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Yin F, Zhao M, Gong L, Nan H, Ma W, Lu M, An H. Genome-wide identification of Rosa roxburghii CML family genes identifies an RrCML13-RrGGP2 interaction involved in calcium-mediated regulation of ascorbate biosynthesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108874. [PMID: 38981208 DOI: 10.1016/j.plaphy.2024.108874] [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: 02/25/2024] [Revised: 06/20/2024] [Accepted: 06/22/2024] [Indexed: 07/11/2024]
Abstract
Calmodulin-like proteins (CMLs) are an essential family of calcium sensors involved in multiple Ca2+-mediated cellular processes in plants. Rosa roxburghii Tratt, known for the abundance of L-ascorbic acid (AsA) in its fruits, is widely distributed in calcium-rich soil of the karst region in southwestern China. The aim of this study was to identify key CMLs that respond to exogenous Ca2+ levels and regulate AsA biosynthesis in R. roxburghii. A genome-wide scan revealed the presence of 41 RrCML genes with 1-4 EF-hand motif (s) unevenly distributed across the 7 chromosomes of R. roxburghii. qRT-PCR analysis revealed that RrCML13, RrCML10, and RrCML36 responded significantly to exogenous Ca2+ treatment, and RrCML13 was positively correlated with GDP-L-galactose phosphorylase encoding gene (RrGGP2) expression and AsA content in the developing fruit. Overexpression of RrCML13 in fruits and roots significantly promoted the transcription of RrGGP2 and the accumulation of AsA, while virus-induced silencing of RrCML13 reduced the transcription of RrGGP2 and the content of AsA. Furthermore, Moreover, the yeast two-hybrid and bimolecular fluorescence complementation (BiFC) analysis confirmed the interaction between RrCML13 and RrGGP2 proteins, indicating that RrCML13 plays a regulatory role in calcium-mediated AsA biosynthesis. This study enhances our understanding of R. roxburghii CMLs and sheds light on the calcium-mediated regulation of AsA biosynthesis.
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Affiliation(s)
- Fei Yin
- Engineering Research Center of National Forestry and Grassland Administration for Rosa roxburghii, Agricultural College, Guizhou University, Guiyang, China
| | - Manqiu Zhao
- Engineering Research Center of National Forestry and Grassland Administration for Rosa roxburghii, Agricultural College, Guizhou University, Guiyang, China
| | - Lisha Gong
- Engineering Research Center of National Forestry and Grassland Administration for Rosa roxburghii, Agricultural College, Guizhou University, Guiyang, China
| | - Hong Nan
- Engineering Research Center of National Forestry and Grassland Administration for Rosa roxburghii, Agricultural College, Guizhou University, Guiyang, China
| | - Wentao Ma
- Engineering Research Center of National Forestry and Grassland Administration for Rosa roxburghii, Agricultural College, Guizhou University, Guiyang, China
| | - Min Lu
- Engineering Research Center of National Forestry and Grassland Administration for Rosa roxburghii, Agricultural College, Guizhou University, Guiyang, China
| | - Huaming An
- Engineering Research Center of National Forestry and Grassland Administration for Rosa roxburghii, Agricultural College, Guizhou University, Guiyang, China.
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Wang Y, Hu Y, Ren H, Zhao X, Yuan Z. Integrated transcriptomic, metabolomic, and functional analyses unravel the mechanism of bagging delaying fruit cracking of pomegranate (Punica granatum L.). Food Chem 2024; 451:139384. [PMID: 38692235 DOI: 10.1016/j.foodchem.2024.139384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/29/2024] [Accepted: 04/13/2024] [Indexed: 05/03/2024]
Abstract
The economic impact of fruit cracking in pomegranate products is substantial. In this study, we present the inaugural comprehensive analysis of transcriptome and metabolome in the outermost pericarp of pomegranate fruit in bagging conditions. Our investigation revealed a notable upregulation of differentially expressed genes (DEGs) associated with the calcium signaling pathway (76.92%) and xyloglucan endotransglucosylase/hydrolase (XTH) genes (87.50%) in the fruit peel of non-cracking fruit under bagging. Metabolomic analysis revealed that multiple phenolics, flavonoids, and tannins were identified in pomegranate. Among these, calmodulin-like 23 (PgCML23) exhibited a significant correlation with triterpenoids and demonstrated a marked upregulation under bagging treatment. The transgenic tomatoes overexpressing PgCML23 exhibited significantly higher cellulose content and xyloglucan endotransglucosylase (XET) enzyme activity in the pericarp at the red ripening stage compared to the wild type. Conversely, water-soluble pectin content, polygalacturonase (PG), and β-galactosidase (β-GAL) enzyme activities were significantly lower in the transgenic tomatoes. Importantly, the heterologous expression of PgCML23 led to a substantial reduction in the fruit cracking rate in tomatoes. Our findings highlight the reduction of fruit cracking in bagging conditions through the manipulation of PgCML23 expression.
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Affiliation(s)
- Yuying Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Yaping Hu
- Key Laboratory of Plant Innovation and Utilization, Institute of Subtropical Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China
| | - Hongfang Ren
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Xueqing Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Zhaohe Yuan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China.
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Niu Y, Zhou Z, Yue Z, Zhang X, Jiang X, Hu L, Liu Q, Zhang X, Dong K. Functional validation of AaCaM3 response to high temperature stress in Amorphophallus albus. BMC PLANT BIOLOGY 2024; 24:615. [PMID: 38937722 PMCID: PMC11212397 DOI: 10.1186/s12870-024-05283-2] [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: 04/03/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024]
Abstract
Amorphophallus is a perennial monocotyledonous herbaceous plant native to the southwestern region of China, widely used in various fields such as food processing, biomedicine and chemical agriculture. However, Amorphophallus is a typical thermolabile plant, and the continuous high temperature in summer have seriously affected the growth, development and economic yield of Amorphophallus in recent years. Calmodulin (CaM), a Ca2+ sensor ubiquitous in eukaryotes, is the most important multifunctional receptor protein in plant cells, which affects plant stress resistance by participating in the activities of a variety of signaling molecules. In this study, the key gene AaCaM3 for the Ca2+-CaM regulatory pathway was obtained from A. albus, the sequence analysis confirmed that it is a typical calmodulin. The qRT-PCR results demonstrated that with the passage of heat treatment time, the expression of AaCaM3 was significantly upregulated in A. albus leaves. Subcellular localization analysis revealed that AaCaM3 localized on the cytoplasm and nucleus. Meanwhile, heterologous transformation experiments have shown that AaCaM3 can significantly improve the heat tolerance of Arabidopsis under heat stress. The promoter region of AaCaM3 was sequenced 1,338 bp by FPNI-PCR and GUS staining assay showed that the promoter of AaCaM3 was a high-temperature inducible promoter. Yeast one-hybrid analysis and Luciferase activity reporting system analysis showed that the AaCaM3 promoter may interact with AaHSFA1, AaHSFA2c, AaHSP70, AaDREB2a and AaDREB2b. In conclusion, this study provides new ideas for further improving the signal transduction network of high-temperature stress in Amorphophallus.
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Affiliation(s)
- Yi Niu
- Yibin Academy of Southwest University, Yibin, China.
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Southwest University, Chongqing, China.
| | - Zixuan Zhou
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Southwest University, Chongqing, China
| | - Zhenyu Yue
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Southwest University, Chongqing, China
| | - Xiaofei Zhang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Southwest University, Chongqing, China
| | - Xuekuan Jiang
- Chongqing SINO Konjac Biotechnology Co., Ltd, Chongqing, China
| | - Lingyu Hu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Southwest University, Chongqing, China
| | - Quanshuo Liu
- Yibin Academy of Southwest University, Yibin, China
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Southwest University, Chongqing, China
| | - Xu Zhang
- Yibin Academy of Southwest University, Yibin, China
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Southwest University, Chongqing, China
| | - Kun Dong
- Institute of Fuyuan Konjac, Yunnan Academy of Agricultural Sciences, Qujing, China
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Zhu Q, Tan Q, Gao Q, Zheng S, Chen W, Galaud J, Li X, Zhu X. Calmodulin-like protein CML15 interacts with PP2C46/65 to regulate papaya fruit ripening via integrating calcium, ABA and ethylene signals. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1703-1723. [PMID: 38319003 PMCID: PMC11123395 DOI: 10.1111/pbi.14297] [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: 03/23/2023] [Revised: 12/13/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024]
Abstract
It is well known that calcium, ethylene and abscisic acid (ABA) can regulate fruit ripening, however, their interaction in the regulation of fruit ripening has not yet been fully clarified. The present study found that the expression of the papaya calcium sensor CpCML15 was strongly linked to fruit ripening. CpCML15 could bind Ca2+ and served as a true calcium sensor. CpCML15 interacted with CpPP2C46 and CpPP2C65, the candidate components of the ABA signalling pathways. CpPP2C46/65 expression was also related to fruit ripening and regulated by ethylene. CpCML15 was located in the nucleus and CpPP2C46/65 were located in both the nucleus and membrane. The interaction between CpCML15 and CpPP2C46/65 was calcium dependent and further repressed the activity of CpPP2C46/65 in vitro. The transient overexpression of CpCML15 and CpPP2C46/65 in papaya promoted fruit ripening and gene expression related to ripening. The reduced expression of CpCML15 and CpPP2C46/65 by virus-induced gene silencing delayed fruit colouring and softening and repressed the expression of genes related to ethylene signalling and softening. Moreover, ectopic overexpression of CpCML15 in tomato fruit also promoted fruit softening and ripening by increasing ethylene production and enhancing gene expression related to ripening. Additionally, CpPP2C46 interacted with CpABI5, and CpPP2C65 interacted with CpERF003-like, two transcriptional factors in ABA and ethylene signalling pathways that are closely related to fruit ripening. Taken together, our results showed that CpCML15 and CpPP2Cs positively regulated fruit ripening, and their interaction integrated the cross-talk of calcium, ABA and ethylene signals in fruit ripening through the CpCML15-CpPP2Cs-CpABI5/CpERF003-like pathway.
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Affiliation(s)
- Qiunan Zhu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
| | - Qinqin Tan
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
| | - Qiyang Gao
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
| | - Senlin Zheng
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
| | - Weixin Chen
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
| | - Jean‐Philippe Galaud
- Laboratoire de Recherche en Sciences VégétalesUniversité de Toulouse, CNRS, UPSCastanet‐TolosanFrance
| | - Xueping Li
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
| | - Xiaoyang Zhu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
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5
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Li L, Guo N, Cao Y, Zhai X, Fan G. Genome-Wide Characterization of Calmodulin and Calmodulin-like Protein Gene Families in Paulownia fortunei and Identification of Their Potential Involvement in Paulownia Witches' Broom. Genes (Basel) 2023; 14:1540. [PMID: 37628592 PMCID: PMC10454933 DOI: 10.3390/genes14081540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/29/2023] [Accepted: 07/17/2023] [Indexed: 08/27/2023] Open
Abstract
As significant Ca2+ sensors, calmodulin (CaM) and calmodulin-like proteins (CML), have been associated with a variety of environmental conditions in plants. However, whether CaMs/CMLs are related to the stress of phytoplasma infection has not been reported in Paulownia fortunei. In the current study, 5 PfCaMs and 58 PfCMLs were detected through a genome-wide investigation. The number of EF-hand motifs in all PfCaMs/CMLs varied. Bioinformatics analyses, including protein characteristics, conserved domain, gene structure, cis-elements, evolutionary relationship, collinearity, chromosomal location, post-translation modification site, subcellular localization and expression pattern analyses, represented the conservation and divergence of PfCaMs/CMLs. Furthermore, some PfCaMs/CMLs might be involved in plants' reaction to phytoplasma infection and exogenous calcium therapy, indicating these genes may play a role in abiotic as well as biotic stress responses. In addition, subcellular localization analysis showed that PfCML10 was located in the cell membrane and nucleus. In summary, these findings establish a stronger platform for their subsequent functional investigation in trees and further characterize their roles in Paulownia witches' broom (PaWB) occurrence.
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Affiliation(s)
- Lijiao Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (L.L.); (N.G.); (Y.C.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
| | - Na Guo
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (L.L.); (N.G.); (Y.C.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
| | - Yabing Cao
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (L.L.); (N.G.); (Y.C.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
| | | | - Guoqiang Fan
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (L.L.); (N.G.); (Y.C.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
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6
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Mir ZA, Chauhan D, Pradhan AK, Srivastava V, Sharma D, Budhlakoti N, Mishra DC, Jadon V, Sahu TK, Grover M, Gangwar OP, Kumar S, Bhardwaj SC, Padaria JC, Singh AK, Rai A, Singh GP, Kumar S. Comparative transcriptome profiling of near isogenic lines PBW343 and FLW29 to unravel defense related genes and pathways contributing to stripe rust resistance in wheat. Funct Integr Genomics 2023; 23:169. [PMID: 37209309 DOI: 10.1007/s10142-023-01104-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/22/2023]
Abstract
Stripe rust (Sr), caused by Puccinia striiformis f. sp. tritici (Pst), is the most devastating disease that poses serious threat to the wheat-growing nations across the globe. Developing resistant cultivars is the most challenging aspect in wheat breeding. The function of resistance genes (R genes) and the mechanisms by which they influence plant-host interactions are poorly understood. In the present investigation, comparative transcriptome analysis was carried out by involving two near-isogenic lines (NILs) PBW343 and FLW29. The seedlings of both the genotypes were inoculated with Pst pathotype 46S119. In total, 1106 differentially expressed genes (DEGs) were identified at early stage of infection (12 hpi), whereas expressions of 877 and 1737 DEGs were observed at later stages (48 and 72 hpi) in FLW29. The identified DEGs were comprised of defense-related genes including putative R genes, 7 WRKY transcriptional factors, calcium, and hormonal signaling associated genes. Moreover, pathways involved in signaling of receptor kinases, G protein, and light showed higher expression in resistant cultivar and were common across different time points. Quantitative real-time PCR was used to further confirm the transcriptional expression of eight critical genes involved in plant defense mechanism against stripe rust. The information about genes are likely to improve our knowledge of the genetic mechanism that controls the stripe rust resistance in wheat, and data on resistance response-linked genes and pathways will be a significant resource for future research.
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Affiliation(s)
- Zahoor Ahmad Mir
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Divya Chauhan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | | | - Vivek Srivastava
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Divya Sharma
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Neeraj Budhlakoti
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | | | - Vasudha Jadon
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Tanmaya Kumar Sahu
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Monendra Grover
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Om Prakash Gangwar
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal, Pradesh, 171002, India
| | - Subodh Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal, Pradesh, 171002, India
| | - S C Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal, Pradesh, 171002, India
| | - Jasdeep C Padaria
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - G P Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India.
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Allan C, Tayagui A, Hornung R, Nock V, Meisrimler CN. A dual-flow RootChip enables quantification of bi-directional calcium signaling in primary roots. FRONTIERS IN PLANT SCIENCE 2023; 13:1040117. [PMID: 36704158 PMCID: PMC9871814 DOI: 10.3389/fpls.2022.1040117] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/13/2022] [Indexed: 06/18/2023]
Abstract
One sentence summary: Bi-directional-dual-flow-RootChip to track calcium signatures in Arabidopsis primary roots responding to osmotic stress. Plant growth and survival is fundamentally linked with the ability to detect and respond to abiotic and biotic factors. Cytosolic free calcium (Ca2+) is a key messenger in signal transduction pathways associated with a variety of stresses, including mechanical, osmotic stress and the plants' innate immune system. These stresses trigger an increase in cytosolic Ca2+ and thus initiate a signal transduction cascade, contributing to plant stress adaptation. Here we combine fluorescent G-CaMP3 Arabidopsis thaliana sensor lines to visualise Ca2+ signals in the primary root of 9-day old plants with an optimised dual-flow RootChip (dfRC). The enhanced polydimethylsiloxane (PDMS) bi-directional-dual-flow-RootChip (bi-dfRC) reported here adds two adjacent inlet channels at the base of the observation chamber, allowing independent or asymmetric chemical stimulation at either the root differentiation zone or tip. Observations confirm distinct early spatio-temporal patterns of salinity (sodium chloride, NaCl) and drought (polyethylene glycol, PEG)-induced Ca2+ signals throughout different cell types dependent on the first contact site. Furthermore, we show that the primary signal always dissociates away from initially stimulated cells. The observed early signaling events induced by NaCl and PEG are surprisingly complex and differ from long-term changes in cytosolic Ca2+ reported in roots. Bi-dfRC microfluidic devices will provide a novel approach to challenge plant roots with different conditions simultaneously, while observing bi-directionality of signals. Future applications include combining the bi-dfRC with H2O2 and redox sensor lines to test root systemic signaling responses to biotic and abiotic factors.
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Affiliation(s)
- Claudia Allan
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Ayelen Tayagui
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
| | | | - Volker Nock
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
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Calcium decoders and their targets: The holy alliance that regulate cellular responses in stress signaling. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 134:371-439. [PMID: 36858741 DOI: 10.1016/bs.apcsb.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Calcium (Ca2+) signaling is versatile communication network in the cell. Stimuli perceived by cells are transposed through Ca2+-signature, and are decoded by plethora of Ca2+ sensors present in the cell. Calmodulin, calmodulin-like proteins, Ca2+-dependent protein kinases and calcineurin B-like proteins are major classes of proteins that decode the Ca2+ signature and serve in the propagation of signals to different parts of cells by targeting downstream proteins. These decoders and their targets work together to elicit responses against diverse stress stimuli. Over a period of time, significant attempts have been made to characterize as well as summarize elements of this signaling machinery. We begin with a structural overview and amalgamate the newly identified Ca2+ sensor protein in plants. Their ability to bind Ca2+, undergo conformational changes, and how it facilitates binding to a wide variety of targets is further embedded. Subsequently, we summarize the recent progress made on the functional characterization of Ca2+ sensing machinery and in particular their target proteins in stress signaling. We have focused on the physiological role of Ca2+, the Ca2+ sensing machinery, and the mode of regulation on their target proteins during plant stress adaptation. Additionally, we also discuss the role of these decoders and their mode of regulation on the target proteins during abiotic, hormone signaling and biotic stress responses in plants. Finally, here, we have enumerated the limitations and challenges in the Ca2+ signaling. This article will greatly enable in understanding the current picture of plant response and adaptation during diverse stimuli through the lens of Ca2+ signaling.
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Application of Exogenous Silicon for Alleviating Photosynthetic Inhibition in Tomato Seedlings under Low−Calcium Stress. Int J Mol Sci 2022; 23:ijms232113526. [DOI: 10.3390/ijms232113526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022] Open
Abstract
To address the low Ca−induced growth inhibition of tomato plants, the mitigation effect of exogenous Si on tomato seedlings under low−Ca stress was investigated using different application methods. We specifically analyzed the effects of root application or foliar spraying of 1 mM Si on growth conditions, leaf photosynthetic properties, stomatal status, chlorophyll content, chlorophyll fluorescence, ATP activity and content, Calvin cycle−related enzymatic activity, and gene expression in tomato seedlings under low vs. adequate calcium conditions. We found that the low−Ca environment significantly affected (reduced) these parameters, resulting in growth limitation. Surprisingly, the application of 1 mM Si significantly increased plant height, stem diameter, and biomass accumulation, protected photosynthetic pigments, improved gas exchange, promoted ATP production, enhanced the activity of Calvin cycle key enzymes and expression of related genes, and ensured efficient photosynthesis to occur in plants under low−Ca conditions. Interestingly, when the same amount of Si was applied, the beneficial effects of Si were more pronounced under low−Ca conditions that under adequate Ca. We speculate that Si might promote the absorption and transport of calcium in plants. The effects of Si also differed depending on the application method; foliar spraying was better in alleviating photosynthetic inhibition in plants under low−Ca stress, whereas root application of Si significantly promoted root growth and development. Enhancing the photosynthetic capacity by foliar Si application is an effective strategy for ameliorating the growth inhibition of plants under low−Ca stress.
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Fu M, Wu C, Li X, Ding X, Guo F. Genome-Wide Identification and Expression Analysis of CsCaM/CML Gene Family in Response to Low-Temperature and Salt Stresses in Chrysanthemum seticuspe. PLANTS 2022; 11:plants11131760. [PMID: 35807712 PMCID: PMC9268918 DOI: 10.3390/plants11131760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 11/29/2022]
Abstract
Calmodulin (CaM) and calmodulin-like proteins (CML) act as significant Ca2+ sensors binding Ca2+ with EF-hand motifs and have been reported to be involved in various environmental stresses in plants. In this study, calmodulin CsCaM/CML gene family members were identified based on the genome of Chrysanthemum seticuspe published recently; a phylogenetic tree was constructed; gene structures and chromosomal locations of CsCaM/CML were depicted; cis-acting regulatory elements were predicted; collinearity and duplicate events of CaM/CML were analyzed using MCScanX software; and the expression levels of CsCaM/CML in response to abiotic stress were analyzed, based on the published RNA-seq data. We identified 86 CsCaM/CML (4 CsCaMs and 82 CsCMLs) genes in total. Promoter sequences of CsCaM/CML contained elements related to abiotic stresses (including low-temperature and anaerobic stresses) and plant hormones (including abscisic acid (ABA), MeJA, and salicylic acid). CsCaM/CML genes were distributed on nine chromosomes unevenly. Collinearity analysis indicated that recent segmental duplications significantly enlarged the scale of the CML family in C. seticuspe. Four CsCMLs (CsCML14, CsCML50, CsCML65, and CsCML79) were statistically differentially regulated under low-temperature and salt stress compared with those in the normal condition. These results indicate diverse roles of CsCaM/CML in plant development and in response to environmental stimuli in C. seticuspe.
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Affiliation(s)
| | | | | | | | - Fangqi Guo
- Correspondence: Correspondence: ; Tel.: +86-0571-8640-4013
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Characterization of the Calmodulin/Calmodulin-like Protein (CAM/CML) Family in Ginkgo biloba, and the Influence of an Ectopically Expressed GbCML Gene (Gb_30819) on Seedling and Fruit Development of Transgenic Arabidopsis. PLANTS 2022; 11:plants11111506. [PMID: 35684283 PMCID: PMC9183014 DOI: 10.3390/plants11111506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 12/05/2022]
Abstract
Calmodulins (CAMs) and calmodulin-like proteins (CMLs) can participate in the regulation of various physiological processes via sensing and decoding Ca2+ signals. To reveal the characteristics of the CAM/CML family in Ginkgo biloba, a comprehensive analysis was performed at the genome-wide level. A total of 26 CAMs/CMLs, consisting of 5 GbCAMs and 21 GbCMLs, was identified on 11 out of 12 chromosomes in G. biloba. They displayed a certain degree of multiplicity in their sequences, albeit with conserved EF hands. Collinearity analysis suggested that tandem rather than segmental or whole-genome duplications were likely to play roles in the evolution of the Ginkgo CAM/CML family. Furthermore, GbCAMs/GbCMLs were grouped into higher, lower, and moderate expression in magnitude. The cis-acting regulatory elements involved in phytohormone-responsiveness within GbCAM/GbCML promotors may explain their varied expression profiles. The ectopic expression of a GbCML gene (Gb_30819) in transgenic Arabidopsis led to phenotypes with significantly shortened root length and seedling height, and decreased yields of both pods and seeds. Moreover, an electrophoresis mobility shift assay demonstrated the Ca2+-binding activity of Gb_30819 in vitro. Altogether, these results contribute to insights into the characteristics of the evolution and expression of GbCAMs/GbCMLs, as well as evidence for Ca2+-CAM/CML pathways functioning within the ancient gymnosperm G. biloba.
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12
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Lu Y, Li Q, Li T. PPA-GCN: A Efficient GCN Framework for Prokaryotic Pathways Assignment. Front Genet 2022; 13:839453. [PMID: 35444686 PMCID: PMC9013948 DOI: 10.3389/fgene.2022.839453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/17/2022] [Indexed: 11/17/2022] Open
Abstract
With the rapid development of sequencing technology, completed genomes of microbes have explosively emerged. For a newly sequenced prokaryotic genome, gene functional annotation and metabolism pathway assignment are important foundations for all subsequent research work. However, the assignment rate for gene metabolism pathways is lower than 48% on the whole. It is even lower for newly sequenced prokaryotic genomes, which has become a bottleneck for subsequent research. Thus, the development of a high-precision metabolic pathway assignment framework is urgently needed. Here, we developed PPA-GCN, a prokaryotic pathways assignment framework based on graph convolutional network, to assist functional pathway assignments using KEGG information and genomic characteristics. In the framework, genomic gene synteny information was used to construct a network, and ideas of self-supervised learning were inspired to enhance the framework’s learning ability. Our framework is applicable to the genera of microbe with sufficient whole genome sequences. To evaluate the assignment rate, genomes from three different genera (Flavobacterium (65 genomes) and Pseudomonas (100 genomes), Staphylococcus (500 genomes)) were used. The initial functional pathway assignment rate of the three test genera were 27.7% (Flavobacterium), 49.5% (Pseudomonas) and 30.1% (Staphylococcus). PPA-GCN achieved excellence performance of 84.8% (Flavobacterium), 77.0% (Pseudomonas) and 71.0% (Staphylococcus) for assignment rate. At the same time, PPA-GCN was proved to have strong fault tolerance. The framework provides novel insights into assignment for metabolism pathways and is likely to inform future deep learning applications for interpreting functional annotations and extends to all prokaryotic genera with sufficient genomes.
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Affiliation(s)
- Yuntao Lu
- Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qi Li
- Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Tao Li
- Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Plant Dehydrins: Expression, Regulatory Networks, and Protective Roles in Plants Challenged by Abiotic Stress. Int J Mol Sci 2021; 22:ijms222312619. [PMID: 34884426 PMCID: PMC8657568 DOI: 10.3390/ijms222312619] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 11/16/2022] Open
Abstract
Dehydrins, also known as Group II late embryogenesis abundant (LEA) proteins, are classic intrinsically disordered proteins, which have high hydrophilicity. A wide range of hostile environmental conditions including low temperature, drought, and high salinity stimulate dehydrin expression. Numerous studies have furnished evidence for the protective role played by dehydrins in plants exposed to abiotic stress. Furthermore, dehydrins play important roles in seed maturation and plant stress tolerance. Hence, dehydrins might also protect plasma membranes and proteins and stabilize DNA conformations. In the present review, we discuss the regulatory networks of dehydrin gene expression including the abscisic acid (ABA), mitogen-activated protein (MAP) kinase cascade, and Ca2+ signaling pathways. Crosstalk among these molecules and pathways may form a complex, diverse regulatory network, which may be implicated in regulating the same dehydrin.
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Chen P, Yang J, Mei Q, Liu H, Cheng Y, Ma F, Mao K. Genome-Wide Analysis of the Apple CBL Family Reveals That Mdcbl10.1 Functions Positively in Modulating Apple Salt Tolerance. Int J Mol Sci 2021; 22:ijms222212430. [PMID: 34830311 PMCID: PMC8624107 DOI: 10.3390/ijms222212430] [Citation(s) in RCA: 4] [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: 10/30/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
Abiotic stresses are increasingly harmful to crop yield and quality. Calcium and its signaling pathway play an important role in modulating plant stress tolerance. As specific Ca2+ sensors, calcineurin B-like (CBL) proteins play vital roles in plant stress response and calcium signaling. The CBL family has been identified in many plant species; however, the characterization of the CBL family and the functional study of apple MdCBL proteins in salt response have yet to be conducted in apple. In this study, 11 MdCBL genes were identified from the apple genome. The coding sequences of these MdCBL genes were cloned, and the gene structure and conserved motifs were analyzed in detail. The phylogenetic analysis indicated that these MdCBL proteins could be divided into four groups. The functional identification in Na+-sensitive yeast mutant showed that the overexpression of seven MdCBL genes could confer enhanced salt stress resistance in transgenic yeast. The function of MdCBL10.1 in regulating salt tolerance was also verified in cisgenic apple calli and apple plants. These results provided valuable insights for future research examining the function and mechanism of CBL proteins in regulating apple salt tolerance.
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Affiliation(s)
| | | | | | | | | | | | - Ke Mao
- Correspondence: (F.M.); (K.M.)
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15
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Basu R, Dutta S, Pal A, Sengupta M, Chattopadhyay S. Calmodulin7: recent insights into emerging roles in plant development and stress. PLANT MOLECULAR BIOLOGY 2021; 107:1-20. [PMID: 34398355 DOI: 10.1007/s11103-021-01177-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 07/27/2021] [Indexed: 05/25/2023]
Abstract
Analyses of the function of Arabidopsis Calmodulin7 (CAM7) in concert with multiple regulatory proteins involved in various signal transduction processes. Calmodulin (CaM) plays various regulatory roles in multiple signaling pathways in eukaryotes. Arabidopsis CALMODULIN 7 (CAM7) is a unique member of the CAM family that works as a transcription factor in light signaling pathways. CAM7 works in concert with CONSTITUTIVE PHOTOMORPHOGENIC 1 and ELONGATED HYPOCOTYL 5, and plays an important role in seedling development. Further, it is involved in the regulation of the activity of various Ca2+-gated channels such as cyclic nucleotide gated channel 6 (CNGC6), CNGC14 and auto-inhibited Ca2+ ATPase 8. Recent studies further indicate that CAM7 is also an integral part of multiple signaling pathways including hormone, immunity and stress. Here, we review the recent advances in understanding the multifaceted role of CAM7. We highlight the open-ended questions, and also discuss the diverse aspects of CAM7 characterization that need to be addressed for comprehensive understanding of its cellular functions.
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Affiliation(s)
- Riya Basu
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur, West Bengal, 713209, India
| | - Siddhartha Dutta
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur, West Bengal, 713209, India
- Department of Biotechnology, University of Engineering and Management, University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
| | - Abhideep Pal
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur, West Bengal, 713209, India
| | - Mandar Sengupta
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur, West Bengal, 713209, India
| | - Sudip Chattopadhyay
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur, West Bengal, 713209, India.
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16
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Bai Q, Shen Y, Huang Y. Advances in Mineral Nutrition Transport and Signal Transduction in Rosaceae Fruit Quality and Postharvest Storage. FRONTIERS IN PLANT SCIENCE 2021; 12:620018. [PMID: 33692815 PMCID: PMC7937644 DOI: 10.3389/fpls.2021.620018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/11/2021] [Indexed: 05/12/2023]
Abstract
Mineral nutrition, taken up from the soil or foliar sprayed, plays fundamental roles in plant growth and development. Among of at least 14 mineral elements, the macronutrients nitrogen (N), potassium (K), phosphorus (P), and calcium (Ca) and the micronutrient iron (Fe) are essential to Rosaceae fruit yield and quality. Deficiencies in minerals strongly affect metabolism with subsequent impacts on the growth and development of fruit trees. This ultimately affects the yield, nutritional value, and quality of fruit. Especially, the main reason of the postharvest storage loss caused by physiological disorders is the improper proportion of mineral nutrient elements. In recent years, many important mineral transport proteins and their regulatory components are increasingly revealed, which make drastic progress in understanding the molecular mechanisms for mineral nutrition (N, P, K, Ca, and Fe) in various aspects including plant growth, fruit development, quality, nutrition, and postharvest storage. Importantly, many studies have found that mineral nutrition, such as N, P, and Fe, not only affects fruit quality directly but also influences the absorption and the content of other nutrient elements. In this review, we provide insights of the mineral nutrients into their function, transport, signal transduction associated with Rosaceae fruit quality, and postharvest storage at physiological and molecular levels. These studies will contribute to provide theoretical basis to improve fertilizer efficient utilization and fruit industry sustainable development.
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Xiong T, Tan Q, Li S, Mazars C, Galaud JP, Zhu X. Interactions between calcium and ABA signaling pathways in the regulation of fruit ripening. JOURNAL OF PLANT PHYSIOLOGY 2021; 256:153309. [PMID: 33197829 DOI: 10.1016/j.jplph.2020.153309] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 05/18/2023]
Abstract
Fruit ripening and senescence are finely controlled by plant hormones such as ethylene and abscisic acid (ABA) but also by calcium ions and by calcium-dependent signaling pathways. Although there are extensive data supporting an interaction between ethylene and calcium in fruit ripening, the regulatory mechanisms resulting from the interaction between ABA and calcium have not yet been fully clarified. In this article, we have reviewed the full roles of calcium and its sensors (CaM, CMLs, CDPKs, CBLs) as well as ABA and the interactions between the two signaling pathways in the regulation of stress responses and in fruit ripening. To illustrate the possible interaction between calcium sensors and ABA signaling components in the control of fruit ripening, we propose an interaction model between the calcium and ABA signaling pathways.
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Affiliation(s)
- Tiantian Xiong
- Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Qinqin Tan
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Shaoshan Li
- Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Chiristian Mazars
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24, chemin de Borde-Rouge, Auzeville, 31320, Castanet-Tolosan, France
| | - Jean-Philippe Galaud
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24, chemin de Borde-Rouge, Auzeville, 31320, Castanet-Tolosan, France.
| | - Xiaoyang Zhu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
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18
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He X, Liu W, Li W, Liu Y, Wang W, Xie P, Kang Y, Liao L, Qian L, Liu Z, Guan C, Guan M, Hua W. Genome-wide identification and expression analysis of CaM/CML genes in Brassica napus under abiotic stress. JOURNAL OF PLANT PHYSIOLOGY 2020; 255:153251. [PMID: 33129076 DOI: 10.1016/j.jplph.2020.153251] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 05/25/2023]
Abstract
Calmodulin (CaM) and calmodulin-like (CML) proteins are primary calcium (Ca2+) sensors and are involved in the regulation of plant development and stress responses by converting calcium signals into transcriptional responses, protein phosphorylation, or metabolic changes. However, the characterization and expression profiling of CaM/CML genes in Brassica napus remain limited. The present study reports that 25 BnaCaM and 168 BnaCML genes were identified in B. napus. The phylogenetics, gene structures, gene motifs, gene chromosomal locations, syntenic and Ka/Ks analysis, promoter cis-acting elements, and expression characteristics in various organs and under abiotic stress were evaluated. The phylogenetic results revealed a total of 11 subgroups, including one unique clade of CaMs distinct from CMLs. Most of group I (CaM), II, III, and X members are intron rich, while members from the other seven groups are intron-less. The majority of CaM/CML proteins have four EF-hands. Syntenic analysis showed that 91.3 % orthologous CaM/CML gene pairs between B. rapa and B. oleracea were retained as homologous gene pairs in B. napus. Ka/Ks analysis indicated that the majority of BnaCaM/CML experienced purifying selection. Expression analysis showed that BnaCaMs genes are highly and ubiquitously expressed in all of the organs and tissues examined, while distinct BnaCMLs are expressed specifically in particular organs and tissues. In total, 129 BnaCaM/CML were induced by abiotic stress and phytohormones. BnaCMLs from group IV, VI, VIII, and X were strongly induced by freezing treatment, but were not or just slightly induced by chilling treatment. The present study is the first to analyze the CaM/CML gene family in B. napus, which is useful for understanding the functions of the BnaCaM/CML in modulating plant responses to abiotic stress, especially freezing stress.
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Affiliation(s)
- Xin He
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan, 410128, China; Oil Crops Research, Hunan Agricultural University, Changsha, Hunan, 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan, 410128, China
| | - Wei Liu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Wenqian Li
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Yan Liu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Weiping Wang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Pan Xie
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Yu Kang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Li Liao
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Lunwen Qian
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Zhongsong Liu
- Oil Crops Research, Hunan Agricultural University, Changsha, Hunan, 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan, 410128, China
| | - Chunyun Guan
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan, 410128, China; Oil Crops Research, Hunan Agricultural University, Changsha, Hunan, 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan, 410128, China
| | - Mei Guan
- Oil Crops Research, Hunan Agricultural University, Changsha, Hunan, 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan, 410128, China.
| | - Wei Hua
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan, 410128, China; Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
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19
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Yang J, Liu S, Ji L, Tang X, Zhu Y, Xie G. Identification of novel OsCML16 target proteins and differential expression analysis under abiotic stresses in rice. JOURNAL OF PLANT PHYSIOLOGY 2020; 249:153165. [PMID: 32408008 DOI: 10.1016/j.jplph.2020.153165] [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: 03/08/2020] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 05/24/2023]
Abstract
Calmodulin-like proteins (CMLs) have been shown to play key regulatory roles in calcium signaling in plants. However, few bona-fide CMLs binding proteins have been characterized in rice, a monocot model plant. Here, through large-scale screening of a yeast-two hybrid (Y2H) cDNA library with OsCML16 as a bait, six new putative interacting partners of OsCML16 were discovered and confirmed by both pairwise Y2H and bimolecular fluorescence complementation (BiFC) assays. Interestingly, the in vitro peptide-binding assays manifested that OsERD2 could bind both OsCaM1 and OsCML16 whereas other five target proteins could specifically bind OsCML16 but not OsCaM1. Furthermore, Ca2+ and TFP, a calmodulin (CaM) antagonist, were involved in the ABA-induced transcription of OsCML16 and its target genes, and they were also obviously induced by cold, drought, and salt stresses. Taken together, our new findings have provided the basis for the novel signaling pathways of OsCML16 in the abiotic stress response in rice.
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Affiliation(s)
- Jun Yang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuang Liu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lingxiao Ji
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xianying Tang
- College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
| | - Yongsheng Zhu
- Institute of Crop Science, Wuhan Academy of Agricultural Sciences, Wuhan 430345, China
| | - Guosheng Xie
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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20
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Wang X, Zhu B, Jiang Z, Wang S. Calcium-mediation of jasmonate biosynthesis and signaling in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 287:110192. [PMID: 31481228 DOI: 10.1016/j.plantsci.2019.110192] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/24/2019] [Accepted: 07/15/2019] [Indexed: 05/22/2023]
Abstract
Jasmonates (JAs) play vital roles in regulating a range of plant growth and development processes including seed germination, seedling development, reproduction, formation and development of storage organs, and senescence. JAs are also involved in the regulation of plant responses to environmental stimuli. The biosynthesis of JAs takes place in three different subcellular compartments, namely, the chloroplast, peroxisome, and cytoplasm. JAs activate the expression of JA-responsive genes by degrading jasmonate zinc-finger-inflorescence meristem (Zim) domain (JAZ) repressors via the E3 ubiquitin-ligase Skp/Cullin/F-box protein CORONATINE INSENSITIVE1 (COI1) complex (SCFCOI1) by using 26S proteasome. Calcium, reactive oxygen species (ROS), mitogen-activated protein kinase (MAPK), and nitric oxide (NO) are involved in the regulation of the biosynthesis and signaling of JAs in plants. Among these signaling molecules, calcium is one of the most important within plant cells. In plants, intracellular calcium levels change in response to JAs, resulting in calcium signatures with temporal and spatial features. Calcium channels are involved in the generation of calcium signatures. Calcium sensors, including calmodulins (CaMs), CaM-like proteins (CMLs), calcineurin B-like proteins (CBLs), and calcium-dependent protein kinases (CDPKs), can act to regulate the biosynthesis and signaling of JAs.
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Affiliation(s)
- Xiaoping Wang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China; Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Biping Zhu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Zhonghao Jiang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Shucai Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China; College of Life Science, Linyi University, Linyi, 276000, China.
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21
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Li C, Meng D, Zhang J, Cheng L. Genome-wide identification and expression analysis of calmodulin and calmodulin-like genes in apple (Malus × domestica). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:600-612. [PMID: 31030028 DOI: 10.1016/j.plaphy.2019.04.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 04/11/2019] [Accepted: 04/11/2019] [Indexed: 05/26/2023]
Abstract
Changes in intracellular calcium (Ca2+) levels in response to developmental processes or external stimuli serve as signals in eukaryotic cells. These Ca2+ signals are likely perceived through sensor proteins that bind Ca2+ by EF-hand (a helix-loop-helix structure) motif. Calmodulins (CaMs), a group of well-characterized Ca2+ sensors, and calmodulin-like (CMLs) are implicated in a large number of diverse cellular processes, including plant development and stress responses. In this study, apple (Malus × domestica) genes encoding CaM and CML proteins that only possess EF-hand motifs with no other functional domains were analyzed. A total of 4 MdCaM and 58 MdCML genes were identified, which are spread among 16 out of the 17 apple chromosomes. Bioinformatics analyses, including protein characteristics, conserved domain, evolutionary relationships and chromosomal locations, demonstrated the conservation and divergence of MdCaMs/CMLs. In addition, expression analysis showed that MdCaMs/CMLs are expressed in more than one tissue, including shoot tips, roots, mature leaves, flowers and fruit. Furthermore, the expression of some MdCaM/CML members responded to plant hormones (abscisic acid, jasmonic acid) and salt stress, suggesting a potential role of these genes in responses to biotic and abiotic stress. Overexpression of stress-induced MdCML3 gene significantly improved the tolerance of apple calli to salinity and ABA. The identification and characterization of MdCaMs/CMLs in apple lays a foundation for future functional studies of these genes.
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Affiliation(s)
- Chunlong Li
- School of Integrative Plant Science, Cornell University, 134A Plant Science, Ithaca, NY, 14853, USA
| | - Dong Meng
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, Beijing, China
| | - Junhong Zhang
- School of Integrative Plant Science, Cornell University, 134A Plant Science, Ithaca, NY, 14853, USA; State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Lin'an, Hangzhou, Zhejiang, PR China
| | - Lailiang Cheng
- School of Integrative Plant Science, Cornell University, 134A Plant Science, Ithaca, NY, 14853, USA.
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Vandelle E, Vannozzi A, Wong D, Danzi D, Digby AM, Dal Santo S, Astegno A. Identification, characterization, and expression analysis of calmodulin and calmodulin-like genes in grapevine (Vitis vinifera) reveal likely roles in stress responses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 129:221-237. [PMID: 29908490 DOI: 10.1016/j.plaphy.2018.06.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 05/09/2018] [Accepted: 06/02/2018] [Indexed: 05/23/2023]
Abstract
Calcium (Ca2+) is an ubiquitous key second messenger in plants, where it modulates many developmental and adaptive processes in response to various stimuli. Several proteins containing Ca2+ binding domain have been identified in plants, including calmodulin (CaM) and calmodulin-like (CML) proteins, which play critical roles in translating Ca2+ signals into proper cellular responses. In this work, a genome-wide analysis conducted in Vitis vinifera identified three CaM- and 62 CML-encoding genes. We assigned gene family nomenclature, analyzed gene structure, chromosomal location and gene duplication, as well as protein motif organization. The phylogenetic clustering revealed a total of eight subgroups, including one unique clade of VviCaMs distinct from VviCMLs. VviCaMs were found to contain four EF-hand motifs whereas VviCML proteins have one to five. Most of grapevine CML genes were intronless, while VviCaMs were intron rich. All the genes were well spread among the 19 grapevine chromosomes and displayed a high level of duplication. The expression profiling of VviCaM/VviCML genes revealed a broad expression pattern across all grape organs and tissues at various developmental stages, and a significant modulation in biotic stress-related responses. Our results highlight the complexity of CaM/CML protein family also in grapevine, supporting the versatile role of its different members in modulating cellular responses to various stimuli, in particular to biotic stresses. This work lays the foundation for further functional and structural studies on specific grapevine CaMs/CMLs in order to better understand the role of Ca2+-binding proteins in grapevine and to explore their potential for further biotechnological applications.
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Affiliation(s)
- Elodie Vandelle
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, 35020 Legnaro, Padova, Italy.
| | - Darren Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton ACT 2601, Australia.
| | - Davide Danzi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
| | - Anne-Marie Digby
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
| | - Silvia Dal Santo
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
| | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
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La Verde V, Dominici P, Astegno A. Towards Understanding Plant Calcium Signaling through Calmodulin-Like Proteins: A Biochemical and Structural Perspective. Int J Mol Sci 2018; 19:E1331. [PMID: 29710867 PMCID: PMC5983762 DOI: 10.3390/ijms19051331] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 11/17/2022] Open
Abstract
Ca2+ ions play a key role in a wide variety of environmental responses and developmental processes in plants, and several protein families with Ca2+-binding domains have evolved to meet these needs, including calmodulin (CaM) and calmodulin-like proteins (CMLs). These proteins have no catalytic activity, but rather act as sensor relays that regulate downstream targets. While CaM is well-studied, CMLs remain poorly characterized at both the structural and functional levels, even if they are the largest class of Ca2+ sensors in plants. The major structural theme in CMLs consists of EF-hands, and variations in these domains are predicted to significantly contribute to the functional versatility of CMLs. Herein, we focus on recent advances in understanding the features of CMLs from biochemical and structural points of view. The analysis of the metal binding and structural properties of CMLs can provide valuable insight into how such a vast array of CML proteins can coexist, with no apparent functional redundancy, and how these proteins contribute to cellular signaling while maintaining properties that are distinct from CaM and other Ca2+ sensors. An overview of the principal techniques used to study the biochemical properties of these interesting Ca2+ sensors is also presented.
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Affiliation(s)
- Valentina La Verde
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
| | - Paola Dominici
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
| | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
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24
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Hu W, Yan Y, Tie W, Ding Z, Wu C, Ding X, Wang W, Xia Z, Guo J, Peng M. Genome-Wide Analyses of Calcium Sensors Reveal Their Involvement in Drought Stress Response and Storage Roots Deterioration after Harvest in Cassava. Genes (Basel) 2018; 9:genes9040221. [PMID: 29671773 PMCID: PMC5924563 DOI: 10.3390/genes9040221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/01/2018] [Accepted: 04/12/2018] [Indexed: 12/18/2022] Open
Abstract
Calcium (Ca2+) plays a crucial role in plant development and responses to environmental stimuli. Currently, calmodulins (CaMs), calmodulin-like proteins (CMLs), and calcineurin B-like proteins (CBLs), such as Ca2+ sensors, are not well understood in cassava (Manihotesculenta Crantz), an important tropical crop. In the present study, 8 CaMs, 48 CMLs, and 9 CBLs were genome-wide identified in cassava, which were divided into two, four, and four groups, respectively, based on evolutionary relationship, protein motif, and gene structure analyses. Transcriptomic analysis revealed the expression diversity of cassava CaMs-CMLs-CBLs in distinct tissues and in response to drought stress in different genotypes. Generally, cassava CaMs-CMLs-CBLs showed different expression profiles between cultivated varieties (Arg7 and SC124) and wild ancestor (W14) after drought treatment. In addition, numerous CaMs-CMLs-CBLs were significantly upregulated at 6 h, 12 h, and 48 h after harvest, suggesting their possible role during storage roots (SR) deterioration. Further interaction network and co-expression analyses suggested that a CBL-mediated interaction network was widely involved in SR deterioration. Taken together, this study provides new insights into CaMs-CMLs-CBLs-mediated drought adaption and SR deterioration at the transcription level in cassava, and identifies some candidates for the genetic improvement of cassava.
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Affiliation(s)
- Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Chunlai Wu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Xupo Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Wenquan Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Zhiqiang Xia
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Jianchun Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Ming Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
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25
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Nie S, Zhang M, Zhang L. Genome-wide identification and expression analysis of calmodulin-like (CML) genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis). BMC Genomics 2017; 18:842. [PMID: 29096605 PMCID: PMC5668983 DOI: 10.1186/s12864-017-4240-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/25/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Calmodulin-like (CML) proteins are a primary family of plant-specific Ca2+ sensors that specifically bind to Ca2+ and deliver a Ca2+ signal. CML proteins have been identified and characterized in many plant species, such as the model plant Arabidopsis and rice. Based on considerable evidence, the roles of CML proteins are crucial in plant growth and development and in the response to various external stimuli. Nevertheless, the characterization and expression profiling of CML genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis) remain limited. RESULTS In this study, a genome-wide search and comprehensive analysis were performed, and a total of 79 BrCML genes were identified in Chinese cabbage. Gene structure analysis revealed that these BrCML genes contained two to four conserved EF-hand motifs. Phylogenetic analysis showed that CML homologs between Chinese cabbage and Arabidopsis shared close relationships. The identified BrCML genes were located across ten chromosomes and three different subgenomes of Chinese cabbage. Moreover, 126 pairs of orthologous CML genes were found among Chinese cabbage, Arabidopsis and Brassica oleracea. Expression analysis revealed that the expression of some BrCML genes was tissue-specific and that of some was susceptible to temperature stress. A putative interaction network of BrCML proteins was proposed, which suggested that BrCML2, BrCML6, BrCML15 and BrCML25 were co-expressed and might play roles in flower development and other relevant biological processes of Chinese cabbage. CONCLUSIONS The results of this study increased the understanding and characterization of BrCML genes in Chinese cabbage, and will be a rich resource for further studies to investigate BrCML protein function in various developmental processes of Chinese cabbage.
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Affiliation(s)
- Shanshan Nie
- College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
| | - Minjuan Zhang
- College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
| | - Lugang Zhang
- College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
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