to provide sufficient metabolism intermediates and energy for tuber development. And, a large number of protein biosynthesis, degradation and assembly-related were up-regulated by JA to promote tuber protein biosynthesis and maintain strict protein quality control during tuber development. CONCLUSIONS This study is the first to integrate physiological and proteomic data to provide useful information about the JA-signaling response mechanism of potato tuber development in vitro. The results revealed that the levels of a number of proteins involved in various cellular processes were regulated by JA during tuber development. The proposed hypothetical model would explain the interaction of these DEPs that associated with tuber development in vitro regulated by JA.
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Affiliation(s)
- Jianlong Yuan
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lixiang Cheng
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Huijun Li
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Congcong An
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuping Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Feng Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
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Comparative Proteomics of Potato Cultivars with a Variable Dormancy Period. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196621. [PMID: 36235158 PMCID: PMC9573702 DOI: 10.3390/molecules27196621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022]
Abstract
The control of the duration of the dormancy phase is a significant challenge in the potato industry and for seed producers. However, the proteome landscape involved in the regulation of the length of the dormancy period over potato cultivars remains largely unexplored. In this study, we performed for the first time a comparative proteome profiling of potato cultivars with differential duration of tuber dormancy. More specifically, the proteome profiling of Agata, Kennebec and Agria commercial potato varieties with short, medium and medium-long dormancy, respectively, was assessed at the endodormancy stage using high-resolution two-dimensional electrophoresis (2-DE) coupled to reversed-phase liquid chromatography–tandem mass spectrometry (LC-TripleTOF MS/MS). A total of 11 proteins/isoforms with statistically significant differential abundance among cultivars were detected on 2-DE gels and confidently identified by LC-TripleTOF MS/MS. Identified proteins have known functions related to tuber development, sprouting and the oxylipins biosynthesis pathway. Fructokinase, a mitochondrial ADP/ATP carrier, catalase isozyme 2 and heat shock 70 kDa were the proteins with the strongest response to dormancy variations. To the best of our knowledge, this study reports the first candidate proteins underlying variable dormancy length in potato cultivars.
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Awasthi S, Chauhan R, Indoliya Y, Chauhan AS, Mishra SK, Agrawal L, Dwivedi S, Singh SN, Srivastava S, Singh PC, Chauhan PS, Chakrabarty D, Srivastava S, Tripathi RD. Comprehensive illustration of transcriptomic and proteomic dataset for mitigation of arsenic toxicity in rice (Oryza sativa L.) by microbial consortium. Data Brief 2022; 43:108377. [PMID: 35761993 PMCID: PMC9232546 DOI: 10.1016/j.dib.2022.108377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/29/2022] Open
Abstract
The present article represents the data for analysis of microbial consortium (P.putida+C.vulgaris) mediated amelioration of arsenic toxicity in rice plant. In the current study the transcriptome profiling of treated rice root and shoot was performed by illumina sequencing (Platform 2000). To process the reads and to analyse differential gene expression, Fastxtoolkit, NGSQCtoolkit, Bowtie 2 (version 2.1.0), Tophat program (version 2.0.8), Cufflinks and Cuffdiff programs were used. For Proteome profiling, total soluble proteins in shoot of rice plant among different treatments were extracted and separated by 2D poly acrylamide gel electrophoresis (PAGE) and then proteins were identified with the help of MALDI-TOF/TOF. In gel based method of protein identification, the isoelectric focusing machine (IPGphor system,Bio-Rad USA), gel unit (SDS-PAGE) and MALDI-TOF/TOF (4800 proteomic analyzer Applied Biosystem, USA) were used for successful separation and positive identification of proteins. To check the differential abundance of proteins among different treatments, PDQuest software was used for data analysis. For protein identification, Mascot search engine (http://www.matrixscience.com) using NCBIprot/SwissProt databases of rice was used. The analyzed data inferred comprehensive picture of key genes and their respective proteins involved in microbial consortium mediated improved plant growth and amelioration of As induced phyto-toxicity in rice. For the more comprehensive information of data, the related full-length article entitled “Microbial consortium mediated growth promotion and Arsenic reduction in Rice: An integrated transcriptome and proteome profiling” may be accessed.
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Affiliation(s)
- Surabhi Awasthi
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
- Plant Stress Biology Laboratory, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, India
| | - Reshu Chauhan
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Yuvraj Indoliya
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Abhishek Singh Chauhan
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001, India
| | - Shashank Kumar Mishra
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Lalit Agrawal
- Department of Agriculture and Allied Science, Doon Business School, Dehradun, Uttarakhand, India
| | - Sanjay Dwivedi
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Shiv Naresh Singh
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Suchi Srivastava
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Poonam C. Singh
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Puneet Singh Chauhan
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Debasis Chakrabarty
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Sudhakar Srivastava
- Plant Stress Biology Laboratory, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, India
- Dr. Sudhakar Srivastava, Assistant Professor, Institute of environment & Sustainable Development, Banaras Hindu University, Varanasi, India
| | - Rudra Deo Tripathi
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
- Corresponding author(s). Dr. Rudra Deo Tripathi, NASI Senior Scientist Platinum Jubilee Fellow, CSIR-National Botanical Research Institute, Lucknow, India
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Ma Z, Chen S, Wang Z, Liu J, Zhang B. Proteome analysis of bermudagrass stolons and rhizomes provides new insights into the adaptation of plant stems to aboveground and underground growth. J Proteomics 2021; 241:104245. [PMID: 33901681 DOI: 10.1016/j.jprot.2021.104245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 12/16/2022]
Abstract
As an important perennial warm-season turfgrass species, bermudagrass (Cynodon dactylon L.) forms underground-growing rhizomes and aboveground-growing stolons simultaneously, making it a fast propagating clonal plant with strong regeneration ability. In the current study, we compared the internode proteomes of rhizomes and stolons at the same developmental stage in the bermudagrass cultivar Yangjiang using iTRAQ. The results indicated that 228 protein species were differentially accumulated in the two specialized stems. In agreement with the different contents of starch, chlorophyll, anthocyanin and H2O2 in the two types of stems, photosynthesis and flavonoid biosynthesis were enriched with differentially accumulated protein species (DAPs) in stolons, whereas starch and sucrose metabolism, glycolysis, and H2O2 metabolism were enriched with DAPs in rhizomes. Burying stolons in the soil resulted in the gradual degradation of chlorophyll and anthocyanin, accumulation of starch, and increment of H2O2, which is similar to the physiological characteristics of rhizomes. These results collectively revealed that stolons and rhizomes of bermudagrass have significant differences at the proteome level and light might play important regulatory roles in the discrepancy of the proteome profiles and specialization of the two stems, providing new insights into the adaptation of plant stems to aboveground and underground growth. BIOLOGICAL SIGNIFICANCE: As two types of specialized stems that grow underground and aboveground respectively, rhizomes and stolons play important roles in overwintering and ecological invasion of many perennial and clonal plants. However, because rhizomes and stolons rarely coexist in single plant species, the differences between the two stems remain unclear at the molecular level. In this study, through an iTRAQ comparative proteomic analysis, we reported the identification of 228 differentially accumulated protein species (DAPs) in rhizomes and stolons of bermudagrass for the first time. We found that the 228 DAPs were interconnected to form protein networks in regulating diverse cellular activities and biochemical reactions. We also observed that stolons growing underground showed similar physiological activities and DAP expression as those of underground-growing rhizomes, suggesting that light might play important regulatory roles in the specialization of stolons and rhizomes. These results expanded our understanding of the mysterious adaption of plant stems to different growth conditions.
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Affiliation(s)
- Ziyan Ma
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Si Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhizhi Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Bing Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
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Sharma S, Deswal R. Dioscorea Alata Tuber Proteome Analysis Uncovers Differentially Regulated Growth-associated Pathways of Tuber Development. PLANT & CELL PHYSIOLOGY 2021; 62:191-204. [PMID: 33313836 DOI: 10.1093/pcp/pcaa151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
During its life cycle, the Dioscorea tuber undergoes multiple morphological and biochemical changes. To gain a better understanding of the metabolic changes associated with tuber growth, a stage-specific gel-free proteome analysis of four distinct morphological stages namely germinating tuber (S1), degrading tuber (S2), new tuber formation (S3) and tuber maturation (S4) was done and validated by principal component analysis. A comprehensive data set identifying 78.2% of the total 3,681 proteins was generated. PANTHER and KEGG MAPPER revealed both expected (carbohydrate metabolism and redox regulation) and novel biological processes (transcription factors and hormonal regulation) characteristic for each developmental stage. Higher abundance of the enzymes of ascorbate-glutathione cycle and carbohydrate metabolism was detected during tuber germination (S1) and tuber formation stages (S3) in comparison with the mature tuber. The presence of ethylene biosynthesis components during tuber formation hints toward its probable role in postharvest shelf life. The data set comprehensively describes the proteome of Dioscorea tuber and provides growth-specific markers for tuber germination (ascorbate peroxidase, monodehydroascorbate reductase, invertase) and tuber formation (sucrose synthase), which were validated by enzyme activity assays and Western blotting. The study provides information that may influence the direction of research for improving the productivity of this under-utilized and largely neglected crop.
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Affiliation(s)
- Shruti Sharma
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi 110007, India
| | - Renu Deswal
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi 110007, India
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A comparative proteomic study of cold responses in potato leaves. Heliyon 2021; 7:e06002. [PMID: 33604464 PMCID: PMC7875832 DOI: 10.1016/j.heliyon.2021.e06002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/17/2020] [Accepted: 01/13/2021] [Indexed: 11/21/2022] Open
Abstract
The potato is an important food crop worldwide. While potatoes are rich in nutrition, the production suffers from yield loss caused by frost and freezing. This study used a common potato cultivar, ‘Zhengshu 6’, as the study system to measure the changes in the contents of soluble protein, malondialdehyde (MDA), proline, and chlorophyll after 1, 3, 5, and 7 days of low temperature treatment. We performed two-dimensional electrophoresis (2-DE) in combination with liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) technology and identified 52 differentially expressed protein spots among these timepoints. Results showed that levels of soluble protein, MDA, and proline increased as the duration of the low temperature treatment increased, and the chlorophyll content decreased. The 52 identified protein spots were classified by function as involved in defense response, energy metabolism, photosynthesis, protein degradation, ribosome formation, signal transduction, cell movement, nitrogen metabolism, and other physiological processes, thus allowing potato plants to achieve metabolic balance at low temperatures.
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Crop Enhancement of Cucumber Plants under Heat Stress by Shungite Carbon. Int J Mol Sci 2020; 21:ijms21144858. [PMID: 32659984 PMCID: PMC7402313 DOI: 10.3390/ijms21144858] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 01/10/2023] Open
Abstract
Heat stress negatively impacts plant growth and yield. The effects of carbon materials on plants in response to abiotic stress and antioxidant activity are poorly understood. In this study, we propose a new method for improving heat tolerance in cucumber (Cucumis sativus L.) using a natural carbon material, shungite, which can be easily mixed into any soil. We analyzed the phenotype and physiological changes in cucumber plants maintained at 35 °C or 40 °C for 1 week. Our results show that shungite-treated cucumber plants had a healthier phenotype, exhibiting dark green leaves, compared to the plants in the control soil group. Furthermore, in the shungite-treated plants, the monodehydroascorbate content (a marker of oxidative damage) of the leaf was 34% lower than that in the control group. In addition, scavengers against reactive oxygen species, such as superoxide dismutase, catalase, and peroxidase were significantly upregulated. These results indicate that the successive pre-treatment of soil with a low-cost natural carbon material can improve the tolerance of cucumber plants to heat stress, as well as improve the corresponding antioxidant activity.
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Gupta S, Mishra SK, Misra S, Pandey V, Agrawal L, Nautiyal CS, Chauhan PS. Revealing the complexity of protein abundance in chickpea root under drought-stress using a comparative proteomics approach. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 151:88-102. [PMID: 32203884 DOI: 10.1016/j.plaphy.2020.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 05/02/2023]
Abstract
Global warming has reached an alarming situation, which led to a dangerous climatic condition. The irregular rainfalls and land degradation are the significant consequences of these climatic changes causing a decrease in crop productivity. The effect of drought and its tolerance mechanism, a comparative roots proteomic analysis of chickpea seedlings grown under hydroponic conditions for three weeks, performed at different time points using 2-Dimensional gel electrophoresis (2-DE). After PD-Quest analysis, 110 differentially expressed spots subjected to MALDI-TOF/TOF and 75 spots identified with a significant score. These identified proteins classified into eight categories based on their functional annotation. Proteins involved in carbon and energy metabolism comprised 23% of total identified proteins include mainly glyceraldehyde-3-phosphate dehydrogenase, malate dehydrogenase, transaldolase, and isocitrate dehydrogenase. Proteins related to stress response (heat-shock protein, CS domain protein, and chitinase 2-like) contributed 16% of total protein spots followed by 13% involved in protein metabolism (adenosine kinase 2, and protein disulfide isomerase). ROS metabolism contributed 13% (glutathione S-transferase, ascorbate peroxidase, and thioredoxin), and 9% for signal transduction (actin-101, and 14-3-3-like protein B). Five percent protein identified for secondary metabolism (cinnamoyl-CoA reductase-1 and chalcone-flavononeisomerase 2) and 7% for nitrogen (N) and amino acid metabolism (glutamine synthetase and homocysteine methyltransferase). The abundance of some proteins validated by using Western blotting and Real-Time-PCR. The detailed information for drought-responsive root protein(s) through comparative proteomics analysis can be utilized in the future for genetic improvement programs to develop drought-tolerant chickpea lines.
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Affiliation(s)
- Swati Gupta
- Microbial Technology Division, Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shashank Kumar Mishra
- Microbial Technology Division, Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Sankalp Misra
- Microbial Technology Division, Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vivek Pandey
- Plant Ecology and Environmental Sciences, Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Lalit Agrawal
- Microbial Technology Division, Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India; Department of Agriculture and Allied Sciences, Doon Business School, Dehradun, 248001, India.
| | - Chandra Shekhar Nautiyal
- Microbial Technology Division, Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India.
| | - Puneet Singh Chauhan
- Microbial Technology Division, Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India.
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Cheng L, Wang D, Wang Y, Xue H, Zhang F. An integrative overview of physiological and proteomic changes of cytokinin-induced potato (Solanum tuberosum L.) tuber development in vitro. PHYSIOLOGIA PLANTARUM 2020; 168:675-693. [PMID: 31343748 DOI: 10.1111/ppl.13014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/21/2019] [Accepted: 07/22/2019] [Indexed: 05/24/2023]
Abstract
Potato tuberization is a complicated biological process regulated by multiple phytohormones, in particular cytokinins (CKs). The information available on the molecular mechanisms regulating tuber development by CKs remains largely unclear. Physiological results initially indicated that low 6-benzylaminopurine (BAP) concentration (3 mg l-1 ) advanced the tuberization beginning time and promoted tuber formation. A comparative proteomics approach was applied to investigate the proteome change of tuber development by two-dimensional gel electrophoresis in vitro, subjected to exogenous BAP treatments (0, 3, 6 and 13 mg l-1 ). Quantitative image analysis showed a total of 83 protein spots with significantly altered abundance (>2.5-fold, P < 0.05), and 55 differentially abundant proteins were identified by MALDI-TOF/TOF MS. Among these proteins, 22 proteins exhibited up-regulation with the increase of exogenous BAP concentration, and 31 proteins were upregulated at 3 mg l-1 BAP whereas being downregulated at higher BAP concentrations. These proteins were involved in metabolism and bioenergy, storage, redox homeostasis, cell defense and rescue, transcription and translation, chaperones, signaling and transport. The favorable effects of low BAP concentrations on tuber development were found in various cellular processes, mainly including the stimulation of starch and storage protein accumulation, the enhancement of the glycolysis pathway and ATP synthesis, the cellular homeostasis maintenance, the activation of pathogen defense, the higher efficiency of transcription and translation, as well as the enhanced metabolite transport. However, higher BAP concentration, especially 13 mg l-1 , showed disadvantageous effects. The proposed hypothetical model would explain the interaction of these proteins associated with CK-induced tuber development in vitro.
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Affiliation(s)
- Lixiang Cheng
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Dongxia Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Yuping Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Hongwei Xue
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
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ul Haq S, Khan A, Ali M, Khattak AM, Gai WX, Zhang HX, Wei AM, Gong ZH. Heat Shock Proteins: Dynamic Biomolecules to Counter Plant Biotic and Abiotic Stresses. Int J Mol Sci 2019; 20:E5321. [PMID: 31731530 PMCID: PMC6862505 DOI: 10.3390/ijms20215321] [Citation(s) in RCA: 206] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 10/15/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
Due to the present scenario of climate change, plants have to evolve strategies to survive and perform under a plethora of biotic and abiotic stresses, which restrict plant productivity. Maintenance of plant protein functional conformation and preventing non-native proteins from aggregation, which leads to metabolic disruption, are of prime importance. Plant heat shock proteins (HSPs), as chaperones, play a pivotal role in conferring biotic and abiotic stress tolerance. Moreover, HSP also enhances membrane stability and detoxifies the reactive oxygen species (ROS) by positively regulating the antioxidant enzymes system. Additionally, it uses ROS as a signal to molecules to induce HSP production. HSP also enhances plant immunity by the accumulation and stability of pathogenesis-related (PR) proteins under various biotic stresses. Thus, to unravel the entire plant defense system, the role of HSPs are discussed with a special focus on plant response to biotic and abiotic stresses, which will be helpful in the development of stress tolerance in plant crops.
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Affiliation(s)
- Saeed ul Haq
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
- Department of Horticulture, University of Agriculture Peshawar, Peshawar 25130, Pakistan;
| | - Abid Khan
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
| | - Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
| | - Abdul Mateen Khattak
- Department of Horticulture, University of Agriculture Peshawar, Peshawar 25130, Pakistan;
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100083, China
| | - Wen-Xian Gai
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
| | - Huai-Xia Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
| | - Ai-Min Wei
- Tianjin Vegetable Research Center, Tianjin 300192, China;
| | - Zhen-Hui Gong
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin 300384, China
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Cao D, Damaris RN, Zhang Y, Liu M, Li M, Yang P. Proteomic analysis showing the signaling pathways involved in the rhizome enlargement process in Nelumbo nucifera. BMC Genomics 2019; 20:766. [PMID: 31640547 PMCID: PMC6805393 DOI: 10.1186/s12864-019-6151-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 09/30/2019] [Indexed: 11/26/2022] Open
Abstract
Background Rhizome is the storage underground stem of lotus (Nelumbo nucifera), which is enlarged before winter season and could be used for asexual propagation. In addition, the enlarged rhizome is a nutritional vegetable with abundant starch, proteins, and vitamins. Enlargement of lotus rhizome is not only significance for itself to survive from the cold winter, but also important for its economic value. Results To explore the mechanism underlying its enlargement, integrative analyses of morphology, physiology and proteomics were conducted on the rhizome at stolon, middle, and enlarged stages. Morphological observation and physiological analyses showed that rhizomes were gradually enlarged during this process, in which the starch accumulation was also initiated. Quantitative proteomic analysis on the rhizomes at these three stages identified 302 stage-specific proteins (SSPs) and 172 differently expressed proteins (DEPs), based on which GO and KEGG enrichment analyses were conducted. The results indicated that light and auxin signal might be transduced through secondary messenger Ca2+, and play important roles in lotus rhizome enlargement. Conclusion These results will provide new insights into understanding the mechanism of lotus rhizome enlargement. Meanwhile, some candidate genes might be useful for further studies on this process, as well as breeding of rhizome lotus.
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Affiliation(s)
- Dingding Cao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rebecca Njeri Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Yue Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meihui Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
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Comparative proteomic analysis provides new insights into the specialization of shoots and stolons in bermudagrass (Cynodon dactylon L.). BMC Genomics 2019; 20:708. [PMID: 31510936 PMCID: PMC6740039 DOI: 10.1186/s12864-019-6077-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/04/2019] [Indexed: 12/26/2022] Open
Abstract
Background Bermudagrass (Cynodon dactylon L.) is an important turfgrass species with two types of stems, shoots and stolons. Despite their importance in determining the morphological variance and plasticity of bermudagrass, the intrinsic differences between stolons and shoots are poorly understood. Results In this study, we compared the proteomes of internode sections of shoots and stolons in the bermudagrass cultivar Yangjiang. The results indicated that 376 protein species were differentially accumulated in the two types of stems. Pathway enrichment analysis revealed that five and nine biochemical pathways were significantly enriched in stolons and shoots, respectively. Specifically, enzymes participating in starch synthesis all preferentially accumulated in stolons, whereas proteins involved in glycolysis and diverse transport processes showed relatively higher abundance in shoots. ADP-glucose pyrophosphorylase (AGPase) and pyruvate kinase (PK), which catalyze rate-limiting steps of starch synthesis and glycolysis, showed high expression levels and enzyme activity in stolons and shoots, respectively, in accordance with the different starch and soluble sugar contents of the two types of stems. Conclusions Our study revealed the differences between the shoots and stolons of bermudagrass at the proteome level. The results not only expand our understanding of the specialization of stolons and shoots but also provide clues for the breeding of bermudagrass and other turfgrasses with different plant architectures. Supplementary material Supplementary information accompanies this paper at 10.1186/s12864-019-6077-3.
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Tappiban P, Smith DR, Triwitayakorn K, Bao J. Recent understanding of starch biosynthesis in cassava for quality improvement: A review. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2018.11.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Cheng L, Wang Y, Liu Y, Zhang Q, Gao H, Zhang F. Comparative proteomics illustrates the molecular mechanism of potato (Solanum tuberosum L.) tuberization inhibited by exogenous gibberellins in vitro. PHYSIOLOGIA PLANTARUM 2018; 163:103-123. [PMID: 29135031 DOI: 10.1111/ppl.12670] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 10/31/2017] [Accepted: 11/08/2017] [Indexed: 05/24/2023]
Abstract
Among the multiple environmental signals and hormonal factors regulating potato tuberization, gibberellins (GAs) are important components of the signaling pathways in these processes. To understand the GAs-signaling response mechanism of potato tuberization, a comparative proteomics approach was applied to analyze proteome change of potato tuberization in vitro subjected to a range of exogenous GA3 treatments (0, 0.01, 0.1 and 1.0 μM) using two-dimensional gel electrophoresis. Quantitative image analyses showed that a total of 37 protein spots have their abundance significantly altered more than 2-fold. Among these proteins, 13 proteins were up-regulated, 13 proteins were down-regulated, one protein was absent and 10 proteins were induced after treatment by exogenous GA3 . The MALDI-TOF/TOF MS analyses led to the identification of differentially abundant proteins that are mainly involved in bioenergy and metabolism, storage, signaling, cell defense and rescue, transcription, chaperones, transport. Furthermore, the comparative analysis of GA3 -responsive proteome allowed for general elucidation of underlying molecular mechanisms of potato tuberization inhibited by exogenous GA3 . Most of these cellular processes were not conducive to the transition from stolon elongation to tuber formation, including a blockage of starch and storage protein accumulation, the accelerated carbohydrate catabolism, a blockage of JA biosynthesis but an elevated endogenous GAs level, the amplification of GA3 signal transduction by other signaling pathways, and the regulation of cellular RNA metabolism for controlling tuberization. Our results firstly integrated physiology and proteome data to provide new insights into GA3 -signaling response mechanisms of potato tuberization in vitro.
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Affiliation(s)
- Lixiang Cheng
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Yuping Wang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Yueshan Liu
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Qingquan Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Huihui Gao
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Feng Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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18
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Xie Y, Xu L, Wang Y, Fan L, Chen Y, Tang M, Luo X, Liu L. Comparative proteomic analysis provides insight into a complex regulatory network of taproot formation in radish ( Raphanus sativus L.). HORTICULTURE RESEARCH 2018; 5:51. [PMID: 30302255 PMCID: PMC6165848 DOI: 10.1038/s41438-018-0057-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/22/2018] [Accepted: 05/30/2018] [Indexed: 05/15/2023]
Abstract
The fleshy taproot of radish is an important storage organ determining its yield and quality. Taproot thickening is a complex developmental process in radish. However, the molecular mechanisms governing this process remain unclear at the proteome level. In this study, a comparative proteomic analysis was performed to analyze the proteome changes at three developmental stages of taproot thickening using iTRAQ approach. In total, 1862 differentially expressed proteins (DEPs) were identified from 6342 high-confidence proteins, among which 256 up-regulated proteins displayed overlapped accumulation in S1 (pre-cortex splitting stage) vs. S2 (cortex splitting stage) and S1 vs. S3 (expanding stage) pairs, whereas 122 up-regulated proteins displayed overlapped accumulation in S1 vs. S3 and S2 vs. S3 pairs. Gene Ontology (GO) and pathway enrichment analysis showed that these DEPs were mainly involved in several processes such as "starch and sucrose metabolism", "plant hormone signal transduction", and "biosynthesis of secondary metabolites". A high concordance existed between iTRAQ and RT-qPCR at the mRNA expression levels. Furthermore, association analysis showed that 187, 181, and 96 DEPs were matched with their corresponding differentially expressed genes (DEGs) in S1 vs. S2, S1 vs. S3, and S2 vs. S3 comparison, respectively. Notably, several functional proteins including cell division cycle 5-like protein (CDC5), expansin B1 (EXPB1), and xyloglucan endotransglucosylase/hydrolase protein 24 (XTH24) were responsible for cell division and expansion during radish taproot thickening process. These results could facilitate a better understanding of the molecular mechanism underlying taproot thickening, and provide valuable information for the identification of critical genes/proteins responsible for taproot thickening in root vegetable crops.
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Affiliation(s)
- Yang Xie
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 PR China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 PR China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 PR China
| | - Lianxue Fan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 PR China
| | - Yinglong Chen
- The UWA Institute of Agriculture, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6001 Australia
| | - Mingjia Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 PR China
| | - Xiaobo Luo
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 PR China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 PR China
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Mishra D, Shekhar S, Singh D, Chakraborty S, Chakraborty N. Heat Shock Proteins and Abiotic Stress Tolerance in Plants. REGULATION OF HEAT SHOCK PROTEIN RESPONSES 2018. [DOI: 10.1007/978-3-319-74715-6_3] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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20
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Yao Y, Geng MT, Wu XH, Sun C, Wang YL, Chen X, Shang L, Lu XH, Li Z, Li RM, Fu SP, Duan RJ, Liu J, Hu XW, Guo JC. Identification, Expression, and Functional Analysis of the Fructokinase Gene Family in Cassava. Int J Mol Sci 2017; 18:E2398. [PMID: 29137155 PMCID: PMC5713366 DOI: 10.3390/ijms18112398] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 12/03/2022] Open
Abstract
Fructokinase (FRK) proteins play important roles in catalyzing fructose phosphorylation and participate in the carbohydrate metabolism of storage organs in plants. To investigate the roles of FRKs in cassava tuber root development, seven FRK genes (MeFRK1-7) were identified, and MeFRK1-6 were isolated. Phylogenetic analysis revealed that the MeFRK family genes can be divided into α (MeFRK1, 2, 6, 7) and β (MeFRK3, 4, 5) groups. All the MeFRK proteins have typical conserved regions and substrate binding residues similar to those of the FRKs. The overall predicted three-dimensional structures of MeFRK1-6 were similar, folding into a catalytic domain and a β-sheet ''lid" region, forming a substrate binding cleft, which contains many residues involved in the binding to fructose. The gene and the predicted three-dimensional structures of MeFRK3 and MeFRK4 were the most similar. MeFRK1-6 displayed different expression patterns across different tissues, including leaves, stems, tuber roots, flowers, and fruits. In tuber roots, the expressions of MeFRK3 and MeFRK4 were much higher compared to those of the other genes. Notably, the expression of MeFRK3 and MeFRK4 as well as the enzymatic activity of FRK were higher at the initial and early expanding tuber stages and were lower at the later expanding and mature tuber stages. The FRK activity of MeFRK3 and MeFRK4 was identified by the functional complementation of triple mutant yeast cells that were unable to phosphorylate either glucose or fructose. The gene expression and enzymatic activity of MeFRK3 and MeFRK4 suggest that they might be the main enzymes in fructose phosphorylation for regulating the formation of tuber roots and starch accumulation at the tuber root initial and expanding stages.
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Affiliation(s)
- Yuan Yao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Meng-Ting Geng
- College of Agriculture, Hainan University, Haikou 570228, China.
| | - Xiao-Hui Wu
- Prisys Biotechnologies Company Limited, Shanghai 201203, China.
| | - Chong Sun
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, China.
| | - Yun-Lin Wang
- College of Agriculture, Hainan University, Haikou 570228, China.
| | - Xia Chen
- College of Agriculture, Hainan University, Haikou 570228, China.
| | - Lu Shang
- College of Agriculture, Hainan University, Haikou 570228, China.
| | - Xiao-Hua Lu
- College of Agriculture, Hainan University, Haikou 570228, China.
| | - Zhan Li
- College of Agriculture, Hainan University, Haikou 570228, China.
| | - Rui-Mei Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Shao-Ping Fu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Rui-Jun Duan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Jiao Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Xin-Wen Hu
- College of Agriculture, Hainan University, Haikou 570228, China.
| | - Jian-Chun Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
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Zhou X, Chen S, Wu H, Yang Y, Xu H. Biochemical and proteomics analyses of antioxidant enzymes reveal the potential stress tolerance in Rhododendron chrysanthum Pall. Biol Direct 2017; 12:10. [PMID: 28476175 PMCID: PMC5418713 DOI: 10.1186/s13062-017-0181-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/27/2017] [Indexed: 12/03/2022] Open
Abstract
Background Rhododendron chrysanthum Pall., an endangered species with significant ornamental and medicinal value, is endemic to the Changbai Mountain of China and can also serve as a significant plant resource for investigating the stress tolerance in plants. Proteomics is an effective analytical tool that provides significant information about plant metabolism and gene expression. However, no proteomics data have been reported for R. chrysanthum previously. In alpine tundra, the abiotic stress will lead to a severe over-accumulation of reactive oxygen species (ROS). Many alpine plants overcome the severe stresses and protect themselves from the oxidative damage by increasing the ratio and activity of antioxidant enzymes. Results In our study, wild type and domesticated Rhododendron chrysanthum Pall. were used as experimental and control groups, respectively. Proteomics method combined with biochemical approach were applied for the stress tolerance investigation of R. chrysanthum at both protein and molecular level. A total of 1,395 proteins were identified, among which 137 proteins were up-regulate in the experimental group. The activities of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidases (APXs), and glutathione peroxidase (GPX) were significantly higher and the expression of APXs and GPX were also increased in the experimental group. Moreover, the interaction network analysis of these enzymes also reveals that the antioxidant enzymes play important roles in the stress resistance in plants. Conclusions This is the first report of the proteome of Rhododendron chrysanthum Pall., and the data reinforce the notion that the antioxidant system plays a significant role in plant stress survival. Our results also verified that R. chrysanthum is highly resistant to abiotic stress and can serve as a significant resource for investigating stress tolerance in plants. Reviewers This article was reviewed by George V. (Yura) Shpakovski and Ramanathan Sowdhamini. Electronic supplementary material The online version of this article (doi:10.1186/s13062-017-0181-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaofu Zhou
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, 136000, China
| | - Silin Chen
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, 136000, China
| | - Hui Wu
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, 136000, China
| | - Yi Yang
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, 136000, China
| | - Hongwei Xu
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, 136000, China.
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Dutt S, Manjul AS, Raigond P, Singh B, Siddappa S, Bhardwaj V, Kawar PG, Patil VU, Kardile HB. Key players associated with tuberization in potato: potential candidates for genetic engineering. Crit Rev Biotechnol 2017; 37:942-957. [PMID: 28095718 DOI: 10.1080/07388551.2016.1274876] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Tuberization in potato (Solanum tuberosum L.) is a complex biological phenomenon which is affected by several environmental cues, genetic factors and plant nutrition. Understanding the regulation of tuber induction is essential to devise strategies to improve tuber yield and quality. It is well established that short-day photoperiods promote tuberization, whereas long days and high-temperatures inhibit or delay tuberization. Worldwide research on this complex biological process has yielded information on the important bio-molecules (proteins, RNAs, plant growth regulators) associated with the tuberization process in potato. Key proteins involved in the regulation of tuberization include StSP6A, POTH1, StBEL5, StPHYB, StCONSTANS, Sucrose transporter StSUT4, StSP5G, etc. Biomolecules that become transported from "source to sink" have also been suggested to be important signaling candidates regulating the tuberization process in potatos. Four molecules, namely StSP6A protein, StBEL5 RNA, miR172 and GAs, have been found to be the main candidates acting as mobile signals for tuberization. These biomolecules can be manipulated (overexpressed/inhibited) for improving the tuberization in commercial varieties/cultivars of potato. In this review, information about the genes/proteins and their mechanism of action associated with the tuberization process is discussed.
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Affiliation(s)
- Som Dutt
- a ICAR-Central Potato Research Institute (ICAR-CPRI) , Shimla , Himachal Pradesh , India
| | - Anshul Sharma Manjul
- a ICAR-Central Potato Research Institute (ICAR-CPRI) , Shimla , Himachal Pradesh , India
| | - Pinky Raigond
- a ICAR-Central Potato Research Institute (ICAR-CPRI) , Shimla , Himachal Pradesh , India
| | - Brajesh Singh
- a ICAR-Central Potato Research Institute (ICAR-CPRI) , Shimla , Himachal Pradesh , India
| | - Sundaresha Siddappa
- a ICAR-Central Potato Research Institute (ICAR-CPRI) , Shimla , Himachal Pradesh , India
| | - Vinay Bhardwaj
- a ICAR-Central Potato Research Institute (ICAR-CPRI) , Shimla , Himachal Pradesh , India
| | - Prashant G Kawar
- a ICAR-Central Potato Research Institute (ICAR-CPRI) , Shimla , Himachal Pradesh , India
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Wardhan V, Pandey A, Chakraborty S, Chakraborty N. Chickpea transcription factor CaTLP1 interacts with protein kinases, modulates ROS accumulation and promotes ABA-mediated stomatal closure. Sci Rep 2016; 6:38121. [PMID: 27934866 PMCID: PMC5146945 DOI: 10.1038/srep38121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 11/07/2016] [Indexed: 11/23/2022] Open
Abstract
Tubby and Tubby-like proteins (TLPs), in mammals, play critical roles in neural development, while its function in plants is largely unknown. We previously demonstrated that the chickpea TLP, CaTLP1, participates in osmotic stress response and might be associated with ABA-dependent network. However, how CaTLP1 is connected to ABA signaling remains unclear. The CaTLP1 was found to be engaged in ABA-mediated gene expression and stomatal closure. Complementation of the yeast yap1 mutant with CaTLP1 revealed its role in ROS scavenging. Furthermore, complementation of Arabidopsis attlp2 mutant displayed enhanced stress tolerance, indicating the functional conservation of TLPs across the species. The presence of ABA-responsive element along with other motifs in the proximal promoter regions of TLPs firmly established their involvement in stress signalling pathways. The CaTLP1 promoter driven GUS expression was restricted to the vegetative organs, especially stem and rosette leaves. Global protein expression profiling of wild-type, attlp2 and complemented Arabidopsis plants revealed 95 differentially expressed proteins, presumably involved in maintaining physiological and biological processes under dehydration. Immunoprecipitation assay revealed that protein kinases are most likely to interact with CaTLP1. This study provides the first demonstration that the TLPs act as module for ABA-mediated stomatal closure possibly via interaction with protein kinase.
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Affiliation(s)
- Vijay Wardhan
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Aarti Pandey
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi-110067, India
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Cheng L, Wang Y, He Q, Li H, Zhang X, Zhang F. Comparative proteomics illustrates the complexity of drought resistance mechanisms in two wheat (Triticum aestivum L.) cultivars under dehydration and rehydration. BMC PLANT BIOLOGY 2016; 16:188. [PMID: 27576435 PMCID: PMC5006382 DOI: 10.1186/s12870-016-0871-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 08/10/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Drought stress is one of the most adverse environmental constraints to plant growth and productivity. Comparative proteomics of drought-tolerant and sensitive wheat genotypes is a strategy to understand the complexity of molecular mechanism of wheat in response to drought. This study attempted to extend findings regarding the potential proteomic dynamics in wheat under drought stress and to enrich the research content of drought tolerance mechanism. RESULTS A comparative proteomics approach was applied to analyze proteome change of Xihan No. 2 (a drought-tolerant cultivar) and Longchun 23 (a drought-sensitive cultivar) subjected to a range of dehydration treatments (18 h, 24 h and 48 h) and rehydration treatment (R24 h) using 2-DE, respectively. Quantitative image analysis showed a total of 172 protein spots in Xihan No. 2 and 215 spots from Longchun 23 with their abundance significantly altered (p < 0.05) more than 2.5-fold. Out of these spots, a total of 84 and 64 differentially abundant proteins were identified by MALDI-TOF/TOF MS in Xihan No. 2 and Longchun 23, respectively. Most of these identified proteins were involved in metabolism, photosynthesis, defence and protein translation/processing/degradation in both two cultivars. In addition, the proteins involved in redox homeostasis, energy, transcription, cellular structure, signalling and transport were also identified. Furthermore, the comparative analysis of drought-responsive proteome allowed for the general elucidation of the major mechanisms associated with differential responses to drought of both two cultivars. These cellular processes work more cooperatively to re-establish homeostasis in Xihan No. 2 than Longchun 23. The resistance mechanisms of Xihan No. 2 mainly included changes in the metabolism of carbohydrates and amino acids as well as in the activation of more antioxidation and defense systems and in the levels of proteins involved in ATP synthesis and protein degradation/refolding. CONCLUSIONS This study revealed that the levels of a number of proteins involved in various cellular processes were affected by drought stress in two wheat cultivars with different drought tolerance. The results showed that there exist specific responses to drought in Xihan No. 2 and Longchun 23. The proposed hypothetical model would explain the interaction of these identified proteins that are associated with drought-responses in two cultivars, and help in developing strategies to improve drought tolerance in wheat.
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Affiliation(s)
- Lixiang Cheng
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
| | - Yuping Wang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
| | - Qiang He
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
| | - Huijun Li
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
- Wuwei Agricultural and Animal Husbandry Bureau, Wuwei, China
| | - Xiaojing Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
- Gansu Dingxi Academy of Agricultural Science, Dingxi, China
| | - Feng Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
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25
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Wang X, Chang L, Tong Z, Wang D, Yin Q, Wang D, Jin X, Yang Q, Wang L, Sun Y, Huang Q, Guo A, Peng M. Proteomics Profiling Reveals Carbohydrate Metabolic Enzymes and 14-3-3 Proteins Play Important Roles for Starch Accumulation during Cassava Root Tuberization. Sci Rep 2016; 6:19643. [PMID: 26791570 PMCID: PMC4726164 DOI: 10.1038/srep19643] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/14/2015] [Indexed: 02/07/2023] Open
Abstract
Cassava is one of the most important root crops as a reliable source of food and carbohydrates. Carbohydrate metabolism and starch accumulation in cassava storage root is a cascade process that includes large amounts of proteins and cofactors. Here, comparative proteomics were conducted in cassava root at nine developmental stages. A total of 154 identified proteins were found to be differentially expressed during starch accumulation and root tuberization. Many enzymes involved in starch and sucrose metabolism were significantly up-regulated, and functional classification of the differentially expressed proteins demonstrated that the majority were binding-related enzymes. Many proteins were took part in carbohydrate metabolism to produce energy. Among them, three 14-3-3 isoforms were induced to be clearly phosphorylated during storage root enlargement. Overexpression of a cassava 14-3-3 gene in Arabidopsis thaliana confirmed that the older leaves of these transgenic plants contained higher sugar and starch contents than the wild-type leaves. The 14-3-3 proteins and their binding enzymes may play important roles in carbohydrate metabolism and starch accumulation during cassava root tuberization. These results not only deepened our understanding of the tuberous root proteome, but also uncovered new insights into carbohydrate metabolism and starch accumulation during cassava root enlargement.
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Affiliation(s)
- Xuchu Wang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.,College of Agriculture, Hainan University, Haikou, Hainan 570228, China
| | - Lili Chang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.,College of Agriculture, Hainan University, Haikou, Hainan 570228, China
| | - Zheng Tong
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Dongyang Wang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.,College of Agriculture, Hainan University, Haikou, Hainan 570228, China
| | - Qi Yin
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.,College of Agriculture, Hainan University, Haikou, Hainan 570228, China
| | - Dan Wang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Xiang Jin
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Qian Yang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Liming Wang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Yong Sun
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Qixing Huang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Anping Guo
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Ming Peng
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.,College of Agriculture, Hainan University, Haikou, Hainan 570228, China
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26
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Agrawal L, Gupta S, Mishra SK, Pandey G, Kumar S, Chauhan PS, Chakrabarty D, Nautiyal CS. Elucidation of Complex Nature of PEG Induced Drought-Stress Response in Rice Root Using Comparative Proteomics Approach. FRONTIERS IN PLANT SCIENCE 2016; 7:1466. [PMID: 27746797 PMCID: PMC5040710 DOI: 10.3389/fpls.2016.01466] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 09/14/2016] [Indexed: 05/22/2023]
Abstract
Along with many adaptive strategies, dynamic changes in protein abundance seem to be the common strategy to cope up with abiotic stresses which can be best explored through proteomics. Understanding of drought response is the key to decipher regulatory mechanism of better adaptation. Rice (Oryza sativa L.) proteome represents a phenomenal source of proteins that govern traits of agronomic importance, such as drought tolerance. In this study, a comparison of root cytoplasmic proteome was done for a drought tolerant rice (Heena) cultivar in PEG induced drought conditions. A total of 510 protein spots were observed by PDQuest analysis and 125 differentially regulated spots were subjected for MALDI-TOF MS-MS analysis out of which 102 protein spots identified which further led to identification of 78 proteins with a significant score. These 78 differentially expressed proteins appeared to be involved in different biological pathways. The largest percentage of identified proteins was involved in bioenergy and metabolism (29%) and mainly consists of malate dehydrogenase, succinyl-CoA, putative acetyl-CoA synthetase, and pyruvate dehydrogenase etc. This was followed by proteins related to cell defense and rescue (22%) such as monodehydroascorbate reductase and stress-induced protein sti1, then by protein biogenesis and storage class (21%) e.g. putative thiamine biosynthesis protein, putative beta-alanine synthase, and cysteine synthase. Further, cell signaling (9%) proteins like actin and prolyl endopeptidase, and proteins with miscellaneous function (19%) like Sgt1 and some hypothetical proteins were also represented a large contribution toward drought regulatory mechanism in rice. We propose that protein biogenesis, cell defense, and superior homeostasis may render better drought-adaptation. These findings might expedite the functional determination of the drought-responsive proteins and their prioritization as potential molecular targets for perfect adaptation.
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Narula K, Pandey A, Gayali S, Chakraborty N, Chakraborty S. Birth of plant proteomics in India: a new horizon. J Proteomics 2015; 127:34-43. [PMID: 25920368 DOI: 10.1016/j.jprot.2015.04.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 01/02/2023]
Abstract
UNLABELLED In the post-genomic era, proteomics is acknowledged as the next frontier for biological research. Although India has a long and distinguished tradition in protein research, the initiation of proteomics studies was a new horizon. Protein research witnessed enormous progress in protein separation, high-resolution refinements, biochemical identification of the proteins, protein-protein interaction, and structure-function analysis. Plant proteomics research, in India, began its journey on investigation of the proteome profiling, complexity analysis, protein trafficking, and biochemical modeling. The research article by Bhushan et al. in 2006 marked the birth of the plant proteomics research in India. Since then plant proteomics studies expanded progressively and are now being carried out in various institutions spread across the country. The compilation presented here seeks to trace the history of development in the area during the past decade based on publications till date. In this review, we emphasize on outcomes of the field providing prospects on proteomic pathway analyses. Finally, we discuss the connotation of strategies and the potential that would provide the framework of plant proteome research. BIOLOGICAL SIGNIFICANCE The past decades have seen rapidly growing number of sequenced plant genomes and associated genomic resources. To keep pace with this increasing body of data, India is in the provisional phase of proteomics research to develop a comparative hub for plant proteomes and protein families, but it requires a strong impetus from intellectuals, entrepreneurs, and government agencies. Here, we aim to provide an overview of past, present and future of Indian plant proteomics, which would serve as an evaluation platform for those seeking to incorporate proteomics into their research programs. This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Kanika Narula
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Aarti Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saurabh Gayali
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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28
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Lee JJ, Kim YH, Kwak YS, An JY, Kim PJ, Lee BH, Kumar V, Park KW, Chang ES, Jeong JC, Lee HS, Kwak SS. A comparative study of proteomic differences between pencil and storage roots of sweetpotato (Ipomoea batatas (L.) Lam.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 87:92-101. [PMID: 25562766 DOI: 10.1016/j.plaphy.2014.12.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/13/2014] [Indexed: 05/25/2023]
Abstract
Fibrous roots of sweetpotato (Ipomoea batatas (L.) Lam.) usually develop into both pencil and storage roots. To understand protein function in root development, a proteomic analysis was conducted on the pencil and storage roots of the light orange-fleshed sweetpotato cultivar, Yulmi. Two-dimensional gel electrophoresis showed that expression of 30 protein spots differed between pencil and storage roots: 15 proteins were up-regulated or expressed in pencil roots and 15 in storage roots. Differentially expressed proteins spots were investigated using matrix-assisted laser desorption/ionization time of flight mass spectrometry, and 10 proteins from pencil roots were identified as binding protein isoform A, catechol oxidase, peroxidases, ascorbate peroxidase, endochitinase, flavanone 3-hydroxylase and unknown proteins. Of the proteins up-regulated in, or restricted to, storage roots, 13 proteins were identified as protein disulfide isomerase, anionic peroxidase, putative ripening protein, sporamin B, sporamin A and sporamin A precursor. An analysis of enzyme activity revealed that catechol oxidase and peroxidase as the first and last enzymes of the lignin biosynthesis pathway, and ascorbate peroxidase had higher activities in pencil than in storage roots. The total concentration of phenolic compounds was also far higher in pencil than in storage roots, and lignin accumulated only in pencil roots. These results provide important insight into sweetpotato proteomics, and imply that lignin biosynthesis and stress-related proteins are up-regulated or uniquely expressed in pencil roots. The results indicate that the reduction of carbon flow toward phenylpropanoid biosynthesis and its delivery to carbohydrate metabolism is a major event in storage root formation.
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Affiliation(s)
- Jeung Joo Lee
- Department of Applied Biology, IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Yun-Hee Kim
- Department of Biology Education, College of Education, IALS, PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Youn-Sig Kwak
- Department of Applied Biology, IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Jae Young An
- Department of Applied Biology, IALS, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Pil Joo Kim
- Division of Applied Life Science (BK21 Program), IALS, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Byung Hyun Lee
- Division of Applied Life Science (BK21 Program), IALS, PMBBRC, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Vikranth Kumar
- Division of Applied Life Science (BK21 Program), PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Kee Woong Park
- Department of Crop Science, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Eun Sil Chang
- Gyeongsangnam-do Agricultural Research & Extension Services, Jinju 660-985, Republic of Korea
| | - Jae Cheol Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea
| | - Haeng-Soon Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea.
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29
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Nawrot R, Zauber H, Schulze WX. Global proteomic analysis of Chelidonium majus and Corydalis cava (Papaveraceae) extracts revealed similar defense-related protein compositions. Fitoterapia 2014; 94:77-87. [DOI: 10.1016/j.fitote.2014.01.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Revised: 01/10/2014] [Accepted: 01/10/2014] [Indexed: 12/31/2022]
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30
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Liu CH, Chao YY, Kao CH. Effect of potassium deficiency on antioxidant status and cadmium toxicity in rice seedlings. BOTANICAL STUDIES 2013; 54:2. [PMID: 28510845 PMCID: PMC5383923 DOI: 10.1186/1999-3110-54-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 05/29/2013] [Indexed: 05/13/2023]
Abstract
BACKGROUND Cadmium (Cd) is one of the most toxic heavy metals and inhibits physiological processes of plants. Potassium (K) is an essential macronutrient in plants. K deficiency and Cd stress represent two different abiotic stress conditions that occur in the field simultaneously. In this study, effects of K deficiency on antioxidant status and Cd toxicity in rice seedlings were investigated. RESULTS K deficiency significantly decreased K concentration in shoots and roots. However, fresh weight and dry weight of rice seedlings were not affected by K deficiency. The activities of antioxidant enzymes (superoxide dismutase, ascorbate peroxidase, glutathione reductase, and catalase) in K-deficient leaves were higher than respective control leaves. However, K deficiency had no effect on the content of antioxidants (ascorbate and glutathione). Cd toxicity was judged by the decrease in biomass production, chlorosis, and induction of oxidative stress. Based on these criteria, we demonstrated that K deficiency protected rice seedling from Cd stress. Moreover, chlorophyll concentration was higher in K-deficient shoots and roots than their respective control shoots and roots. CONCLUSIONS Our results indicated that K deficiency protects rice seedlings from Cd toxicity. This protective effect of K deficiency is mainly due to enhanced antioxidant enzyme activities but not inhibition of Cd uptake.
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Affiliation(s)
- Chun-Hsin Liu
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC
| | - Yun-Yang Chao
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC
| | - Ching Huei Kao
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC
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31
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Agrawal L, Narula K, Basu S, Shekhar S, Ghosh S, Datta A, Chakraborty N, Chakraborty S. Comparative Proteomics Reveals a Role for Seed Storage Protein AmA1 in Cellular Growth, Development, and Nutrient Accumulation. J Proteome Res 2013; 12:4904-30. [DOI: 10.1021/pr4007987] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lalit Agrawal
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Kanika Narula
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Swaraj Basu
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Shubhendu Shekhar
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Sudip Ghosh
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Asis Datta
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Niranjan Chakraborty
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
| | - Subhra Chakraborty
- Laboratory 104 and ‡Laboratory 105, National Institute of Plant Genome Research, Aruna
Asaf Ali Marg, New Delhi 110067, India
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32
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Deswal R, Gupta R, Dogra V, Singh R, Abat JK, Sarkar A, Mishra Y, Rai V, Sreenivasulu Y, Amalraj RS, Raorane M, Chaudhary RP, Kohli A, Giri AP, Chakraborty N, Zargar SM, Agrawal VP, Agrawal GK, Job D, Renaut J, Rakwal R. Plant proteomics in India and Nepal: current status and challenges ahead. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2013; 19:461-477. [PMID: 24431515 PMCID: PMC3781272 DOI: 10.1007/s12298-013-0198-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Plant proteomics has made tremendous contributions in understanding the complex processes of plant biology. Here, its current status in India and Nepal is discussed. Gel-based proteomics is predominantly utilized on crops and non-crops to analyze majorly abiotic (49 %) and biotic (18 %) stress, development (11 %) and post-translational modifications (7 %). Rice is the most explored system (36 %) with major focus on abiotic mainly dehydration (36 %) stress. In spite of expensive proteomics setup and scarcity of trained workforce, output in form of publications is encouraging. To boost plant proteomics in India and Nepal, researchers have discussed ground level issues among themselves and with the International Plant Proteomics Organization (INPPO) to act in priority on concerns like food security. Active collaboration may help in translating this knowledge to fruitful applications.
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Affiliation(s)
- Renu Deswal
- />Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, India
| | - Ravi Gupta
- />Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, India
| | - Vivek Dogra
- />Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh India
| | - Raksha Singh
- />Department of Plant Molecular Biology, College of Life Science, Sejong University, Seoul, Republic of Korea
| | - Jasmeet Kaur Abat
- />Department of Botany, Gargi College, University of Delhi, New Delhi, India
| | - Abhijit Sarkar
- />Department of Botany, Banaras Hindu University, Varanasi, India
- />Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal
| | - Yogesh Mishra
- />Department of Plant Physiology, Umeå Plant Science Center, Umeå University, Umeå, Sweden
| | - Vandana Rai
- />National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, India
| | - Yelam Sreenivasulu
- />Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh India
| | - Ramesh Sundar Amalraj
- />Plant Pathology Section, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Tamil Nadu, India
| | - Manish Raorane
- />Plant Molecular Biology Laboratory, Plant Breeding, Genetics and Biotechnology, International Rice Research Institute, Manila, Philippines
| | - Ram Prasad Chaudhary
- />Central Department of Botany, and Research Centre for Applied Science and Technology, Tribhuvan University, Kirtipur, Nepal
| | - Ajay Kohli
- />Plant Molecular Biology Laboratory, Plant Breeding, Genetics and Biotechnology, International Rice Research Institute, Manila, Philippines
| | - Ashok Prabhakar Giri
- />Plant Molecular Biology Unit, Division of Biochemical Sciences, National Chemical Laboratory, Pune, India
| | | | - Sajad Majeed Zargar
- />School of Biotechnology, SK University of Agricultural Sciences and Technology, Chatha, Jammu, 180009 Jammu and Kashmir India
| | | | - Ganesh Kumar Agrawal
- />Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal
| | - Dominique Job
- />CNRS/Bayer Crop Science (UMR 5240) Joint Laboratory, Lyon, France
| | - Jenny Renaut
- />Department of Environment and Agrobiotechnologies, Centre de Recherche Public-Gabriel Lippmann, Belvaux, GD Luxembourg
| | - Randeep Rakwal
- />Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal
- />Organization for Educational Initiatives, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577 Japan
- />Department of Anatomy I, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa, Tokyo 142-8555 Japan
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Yu JW, Choi JS, Upadhyaya CP, Kwon SO, Gururani MA, Nookaraju A, Nam JH, Choi CW, Kim SI, Ajappala H, Kim HS, Jeon JH, Park SW. Dynamic proteomic profile of potato tuber during its in vitro development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 195:1-9. [PMID: 22920994 DOI: 10.1016/j.plantsci.2012.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 06/14/2012] [Accepted: 06/15/2012] [Indexed: 05/07/2023]
Abstract
Potato tuberization is a complicated biochemical process, which is dependent on external environmental factors. Tuber development in potato consists of a series of biochemical and morphological processes at the stolon tip. Signal transduction proteins are involved in the source-sink transition during potato tuberization. In the present study, we examined protein profiles under in vitro tuber-inducing conditions using a shotgun proteomic approach involving denaturing gel electrophoresis and liquid chromatography-mass spectrometry. A total of 251 proteins were identified and classified into 9 groups according to distinctive expression patterns during the tuberization stage. Stolon stage-specific proteins were primarily involved in the photosynthetic machinery. Proteins specific to the initial tuber stage included patatin. Proteins specific to the developing tuber stage included 6-fructokinase, phytoalexin-deficient 4-1, metallothionein II-like protein, and malate dehydrogenase. Novel stage-specific proteins identified during in vitro tuberization were ferredoxin-NADP reductase, 34 kDa porin, aquaporin, calmodulin, ripening-regulated protein, and starch synthase. Superoxide dismutase, dehydroascorbate reductase, and catalase I were most abundantly expressed in the stolon; however, the enzyme activities of these proteins were most activated at the initial tuber. The present shotgun proteomic study provides insights into the proteins that show altered expression during in vitro potato tuberization.
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Affiliation(s)
- Jae Woong Yu
- Department of Molecular Biotechnology, Konkuk University, 1, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
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Lee JJ, Park KW, Kwak YS, Ahn JY, Jung YH, Lee BH, Jeong JC, Lee HS, Kwak SS. Comparative proteomic study between tuberous roots of light orange- and purple-fleshed sweetpotato cultivars. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 193-194:120-129. [PMID: 22794925 DOI: 10.1016/j.plantsci.2012.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 06/05/2012] [Accepted: 06/06/2012] [Indexed: 05/15/2023]
Abstract
This study compares the differences in proteomes expressed in tuberous roots of a light orange-fleshed sweetpotato (Ipomoea batatas (L.) Lam. cultivar Yulmi) and a purple-fleshed sweetpotato cultivar (Shinjami). More than 370 protein spots were reproducibly detected by two-dimensional gel electrophoresis, in which 35 spots were up-regulated (Yulmi vs. Shinjami) or uniquely expressed (only Yulmi or Shinjami) in either of the two cultivars. Of these 35 protein spots, 23 were expressed in Yulmi and 12 were expressed in Shinjami. These protein spots were analyzed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry and electrospray ionization tandem mass spectrometry. Fifteen proteins in Yulmi and eight proteins in Shinjami were identified from the up-regulated (Yulmi vs. Shinjami) or uniquely expressed (only Yulmi or Shinjami) proteins, respectively. In Yulmi, α-amylase and isomerase precursor-like protein were uniquely expressed or up-regulated and activities of α-amylase, monodehydroascorbate reductase, and dehydroascorbate reductase were higher than in Shinjami. In Shinjami, peroxidase precursor and aldo-keto reductase were uniquely expressed or up-regulated and peroxidase and aldo-keto reductase activities were higher than in Yulmi. PSG-RGH7 uniquely expressed only in Shinjami and the cultivar was evaluated more resistant than Yulmi against the root-knot nematode, Meloidogyne incognita (Kofold and White, 1919) Chitwood 1949 on the basis of shoot and root growth. Egg mass formation was 14.9-fold less in Shinjami than in Yulmi. These results provide important clues that can provide a foundation for sweetpotato proteomics and lead to the characterization of the physiological function of differentially expressed proteins.
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Affiliation(s)
- Jeung Joo Lee
- Department of Applied Biology, IALS, Gyeongsang National University, Jinju 660-751, Republic of Korea
| | - Kee Woong Park
- Department of Crop Science, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Youn-Sig Kwak
- Department of Applied Biology, IALS, Gyeongsang National University, Jinju 660-751, Republic of Korea
| | - Jae Young Ahn
- Department of Applied Biology, IALS, Gyeongsang National University, Jinju 660-751, Republic of Korea
| | - Young Hak Jung
- Division of Applied Life Science (BK21 Program), IALS, PMBBRC, Gyeongsang National University, Jinju 660-751, Republic of Korea
| | - Byung-Hyun Lee
- Division of Applied Life Science (BK21 Program), IALS, PMBBRC, Gyeongsang National University, Jinju 660-751, Republic of Korea
| | - Jae Cheol Jeong
- Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Haeng-Soon Lee
- Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Sang-Soo Kwak
- Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea.
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Lim S, Chisholm K, Coffin RH, Peters RD, Al-Mughrabi KI, Wang-Pruski G, Pinto DM. Protein Profiling in Potato (Solanum tuberosum L.) Leaf Tissues by Differential Centrifugation. J Proteome Res 2012; 11:2594-601. [DOI: 10.1021/pr201004k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Sanghyun Lim
- Department of Plant and Animal
Sciences, Nova Scotia Agricultural College, Truro, Nova Scotia, Canada
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Kenneth Chisholm
- National Research Council Institute for Marine Biosciences, Halifax, Nova
Scotia, Canada
| | | | | | | | - Gefu Wang-Pruski
- Department of Plant and Animal
Sciences, Nova Scotia Agricultural College, Truro, Nova Scotia, Canada
| | - Devanand M. Pinto
- National Research Council Institute for Marine Biosciences, Halifax, Nova
Scotia, Canada
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36
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Afify AEMMR, El-Beltagi HS, Aly AA, El-Ansary AE. Antioxidant enzyme activities and lipid peroxidation as biomarker compounds for potato tuber stored by gamma radiation. Asian Pac J Trop Biomed 2012. [DOI: 10.1016/s2221-1691(12)60451-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Vairamani M, Prabhakar S. Mass spectrometry in India. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2012; 18:1-35. [PMID: 22792611 DOI: 10.1255/ejms.1165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This review emphasizes the mass spectrometry research being performed at academic and established research institutions in India. It consists of three main parts covering the work done in organic, atomic and biological mass spectrometry. The review reveals that the use of mass spectrometry techniques started in the middle of the 20th century and was applied to research in the fields of organic, nuclear, geographical and atomic chemistry. Later, with the advent of soft and atmospheric ionization techniques it has been applied to pharmaceutical and biological research. In due course, several research centers with advanced mass spectrometry facilities have been established for specific areas of research such as gas-phase ion chemistry, ion-molecule reactions, proscribed chemicals, pesticide residues, pharmacokinetics, protein/peptide chemistry, nuclear chemistry, geochronological studies, archeology, petroleum industry, proteomics, lipidomics and metabolomics. Day-by-day the mass spectrometry centers/facilities in India have attracted young students for their doctoral research and other advanced research applications.
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Affiliation(s)
- M Vairamani
- National Centre for Mass Spectrometry, Indian Institute of Chemical Technology, Hyderabad-500 007, Andhra Pradesh, India.
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Urbany C, Colby T, Stich B, Schmidt L, Schmidt J, Gebhardt C. Analysis of Natural Variation of the Potato Tuber Proteome Reveals Novel Candidate Genes for Tuber Bruising. J Proteome Res 2011; 11:703-16. [DOI: 10.1021/pr2006186] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Claude Urbany
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Thomas Colby
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Benjamin Stich
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Lysann Schmidt
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Jürgen Schmidt
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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Agrawal GK, Bourguignon J, Rolland N, Ephritikhine G, Ferro M, Jaquinod M, Alexiou KG, Chardot T, Chakraborty N, Jolivet P, Doonan JH, Rakwal R. Plant organelle proteomics: collaborating for optimal cell function. MASS SPECTROMETRY REVIEWS 2011; 30:772-853. [PMID: 21038434 DOI: 10.1002/mas.20301] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 02/02/2010] [Accepted: 02/02/2010] [Indexed: 05/10/2023]
Abstract
Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), P.O. Box 13265, Sanepa, Kathmandu, Nepal.
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Lozano-Juste J, León J. Nitric oxide regulates DELLA content and PIF expression to promote photomorphogenesis in Arabidopsis. PLANT PHYSIOLOGY 2011; 156:1410-23. [PMID: 21562334 PMCID: PMC3135954 DOI: 10.1104/pp.111.177741] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 05/06/2011] [Indexed: 05/19/2023]
Abstract
The transition from etiolated to green seedlings involves a shift from hypocotyl growth-promoting conditions to growth restraint. These changes occur through a complex light-driven process involving multiple and tightly coordinated hormonal signaling pathways. Nitric oxide (NO) has been lately characterized as a regulator of plant development interacting with hormone signaling. Here, we show that Arabidopsis (Arabidopsis thaliana) NO-deficient mutant hypocotyls are longer than those from wild-type seedlings under red light but not under blue or far-red light. Accordingly, exogenous treatment with the NO donor sodium nitroprusside and mutant plants with increased endogenous NO levels resulted in reduced hypocotyl length. In addition to increased hypocotyl elongation, NO deficiency led to increased anthocyanin levels and reduced PHYB content under red light, all processes governed by phytochrome-interacting factors (PIFs). NO-deficient plants accordingly showed an enhanced expression of PIF3, PIF1, and PIF4. Moreover, exogenous NO increased the levels of the gibberellin (GA)-regulated DELLA proteins and shortened hypocotyls, likely through the negative regulation of the GA Insensitive Dwarf1 (GID1)-Sleepy1 (SLY1) module. Consequently, NO-deficient seedlings displayed up-regulation of SLY1, defective DELLA accumulation, and altered GA sensitivity, thus resulting in defective deetiolation under red light. Accumulation of NO in wild-type seedlings undergoing red light-triggered deetiolation and elevated levels of NO in the GA-deficient ga1-3 mutant in darkness suggest a mutual NO-GA antagonism in controlling photomorphogenesis. PHYB-dependent NO production promotes photomorphogenesis by a GID1-GA-SLY1-mediated mechanism based on the coordinated repression of growth-promoting PIF genes and the increase in the content of DELLA proteins.
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41
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Takáč T, Pechan T, Samaj J. Differential proteomics of plant development. J Proteomics 2011; 74:577-88. [PMID: 21315196 DOI: 10.1016/j.jprot.2011.02.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 01/28/2011] [Accepted: 02/01/2011] [Indexed: 10/18/2022]
Abstract
In this mini-review, recent advances in plant developmental proteomics are summarized. The growing interest in plant proteomics continually produces large numbers of developmental studies on plant cell division, elongation, differentiation, and formation of various organs. The brief overview of changes in proteome profiles emphasizes the participation of stress-related proteins in all developmental processes, which substantially changes the view on functional classification of these proteins. Next, it is noteworthy that proteomics helped to recognize some metabolic and housekeeping proteins as important signaling inducers of developmental pathways. Further, cell division and elongation are dependent on proteins involved in membrane trafficking and cytoskeleton dynamics. These protein groups are less prevalently represented in studies concerning cell differentiation and organ formation, which do not target primarily cell division. The synthesis of new proteins, generally observed during developmental processes, is followed by active protein folding. In this respect, disulfide isomerase was found to be commonly up-regulated during several developmental processes. The future progress in plant proteomics requires new and/or complementary approaches including cell fractionation, specific chemical treatments, molecular cloning and subcellular localization of proteins combined with more sensitive methods for protein detection and identification.
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Affiliation(s)
- Tomáš Takáč
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
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42
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Abelenda JA, Navarro C, Prat S. From the model to the crop: genes controlling tuber formation in potato. Curr Opin Biotechnol 2010; 22:287-92. [PMID: 21168321 DOI: 10.1016/j.copbio.2010.11.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 11/25/2010] [Accepted: 11/25/2010] [Indexed: 12/15/2022]
Abstract
Photoperiod regulates many different developmental processes, including floral induction in several species and tuber formation in potato. Research in Arabidopsis led to the identification of FLOWERING LOCUS T (FT) as a main component of the florigen or mobile flowering promoting signal produced in the leaves. A similar mobile signal or tuberigen has been reported to induce tuber formation in potato, recent evidence obtained in our laboratory indicates that a potato homolog of FT encodes this signal. Flowering regulators, like CONSTANS and miR172, also play a role in tuberization, although it remains unclear whether these regulators function in identical pathways. Here, we highlight differential regulation of these genes in flowering and tuberization control and discuss on their possible tuberization-related function.
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Affiliation(s)
- José A Abelenda
- Dpto. de Genética Molecular de Plantas, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, c/Darwin 3, 28049 Madrid, Spain
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Delaplace P, Fauconnier ML, Sergeant K, Dierick JF, Oufir M, van der Wal F, America AHP, Renaut J, Hausman JF, du Jardin P. Potato (Solanum tuberosum L.) tuber ageing induces changes in the proteome and antioxidants associated with the sprouting pattern. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:1273-88. [PMID: 19204031 PMCID: PMC2657538 DOI: 10.1093/jxb/erp008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
During post-harvest storage, potato tubers age as they undergo an evolution of their physiological state influencing their sprouting pattern. In the present study, physiological and biochemical approaches were combined to provide new insights on potato (Solanum tuberosum L. cv. Désirée) tuber ageing. An increase in the physiological age index (PAI) value from 0.14 to 0.83 occurred during storage at 4 degrees C over 270 d. Using this reference frame, a proteomic approach was followed based on two-dimensional electrophoresis. In the experimental conditions of this study, a marked proteolysis of patatin occurred after the PAI reached a value of 0.6. In parallel, several glycolytic enzymes were up-regulated and cellular components influencing protein conformation and the response to stress were altered. The equilibrium between the 20S and 26S forms of the proteasome was modified, the 20S form that recycles oxidized proteins being up-regulated. Two proteins belonging to the cytoskeleton were also differentially expressed during ageing. As most of these changes are also observed in an oxidative stress context, an approach focused on antioxidant compounds and enzymes as well as oxidative damage on polyunsaturated fatty acids and proteins was conducted. All the changes observed during ageing seemed to allow the potato tubers to maintain their radical scavenging activity until the end of the storage period as no accumulation of oxidative damage was observed. These data are interpreted considering the impact of reactive oxygen species on the development and the behaviour of other plant systems undergoing ageing or senescence processes.
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Affiliation(s)
- Pierre Delaplace
- Gembloux Agricultural University, Plant Biology Unit, Avenue de la Faculté d'Agronomie 2A, 5030 Gembloux, Belgium.
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