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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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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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Terletskaya NV, Shadenova EA, Litvinenko YA, Ashimuly K, Erbay M, Mamirova A, Nazarova I, Meduntseva ND, Kudrina NO, Korbozova NK, Djangalina ED. Influence of Cold Stress on Physiological and Phytochemical Characteristics and Secondary Metabolite Accumulation in Microclones of Juglans regia L. Int J Mol Sci 2024; 25:4991. [PMID: 38732208 PMCID: PMC11084536 DOI: 10.3390/ijms25094991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
The current study investigated the impact of cold stress on the morphological, physiological, and phytochemical properties of Juglans regia L. (J. regia) using in vitro microclone cultures. The study revealed significant stress-induced changes in the production of secondary antioxidant metabolites. According to gas chromatography-mass spectrometry (GC-MS) analyses, the stress conditions profoundly altered the metabolism of J. regia microclones. Although the overall spectrum of metabolites was reduced, the production of key secondary antioxidant metabolites significantly increased. Notably, there was a sevenfold (7×) increase in juglone concentration. These findings are crucial for advancing walnut metabolomics and enhancing our understanding of plant responses to abiotic stress factors. Additionally, study results aid in identifying the role of individual metabolites in these processes, which is essential for developing strategies to improve plant resilience and tolerance to adverse conditions.
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Affiliation(s)
- Nina V. Terletskaya
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan; (M.E.); (A.M.); (N.O.K.); (N.K.K.)
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
| | - Elvira A. Shadenova
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
| | - Yuliya A. Litvinenko
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
- Faculty of Chemistry, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan
| | - Kazhybek Ashimuly
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
- Faculty of Chemistry, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan
| | - Malika Erbay
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan; (M.E.); (A.M.); (N.O.K.); (N.K.K.)
- Faculty of Chemistry, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan
| | - Aigerim Mamirova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan; (M.E.); (A.M.); (N.O.K.); (N.K.K.)
| | - Irada Nazarova
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
- Faculty of Chemistry, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan
| | - Nataliya D. Meduntseva
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
| | - Nataliya O. Kudrina
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan; (M.E.); (A.M.); (N.O.K.); (N.K.K.)
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
| | - Nazym K. Korbozova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan; (M.E.); (A.M.); (N.O.K.); (N.K.K.)
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
| | - Erika D. Djangalina
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
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Foresti C, Orduña L, Matus JT, Vandelle E, Danzi D, Bellon O, Tornielli GB, Amato A, Zenoni S. NAC61 regulates late- and post-ripening osmotic, oxidative, and biotic stress responses in grapevine. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2330-2350. [PMID: 38159048 PMCID: PMC11016852 DOI: 10.1093/jxb/erad507] [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: 05/17/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
During late- and post-ripening stages, grape berry undergoes profound biochemical and physiological changes whose molecular control is poorly understood. Here, we report the role of NAC61, a grapevine NAC transcription factor, in regulating different processes involved in berry ripening progression. NAC61 is highly expressed during post-harvest berry dehydration and its expression pattern is closely related to sugar concentration. The ectopic expression of NAC61 in Nicotiana benthamiana leaves resulted in low stomatal conductance, high leaf temperature, tissue collapse and a higher relative water content. Transcriptome analysis of grapevine leaves transiently overexpressing NAC61 and DNA affinity purification and sequencing analyses allowed us to narrow down a list of NAC61-regulated genes. Direct regulation of the stilbene synthase regulator MYB14, the osmotic stress-related gene DHN1b, the Botrytis cinerea susceptibility gene WRKY52, and NAC61 itself was validated. We also demonstrate that NAC61 interacts with NAC60, a proposed master regulator of grapevine organ maturation, in the activation of MYB14 and NAC61 expression. Overall, our findings establish NAC61 as a key player in a regulatory network that governs stilbenoid metabolism and osmotic, oxidative, and biotic stress responses that are the hallmark of late- and post-ripening grape stages.
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Affiliation(s)
- Chiara Foresti
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
| | - Elodie Vandelle
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Davide Danzi
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Oscar Bellon
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Alessandra Amato
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Sara Zenoni
- Department of Biotechnology, University of Verona, Verona, Italy
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Fu N, Wang L, Han X, Yang Q, Zhang Y, Tong Z, Zhang J. Genome-Wide Identification and Expression Analysis of Calmodulin and Calmodulin-like Genes, Revealing CaM3 and CML13 Participating in Drought Stress in Phoebe bournei. Int J Mol Sci 2023; 25:545. [PMID: 38203715 PMCID: PMC10778748 DOI: 10.3390/ijms25010545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Calmodulin (CaM) and calmodulin-like (CML) proteins are major Ca2+ sensors involved in the regulation of plant development and stress responses by converting Ca2+ signals into appropriate cellular responses. However, characterization and expression analyses of CaM/CML genes in the precious species, Phoebe bournei, remain limited. In this study, five PbCaM and sixty PbCML genes were identified that only had EF-hand motifs with no other functional domains. The phylogenetic tree was clustered into 11 subgroups, including a unique clade of PbCaMs. The PbCaMs were intron-rich with four EF-hand motifs, whereas PbCMLs had two to four EF-hands and were mostly intronless. PbCaMs/CMLs were unevenly distributed across the 12 chromosomes of P. bournei and underwent purifying selection. Fragment duplication was the main driving force for the evolution of the PbCaM/CML gene family. Cis-acting element analysis indicated that PbCaMs/CMLs might be related to hormones, growth and development, and stress response. Expression analysis showed that PbCaMs were generally highly expressed in five different tissues and under drought stress, whereas PbCMLs showed specific expression patterns. The expression levels of 11 candidate PbCaMs/CMLs were responsive to ABA and MeJA, suggesting that these genes might act through multiple signaling pathways. The overexpression of PbCaM3/CML13 genes significantly increased the tolerance of yeast cells to drought stress. The identification and characterization of the CaM/CML gene family in P. bournei laid the foundation for future functional studies of these genes.
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Affiliation(s)
| | | | | | | | | | - Zaikang Tong
- State Key Laboratory of Subtropical Silviculture, School of Forestry & Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (N.F.); (L.W.); (X.H.); (Q.Y.); (Y.Z.)
| | - Junhong Zhang
- State Key Laboratory of Subtropical Silviculture, School of Forestry & Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (N.F.); (L.W.); (X.H.); (Q.Y.); (Y.Z.)
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7
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Pedretti M, Favretto F, Troilo F, Giovannoni M, Conter C, Mattei B, Dominici P, Travaglini-Allocatelli C, Di Matteo A, Astegno A. Role of myristoylation in modulating PCaP1 interaction with calmodulin. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108003. [PMID: 37717348 DOI: 10.1016/j.plaphy.2023.108003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/09/2023] [Accepted: 09/04/2023] [Indexed: 09/19/2023]
Abstract
Plasma membrane-associated Cation-binding Protein 1 (PCaP1) belongs to the plant-unique DREPP protein family with largely unknown biological functions but ascertained roles in plant development and calcium (Ca2+) signaling. PCaP1 is anchored to the plasma membrane via N-myristoylation and a polybasic cluster, and its N-terminal region can bind Ca2+/calmodulin (CaM). However, the molecular determinants of PCaP1-Ca2+-CaM interaction and the functional impact of myristoylation in the complex formation and Ca2+ sensitivity of CaM remained to be elucidated. Herein, we investigated the direct interaction between Arabidopsis PCaP1 (AtPCaP1) and CaM1 (AtCaM1) using both myristoylated and non-myristoylated peptides corresponding to the N-terminal region of AtPCaP1. ITC analysis showed that AtCaM1 forms a high affinity 1:1 complex with AtPCaP1 peptides and the interaction is strictly Ca2+-dependent. Spectroscopic and kinetic Ca2+ binding studies showed that the myristoylated peptide dramatically increased the Ca2+-binding affinity of AtCaM1 and slowed the Ca2+ dissociation rates from both the C- and N-lobes, thus suggesting that the myristoylation modulates the mechanism of AtPCaP1 recognition by AtCaM1. Furthermore, NMR and CD spectroscopy revealed that the structure of both the N- and C-lobes of Ca2+-AtCaM1 changes markedly in the presence of the myristoylated AtPCaP1 peptide, which assumes a helical structure in the final complex. Overall, our results indicate that AtPCaP1 biological function is strictly related to the presence of multiple ligands, i.e., the myristoyl moiety, Ca2+ ions and AtCaM1 and only a full characterization of their equilibria will allow for a complete molecular understanding of the putative role of PCaP1 as signal protein.
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Affiliation(s)
- Marco Pedretti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Filippo Favretto
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Francesca Troilo
- CNR Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Moira Giovannoni
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Carolina Conter
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Benedetta Mattei
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Paola Dominici
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | | | - Adele Di Matteo
- CNR Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185, Rome, Italy.
| | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
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Agho CA, Kaurilind E, Tähtjärv T, Runno-Paurson E, Niinemets Ü. Comparative transcriptome profiling of potato cultivars infected by late blight pathogen Phytophthora infestans: Diversity of quantitative and qualitative responses. Genomics 2023; 115:110678. [PMID: 37406973 PMCID: PMC10548088 DOI: 10.1016/j.ygeno.2023.110678] [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: 01/02/2023] [Revised: 06/30/2023] [Accepted: 07/02/2023] [Indexed: 07/07/2023]
Abstract
The Estonia potato cultivar Ando has shown elevated field resistance to Phytophthora infestans, even after being widely grown for over 40 years. A comprehensive transcriptional analysis was performed using RNA-seq from plant leaf tissues to gain insight into the mechanisms activated for the defense after infection. Pathogen infection in Ando resulted in about 5927 differentially expressed genes (DEGs) compared to 1161 DEGs in the susceptible cultivar Arielle. The expression levels of genes related to plant disease resistance such as serine/threonine kinase activity, signal transduction, plant-pathogen interaction, endocytosis, autophagy, mitogen-activated protein kinase (MAPK), and others were significantly enriched in the upregulated DEGs in Ando, whereas in the susceptible cultivar, only the pathway related to phenylpropanoid biosynthesis was enriched in the upregulated DEGs. However, in response to infection, photosynthesis was deregulated in Ando. Multi-signaling pathways of the salicylic-jasmonic-ethylene biosynthesis pathway were also activated in response to Phytophthora infestans infection.
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Affiliation(s)
- C A Agho
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia.
| | - E Kaurilind
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia
| | - T Tähtjärv
- Centre of Estonian Rural Research and Knowledge, J. Aamisepa 1, 48309 Jõgeva, Estonia
| | - E Runno-Paurson
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia
| | - Ü Niinemets
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia; Estonian Academy of Sciences, Kohtu 6, Tallinn 10130, Estonia
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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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Xue N, Sun M, Gai Z, Bai M, Sun J, Sai S, Zhang L. Genome-Wide Identification and Expression Analysis of Calmodulin (CaM) and Calmodulin-Like (CML) Genes in the Brown Algae Saccharina japonica. PLANTS (BASEL, SWITZERLAND) 2023; 12:1934. [PMID: 37653850 PMCID: PMC10222329 DOI: 10.3390/plants12101934] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/30/2023] [Accepted: 05/02/2023] [Indexed: 09/02/2023]
Abstract
Calmodulins (CaMs) and Calmodulin-like proteins (CMLs) are vital in plant growth, development, and stress responses. However, CaMs and CMLs have not been fully identified and characterized in brown algae, which has been evolving independently of the well-studied green plant lineage. In this study, whole-genome searches revealed one SjCaM and eight SjCMLs in Saccharina japonica, and one EsCaM and eleven EsCMLs in Ectocarpus sp. SjCaM and EsCaM encoded identical protein products and shared 88.59-89.93% amino acid identities with Arabidopsis thaliana AtCaMs, thereby indicating that brown algae CaMs retained a similar Ca2+ sensors function as in plants. The phylogenetic and gene structure analysis results showed that there was significant divergence in the gene sequences among brown algae CMLs. Furthermore, evolutionary analysis indicated that the function of brown alga CMLs was relatively conserved, which may be related to the fact that brown algae do not need to face complex environments like terrestrial plants. Regulatory elements prediction and the expression analysis revealed the probable functioning of SjCaM/CML genes in gametophyte development and the stress response in S. japonica. In addition, the SjCaM/SjCMLs interacting proteins and chemicals were preliminarily predicted, suggesting that SjCaM/SjCMLs might play putative roles in Ca2+/CaM-mediated growth and development processes and stimulus responses. Therefore, these results will facilitate our understanding of the evolution of brown algae CaMs/CMLs and the functional identification of SjCaM/SjCMLs.
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Affiliation(s)
- Nianchao Xue
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Minghui Sun
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Zihan Gai
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Meihan Bai
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Juan Sun
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Shandong Technology Innovation Center of Algae and Sea Cucumber, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-Tech Co., Ltd., Yantai 264003, China
| | - Shan Sai
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Shandong Technology Innovation Center of Algae and Sea Cucumber, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-Tech Co., Ltd., Yantai 264003, China
| | - Linan Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
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11
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Hosseini SS, Ramezanpour SS, Soltanloo H, Seifati SE. RNA-seq analysis and reconstruction of gene networks involved in response to salinity stress in quinoa (cv. Titicaca). Sci Rep 2023; 13:7308. [PMID: 37147414 PMCID: PMC10163252 DOI: 10.1038/s41598-023-34534-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/03/2023] [Indexed: 05/07/2023] Open
Abstract
To better understand the mechanisms involved in salinity stress, the adaptability of quinoa cv. Titicaca-a halophytic plant-was investigated at the transcriptome level under saline and non-saline conditions. RNA-sequencing analysis of leaf tissue at the four-leaf stage by Illumina paired-end method was used to compare salt stress treatment (four days after stress at 13.8 dsm-1) and control. Among the obtained 30,846,354 transcripts sequenced, 30,303 differentially expressed genes from the control and stress treatment samples were identified, with 3363 genes expressed ≥ 2 and false discovery rate (FDR) of < 0.001. Six differential expression genes were then selected and qRT-PCR was used to confirm the RNA-seq results. Some of the genes (Include; CML39, CBSX5, TRX1, GRXC9, SnRKγ1 and BAG6) and signaling pathways discussed in this paper not been previously studied in quinoa. Genes with ≥ 2 were used to design the gene interaction network using Cytoscape software, and AgriGO software and STRING database were used for gene ontology. The results led to the identification of 14 key genes involved in salt stress. The most effective hub genes involved in salt tolerance were the heat shock protein gene family. The transcription factors that showed a significant increase in expression under stress conditions mainly belonged to the WRKY, bZIP and MYB families. Ontology analysis of salt stress-responsive genes and hub genes revealed that metabolic pathways, binding, cellular processes and cellular anatomical entity are among the most effective processes involved in salt stress.
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Affiliation(s)
- Sahar Sadat Hosseini
- Department of Plant Breeding and Plant Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Golestan, Iran
| | - Seyedeh Sanaz Ramezanpour
- Department of Plant Breeding and Plant Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Golestan, Iran.
| | - Hassan Soltanloo
- Department of Arid Land and Desert Management, School of Natural Resources and Desert Studies, Yazd University, Yazd, Iran
| | - Seyed Ebrahim Seifati
- Department of Arid Land and Desert Management, School of Natural Resources and Desert Studies, Yazd University, Yazd, Iran
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Han L, Wu X, Hou K, Zhang H, Liang X, Chen C, Wang Z, Shen C. Identification and functional analysis of calcium sensor calmodulins from heavy metal hyperaccumulator Noccaea caerulescens. FUNCTIONAL PLANT BIOLOGY : FPB 2023; 50:294-302. [PMID: 36683141 DOI: 10.1071/fp22243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Noccaea caerulescens (J. Presl & C. Presl) F. K. Mey. is a heavy metal hyperaccumulator exhibiting extreme tolerance to various environmental stresses. To date, the functional role of Ca2+ -binding protein in this plant is largely unknown. To investigate the function of calmodulins (CaMs) in N. caerulescens , CaM2 , a Ca2+ sensor encoding gene, was identified and functionally characterised. Protein structure analysis showed that NcCaM2 contains four classic exchange factor (EF)-hand motifs with high sequence similarity to the CaM proteins from model plant Arabidopsis thaliana L. Tissue specific expression analysis showed that NcCaM2 is constitutively expressed in stems, leaves, and roots. Expression level of NcCaM2 was significantly upregulated under various environmental stimulus, indicating a potential involvement of NcCaM2 in the tolerance to abiotic stresses. The heterologous expression of NcCaM2 in a yeast mutant strain increased the heavy metal tolerance in yeast cells. Furthermore, the constitutive expression of NcCaM2 enhanced the heavy metal tolerance capability of transgenic tobacco (Nicotiana tabacum L.) plants. Our data suggested an important role of NcCaM2 in the responses to environmental stresses and provided a potential target gene to enhance of the ability to hyperaccumulate metals.
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Affiliation(s)
- Lu Han
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China; and Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Xiaohua Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China; and Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Kailin Hou
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China; and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Hongshan Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China; and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Xueshuang Liang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China; and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Cheng Chen
- College of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Zhijing Wang
- College of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China; and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
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Li C, Wang Y, Wei M, Wang X. The involvement of a novel calmodulin-like protein isoform from oyster Crassostrea gigas in transcription factor regulation provides new insight into acclimation to ocean acidification. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 257:106423. [PMID: 36822075 DOI: 10.1016/j.aquatox.2023.106423] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Marine organisms need to adapt to improve organismal fitness under ocean acidification (OA). Recent studies have shown that marine calcifiers can achieve acclimation by stimulating calcium binding/signaling pathways. Here, a CaM-like gene (CgCaLP-2) from oyster Crassostrea gigas which typically responded to long-term CO2 exposure (two months) rather than short-term exposure (one week) was characterized. The cloned cDNA was 678 bp and was shorter than the retrieved sequence from NCBI (1125 bp). The two sequences, designated as CgCaLP-2-v1 and CgCaLP-2-v2, were demonstrated to be different splice variants by the genome sequence analysis. Western blotting analysis revealed two bands of 23 kD and 43 kD in mantle and hemocytes, corresponding to predicted molecular weight of CgCaLP-2-v1 and CgCaLP-2-v2, respectively. The isoform CgCaLP-2-v1 (the 23 kD band) was highly stimulated in response to long-term CO2 exposure (42-day and 56-day treatment) in hemocytes and mantle tissue. The fluorescence signal of CgCaLP-2 in mantle and hemocytes became more intensive after long-term CO2 exposure. Besides, in hemocytes, CgCaLP-2 presented a higher localization on the nuclear membrane after long-term CO2 exposure (56 d). The target gene network of CgCaLP-2 was predicted, and a transcription factor (TF) gene annotated as Homeobox protein SIX4 (CgSIX4) showed a similar expressive trend to CgCaLP-2 during CO2 exposure. Suppression of CgCaLP-2 via RNA interference significantly reduced the mRNA expression of CgSIX4. The results suggested that CgCaLP-2 might mediate the Ca2+-CaLP-TF signal transduction pathway under long-term CO2 exposure. This study serves as an example to reveal that alternative splicing is an important mechanism for generation multiple protein isoforms and thus shape the plastic responses under CO2 exposure, providing new insight into the potential acclimation ability of marine calcifiers to future OA.
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Affiliation(s)
- Changmei Li
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yilin Wang
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Manman Wei
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Xiudan Wang
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China; College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China.
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Yang M, Chen J, Liu T, Xiang L, Zhou BF. Genome-Wide Identification and Expression Analysis of Calmodulin-Like Gene Family in Paspalums vaginatium Revealed Their Role in Response to Salt and Cold Stress. Curr Issues Mol Biol 2023; 45:1693-1711. [PMID: 36826054 PMCID: PMC9954852 DOI: 10.3390/cimb45020109] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/05/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
The calmodulin-like (CML) family is an important calcium (Ca2+) sensor in plants and plays a pivotal role in the response to abiotic and biotic stresses. As one of the most salt-tolerant grass species, Paspalums vaginatum is resistant to multiple abiotic stresses, such as salt, cold, and drought. However, investigations of PvCML proteins in P. vaginatum have been limited. Based on the recently published P. vaginatum genome, we identified forty-nine PvCMLs and performed a comprehensive bioinformatics analysis of PvCMLs. The main results showed that the PvCMLs were unevenly distributed on all chromosomes and that the expansion of PvCMLs was shaped by tandem and segmental duplications. In addition, cis-acting element analysis, expression profiles, and qRT-PCR analysis revealed that PvCMLs were involved in the response to salt and cold stress. Most interestingly, we found evidence of a tandem gene cluster that independently evolved in P. vaginatum and may participate in cold resistance. In summary, our work provides important insight into how grass species are resistant to abiotic stresses such as salt and cold and could be the basis of further gene function research on CMLs in P. vaginatum.
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Affiliation(s)
- Meizhen Yang
- Guangdong Engineering Research Center for Grassland Science, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jingjin Chen
- Guangdong Engineering Research Center for Grassland Science, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Tingting Liu
- Guangdong Engineering Research Center for Grassland Science, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Leilei Xiang
- Guangdong Engineering Research Center for Grassland Science, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Biao-Feng Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Correspondence: ; Tel.: +86-17665141041
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Wang H, Feng M, Zhong X, Yu Q, Que Y, Xu L, Guo J. Identification of Saccharum CaM gene family and function characterization of ScCaM1 during cold and oxidant exposure in Pichia pastoris. Genes Genomics 2023; 45:103-122. [PMID: 35608775 DOI: 10.1007/s13258-022-01263-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/03/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Calmodulin (CaM) plays an essential role in binding calcium ions and mediating the interpretation of Ca2+ signals in plants under various stresses. However, the evolutionary relationship of CaM family proteins in Saccharum has not been elucidated. OBJECTIVE To deduce and explore the evolution and function of Saccharum CaM family. METHODS A total of 104 typical CaMs were obtained from Saccharum spontaneum and other 18 plant species. The molecular characteristics and evolution of those CaM proteins were analyzed. A typical CaM gene, ScCaM1, was subsequently cloned from sugarcane (Saccharum spp. hybrid). Its expression patterns in different tissues and under various abiotic stresses were assessed by quantitative real-time PCR. Then the green fluorescent protein was used to determine the subcellular localization of ScCaM1. Finally, the function of ScCaM1 was evaluated via heterologous yeast expression systems. RESULTS Three typical CaM members (SsCaM1, SsCaM2, and SsCaM3) were identified from the S. spontaneum genome database. CaMs were originated from the two last common ancestors before the origin of angiosperms. The number of CaM family members did not correlate to the genome size but correlated with allopolyploidization events. The ScCaM1 was more highly expressed in buds and roots than in other tissues. The expression patterns of ScCaM1 suggested that it was involved in responses to various abiotic stresses in sugarcane via different hormonal signaling pathways. Noteworthily, its expression levels appeared relatively stable during the cold exposure in the cold-tolerant variety but significantly suppressed in the cold-susceptible variety. Moreover, the recombinant yeast (Pichia pastoris) overexpressing ScCaM1 grew better than the wild-type yeast strain under cold and oxidative stresses. It was revealed that the ScCaM1 played a positive role in reactive oxygen species scavenging and conferred enhanced cold and oxidative stress tolerance to cells. CONCLUSION This study provided comprehensive information on the CaM gene family in Saccharum and would facilitate further investigation of their functional characterization.
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Affiliation(s)
- Hengbo Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meichang Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoqiang Zhong
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qing Yu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jinlong Guo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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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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Ananev AA, Suprun AR, Aleynova OA, Nityagovsky NN, Ogneva ZV, Dubrovina AS, Kiselev KV. Effect of VaMyb40 and VaMyb60 Overexpression on Stilbene Biosynthesis in Cell Cultures of Grapevine Vitis amurensis Rupr. PLANTS 2022; 11:plants11151916. [PMID: 35893620 PMCID: PMC9330820 DOI: 10.3390/plants11151916] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/08/2022] [Accepted: 07/21/2022] [Indexed: 01/10/2023]
Abstract
Stilbenes are plant defense compounds known to rapidly accumulate in grapevine and some other plant species in response to microbial infection and several abiotic stresses. Stilbenes have attracted considerable attention due to valuable biological effects with multi-spectrum therapeutic application. However, there is a lack of information on natural signaling pathways and transcription factors regulating stilbene biosynthesis. It has been previously shown that MYB R2R3 transcription factor genes VaMyb40 and VaMyb60 were up-regulated in cell cultures of wild-growing grapevine Vitis amurensis Rupr. in response to UV irradiation. In this study, the effects of VaMyb40 or VaMyb60 overexpression in cell cultures of V. amurensis on their capability to produce stilbenes were investigated. Overexpression of the VaMyb60 gene led to a considerable increase in the content of stilbenes in three independently transformed transgenic lines in 5.9–13.9 times, while overexpression of the VaMyb40 gene also increased the content of stilbenes, although to a lesser extent (in 3.4–4.0 times) in comparison with stilbene levels in the empty vector-transformed calli. Stilbene content and stilbene production in the VaMyb60-transgenic calli reached 18.8 mg/g of dry weight (DW) and 150.8 mg/L, respectively. Using HPLC analysis, we detected eight individual stilbenes: t-resveratrol diglucoside, t-piceid, t-resveratrol, ε-viniferin, δ-viniferin, cis-resveratrol, cis-piceid, t-piceatannol. T-resveratrol prevailed over other stilbenoid compounds (53.1–89.5% of all stilbenes) in the VaMyb-overexpressing cell cultures. Moreover, the VaMyb40- and VaMyb60-transformed calli were capable of producing anthocyanins up to 0.035 mg/g DW, while the control calli did not produce anthocyanins. These findings show that the VaMyb40 and VaMyb60 genes positively regulate the stilbene biosynthesis as strong positive transcription regulators and can be used in biotechnological applications for stilbene production or high-quality viticulture and winemaking.
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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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Kadri SUT, Mulla SI, Babu R N, Suchithra B, Bilal M, Ameen F, Bharagava RN, Saratale GD, Ferreira LFR, Américo-Pinheiro JHP. Transcriptome-wide identification and computational insights into protein modeling and docking of CAMTA transcription factors in Eleusine coracana L (finger millet). Int J Biol Macromol 2022; 206:768-776. [DOI: 10.1016/j.ijbiomac.2022.03.073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/12/2022] [Accepted: 03/12/2022] [Indexed: 12/14/2022]
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Full-Length Transcriptome Sequencing-Based Analysis of Pinus sylvestris var. mongolica in Response to Sirex noctilio Venom. INSECTS 2022; 13:insects13040338. [PMID: 35447780 PMCID: PMC9029201 DOI: 10.3390/insects13040338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Sirex noctilio, as a devastating international forestry quarantine pest whose venom can cause a series of physiological changes in the host plants, such as needle wilting, yellowing, decreased transpiration rate and increased respiration rate, etc. In this study, a full-length reference transcript of Pinus sylvestris var. mongolica was constructed by combining second- and third-generation transcriptome sequencing technologies. We also identified the specific expression genes and transcription factors of P. sylvestris var. mongolica under S. noctilio venom and wounding stress. S. noctilio venom mainly induced the expression of genes related to ROS, GAPDH and GPX, and mechanical damage mainly induced the photosynthesis−related genes. The results provide a better understanding of the molecular regulation of pine trees in response to S. noctilio venom. Abstract Sirex noctilio is a major international quarantine pest that recently emerged in northeast China to specifically invade conifers. During female oviposition, venom is injected into the host together with its symbiotic fungus to alter the normal Pinus physiology and weaken or even kill the tree. In China, the Mongolian pine (Pinus sylvestris var. mongolica), an important wind-proof and sand-fixing species, is the unique host of S. noctilio. To explore the interplay between S. noctilio venom and Mongolian pine, we performed a transcriptome comparative analysis of a 10-year-old Mongolian pine after wounding and inoculation with S. noctilio venom. The analysis was performed at 12 h, 24 h and 72 h. PacBio ISO-seq was used and integrated with RNA-seq to construct an accurate full-length transcriptomic database. We obtained 52,963 high-precision unigenes, consisting of 48,654 (91.86%) unigenes that were BLASTed to known sequences in the public database and 4309 unigenes without any annotation information, which were presumed to be new genes. The number of differentially expressed genes (DEGs) increased with the treatment time, and the DEGs were most abundant at 72 h. A total of 706 inoculation-specific DEGs (475 upregulated and 231 downregulated) and 387 wounding-specific DEGs (183 upregulated and 204 downregulated) were identified compared with the control. Under venom stress, we identified 6 DEGs associated with reactive oxygen species (ROS) and 20 resistance genes in Mongolian pine. Overall, 52 transcription factors (TFs) were found under venom stress, 45 of which belonged to the AP2/ERF TF family and were upregulated. A total of 13 genes related to the photosystem, 3 genes related photo-regulation, and 9 TFs were identified under wounding stress. In conclusion, several novel putative genes were found in Mongolian pine by PacBio ISO seq. Meanwhile, we also identified various genes that were resistant to S. noctilio venom, such as GAPDH, GPX, CAT, FL2, CERK1, and HSP83A, etc.
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Ramírez-Pool JA, Xoconostle-Cázares B, Calderón-Pérez B, Ibarra-Laclette E, Villafán E, Lira-Carmona R, Ruiz-Medrano R. Transcriptomic Analysis of the Host Response to Mild and Severe CTV Strains in Naturally Infected Citrus sinensis Orchards. Int J Mol Sci 2022; 23:ijms23052435. [PMID: 35269578 PMCID: PMC8910659 DOI: 10.3390/ijms23052435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/03/2022] [Accepted: 02/15/2022] [Indexed: 12/14/2022] Open
Abstract
Citrus tristeza virus (CTV) is an important threat to the global citrus industry, causing severe economic losses worldwide. The disease management strategies are focused on vector control, tree culling, and the use of resistant varieties and rootstocks. Sweet orange (Citrus sinensis) trees showing either severe or mild CTV symptoms have been observed in orchards in Veracruz, Mexico, and were probably caused by different virus strains. To understand these symptomatic differences, transcriptomic analyses were conducted using asymptomatic trees. CTV was confirmed to be associated with infected plants, and mild and severe strains were successfully identified by a polymorphism in the coat protein (CP) encoding gene. RNA-Seq analysis revealed more than 900 significantly differentially expressed genes in response to mild and severe strains, with some overlapping genes. Importantly, multiple sequence reads corresponding to Citrus exocortis viroid and Hop stunt viroid were found in severe symptomatic and asymptomatic trees, but not in plants with mild symptoms. The differential gene expression profiling obtained in this work provides an overview of molecular behavior in naturally CTV-infected trees. This work may contribute to our understanding of citrus-virus interaction in more natural settings, which can help develop strategies for integrated crop management.
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Affiliation(s)
- José Abrahán Ramírez-Pool
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco 07360, Mexico; (J.A.R.-P.); (B.X.-C.); (B.C.-P.)
| | - Beatriz Xoconostle-Cázares
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco 07360, Mexico; (J.A.R.-P.); (B.X.-C.); (B.C.-P.)
| | - Berenice Calderón-Pérez
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco 07360, Mexico; (J.A.R.-P.); (B.X.-C.); (B.C.-P.)
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Carretera Antigua a Coatepec 351, El Haya, Xalapa 91070, Mexico; (E.I.-L.); (E.V.)
| | - Emanuel Villafán
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Carretera Antigua a Coatepec 351, El Haya, Xalapa 91070, Mexico; (E.I.-L.); (E.V.)
| | - Rosalía Lira-Carmona
- Laboratorio de Virología, UIMEIP, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, Av. Cuauhtémoc 330, Col. Doctores, Alcaldía Cuauhtémoc 06720, Mexico;
| | - Roberto Ruiz-Medrano
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco 07360, Mexico; (J.A.R.-P.); (B.X.-C.); (B.C.-P.)
- Correspondence: ; Tel.: +52-5557473800
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Aleynova OA, Suprun AR, Ananev AA, Nityagovsky NN, Ogneva ZV, Dubrovina AS, Kiselev KV. Effect of Calmodulin-like Gene (CML) Overexpression on Stilbene Biosynthesis in Cell Cultures of Vitis amurensis Rupr. PLANTS 2022; 11:plants11020171. [PMID: 35050059 PMCID: PMC8778512 DOI: 10.3390/plants11020171] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 01/05/2022] [Indexed: 12/23/2022]
Abstract
Stilbenes are plant phenolics known to rapidly accumulate in grapevine and other plants in response to injury or pathogen attack and to exhibit a great variety of healing beneficial effects. It has previously been shown that several calmodulin-like protein (CML) genes were highly up-regulated in cell cultures of wild-growing grapevine Vitis amurensis Rupr. in response to stilbene-modulating conditions, such as stress hormones, UV-C, and stilbene precursors. Both CML functions and stilbene biosynthesis regulation are still poorly understood. In this study, we investigated the effect of overexpression of five VaCML genes on stilbene and biomass accumulation in the transformed cell cultures of V. amurensis. We obtained 16 transgenic cell lines transformed with the VaCML52, VaCML65, VaCML86, VaCML93, and VaCML95 genes (3–4 independent lines per gene) under the control of the double CaMV 35S promoter. HPLC-MS analysis showed that overexpression of the VaCML65 led to a considerable and consistent increase in the content of stilbenes of 3.8–23.7 times in all transformed lines in comparison with the control calli, while biomass accumulation was not affected. Transformation of the V. amurensis cells with other analyzed VaCML genes did not lead to a consistent and considerable effect on stilbene biosynthesis in the cell lines. The results indicate that the VaCML65 gene is implicated in the signaling pathway regulating stilbene biosynthesis as a strong positive regulator and can be useful in viticulture and winemaking for obtaining grape cultivars with a high content of stilbenes and stress resistance.
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Affiliation(s)
- Olga A. Aleynova
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, FEB RAS, 690022 Vladivostok, Russia; (O.A.A.); (A.R.S.); (A.A.A.); (N.N.N.); (Z.V.O.); (A.S.D.)
| | - Andrey R. Suprun
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, FEB RAS, 690022 Vladivostok, Russia; (O.A.A.); (A.R.S.); (A.A.A.); (N.N.N.); (Z.V.O.); (A.S.D.)
| | - Alexey A. Ananev
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, FEB RAS, 690022 Vladivostok, Russia; (O.A.A.); (A.R.S.); (A.A.A.); (N.N.N.); (Z.V.O.); (A.S.D.)
- Department of Biochemistry and Biotechnology, Institute of the World Ocean, Far Eastern Federal University, 690090 Vladivostok, Russia
| | - Nikolay N. Nityagovsky
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, FEB RAS, 690022 Vladivostok, Russia; (O.A.A.); (A.R.S.); (A.A.A.); (N.N.N.); (Z.V.O.); (A.S.D.)
| | - Zlata V. Ogneva
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, FEB RAS, 690022 Vladivostok, Russia; (O.A.A.); (A.R.S.); (A.A.A.); (N.N.N.); (Z.V.O.); (A.S.D.)
| | - Alexandra S. Dubrovina
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, FEB RAS, 690022 Vladivostok, Russia; (O.A.A.); (A.R.S.); (A.A.A.); (N.N.N.); (Z.V.O.); (A.S.D.)
| | - Konstantin V. Kiselev
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, FEB RAS, 690022 Vladivostok, Russia; (O.A.A.); (A.R.S.); (A.A.A.); (N.N.N.); (Z.V.O.); (A.S.D.)
- Correspondence: ; Tel.: +8-423-2310410; Fax: +8-4232-310193
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Cai K, Kuang L, Yue W, Xie S, Xia X, Zhang G, Wang J. Calmodulin and calmodulin-like gene family in barley: Identification, characterization and expression analyses. FRONTIERS IN PLANT SCIENCE 2022; 13:964888. [PMID: 36061813 PMCID: PMC9439640 DOI: 10.3389/fpls.2022.964888] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/29/2022] [Indexed: 05/11/2023]
Abstract
Calmodulin (CaM) and calmodulin-like (CML) proteins are Ca2+ relays and play diverse and multiple roles in plant growth, development and stress responses. However, CaM/CML gene family has not been identified in barley (Hordeum vulgare). In the present study, 5 HvCaMs and 80 HvCMLs were identified through a genome-wide analysis. All HvCaM proteins possessed 4 EF-hand motifs, whereas HvCMLs contained 1 to 4 EF-hand motifs. HvCaM2, HvCaM3 and HvCaM5 coded the same polypeptide although they differed in nucleotide sequence, which was identical to the polypeptides coded by OsCaM1-1, OsCaM1-2 and OsCaM1-3. HvCaMs/CMLs were unevenly distributed over barley 7 chromosomes, and could be phylogenetically classified into 8 groups. HvCaMs/CMLs differed in gene structure, cis-acting elements and tissue expression patterns. Segmental and tandem duplication were observed among HvCaMs/CMLs during evolution. HvCML16, HvCML18, HvCML50 and HvCML78 were dispensable genes and the others were core genes in barley pan-genome. In addition, 14 HvCaM/CML genes were selected to examine their responses to salt, osmotic and low potassium stresses by qRT-PCR, and their expression were stress-and time-dependent. These results facilitate our understanding and further functional identification of HvCaMs/CMLs.
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Affiliation(s)
- Kangfeng Cai
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- National Barley Improvement Centre, Hangzhou, China
| | - Liuhui Kuang
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Wenhao Yue
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- National Barley Improvement Centre, Hangzhou, China
| | - Shanggeng Xie
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Xue Xia
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guoping Zhang
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Junmei Wang
- Key Laboratory of Digital Dry Land Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- National Barley Improvement Centre, Hangzhou, China
- *Correspondence: Junmei Wang,
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25
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Yadav M, Pandey J, Chakraborty A, Hassan MI, Kundu JK, Roy A, Singh IK, Singh A. A Comprehensive Analysis of Calmodulin-Like Proteins of Glycine max Indicates Their Role in Calcium Signaling and Plant Defense Against Insect Attack. FRONTIERS IN PLANT SCIENCE 2022; 13:817950. [PMID: 35371141 PMCID: PMC8965522 DOI: 10.3389/fpls.2022.817950] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/25/2022] [Indexed: 05/09/2023]
Abstract
The calcium (Ca2+) signaling is a crucial event during plant-herbivore interaction, which involves a transient change in cytosolic Ca2+ concentration, which is sensed by Ca2+-sensors, and the received message is transduced to downstream target proteins leading to appropriate defense response. Calmodulin-like proteins (CMLs) are calcium-sensing plant-specific proteins. Although CMLs have been identified in a few plants, they remained uncharacterized in leguminous crop plants. Therefore, a wide-range analysis of CMLs of soybean was performed, which identified 41 true CMLs with greater than 50% similarity with Arabidopsis CMLs. The phylogenetic study revealed their evolutionary relatedness with known CMLs. Further, the identification of conserved motifs, gene structure analysis, and identification of cis-acting elements strongly supported their identity as members of this family and their involvement in stress responses. Only a few Glycine max CMLs (GmCMLs) exhibited differential expression in different tissue types, and rest of them had minimal expression. Additionally, differential expression patterns of GmCMLs were observed during Spodoptera litura-feeding, wounding, and signaling compound treatments, indicating their role in plant defense. The three-dimensional structure prediction, identification of interactive domains, and docking with Ca2+ ions of S. litura-inducible GmCMLs, indicated their identity as calcium sensors. This study on the characterization of GmCMLs provided insights into their roles in calcium signaling and plant defense during herbivory.
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Affiliation(s)
- Manisha Yadav
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Jyotsna Pandey
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Amrita Chakraborty
- EVA4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Jiban Kumar Kundu
- Plant Virus and Vector Interactions Group, Crop Research Institute, Prague, Czechia
| | - Amit Roy
- EVA4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
- *Correspondence: Amit Roy,
| | - Indrakant Kumar Singh
- Molecular Biology Research Laboratory, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
- DBC-i4 Center, Deshbandhu College, University of Delhi, New Delhi, India
- Indrakant Kumar Singh,
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
- Archana Singh,
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26
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Vandelle E, Ariani P, Regaiolo A, Danzi D, Lovato A, Zadra C, Vitulo N, Gambino G, Polverari A. The Grapevine E3 Ubiquitin Ligase VriATL156 Confers Resistance against the Downy Mildew Pathogen Plasmopara viticola. Int J Mol Sci 2021; 22:ijms22020940. [PMID: 33477914 PMCID: PMC7833427 DOI: 10.3390/ijms22020940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 12/13/2022] Open
Abstract
Downy mildew, caused by Plasmopara viticola, is one of the most severe diseases of grapevine (Vitis vinifera L.). Genetic resistance is an effective and sustainable control strategy, but major resistance genes (encoding receptors for specific pathogen effectors) introgressed from wild Vitis species, although effective, may be non-durable because the pathogen can evolve to avoid specific recognition. Previous transcriptomic studies in the resistant species Vitis riparia highlighted the activation of signal transduction components during infection. The transfer of such components to V. vinifera might confer less specific and therefore more durable resistance. Here, we describe the generation of transgenic V. vinifera lines constitutively expressing the V. riparia E3 ubiquitin ligase gene VriATL156. Phenotypic and molecular analysis revealed that the transgenic plants were less susceptible to P. viticola than vector-only controls, confirming the role of this E3 ubiquitin ligase in the innate immune response. Two independent transgenic lines were selected for detailed analysis of the resistance phenotype by RNA-Seq and microscopy, revealing the profound reprogramming of transcription to achieve resistance that operates from the earliest stages of pathogen infection. The introduction of VriATL156 into elite grapevine cultivars could therefore provide an effective and sustainable control measure against downy mildew.
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Affiliation(s)
- Elodie Vandelle
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, CV1, 37134 Verona, Italy; (P.A.); (A.R.); (D.D.); (A.L.); (N.V.)
- Correspondence: (E.V.); (A.P.); Tel.: +39-045-802-7826 (E.V.); +39-045-802-7064 (A.P.)
| | - Pietro Ariani
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, CV1, 37134 Verona, Italy; (P.A.); (A.R.); (D.D.); (A.L.); (N.V.)
| | - Alice Regaiolo
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, CV1, 37134 Verona, Italy; (P.A.); (A.R.); (D.D.); (A.L.); (N.V.)
| | - Davide Danzi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, CV1, 37134 Verona, Italy; (P.A.); (A.R.); (D.D.); (A.L.); (N.V.)
| | - Arianna Lovato
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, CV1, 37134 Verona, Italy; (P.A.); (A.R.); (D.D.); (A.L.); (N.V.)
| | - Claudia Zadra
- Department of Pharmaceutical Sciences, University of Perugia, Borgo XX Giugno 72, 06121 Perugia, Italy;
| | - Nicola Vitulo
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, CV1, 37134 Verona, Italy; (P.A.); (A.R.); (D.D.); (A.L.); (N.V.)
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135 Torino, Italy;
| | - Annalisa Polverari
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, CV1, 37134 Verona, Italy; (P.A.); (A.R.); (D.D.); (A.L.); (N.V.)
- Correspondence: (E.V.); (A.P.); Tel.: +39-045-802-7826 (E.V.); +39-045-802-7064 (A.P.)
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27
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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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28
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Amna S, Qamar S, Turab Naqvi AA, Al-Huqail AA, Qureshi MI. Role of sulfur in combating arsenic stress through upregulation of important proteins, and in-silico analysis to study the interaction between phosphate transporter (PHO1), arsenic and phosphate in spinach. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 157:348-358. [PMID: 33189055 DOI: 10.1016/j.plaphy.2020.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/02/2020] [Indexed: 06/11/2023]
Abstract
An adequate amount of Sulfur (S) is essential for proper plant growth and defence against abiotic stresses including metals and metalloids. Arsenic (As) contamination is increasing in agricultural soils rapidly due to anthropogenic activities. Sulfur deficiency and arsenic stress could be more harmful than these individual stresses alone. To understand the impact of S-deficiency and arsenic (31 ppm Na3AsO4 of soil) on ecophysiology, growth, inorganic phosphate level, and proteomic profile of spinach, the present study was conducted. Interaction of arsenic with phosphate transporters, phytochelatins, and glutathione was also analyzed in silico. Comparative 2D MS/MS proteomics helped in the identification of important proteins which might be the key players under S-deficiency and As stress. Upregulation and downregulation of 36 and 21 proteins under As stress; 19 and 36 proteins under S-deficiency; 38 and 31 proteins under combined stress, respectively was observed. A total, 87 proteins subjected to identification via MS/MS ion search were found to be associated with important plant functions. PHO1 abundance was highly influenced by As stress; hence an in-silico homology modeling based molecular docking was performed which indicated high interaction between PHO1 and As/phosphate. Varied proximity of arsenic with phosphate transporters, phytochelatin, and glutathione revealed these components as a potential target of As toxicity/detoxification in Spinach, reflecting sulfur as an important criterion for arsenic tolerance.
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Affiliation(s)
- Syeda Amna
- Proteomics and Bioinformatics Lab, Department of Biotechnology, Jamia Millia Islamia, Delhi, India.
| | - Sadia Qamar
- Proteomics and Bioinformatics Lab, Department of Biotechnology, Jamia Millia Islamia, Delhi, India.
| | - Ahmad Abu Turab Naqvi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Delhi, India.
| | - Asma A Al-Huqail
- Botany & Microbiology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, Saudi Arabia.
| | - M Irfan Qureshi
- Proteomics and Bioinformatics Lab, Department of Biotechnology, Jamia Millia Islamia, Delhi, India.
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29
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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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The Grapevine Calmodulin-Like Protein Gene CML21 Is Regulated by Alternative Splicing and Involved in Abiotic Stress Response. Int J Mol Sci 2020; 21:ijms21217939. [PMID: 33114685 PMCID: PMC7663043 DOI: 10.3390/ijms21217939] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 01/09/2023] Open
Abstract
Calmodulin-like proteins (CMLs) represent a large family of plant calcium sensor proteins involved in the regulation of plant responses to environmental cues and developmental processes. In the present work, we identified four alternatively spliced mRNA forms of the grapevine CML21 gene that encoded proteins with distinct N-terminal regions. We studied the transcript abundance of CML21v1, CML21v2, CML21v3, and CML21v4 in wild-growing grapevine Vitis amurensis Rupr. in response to desiccation, heat, cold, high salinity, and high mannitol stress using quantitative real-time RT-PCR. The levels of all four splice variants of VaCML21 were highly induced in response to cold stress. In addition, VaCML21v1 and VaCML21v2 forms were highly modulated by all other abiotic stress treatments. Constitutive expression of VaCML21v2 and VaCML21v4 improved biomass accumulation of V. amurensis callus cell cultures under prolonged low temperature stress. Heterologous expression of the grapevine CML21v2 and VaCML21v4 splice variants in Arabidopsis improved survival rates of the transgenic plants after freezing. The VaCML21v2 overexpression enhanced activation of the cold stress-responsive marker genes AtDREB1A and AtDREB2A, while VaCML21v4 overexpression—AtCOR47, AtRD29A, AtRD29B, and AtKIN1 genes after freezing stress in the transgenic Arabidopsis. The results indicate that the grapevine CML21 gene acts as a positive regulator in the plant response to cold stress. The detected variety of CML21 transcripts and their distinct transcriptional responses suggested that this expansion of mRNA variants could contribute to the diversity of grapevine adaptive reactions.
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Transcriptomic analysis of Dubas bug (Ommatissus lybicus Bergevin) infestation to Date Palm. Sci Rep 2020; 10:11505. [PMID: 32661358 DOI: 10.1038/s41598-020-67438-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 06/08/2020] [Indexed: 01/03/2023] Open
Abstract
Date palm (Phoenix dactylifera L.) and its fruit possess sociocultural, health and economic importance in Middle East. The date palm plantations are prone to Dubas bug (DB; Ommatissus lybicus DeBergevin; Homoptera: Tropiduchidae) attacks that severely damages the tree's growth and reduces fruit production. However, the transcriptome related datasets are not known to understand how DB activates physiological and gene regulatory mechanisms during infestation. Hence, we performed RNA-Seq of leaf infected with or without DB to understand the molecular responses of date palm seedlings. Before doing that, we noticed that DB infestation significantly increase superoxide anion and malondialdehyde production to two-folds as compared to healthy control. Stress-responsive genes such as proline transporter 2, NADP-dependent glyceraldehyde and superoxide dismutase were found significantly upregulated in infected seedlings. The infection repercussions were also revealed by significantly higher contents of endogenous phytohormonal signaling of jasmonic acid (JA) and salicylic acid (SA) compared with control. These findings persuaded to dig out intrinsic mechanisms and gene regulatory networks behind DB infestation to date palm by RNA-Seq analysis. Transcriptome analysis revealed upregulation of 6,919 genes and down-regulation of 2,695 genes in leaf during the infection process. The differentially expressed genes were mostly belongs to cellular functions (calcium and MAPK), phytohormones (auxin, gibberellins, abscisic acid, JA and SA), and secondary metabolites (especially coumarinates and gossypol). The data showed that defense responses were aggravated by gene networks involved in hypersensitive responses (PAR1, RIN4, PBS1 etc.). In conclusion, the results revealed that date palm's leaf up-regulates both cellular and phytohormonal determinants, followed by intrinsic hypersensitive responses to counter infestation process by Dubas bug.
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Shi J, Du X. Identification, characterization and expression analysis of calmodulin and calmodulin-like proteins in Solanum pennellii. Sci Rep 2020; 10:7474. [PMID: 32366918 PMCID: PMC7198499 DOI: 10.1038/s41598-020-64178-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 02/26/2020] [Indexed: 01/09/2023] Open
Abstract
In plants, the calmodulin (CaM) proteins is an important calcium-binding protein, which play a crucial role in both regulating plant growth and development, as well as in the resistance mechanisms to various biotic and abiotic stresses. However, there is limited knowledge available on the CaM family functions in Solanum pennellii, a wild tomato species utilized as a genetic resource for cultivated tomatoes. In this study, 6 CaM (SpCaM) and 45 CaM-like (SpCML) genes from Solanum pennellii were selected for bioinformatics analysis to obtain insights into their phylogenetic relationships, gene structures, conserved motifs, chromosomal locations, and promoters. The results showed that the 6 SpCaM proteins contained 4 EF-hand domains each, and the 45 SpCML proteins had 2-4 EF-hand domains. The 51 CaM and CaM-like genes contained different intron/exon patterns and they were unevenly distributed across the 12 chromosomes of S. pennellii. The results of the analysis of the conserved motifs and promoter cis-regulatory elements also indicated that these proteins were involved in the responses to biotic and abiotic stresses. qRT-PCR analysis indicated that the SpCaM and SpCML genes had broad expression patterns in abiotic stress conditions and with hormone treatments, in different tissues. The findings of this study will be important for further investigations of the calcium signal transduction mechanisms under stress conditions and lay a theoretical foundation for further exploration of the molecular mechanisms of plant resistance.
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Affiliation(s)
- Jinyan Shi
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiangge Du
- College of Plant Protection, China Agricultural University, Beijing, China.
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The Effect of Abiotic Stress Conditions on Expression of Calmodulin ( CaM) and Calmodulin-Like ( CML) Genes in Wild-Growing Grapevine Vitis amurensis. PLANTS 2019; 8:plants8120602. [PMID: 31847201 PMCID: PMC6963546 DOI: 10.3390/plants8120602] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/07/2019] [Accepted: 12/10/2019] [Indexed: 12/22/2022]
Abstract
Plant calmodulins (CaMs) and calmodulin-like proteins (CMLs) are important plant Ca2+-binding proteins that sense and decode changes in the intracellular Ca2+ concentration arising in response to environmental stimuli. Protein Ca2+ sensors are presented by complex gene families in plants and perform diverse biological functions. In this study, we cloned, sequenced, and characterized three CaM and 54 CML mRNA transcripts of Vitis amurensis Rupr., a wild-growing grapevine with a remarkable stress tolerance. Using real-time quantitative RT-PCR, we analyzed transcript abundance of the identified VaCaMs and VaCMLs in response to water deficit, high salinity, high mannitol, cold and heat stresses. Expression of VaCaMs and 32 VaCMLs actively responded to the abiotic stresses and exhibited both positive and negative regulation patterns. Other VaCML members showed slight transcriptional regulation, remained essentially unresponsive or responded only after one time interval of the treatments. The substantial alterations in the VaCaM and VaCML transcript levels revealed their involvement in the adaptation of wild-growing grapevine to environmental stresses.
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Gu W, Zhang A, Sun H, Gu Y, Chao J, Tian R, Duan JA. Identifying resurrection genes through the differentially expressed genes between Selaginella tamariscina (Beauv.) spring and Selaginella moellendorffii Hieron under drought stress. PLoS One 2019; 14:e0224765. [PMID: 31721818 PMCID: PMC6853609 DOI: 10.1371/journal.pone.0224765] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 10/21/2019] [Indexed: 02/06/2023] Open
Abstract
Selaginella tamariscina (Beauv.) spring, a primitive vascular resurrection plant, can survive extreme drought and recover when water becomes available. To identify drought-inducible genes and to clarify the molecular mechanism of drought tolerance, a comparative transcriptional pattern analysis was conducted between S. tamariscina and Selaginella moellendorffii Hieron (drought sensitive). 133 drought related genes were identified, including 72 functional genes and 61 regulatory genes. And several drought responsive reactions, such as antioxidant activity, osmotic balance, cuticle defense and signal transduction were highlighted in S. tamariscina under drought. Notably, besides peroxidase, catalase and L-ascorbate oxidase genes, DEGs associated with phenylalanine metabolism and polyamine catabolism could be alternative ways to enhance antioxidant ability in S. tamariscina. DEGs related to soluble carbohydrate metabolism, late embryogenesis abundant protein (LEA) and aquaporin protein (AQP) confirmed that osmotic adjustment could resist drought during desiccation. DEGs involved in xyloglucan metabolic process, pectin metabolic process and cutin biosynthesis may also contribute to drought tolerance of S. tamariscina by cuticle defense. Drought-responsive genes encoding protein kinases, calcium sensors, transcription factors (TFs) and plant hormones also help to drought resistance of S. tamariscina. The preliminary validation experiments were performed and the results were consistent with our hypothetical integrated regulatory network. The results of this study provide candidate resurrection genes and an integrated regulatory network for further studies on the molecular mechanisms of stress tolerance in S. tamariscina.
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Affiliation(s)
- Wei Gu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Aqin Zhang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hongmei Sun
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuchen Gu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jianguo Chao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Rong Tian
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jin-Ao Duan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
- * E-mail:
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Trande M, Pedretti M, Bonza MC, Di Matteo A, D'Onofrio M, Dominici P, Astegno A. Cation and peptide binding properties of CML7, a calmodulin-like protein from Arabidopsis thaliana. J Inorg Biochem 2019; 199:110796. [PMID: 31419675 DOI: 10.1016/j.jinorgbio.2019.110796] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/26/2019] [Accepted: 07/31/2019] [Indexed: 12/12/2022]
Abstract
Plants contain a large family of so-called calmodulin-like proteins (CMLs) which differ from canonical calmodulin in that they show greater variability in sequence, length, and number of EF-hand domains. The presence of this extended CML family has raised questions regarding the role of these proteins: are they functionally redundant or do they play specific functions in physiological plant processes? To answer these questions, comprehensive biochemical and structural information on CML proteins is fundamental. Among the 50 CMLs from Arabidopsis thaliana, herein we described the ability of CML7 to bind metal ions focusing on the Ca2+ and Mg2+ sensing properties, as well as on metal-induced conformational changes. Circular dichroism and nuclear magnetic resonance (NMR) studies indicated that both Ca2+ and Mg2+ stabilize CML7, as reflected in conformational rearrangements in secondary and tertiary structure and in increases in thermal stability of the protein. However, the conformational changes that binding induces differ between the two metal ions, and only Ca2+ binding controls a structural transition that leads to hydrophobic exposure, as suggested by 8-anilino-1-naphthalenesulfonic acid fluorescence. Isothermal titration calorimetry data coupled with NMR experiments revealed the presence of two high affinity Ca2+-binding sites in the C-lobe of CML7 and two weaker sites in the N-lobe. The paired nature of these CML7 EF-hands enables them to bind Ca2+ with positive cooperativity within each globular domain. Our results clearly place CML7 in the category of Ca2+ sensors. Along with this, the protein can bind to a model target peptide (melittin) in a Ca2+-dependent manner.
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Affiliation(s)
- Matteo Trande
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Marco Pedretti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Maria Cristina Bonza
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Adele Di Matteo
- Institute of Molecular Biology and Pathology, CNR, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Mariapina D'Onofrio
- 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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Galati G, Gandin A, Jolivet Y, Larbat R, Hehn A. Untargeted Metabolomics Approach Reveals Diverse Responses of Pastinaca Sativa to Ozone and Wounding Stresses. Metabolites 2019; 9:E153. [PMID: 31340592 PMCID: PMC6681050 DOI: 10.3390/metabo9070153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/08/2019] [Accepted: 07/20/2019] [Indexed: 12/01/2022] Open
Abstract
Stresses such as wounding or atmospheric pollutant exposure have a significant impact on plant fitness. Since it has been widely described that the metabolome directly reflects plant physiological status, a way to assess this impact is to perform a global metabolomic analysis. In this study, we investigated the effect of two abiotic stresses (mechanical wounding and ozone exposure) on parsnip metabolic balance using a liquid chromatography-mass spectrometry-based untargeted metabolomic approach. For this purpose, parsnip leaves were submitted to an acute ozone exposure or were mechanically wounded and sampled 24, 48, and 72 h post-treatment. Multivariate and univariate statistical analyses highlighted numerous differentially-accumulated metabolic features as a function of time and treatment. Mechanical wounding led to a more differentiated response than ozone exposure. We found that the levels of coumarins and fatty acyls increased in wounded leaves, while flavonoid concentration decreased in the same conditions. These results provide an overview of metabolic destabilization through differentially-accumulated compounds and provide a better understanding of global plant metabolic changes in defense mechanisms.
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Affiliation(s)
- Gianni Galati
- INRA, LAE, Université de Lorraine, 54000 Nancy France
| | - Anthony Gandin
- Université de Lorraine, AgroParisTech, INRA, UMR Silva, 54000 Nancy, France
| | - Yves Jolivet
- Université de Lorraine, AgroParisTech, INRA, UMR Silva, 54000 Nancy, France
| | - Romain Larbat
- INRA, LAE, Université de Lorraine, 54000 Nancy France.
| | - Alain Hehn
- INRA, LAE, Université de Lorraine, 54000 Nancy France
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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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Xu M, Liu CL, Luo J, Qi Z, Yan Z, Fu Y, Wei SS, Tang H. Transcriptomic de novo analysis of pitaya (Hylocereus polyrhizus) canker disease caused by Neoscytalidium dimidiatum. BMC Genomics 2019; 20:10. [PMID: 30616517 PMCID: PMC6323817 DOI: 10.1186/s12864-018-5343-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/30/2018] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Canker disease caused by Neoscytalidium dimidiatum is the most serious disease that attacks the pitaya industry. One pathogenic fungus, referred to as ND8, was isolated from the wild-type red-fleshed pitaya (Hylocereus polyrhizus) of Hainan Province. In the early stages of this disease, stems show little spots and a loss of green color. These spots then gradually spread until the stems became rotten due to infection by various strains. Canker disease caused by Neoscytalidium dimidiatum poses a significant threat to pitaya commercial plantations with the growth of stems and the yields, quality of pitaya fruits. However, a lack of transcriptomic and genomic information hinders our understanding of the molecular mechanisms underlying the pitaya defense response. RESULTS We investigated the host responses of red-fleshed pitaya (H. polyrhizus) cultivars against N. dimidiatum using Illumina RNA-Seq technology. Significant expression profiles of 23 defense-related genes were further analyzed by qRT-PCR. The total read length based on RNA-Seq was 25,010,007; mean length was 744, the N50 was 1206, and the guanine-cytosine content was 44.48%. Our investigation evaluated 33,584 unigenes, of which 6209 (18.49%) and 27,375 (81.51%) were contigs and singlets, respectively. These unigenes shared a similarity of 16.62% with Vitis vinifera, 7.48% with Theobroma cacao, 6.6% with Nelumbo nucifera and 5.35% with Jatropha curcas. The assembled unigenes were annotated into non-redundant (NR, 25161 unigenes), Kyoto Encyclopedia of Genes and Genomes (KEGG, 17895 unigenes), Clusters of Orthologous Groups (COG, 10475 unigenes), InterPro (19,045 unigenes), and Swiss-Prot public protein databases (16,458 unigenes). In addition, 24 differentially expressed genes, which were mainly associated with plant pathology pathways, were analyzed in-depth. CONCLUSIONS This study provides a basis for further in-depth research on the protein function of the annotated unigene assembly with cDNA sequences.
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Affiliation(s)
- Min Xu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, No.58 Renmin Avenue, Haikou, 570228 Hainan People’s Republic of China
| | - Cheng-Li Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, No.58 Renmin Avenue, Haikou, 570228 Hainan People’s Republic of China
| | - Juan Luo
- University of Sanya, No.191 Yingbin Avenue Xueyuan Road, Sanya, 572000 Hainan People’s Republic of China
| | - Zhao Qi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, No.58 Renmin Avenue, Haikou, 570228 Hainan People’s Republic of China
| | - Zhen Yan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, No.58 Renmin Avenue, Haikou, 570228 Hainan People’s Republic of China
| | - Yu Fu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, No.58 Renmin Avenue, Haikou, 570228 Hainan People’s Republic of China
| | - Shuang-Shuang Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, No.58 Renmin Avenue, Haikou, 570228 Hainan People’s Republic of China
| | - Hua Tang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, No.58 Renmin Avenue, Haikou, 570228 Hainan People’s Republic of China
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