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Tian F, Wang J, Ding F, Wang L, Yang Y, Bai X, Tan C, Liao X. Comparative transcriptomics and proteomics analysis of the symbiotic germination of Paphiopedilum barbigerum with Epulorhiza sp. FQXY019. Front Microbiol 2024; 15:1358137. [PMID: 38562471 PMCID: PMC10982344 DOI: 10.3389/fmicb.2024.1358137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction Paphiopedilum barbigerum is currently the rarest and most endangered species of orchids in China and has significant ornamental value. The mature seeds of P. barbigerum are difficult to germinate owing to the absence of an endosperm and are highly dependent on mycorrhizal fungi for germination and subsequent development. However, little is known about the regulation mechanisms of symbiosis and symbiotic germination of P. barbigerum seeds. Methods Herein, transcriptomics and proteomics were used to explore the changes in the P. barbigerum seeds after inoculation with (FQXY019 treatment group) or without (control group) Epulorhiza sp. FQXY019 at 90 days after germination. Results Transcriptome sequencing revealed that a total of 10,961 differentially expressed genes (DEGs; 2,599 upregulated and 8,402 downregulated) were identified in the control and FQXY019 treatment groups. These DEGs were mainly involved in carbohydrate, fatty acid, and amino acid metabolism. Furthermore, the expression levels of candidate DEGs related to nodulin, Ca2+ signaling, and plant lectins were significantly affected in P. barbigerum in the FQXY019 treatment groups. Subsequently, tandem mass tag-based quantitative proteomics was performed to recognize the differentially expressed proteins (DEPs), and a total of 537 DEPs (220 upregulated and 317 downregulated) were identified that were enriched in processes including photosynthesis, photosynthesis-antenna proteins, and fatty acid biosynthesis and metabolism. Discussion This study provides novel insight on the mechanisms underlying the in vitro seed germination and protocorm development of P. barbigerum by using a compatible fungal symbiont and will benefit the reintroduction and mycorrhizal symbiotic germination of endangered orchids.
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Affiliation(s)
- Fan Tian
- Guizhou Academy of Forestry, Guiyang, Guizhou, China
- Key Laboratory for Biodiversity Conservation in the Karst Mountain Area of Southwestern China, National Forestry and Grassland Administration, Guiyang, Guizhou, China
| | - Juncai Wang
- Guizhou Academy of Sciences, Guiyang, Guizhou, China
| | - Fangjun Ding
- Guizhou Academy of Forestry, Guiyang, Guizhou, China
- Key Laboratory for Biodiversity Conservation in the Karst Mountain Area of Southwestern China, National Forestry and Grassland Administration, Guiyang, Guizhou, China
| | - Lianhui Wang
- Guizhou Academy of Forestry, Guiyang, Guizhou, China
- Key Laboratory for Biodiversity Conservation in the Karst Mountain Area of Southwestern China, National Forestry and Grassland Administration, Guiyang, Guizhou, China
| | - Yanbing Yang
- Guizhou Academy of Forestry, Guiyang, Guizhou, China
- Key Laboratory for Biodiversity Conservation in the Karst Mountain Area of Southwestern China, National Forestry and Grassland Administration, Guiyang, Guizhou, China
| | - Xinxiang Bai
- College of Forestry, Guizhou University, Guiyang, Guizhou, China
| | - Chengjiang Tan
- Guizhou Maolan National Nature Reserve Administration, Libo, Guizhou, China
| | - Xiaofeng Liao
- Guizhou Academy of Sciences, Guiyang, Guizhou, China
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Wang M, Tang W, Xiang L, Chen X, Shen X, Yin C, Mao Z. Involvement of MdWRKY40 in the defense of mycorrhizal apple against fusarium solani. BMC PLANT BIOLOGY 2022; 22:385. [PMID: 35918651 PMCID: PMC9344649 DOI: 10.1186/s12870-022-03753-z] [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: 09/17/2021] [Accepted: 07/08/2022] [Indexed: 05/06/2023]
Abstract
BACKGROUND Apple (Malus domestica Borkh.) is an important economic crop. The pathological effects of Fusarium solani, a species complex of soilborne pathogens, on the root systems of apple plants was unknown. It was unclear how mycorrhizal apple seedlings resist infection by F. solani. The transcriptional profiles of mycorrhizal and non-mycorrhizal plants infected by F. solani were compared using RNA-Seq. RESULTS Infection with F. solani significantly reduced the dry weight of apple roots, and the roots of mycorrhizal apple plants were less damaged when the plants were infected with F. solani. They also had enhanced activity of antioxidant enzymes and a reduction in the oxidation of membrane lipids. A total of 1839 differentially expressed genes (DEGs) were obtained after mycorrhizal and non-mycorrhizal apple plants were infected with F. solani. A gene ontogeny (GO) analysis showed that most of the DEGs were involved in the binding of ADP and calcium ions. In addition, based on a MapMan analysis, a large number of DEGs were found to be involved in the response of mycorrhizal plants to stress. Among them, the overexpressed transcription factor MdWRKY40 significantly improved the resistance of the apple 'Orin' callus to F. solani and the expression of the resistance gene MdGLU by binding the promoter of MdGLU. CONCLUSION This paper outlines how the inoculation of apple seedlings roots by arbuscular mycorrhizal fungi responded to infection with F. solani at the transcriptional level. In addition, MdWRKY40 played an important role in the resistance of mycorrhizal apple seedlings to infection with F. solani.
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Affiliation(s)
- Mei Wang
- State Key Laboratory of Crop Biology / College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
- Forestry College of Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Weixiao Tang
- State Key Laboratory of Crop Biology / College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Li Xiang
- State Key Laboratory of Crop Biology / College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Xuesen Chen
- State Key Laboratory of Crop Biology / College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Xiang Shen
- State Key Laboratory of Crop Biology / College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Chengmiao Yin
- State Key Laboratory of Crop Biology / College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
| | - Zhiquan Mao
- State Key Laboratory of Crop Biology / College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
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Anandan A, Panda S, Sabarinathan S, Travis AJ, Norton GJ, Price AH. Superior Haplotypes for Early Root Vigor Traits in Rice Under Dry Direct Seeded Low Nitrogen Condition Through Genome Wide Association Mapping. FRONTIERS IN PLANT SCIENCE 2022; 13:911775. [PMID: 35874029 PMCID: PMC9305665 DOI: 10.3389/fpls.2022.911775] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/13/2022] [Indexed: 06/14/2023]
Abstract
Water and land resources have been aggressively exploited in the recent decades to meet the growing demands for food. The changing climate has prompted rice scientists and farmers of the tropics and subtropics to adopt the direct seeded rice (DSR) system. DSR system of rice cultivation significantly reduces freshwater consumption and labor requirements, while increasing system productivity, resource use efficiency, and reducing greenhouse gas emissions. Early root vigor is an essential trait required in an ideal DSR system of rice cultivation to ensure a good crop stand, adequate uptake of water, nutrients and compete with weeds. The aus subpopulation which is adapted for DSR was evaluated to understand the biology of early root growth under limited nitrogen conditions over two seasons under two-time points (14 and 28 days). The correlation study identified a positive association between shoot dry weight and root dry weight. The genome-wide association study was conducted on root traits of 14 and 28 days with 2 million single-nucleotide polymorphisms (SNPs) using an efficient mixed model. QTLs over a significant threshold of p < 0.0001 and a 10% false discovery rate were selected to identify genes involved in root growth related to root architecture and nutrient acquisition from 97 QTLs. Candidate genes under these QTLs were explored. On chromosome 4, around 30 Mbp are two important peptide transporters (PTR5 and PTR6) involved in mobilizing nitrogen in the root during the early vegetative stage. In addition, several P transporters and expansin genes with superior haplotypes are discussed. A novel QTL from 21.12 to 21.46 Mb on chromosome 7 with two linkage disequilibrium (LD) blocks governing root length at 14 days were identified. The QTLs/candidate genes with superior haplotype for early root vigor reported here could be explored further to develop genotypes for DSR conditions.
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Affiliation(s)
- Annamalai Anandan
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, India
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Seed Science (IISS), Bengaluru, India
| | - Siddharth Panda
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, India
- Department of Plant Breeding and Genetics, Odisha University of Agriculture & Technology, Bhubaneswar, India
| | - S. Sabarinathan
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, India
| | - Anthony J. Travis
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Gareth J. Norton
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Adam H. Price
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
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Khalid MHB, Raza MA, Yu HQ, Khan I, Sun FA, Feng LY, Qu JT, Fu FL, Li WC. Expression, Subcellular Localization, and Interactions of CPK Family Genes in Maize. Int J Mol Sci 2019; 20:E6173. [PMID: 31817801 PMCID: PMC6940914 DOI: 10.3390/ijms20246173] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 11/30/2019] [Accepted: 12/05/2019] [Indexed: 12/20/2022] Open
Abstract
Calcium-dependent protein kinase (CPKs) is a key player in the calcium signaling pathway to decode calcium signals into various physiological responses. cDNA sequences of 9 ZmCPK genes were successfully cloned from all four phylogenetic groups in maize. qRT-PCR analysis showed the expression variation of these selected genes under abscisic acid (ABA) and calcium chloride (CaCl2) treatment. Due to the presence of N-myristoylation/palmitoylation sites, the selected ZmCPK members were localized in a plasma membrane. To clarify whether ZmCPK, a key player in calcium signaling, interacts with key players of ABA, protein phosphatase 2Cs (PP2Cs) and the SNF1-related protein kinase 2s (SnRK2s) and mitogen-activated protein kinase (MAPK) signaling pathways in maize, we examined the interaction between 9 CPKs, 8 PP2Cs, 5 SnRKs, and 20 members of the MPK family in maize by using yeast two-hybrid assay. Our results showed that three ZmCPKs interact with three different members of ZmSnRKs while four ZmCPK members had a positive interaction with 13 members of ZmMPKs in different combinations. These four ZmCPK proteins are from three different groups in maize. These findings of physical interactions between ZmCPKs, ZmSnRKs, and ZmMPKs suggested that these signaling pathways do not only have indirect influence but also have direct crosstalk that may involve the defense mechanism in maize. The present study may improve the understanding of signal transduction in plants.
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Affiliation(s)
- Muhammad Hayder Bin Khalid
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (M.H.B.K.); (H.Q.Y.); (F.A.S.); (J.T.Q.)
| | - Muhammad Ali Raza
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (M.A.R.); (L.Y.F.)
| | - Hao Qiang Yu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (M.H.B.K.); (H.Q.Y.); (F.A.S.); (J.T.Q.)
| | - Imran Khan
- Department of Grassland Science, Sichuan Agricultural University, Chengdu 611130, China;
| | - Fu Ai Sun
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (M.H.B.K.); (H.Q.Y.); (F.A.S.); (J.T.Q.)
| | - Ling Yang Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (M.A.R.); (L.Y.F.)
| | - Jing Tao Qu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (M.H.B.K.); (H.Q.Y.); (F.A.S.); (J.T.Q.)
| | - Feng Ling Fu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (M.H.B.K.); (H.Q.Y.); (F.A.S.); (J.T.Q.)
| | - Wan Chen Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (M.H.B.K.); (H.Q.Y.); (F.A.S.); (J.T.Q.)
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Mohanta TK, Yadav D, Khan AL, Hashem A, Abd Allah EF, Al-Harrasi A. Molecular Players of EF-hand Containing Calcium Signaling Event in Plants. Int J Mol Sci 2019; 20:E1476. [PMID: 30909616 PMCID: PMC6471108 DOI: 10.3390/ijms20061476] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 02/21/2019] [Accepted: 02/27/2019] [Indexed: 11/28/2022] Open
Abstract
Ca2+ is a universal second messenger that plays a pivotal role in diverse signaling mechanisms in almost all life forms. Since the evolution of life from an aquatic to a terrestrial environment, Ca2+ signaling systems have expanded and diversified enormously. Although there are several Ca2+ sensing molecules found in a cell, EF-hand containing proteins play a principal role in calcium signaling event in plants. The major EF-hand containing proteins are calmodulins (CaMs), calmodulin like proteins (CMLs), calcineurin B-like (CBL) and calcium dependent protein kinases (CDPKs/CPKs). CaMs and CPKs contain calcium binding conserved D-x-D motifs in their EF-hands (one motif in each EF-hand) whereas CMLs contain a D-x₃-D motif in the first and second EF-hands that bind the calcium ion. Calcium signaling proteins form a complex interactome network with their target proteins. The CMLs are the most primitive calcium binding proteins. During the course of evolution, CMLs are evolved into CaMs and subsequently the CaMs appear to have merged with protein kinase molecules to give rise to calcium dependent protein kinases with distinct and multiple new functions. Ca2+ signaling molecules have evolved in a lineage specific manner with several of the calcium signaling genes being lost in the monocot lineage.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman.
| | - Dhananjay Yadav
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea.
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman.
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
- Mycology and Plant Survey Department, Plant Pathology Research Institute, ARC, Giza 12511, Egypt.
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agriculture Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman.
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Montero H, Choi J, Paszkowski U. Arbuscular mycorrhizal phenotyping: the dos and don'ts. THE NEW PHYTOLOGIST 2019; 221:1182-1186. [PMID: 30222191 PMCID: PMC7463165 DOI: 10.1111/nph.15489] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 09/07/2018] [Indexed: 05/20/2023]
Affiliation(s)
- Hector Montero
- Department of Plant SciencesUniversity of CambridgeCambridgeCB2 3EAUK
| | - Jeongmin Choi
- Department of Plant SciencesUniversity of CambridgeCambridgeCB2 3EAUK
| | - Uta Paszkowski
- Department of Plant SciencesUniversity of CambridgeCambridgeCB2 3EAUK
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7
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Wang J, Wang S, Hu K, Yang J, Xin X, Zhou W, Fan J, Cui F, Mou B, Zhang S, Wang G, Sun W. The Kinase OsCPK4 Regulates a Buffering Mechanism That Fine-Tunes Innate Immunity. PLANT PHYSIOLOGY 2018; 176:1835-1849. [PMID: 29242377 PMCID: PMC5813524 DOI: 10.1104/pp.17.01024] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/12/2017] [Indexed: 05/06/2023]
Abstract
The calcium-dependent protein kinase OsCPK4 has been demonstrated to play important roles in salt and drought tolerance, plant growth, and development in rice (Oryza sativa). However, little is known about molecular mechanisms underlying OsCPK4 function in rice immunity. In this study, we demonstrated that the generation of oxidative burst and pathogenesis-related gene expression triggered by microbe-associated molecular patterns were significantly enhanced in the oscpk4 mutants. These mutant lines are more resistant to bacterial blight and fungal blast diseases than the wild-type plants, indicating that OsCPK4 negatively regulates innate immunity in rice. OsCPK4 was further identified to interact with a receptor-like cytoplasmic kinase OsRLCK176. OsRLCK176 accumulation is negatively regulated by OsCPK4. Interestingly, the kinase-dead OsCPK4 promotes OsRLCK176 degradation more strongly than the wild-type protein. OsCPK4 and OsRLCK176 mutually phosphorylate each other and form a feedback loop. Moreover, the kinase activity and phosphorylation of OsCPK4 and OsRLCK176 contribute to the stability of OsRLCK176. These findings indicate that the kinase-inactive OsCPK4 promotes OsRLCK176 degradation and restricts plant defenses, whereas the activation of OsCPK4-OsRLCK176 phosphorylation circuit invalidates the OsRLCK176 degradation machinery, thus enhancing plant immunity. Collectively, the study proposes a novel defense buffering mechanism mediated by OsCPK4, which fine-tunes microbe-associated molecular pattern-triggered immunity in rice.
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Affiliation(s)
- Jiyang Wang
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China
| | - Shanzhi Wang
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China
| | - Ke Hu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jun Yang
- Rice Research Institute, Shandong Academy of Agricultural Science, Jinan 250100, Shandong Province, China
| | - Xiaoyun Xin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wenqing Zhou
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China
| | - Jiangbo Fan
- Department of Plant Pathology, Ohio State University, Columbus, Ohio 43210
| | - Fuhao Cui
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China
| | - Baohui Mou
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China
| | - Shiyong Zhang
- Rice Research Institute, Shandong Academy of Agricultural Science, Jinan 250100, Shandong Province, China
| | - Guoliang Wang
- Department of Plant Pathology, Ohio State University, Columbus, Ohio 43210
| | - Wenxian Sun
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China
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Wen Z, Tyerman SD, Dechorgnat J, Ovchinnikova E, Dhugga KS, Kaiser BN. Maize NPF6 Proteins Are Homologs of Arabidopsis CHL1 That Are Selective for Both Nitrate and Chloride. THE PLANT CELL 2017; 29:2581-2596. [PMID: 28887406 PMCID: PMC5774558 DOI: 10.1105/tpc.16.00724] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 07/21/2017] [Accepted: 09/05/2017] [Indexed: 05/02/2023]
Abstract
Nitrate uptake by plant cells requires both high- and low-affinity transport activities. Arabidopsis thaliana nitrate transporter 1/peptide transporter family (NPF) 6.3 is a dual-affinity plasma membrane transport protein that has both high- and low-affinity functions. At-NPF6.3 imports and senses nitrate and is regulated by phosphorylation at Thr-101 (T101). A detailed functional analysis of two maize (Zea mays) homologs of At-NPF6.3 (Zm-NPF6.6 and Zm-NPF6.4) showed that Zm-NPF6.6 was a pH-dependent nonbiphasic high-affinity nitrate-specific transport protein. By contrast, maize NPF6.4 was a low-affinity nitrate transporter with efflux activity. When supplied chloride, NPF6.4 switched to a high-affinity chloride selective transporter, while NPF6.6 had only a low-affinity chloride transport activity. Structural predictions identified a nitrate binding His (H362) in NPF6.6 but not in NPF6.4. Mutation of NPF6.4 Tyr-370 to His (Y370H) resulted in saturable high-affinity nitrate transport activity and nitrate selectivity. Loss of H362 in NPF6.6 (H362Y) eliminated both nitrate and chloride transport. Furthermore, alterations to Thr-104, a conserved phosphorylation site in NPF6.6, resulted in a similar high-affinity nitrate transport activity with increased Km, whereas equivalent changes in NPF6.4 (T106) disrupted high-affinity chloride transport activity. NPF6 proteins exhibit different substrate specificity in plants and regulate nitrate transport affinity/selectivity using a conserved His residue.
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Affiliation(s)
- Zhengyu Wen
- School of Life and Environmental Sciences, University of Sydney, Camden, NSW 2570, Australia
- School of Agriculture, Food, and Wine, University of Adelaide, Urrbrae, SA 5064, Australia
| | - Stephen D Tyerman
- Australian Research Centre of Excellence in Plant Energy Biology, School of Agriculture, Food, and Wine, University of Adelaide, Urrbrae, SA 5064, Australia
| | - Julie Dechorgnat
- School of Life and Environmental Sciences, University of Sydney, Camden, NSW 2570, Australia
| | - Evgenia Ovchinnikova
- School of Life and Environmental Sciences, University of Sydney, Camden, NSW 2570, Australia
| | | | - Brent N Kaiser
- School of Life and Environmental Sciences, University of Sydney, Camden, NSW 2570, Australia
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Podgorny OV, Lazarev VN. Laser microdissection: A promising tool for exploring microorganisms and their interactions with hosts. J Microbiol Methods 2017; 138:82-92. [PMID: 26775287 DOI: 10.1016/j.mimet.2016.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 11/11/2015] [Accepted: 01/01/2016] [Indexed: 12/14/2022]
Abstract
Laser microdissection is a method that allows for the isolation of homogenous cell populations from their native niches in tissues for downstream molecular assays. This method is widely used for genomic analysis, gene expression profiling and proteomic and metabolite assays in various fields of biology, but it remains an uncommon approach in microbiological research. In spite of the limited number of publications, laser microdissection was shown to be an extremely useful method for studying host-microorganism interactions in animals and plants, investigating bacteria within biofilms, identifying uncultivated bacteria and performing single prokaryotic cell analysis. The current paper describes the methodological aspects of commercially available laser microdissection instruments and representative examples that demonstrate the advantages of this method for resolving a variety of issues in microbiology.
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Affiliation(s)
- Oleg V Podgorny
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str., Moscow 119435, Russia; Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, 26 Vavilov Str., Moscow 119334, Russia.
| | - Vassili N Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str., Moscow 119435, Russia
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Almadanim MC, Alexandre BM, Rosa MTG, Sapeta H, Leitão AE, Ramalho JC, Lam TT, Negrão S, Abreu IA, Oliveira MM. Rice calcium-dependent protein kinase OsCPK17 targets plasma membrane intrinsic protein and sucrose-phosphate synthase and is required for a proper cold stress response. PLANT, CELL & ENVIRONMENT 2017; 40:1197-1213. [PMID: 28102545 DOI: 10.1111/pce.12916] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/10/2017] [Accepted: 01/15/2017] [Indexed: 05/20/2023]
Abstract
Calcium-dependent protein kinases (CDPKs) are involved in plant tolerance mechanisms to abiotic stresses. Although CDPKs are recognized as key messengers in signal transduction, the specific role of most members of this family remains unknown. Here, we test the hypothesis that OsCPK17 plays a role in rice cold stress response by analysing OsCPK17 knockout, silencing and overexpressing rice lines under low temperature. Altered OsCPK17 gene expression compromises cold tolerance performance, without affecting the expression of key cold stress-inducible genes. A comparative phosphoproteomic approach led to the identification of six potential in vivo OsCPK17 targets, which are associated with sugar and nitrogen metabolism, and with osmotic regulation. To test direct interaction, in vitro kinase assays were performed, showing that the sucrose-phosphate synthase OsSPS4 and the aquaporin OsPIP2;1/OsPIP2;6 are phosphorylated by OsCPK17 in a calcium-dependent manner. Altogether, our data indicates that OsCPK17 is required for a proper cold stress response in rice, likely affecting the activity of membrane channels and sugar metabolism.
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Affiliation(s)
- M Cecília Almadanim
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Bruno M Alexandre
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - Margarida T G Rosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Helena Sapeta
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - António E Leitão
- Plant Stress and Biodiversity, Linking Landscape, Environment, Agriculture and Food (LEAF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia, Universidade de Lisboa, 2784-505, Oeiras, Portugal
| | - José C Ramalho
- Plant Stress and Biodiversity, Linking Landscape, Environment, Agriculture and Food (LEAF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia, Universidade de Lisboa, 2784-505, Oeiras, Portugal
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520-8024, USA
- MS and Proteomics Resource, WM Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT, 06520-8024, USA
| | - Sónia Negrão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Isabel A Abreu
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - M Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
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11
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Carotenuto G, Chabaud M, Miyata K, Capozzi M, Takeda N, Kaku H, Shibuya N, Nakagawa T, Barker DG, Genre A. The rice LysM receptor-like kinase OsCERK1 is required for the perception of short-chain chitin oligomers in arbuscular mycorrhizal signaling. THE NEW PHYTOLOGIST 2017; 214:1440-1446. [PMID: 28369864 DOI: 10.1111/nph.14539] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/28/2017] [Indexed: 05/18/2023]
Abstract
The rice lysin-motif (LysM) receptor-like kinase OsCERK1 is now known to have a dual role in both pathogenic and symbiotic interactions. Following the recent discovery that the Oscerk1 mutant is unable to host arbuscular mycorrhizal (AM) fungi, we have examined whether OsCERK1 is directly involved in the perception of the short-chain chitin oligomers (Myc-COs) identified in AM fungal exudates and shown to activate nuclear calcium (Ca2+ ) spiking in the rice root epidermis. An Oscerk1 knockout mutant expressing the cameleon NLS-YC2.60 was used to monitor nuclear Ca2+ signaling following root treatment with either crude fungal exudates or purified Myc-COs. Compared with wild-type rice, Ca2+ spiking responses to AM fungal elicitation were absent in root atrichoblasts of the Oscerk1 mutant. By contrast, rice lines mutated in OsCEBiP, encoding the LysM receptor-like protein which associates with OsCERK1 to perceive chitin elicitors of the host immune defense pathway, responded positively to Myc-COs. These findings provide direct evidence that the bi-functional OsCERK1 plays a central role in perceiving short-chain Myc-CO signals and activating the downstream conserved symbiotic signal transduction pathway.
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Affiliation(s)
- Gennaro Carotenuto
- Department of Life Sciences and Systems Biology, University of Torino, Torino, 10125, Italy
| | - Mireille Chabaud
- Laboratory of Plant-Microbe Interactions (LIPM), INRA-CNRS-Toulouse University, Castanet-Tolosan, 31326, France
| | - Kana Miyata
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571, Japan
| | - Martina Capozzi
- Department of Life Sciences and Systems Biology, University of Torino, Torino, 10125, Italy
| | - Naoya Takeda
- National Institute for Basic Biology (NIBB)/SOKENDAI, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Hanae Kaku
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571, Japan
| | - Naoto Shibuya
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571, Japan
| | - Tomomi Nakagawa
- National Institute for Basic Biology (NIBB)/SOKENDAI, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - David G Barker
- Laboratory of Plant-Microbe Interactions (LIPM), INRA-CNRS-Toulouse University, Castanet-Tolosan, 31326, France
| | - Andrea Genre
- Department of Life Sciences and Systems Biology, University of Torino, Torino, 10125, Italy
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12
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Bundó M, Coca M. Calcium-dependent protein kinase OsCPK10 mediates both drought tolerance and blast disease resistance in rice plants. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2963-2975. [PMID: 28472292 PMCID: PMC5853374 DOI: 10.1093/jxb/erx145] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/05/2017] [Indexed: 05/21/2023]
Abstract
Plant growth and productivity is negatively affected by different stresses. Most stresses trigger calcium signals that initiate acclimation responses in plants. The multigene family of plant calcium-dependent protein kinases (CPKs) functions in multiple stress responses by transducing calcium signals into phosphorylation events. This work reports that the OsCPK10 isoform positively mediates tolerance to different stresses in rice plants by enhancing their antioxidant capacity and protecting them from reactive oxygen species (ROS) damage, with the uncontrolled generation of ROS being a common feature of these stresses. Here, we show that the constitutive accumulation of an HA-tagged OsCPK10 full-length protein enhances the hydrogen peroxide detoxifying capacity of rice plants during desiccation. This is achived by modulating the accumulation of catalase proteins, which reduces the extent of lipid peroxidation and protects the integrity of cell membranes, resulting in drought tolerance. OsCPK10HA accumulation also confers blast disease resistance by interfering with fungal necrotrophic growth via a reduction in the accumulation of hydrogen peroxide. Furthermore, we show by bimolecular complementation assays that OsCPK10 is a plasma membrane protein that physically interacts in vivo with catalase A. OsCPK10 therefore appears to be a good molecular target to improve tolerance to abiotic stresses as well as to blast disease, which limit rice crop productivity.
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Affiliation(s)
| | - María Coca
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus de la UAB, Bellaterra, Barcelona, Spain
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13
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Mauch-Mani B, Baccelli I, Luna E, Flors V. Defense Priming: An Adaptive Part of Induced Resistance. ANNUAL REVIEW OF PLANT BIOLOGY 2017; 68:485-512. [PMID: 28226238 DOI: 10.1146/annurev-arplant-042916-041132] [Citation(s) in RCA: 428] [Impact Index Per Article: 61.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Priming is an adaptive strategy that improves the defensive capacity of plants. This phenomenon is marked by an enhanced activation of induced defense mechanisms. Stimuli from pathogens, beneficial microbes, or arthropods, as well as chemicals and abiotic cues, can trigger the establishment of priming by acting as warning signals. Upon stimulus perception, changes may occur in the plant at the physiological, transcriptional, metabolic, and epigenetic levels. This phase is called the priming phase. Upon subsequent challenge, the plant effectively mounts a faster and/or stronger defense response that defines the postchallenge primed state and results in increased resistance and/or stress tolerance. Priming can be durable and maintained throughout the plant's life cycle and can even be transmitted to subsequent generations, therefore representing a type of plant immunological memory.
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Affiliation(s)
- Brigitte Mauch-Mani
- Institute of Biology, Faculty of Science, University of Neuchâtel, 2000 Neuchâtel, Switzerland; ,
| | - Ivan Baccelli
- Institute of Biology, Faculty of Science, University of Neuchâtel, 2000 Neuchâtel, Switzerland; ,
| | - Estrella Luna
- Plant Production and Protection (P3) Institute for Translational Plant and Soil Biology, Department of Animal and Plant Sciences, The University of Sheffield, Sheffield S10 2TN, United Kingdom;
| | - Victor Flors
- Metabolic Integration and Cell Signaling Group, Departamento de Ciencias Agrarias y del Medio Natural, Universitat Jaume I, 12071 Castellón, Spain;
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14
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Sheshadri SA, Nishanth MJ, Simon B. Stress-Mediated cis-Element Transcription Factor Interactions Interconnecting Primary and Specialized Metabolism in planta. FRONTIERS IN PLANT SCIENCE 2016; 7:1725. [PMID: 27933071 PMCID: PMC5122738 DOI: 10.3389/fpls.2016.01725] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 11/02/2016] [Indexed: 05/07/2023]
Abstract
Plant specialized metabolites are being used worldwide as therapeutic agents against several diseases. Since the precursors for specialized metabolites come through primary metabolism, extensive investigations have been carried out to understand the detailed connection between primary and specialized metabolism at various levels. Stress regulates the expression of primary and specialized metabolism genes at the transcriptional level via transcription factors binding to specific cis-elements. The presence of varied cis-element signatures upstream to different stress-responsive genes and their transcription factor binding patterns provide a prospective molecular link among diverse metabolic pathways. The pattern of occurrence of these cis-elements (overrepresentation/common) decipher the mechanism of stress-responsive upregulation of downstream genes, simultaneously forming a molecular bridge between primary and specialized metabolisms. Though many studies have been conducted on the transcriptional regulation of stress-mediated primary or specialized metabolism genes, but not much data is available with regard to cis-element signatures and transcription factors that simultaneously modulate both pathway genes. Hence, our major focus would be to present a comprehensive analysis of the stress-mediated interconnection between primary and specialized metabolism genes via the interaction between different transcription factors and their corresponding cis-elements. In future, this study could be further utilized for the overexpression of the specific transcription factors that upregulate both primary and specialized metabolism, thereby simultaneously improving the yield and therapeutic content of plants.
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Affiliation(s)
| | | | - Bindu Simon
- School of Chemical and Biotechnology, SASTRA UniversityThanjavur, India
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15
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de Michele R, McFarlane HE, Parsons HT, Meents MJ, Lao J, González Fernández-Niño SM, Petzold CJ, Frommer WB, Samuels AL, Heazlewood JL. Free-Flow Electrophoresis of Plasma Membrane Vesicles Enriched by Two-Phase Partitioning Enhances the Quality of the Proteome from Arabidopsis Seedlings. J Proteome Res 2016; 15:900-13. [PMID: 26781341 DOI: 10.1021/acs.jproteome.5b00876] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The plant plasma membrane is the interface between the cell and its environment undertaking a range of important functions related to transport, signaling, cell wall biosynthesis, and secretion. Multiple proteomic studies have attempted to capture the diversity of proteins in the plasma membrane using biochemical fractionation techniques. In this study, two-phase partitioning was combined with free-flow electrophoresis to produce a population of highly purified plasma membrane vesicles that were subsequently characterized by tandem mass spectroscopy. This combined high-quality plasma membrane isolation technique produced a reproducible proteomic library of over 1000 proteins with an extended dynamic range including plasma membrane-associated proteins. The approach enabled the detection of a number of putative plasma membrane proteins not previously identified by other studies, including peripheral membrane proteins. Utilizing multiple data sources, we developed a PM-confidence score to provide a value indicating association to the plasma membrane. This study highlights over 700 proteins that, while seemingly abundant at the plasma membrane, are mostly unstudied. To validate this data set, we selected 14 candidates and transiently localized 13 to the plasma membrane using a fluorescent tag. Given the importance of the plasma membrane, this data set provides a valuable tool to further investigate important proteins. The mass spectrometry data are available via ProteomeXchange, identifier PXD001795.
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Affiliation(s)
- Roberto de Michele
- Department of Plant Biology, Carnegie Institution for Science , Stanford, California 94305, United States.,Institute of Biosciences and Bioresources (CNR-IBBR), National Research Council of Italy , Palermo 90129, Italy
| | - Heather E McFarlane
- Department of Botany, University of British Columbia , Vancouver, BC V6T 1Z4, Canada.,Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany
| | - Harriet T Parsons
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.,Department of Plant and Environmental Sciences, University of Copenhagen , Copenhagen C-1871, Denmark
| | - Miranda J Meents
- Department of Botany, University of British Columbia , Vancouver, BC V6T 1Z4, Canada
| | - Jeemeng Lao
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Susana M González Fernández-Niño
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Christopher J Petzold
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution for Science , Stanford, California 94305, United States
| | - A Lacey Samuels
- Department of Botany, University of British Columbia , Vancouver, BC V6T 1Z4, Canada
| | - Joshua L Heazlewood
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.,ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne , Melbourne, Victoria 3010, Australia
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16
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Jaiswal V, Gahlaut V, Mathur S, Agarwal P, Khandelwal MK, Khurana JP, Tyagi AK, Balyan HS, Gupta PK. Identification of Novel SNP in Promoter Sequence of TaGW2-6A Associated with Grain Weight and Other Agronomic Traits in Wheat (Triticum aestivum L.). PLoS One 2015; 10:e0129400. [PMID: 26076351 PMCID: PMC4468092 DOI: 10.1371/journal.pone.0129400] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 05/07/2015] [Indexed: 11/18/2022] Open
Abstract
TaGW2 is an orthologue of rice gene OsGW2, which encodes E3 RING ubiquitin ligase and controls the grain size in rice. In wheat, three copies of TaGW2 have been identified and mapped on wheat homoeologous group 6 viz. TaGW2-6A, TaGW2-6B and TaGW2-6D. In the present study, using as many as 207 Indian wheat genotypes, we identified four SNPs including two novel SNPs (SNP-988 and SNP-494) in the promoter sequence of TaGW2-6A. All the four SNPs were G/A or A/G substitutions (transitions). Out of the four SNPs, SNP-494 was causal, since it was found associated with grain weight. The mean TGW (41.1 g) of genotypes with the allele SNP-494_A was significantly higher than mean TGW (38.6 g) of genotypes with the allele SNP-494_G. SNP-494 also regulates the expression of TaGW2-6A so that the wheat genotypes with SNP-494_G have higher expression and lower TGW and the genotypes with SNP-494_A have lower expression but higher TGW. Besides, SNP-494 was also found associated with grain length-width ratio, awn length, spike length, grain protein content, peduncle length and plant height. This suggested that gene TaGW2-6A not only controls grain size, but also controls other agronomic traits. In the promoter region, SNP-494 was present in 'CGCG' motif that plays an important role in Ca2+/calmodulin mediated regulation of genes. A user-friendly CAPS marker was also developed to identify the desirable allele of causal SNP (SNP-494) for use in marker-assisted selection for improvement of grain weight in wheat. Using four SNPs, five haplotypes were identified; of these, Hap_5 (G_A_G_A) was found to be a desirable haplotype having significantly higher grain weight (41.13g) relative to other four haplotypes (36.33-39.16 g).
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Affiliation(s)
- Vandana Jaiswal
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Vijay Gahlaut
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Saloni Mathur
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi, India
| | - Priyanka Agarwal
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | | | - Jitendra Paul Khurana
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | | | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
- * E-mail:
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17
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Manimaran P, Mangrauthia SK, Sundaram RM, Balachandran SM. Constitutive expression and silencing of a novel seed specific calcium dependent protein kinase gene in rice reveals its role in grain filling. JOURNAL OF PLANT PHYSIOLOGY 2015; 174:41-8. [PMID: 25462965 DOI: 10.1016/j.jplph.2014.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/20/2014] [Accepted: 09/20/2014] [Indexed: 05/04/2023]
Abstract
Ca(2+) sensor protein kinases are prevalent in most plant species including rice. They play diverse roles in plant signaling mechanism. Thirty one CDPK genes have been identified in rice and some are functionally characterized. In the present study, the newly identified rice CDPK gene OsCPK31 was functionally validated by overexpression and silencing in Taipei 309 rice cultivar. Spikelets of overexpressing plants showed hard dough stage within 15d after pollination (DAP) with rapid grain filling and early maturation. Scanning electron microscopy of endosperm during starch granule formation confirmed early grain filling. Further, seeds of overexpressing transgenic lines matured early (20-22 DAP) and the average number of maturity days reduced significantly. On the other hand, silencing lines showed more number of unfilled spikelet without any difference in maturity duration. It will be interesting to further decipher the role of OsCPK31 in biological pathways associated with distribution of photosynthetic assimilates during grain filling stage.
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Affiliation(s)
- P Manimaran
- Biotechnology Laboratory, Directorate of Rice Research, Rajendranagar, Hyderabad 500 030, Andhra Pradesh, India
| | - Satendra K Mangrauthia
- Biotechnology Laboratory, Directorate of Rice Research, Rajendranagar, Hyderabad 500 030, Andhra Pradesh, India
| | - R M Sundaram
- Biotechnology Laboratory, Directorate of Rice Research, Rajendranagar, Hyderabad 500 030, Andhra Pradesh, India
| | - S M Balachandran
- Biotechnology Laboratory, Directorate of Rice Research, Rajendranagar, Hyderabad 500 030, Andhra Pradesh, India.
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18
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The CarERF genes in chickpea (Cicer arietinum L.) and the identification of CarERF116 as abiotic stress responsive transcription factor. Funct Integr Genomics 2014; 15:27-46. [PMID: 25274312 DOI: 10.1007/s10142-014-0399-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 08/21/2014] [Accepted: 08/31/2014] [Indexed: 10/24/2022]
Abstract
The AP2/ERF family is one of the largest transcription factor gene families that are involved in various plant processes, especially in response to biotic and abiotic stresses. Complete genome sequences of one of the world's most important pulse crops chickpea (Cicer arietinum L.), has provided an important opportunity to identify and characterize genome-wide ERF genes. In this study, we identified 120 putative ERF genes from chickpea. The genomic organization of the chickpea ERF genes suggested that the gene family might have been expanded through the segmental duplications. The 120 member ERF family was classified into eleven distinct groups (I-X and VI-L). Transcriptional factor CarERF116, which is differentially expressed between drought tolerant and susceptible chickpea cultivar under terminal drought stress has been identified and functionally characterized. The CarERF116 encodes a putative protein of 241 amino acids and classified into group IX of ERF family. An in vitro CarERF116 protein-DNA binding assay demonstrated that CarERF116 protein specifically interacts with GCC box. We demonstrate that CarERF116 is capable of transactivation activity of and show that the functional transcriptional domain lies at the C-terminal region of the CarERF116. In transgenic Arabidopsis plants overexpressing CarERF116, significant up-regulation of several stress related genes were observed. These plants also exhibit resistance to osmotic stress and reduced sensitivity to ABA during seed germination. Based on these findings, we conclude that CarERF116 is an abiotic stress responsive gene, which plays an important role in stress tolerance. In addition, the present study leads to genome-wide identification and evolutionary analyses of chickpea ERF gene family, which will facilitate further research on this important group of genes and provides valuable resources for comparative genomics among the grain legumes.
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19
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Xie K, Chen J, Wang Q, Yang Y. Direct phosphorylation and activation of a mitogen-activated protein kinase by a calcium-dependent protein kinase in rice. THE PLANT CELL 2014; 26:3077-89. [PMID: 25035404 PMCID: PMC4145133 DOI: 10.1105/tpc.114.126441] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/18/2014] [Accepted: 06/16/2014] [Indexed: 05/18/2023]
Abstract
The mitogen-activated protein kinase (MAPK) is a pivotal point of convergence for many signaling pathways in eukaryotes. In the classical MAPK cascade, a signal is transmitted via sequential phosphorylation and activation of MAPK kinase kinase, MAPK kinase (MKK), and MAPK. The activation of MAPK is dependent on dual phosphorylation of a TXY motif by an MKK, which is considered the sole kinase to phosphorylate and activate MAPK. Here, we report a novel regulatory mechanism of MAPK phosphorylation and activation besides the canonical MAPK cascade. A rice (Oryza sativa) calcium-dependent protein kinase (CDPK), CPK18, was identified as an upstream kinase of MAPK (MPK5) in vitro and in vivo. Curiously, CPK18 was shown to phosphorylate and activate MPK5 without affecting the phosphorylation of its TXY motif. Instead, CPK18 was found to predominantly phosphorylate two Thr residues (Thr-14 and Thr-32) that are widely conserved in MAPKs from land plants. Further analyses reveal that the newly identified CPK18-MPK5 pathway represses defense gene expression and negatively regulates rice blast resistance. Our results suggest that land plants have evolved an MKK-independent phosphorylation pathway that directly connects calcium signaling to the MAPK machinery.
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Affiliation(s)
- Kabin Xie
- Department of Plant Pathology and Environmental Microbiology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Jianping Chen
- Department of Plant Pathology and Environmental Microbiology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Qin Wang
- Department of Plant Pathology and Environmental Microbiology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Yinong Yang
- Department of Plant Pathology and Environmental Microbiology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
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20
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Campo S, Baldrich P, Messeguer J, Lalanne E, Coca M, San Segundo B. Overexpression of a Calcium-Dependent Protein Kinase Confers Salt and Drought Tolerance in Rice by Preventing Membrane Lipid Peroxidation. PLANT PHYSIOLOGY 2014; 165:688-704. [PMID: 24784760 PMCID: PMC4044838 DOI: 10.1104/pp.113.230268] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 05/01/2014] [Indexed: 05/18/2023]
Abstract
The OsCPK4 gene is a member of the complex gene family of calcium-dependent protein kinases in rice (Oryza sativa). Here, we report that OsCPK4 expression is induced by high salinity, drought, and the phytohormone abscisic acid. Moreover, a plasma membrane localization of OsCPK4 was observed by transient expression assays of green fluorescent protein-tagged OsCPK4 in onion (Allium cepa) epidermal cells. Overexpression of OsCPK4 in rice plants significantly enhances tolerance to salt and drought stress. Knockdown rice plants, however, are severely impaired in growth and development. Compared with control plants, OsCPK4 overexpressor plants exhibit stronger water-holding capability and reduced levels of membrane lipid peroxidation and electrolyte leakage under drought or salt stress conditions. Also, salt-treated OsCPK4 seedlings accumulate less Na+ in their roots. We carried out microarray analysis of transgenic rice overexpressing OsCPK4 and found that overexpression of OsCPK4 has a low impact on the rice transcriptome. Moreover, no genes were found to be commonly regulated by OsCPK4 in roots and leaves of rice plants. A significant number of genes involved in lipid metabolism and protection against oxidative stress appear to be up-regulated by OsCPK4 in roots of overexpressor plants. Meanwhile, OsCPK4 overexpression has no effect on the expression of well-characterized abiotic stress-associated transcriptional regulatory networks (i.e. ORYZA SATIVA DEHYDRATION-RESPONSIVE ELEMENT BINDING PROTEIN1 and ORYZA SATIVA No Apical Meristem, Arabidopsis Transcription Activation Factor1-2, Cup-Shaped Cotyledon6 genes) and LATE EMBRYOGENESIS ABUNDANT genes in their roots. Taken together, our data show that OsCPK4 functions as a positive regulator of the salt and drought stress responses in rice via the protection of cellular membranes from stress-induced oxidative damage.
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Affiliation(s)
- Sonia Campo
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, Campus UAB, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain (S.C., P.B., J.M., M.C., B.S.S.); andOryzon Genomics, Cornella de Llobregat, 08940 Barcelona, Spain (E.L.)
| | - Patricia Baldrich
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, Campus UAB, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain (S.C., P.B., J.M., M.C., B.S.S.); andOryzon Genomics, Cornella de Llobregat, 08940 Barcelona, Spain (E.L.)
| | - Joaquima Messeguer
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, Campus UAB, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain (S.C., P.B., J.M., M.C., B.S.S.); andOryzon Genomics, Cornella de Llobregat, 08940 Barcelona, Spain (E.L.)
| | - Eric Lalanne
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, Campus UAB, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain (S.C., P.B., J.M., M.C., B.S.S.); andOryzon Genomics, Cornella de Llobregat, 08940 Barcelona, Spain (E.L.)
| | - María Coca
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, Campus UAB, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain (S.C., P.B., J.M., M.C., B.S.S.); andOryzon Genomics, Cornella de Llobregat, 08940 Barcelona, Spain (E.L.)
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, Campus UAB, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain (S.C., P.B., J.M., M.C., B.S.S.); andOryzon Genomics, Cornella de Llobregat, 08940 Barcelona, Spain (E.L.)
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Jiang S, Zhang D, Wang L, Pan J, Liu Y, Kong X, Zhou Y, Li D. A maize calcium-dependent protein kinase gene, ZmCPK4, positively regulated abscisic acid signaling and enhanced drought stress tolerance in transgenic Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 71:112-20. [PMID: 23911729 DOI: 10.1016/j.plaphy.2013.07.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/10/2013] [Indexed: 05/21/2023]
Abstract
Calcium-dependent protein kinases (CDPKs) play essential roles in calcium-mediated signal transductions in plant response to abiotic stress. Several members have been identified to be regulators for plants response to abscisic acid (ABA) signaling. Here, we isolated a subgroup I CDPK gene, ZmCPK4, from maize. Quantitative real time PCR (qRT-PCR) analysis revealed that the ZmCPK4 transcripts were induced by various stresses and signal molecules. Transient and stable expression of the ZmCPK4-GFP fusion proteins revealed ZmCPK4 localized to the membrane. Moreover, overexpression of ZmCPK4 in the transgenic Arabidopsis enhanced ABA sensitivity in seed germination, seedling growth and stomatal movement. The transgenic plants also enhanced drought stress tolerance. Taken together, the results suggest that ZmCPK4 might be involved in ABA-mediated regulation of stomatal closure in response to drought stress.
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Affiliation(s)
- Shanshan Jiang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, 61 Dai Zong Street, Tai'an, 271018 Shandong, PR China
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Bai H, Euring D, Volmer K, Janz D, Polle A. The nitrate transporter (NRT) gene family in poplar. PLoS One 2013; 8:e72126. [PMID: 23977227 PMCID: PMC3747271 DOI: 10.1371/journal.pone.0072126] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 07/03/2013] [Indexed: 11/29/2022] Open
Abstract
Nitrate is an important nutrient required for plant growth. It also acts as a signal regulating plant development. Nitrate is actively taken up and transported by nitrate transporters (NRT), which form a large family with many members and distinct functions. In contrast to Arabidopsis and rice there is little information about the NRT family in woody plants such as Populus. In this study, a comprehensive analysis of the Populus NRT family was performed. Sixty-eight PtNRT1/PTR, 6 PtNRT2, and 5 PtNRT3 genes were identified in the P. trichocarpa genome. Phylogenetic analysis confirmed that the genes of the NRT family are divided into three clades: NRT1/PTR with four subclades, NRT2, and NRT3. Topological analysis indicated that all members of PtNRT1/PTR and PtNRT2 have 8 to 12 trans-membrane domains, whereas the PtNRT3 proteins have no or up to two trans-membrane domains. Four PtNRT3 members were predicted as secreted proteins. Microarray analyses revealed tissue-specific expression patterns of PtNRT genes with distinct clusters of NRTs for roots, for the elongation zone of the apical stem segment and the developing xylem and a further cluster for leaves, bark and wood. A comparison of different poplar species (P. trichocarpa, P. tremula, P. euphratica, P. fremontii x P. angustifolia, and P. x canescens) showed that the tissue-specific patterns of the NRT genes varied to some extent with species. Bioinformatic analysis of putative cis-regulatory elements in the promoter regions of PtNRT family retrieved motifs suggesting the regulation of the NRT genes by N metabolism, by energy and carbon metabolism, and by phytohormones and stress. Multivariate analysis suggested that the combination and abundance of motifs in distinct promoters may lead to tissue-specificity. Our genome wide analysis of the PtNRT genes provides a valuable basis for functional analysis towards understanding the role of nitrate transporters for tree growth.
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Affiliation(s)
- Hua Bai
- Forstbotanik und Baumphysiologie, Georg-August Universität Göttingen, Göttingen, Germany
| | - Dejuan Euring
- Forstbotanik und Baumphysiologie, Georg-August Universität Göttingen, Göttingen, Germany
| | - Katharina Volmer
- Forstbotanik und Baumphysiologie, Georg-August Universität Göttingen, Göttingen, Germany
| | - Dennis Janz
- Forstbotanik und Baumphysiologie, Georg-August Universität Göttingen, Göttingen, Germany
| | - Andrea Polle
- Forstbotanik und Baumphysiologie, Georg-August Universität Göttingen, Göttingen, Germany
- * E-mail:
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Zhao MM, Zhang G, Zhang DW, Hsiao YY, Guo SX. ESTs analysis reveals putative genes involved in symbiotic seed germination in Dendrobium officinale. PLoS One 2013; 8:e72705. [PMID: 23967335 PMCID: PMC3742586 DOI: 10.1371/journal.pone.0072705] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 07/15/2013] [Indexed: 01/05/2023] Open
Abstract
Dendrobiumofficinale (Orchidaceae) is one of the world's most endangered plants with great medicinal value. In nature, D. officinale seeds must establish symbiotic relationships with fungi to germinate. However, the molecular events involved in the interaction between fungus and plant during this process are poorly understood. To isolate the genes involved in symbiotic germination, a suppression subtractive hybridization (SSH) cDNA library of symbiotically germinated D. officinale seeds was constructed. From this library, 1437 expressed sequence tags (ESTs) were clustered to 1074 Unigenes (including 902 singletons and 172 contigs), which were searched against the NCBI non-redundant (NR) protein database (E-value cutoff, e(-5)). Based on sequence similarity with known proteins, 579 differentially expressed genes in D. officinale were identified and classified into different functional categories by Gene Ontology (GO), Clusters of orthologous Groups of proteins (COGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The expression levels of 15 selected genes emblematic of symbiotic germination were confirmed via real-time quantitative PCR. These genes were classified into various categories, including defense and stress response, metabolism, transcriptional regulation, transport process and signal transduction pathways. All transcripts were upregulated in the symbiotically germinated seeds (SGS). The functions of these genes in symbiotic germination were predicted. Furthermore, two fungus-induced calcium-dependent protein kinases (CDPKs), which were upregulated 6.76- and 26.69-fold in SGS compared with un-germinated seeds (UGS), were cloned from D. officinale and characterized for the first time. This study provides the first global overview of genes putatively involved in D. officinale symbiotic seed germination and provides a foundation for further functional research regarding symbiotic relationships in orchids.
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Affiliation(s)
- Ming-Ming Zhao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Medical Laboratory College, Beihua University, Jilin, People’s Republic of China
| | - Gang Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Da-Wei Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Yu-Yun Hsiao
- Department of Life Sciences, Orchid Research Center, National Cheng Kung University, Tainan, Taiwan
| | - Shun-Xing Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
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Kong X, Lv W, Jiang S, Zhang D, Cai G, Pan J, Li D. Genome-wide identification and expression analysis of calcium-dependent protein kinase in maize. BMC Genomics 2013; 14:433. [PMID: 23815483 PMCID: PMC3704972 DOI: 10.1186/1471-2164-14-433] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 06/28/2013] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Calcium-dependent protein kinases (CDPKs) have been shown to play important roles in various physiological processes, including plant growth and development, abiotic and biotic stress responses and plant hormone signaling in plants. RESULTS In this study, we performed a bioinformatics analysis of the entire maize genome and identified 40 CDPK genes. Phylogenetic analysis indicated that 40 ZmCPKs can be divided into four groups. Most maize CDPK genes exhibited different expression levels in different tissues and developmental stages. Twelve CDPK genes were selected to respond to various stimuli, including salt, drought and cold, as well as ABA and H2O2. Expression analyses suggested that maize CDPK genes are important components of maize development and multiple transduction pathways. CONCLUSION Here, we present a genome-wide analysis of the CDPK gene family in maize for the first time, and this genomic analysis of maize CDPK genes provides the first step towards a functional study of this gene family in maize.
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Affiliation(s)
- Xiangpei Kong
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
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Yazawa T, Kawahigashi H, Matsumoto T, Mizuno H. Simultaneous transcriptome analysis of Sorghum and Bipolaris sorghicola by using RNA-seq in combination with de novo transcriptome assembly. PLoS One 2013; 8:e62460. [PMID: 23638091 PMCID: PMC3640049 DOI: 10.1371/journal.pone.0062460] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 03/21/2013] [Indexed: 12/20/2022] Open
Abstract
The recent development of RNA sequencing (RNA-seq) technology has enabled us to analyze the transcriptomes of plants and their pathogens simultaneously. However, RNA-seq often relies on aligning reads to a reference genome and is thus unsuitable for analyzing most plant pathogens, as their genomes have not been fully sequenced. Here, we analyzed the transcriptomes of Sorghum bicolor (L.) Moench and its pathogen Bipolaris sorghicola simultaneously by using RNA-seq in combination with de novo transcriptome assembly. We sequenced the mixed transcriptome of the disease-resistant sorghum cultivar SIL-05 and B. sorghicola in infected leaves in the early stages of infection (12 and 24 h post-inoculation) by using Illumina mRNA-Seq technology. Sorghum gene expression was quantified by aligning reads to the sorghum reference genome. For B. sorghicola, reads that could not be aligned to the sorghum reference genome were subjected to de novo transcriptome assembly. We identified genes of B. sorghicola for growth of this fungus in sorghum, as well as genes in sorghum for the defense response. The genes of B. sorghicola included those encoding Woronin body major protein, LysM domain-containing intracellular hyphae protein, transcriptional factors CpcA and HacA, and plant cell-wall degrading enzymes. The sorghum genes included those encoding two receptors of the simple eLRR domain protein family, transcription factors that are putative orthologs of OsWRKY45 and OsWRKY28 in rice, and a class III peroxidase that is a homolog involved in disease resistance in the Poaceae. These defense-related genes were particularly strongly induced among paralogs annotated in the sorghum genome. Thus, in the absence of genome sequences for the pathogen, simultaneous transcriptome analysis of plant and pathogen by using de novo assembly was useful for identifying putative key genes in the plant-pathogen interaction.
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Affiliation(s)
- Takayuki Yazawa
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki, Japan
- Hitachi Government & Public Corporation System Engineering, Ltd, Koto-ku, Tokyo, Japan
| | - Hiroyuki Kawahigashi
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki, Japan
| | - Takashi Matsumoto
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki, Japan
| | - Hiroshi Mizuno
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki, Japan
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