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Wang G, Xu Y, Guan SL, Zhang J, Jia Z, Hu L, Zhai M, Mo Z, Xuan J. Comprehensive genomic analysis of CiPawPYL-PP2C-SnRK family genes in pecan (Carya illinoinensis) and functional characterization of CiPawSnRK2.1 under salt stress responses. Int J Biol Macromol 2024; 279:135366. [PMID: 39244129 DOI: 10.1016/j.ijbiomac.2024.135366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 09/04/2024] [Accepted: 09/04/2024] [Indexed: 09/09/2024]
Abstract
Abscisic acid (ABA) is a pivotal regulator of plant growth, development, and responses to environmental stresses. The ABA signaling pathway involves three key components: ABA receptors known as PYLs, PP2Cs, and SnRK2s, which are conserved across higher plants. This study comprehensively investigated the PYL-PP2C-SnRK gene family in pecan, identifying 14 PYL genes, 97 PP2C genes, and 44 SnRK genes, which were categorized into subgroups through phylogenetic and sequence structure analysis. Whole-genome duplication (WGD) and dispersed duplication (DSD) were identified as major drivers of family expansion, and purifying selection was the primary evolutionary force. Tissue-specific expression analysis suggested diverse functions in different pecan tissues. qRT-PCR validation confirmed the involvement of CiPawPYLs, CiPawPP2CAs, and CiPawSnRK2s in salt stress response. Subcellular localization analysis revealed CiPawPP2C1 in the nucleus and CiPawPYL1 and CiPawSnRK2.1 in both the nucleus and the plasma membrane. In addition, VIGS indicated that CiPawSnRK2.1-silenced pecan seedling leaves display significantly reduced salt tolerance. Y2H and LCI assays verified that CiPawPP2C3 can interact with CiPawPYL5, CiPawPYL8, and CiPawSnRK2.1. This study characterizes the role of CiPawSnRK2.1 in salt stress and lays the groundwork for exploring the CiPawPYL-PP2C-SnRK module, highlighting the need to investigate the roles of other components in the pecan ABA signaling pathway.
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Affiliation(s)
- Guoming Wang
- Jiangsu Engineering Research Center for Germplasm Innovation and Utilization of Pecan, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Ying Xu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Sophia Lee Guan
- College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park, MD 20742, United States
| | - Jiyu Zhang
- Jiangsu Engineering Research Center for Germplasm Innovation and Utilization of Pecan, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Zhanhui Jia
- Jiangsu Engineering Research Center for Germplasm Innovation and Utilization of Pecan, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Longjiao Hu
- Jiangsu Engineering Research Center for Germplasm Innovation and Utilization of Pecan, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Min Zhai
- Jiangsu Engineering Research Center for Germplasm Innovation and Utilization of Pecan, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Zhenghai Mo
- Jiangsu Engineering Research Center for Germplasm Innovation and Utilization of Pecan, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Jiping Xuan
- Jiangsu Engineering Research Center for Germplasm Innovation and Utilization of Pecan, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
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Yao P, Zhang C, Bi Z, Liu Y, Liu Z, Wei J, Su X, Bai J, Cui J, Sun C. Overexpression of Potato PYL16 Gene in Tobacco Enhances the Transgenic Plant Tolerance to Drought Stress. Int J Mol Sci 2024; 25:8644. [PMID: 39201331 PMCID: PMC11354512 DOI: 10.3390/ijms25168644] [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: 07/24/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 09/02/2024] Open
Abstract
PYR/PYL/RCAR proteins are abscisic acid (ABA) receptors that play a crucial role in plant responses to abiotic stresses. However, there have been no research reports on potato PYL so far. In this study, a potato PYL gene named StPYL16 was identified based on transcriptome data under drought stress. Molecular characteristics analysis revealed that the StPYL16 protein possesses an extremely conserved PYL family domain. The tissue expression results indicated that the StPYL16 is predominantly expressed at high levels in the underground parts, particularly in tubers. Abiotic stress response showed that StPYL16 has a significant response to drought treatment. Further research on the promoter showed that drought stress could enhance the activation activity of the StPYL16 promoter on the reporter gene. Then, transient and stable expression of StPYL16 in tobacco enhanced the drought resistance of transgenic plants, resulting in improved plant height, stem thickness, and root development. In addition, compared with wild-type plants, StPYL16 transgenic tobacco exhibited lower malondialdehyde (MDA) content, higher proline accumulation, and stronger superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities. Meanwhile, StPYL16 also up-regulated the expression levels of stress-related genes (NtSOD, NtCAT, NtPOD, NtRD29A, NtLEA5, and NtP5CS) in transgenic plants under drought treatment. These findings indicated that the StPYL16 gene plays a positive regulatory role in potato responses to drought stress.
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Affiliation(s)
- Panfeng Yao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (Z.B.); (Y.L.); (Z.L.); (J.W.); (X.S.); (J.B.); (J.C.)
| | - Chunli Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (Z.B.); (Y.L.); (Z.L.); (J.W.); (X.S.); (J.B.); (J.C.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (Z.B.); (Y.L.); (Z.L.); (J.W.); (X.S.); (J.B.); (J.C.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (Z.B.); (Y.L.); (Z.L.); (J.W.); (X.S.); (J.B.); (J.C.)
| | - Zhen Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (Z.B.); (Y.L.); (Z.L.); (J.W.); (X.S.); (J.B.); (J.C.)
| | - Jia Wei
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (Z.B.); (Y.L.); (Z.L.); (J.W.); (X.S.); (J.B.); (J.C.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xinglong Su
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (Z.B.); (Y.L.); (Z.L.); (J.W.); (X.S.); (J.B.); (J.C.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (Z.B.); (Y.L.); (Z.L.); (J.W.); (X.S.); (J.B.); (J.C.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Junmei Cui
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (Z.B.); (Y.L.); (Z.L.); (J.W.); (X.S.); (J.B.); (J.C.)
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (Z.B.); (Y.L.); (Z.L.); (J.W.); (X.S.); (J.B.); (J.C.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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Chen J, Wang Y, Wu Y, Huang X, Qiu X, Chen J, Lin Q, Zhao H, Chen F, Gao G. Genome-wide identification and expression analysis of the PP2C gene family in Apocynum venetum and Apocynum hendersonii. BMC PLANT BIOLOGY 2024; 24:652. [PMID: 38982365 PMCID: PMC11232223 DOI: 10.1186/s12870-024-05328-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/24/2024] [Indexed: 07/11/2024]
Abstract
BACKGROUND Protein phosphatase class 2 C (PP2C) is the largest protein phosphatase family in plants. Members of the PP2C gene family are involved in a variety of physiological pathways in plants, including the abscisic acid signalling pathway, the regulation of plant growth and development, etc., and are capable of responding to a wide range of biotic and abiotic stresses, and play an important role in plant growth, development, and response to stress. Apocynum is a perennial persistent herb, divided into Apocynum venetum and Apocynum hendersonii. It mainly grows in saline soil, deserts and other harsh environments, and is widely used in saline soil improvement, ecological restoration, textiles and medicine. A. hendersonii was found to be more tolerant to adverse conditions. The main purpose of this study was to investigate the PP2C gene family and its expression pattern under salt stress and to identify important candidate genes related to salt tolerance. RESULTS In this study, 68 AvPP2C genes and 68 AhPP2C genes were identified from the genomes of A. venetum and A. hendersonii, respectively. They were classified into 13 subgroups based on their phylogenetic relationships and were further analyzed for their subcellular locations, gene structures, conserved structural domains, and cis-acting elements. The results of qRT-PCR analyses of seven AvPP2C genes and seven AhPP2C genes proved that they differed significantly in gene expression under salt stress. It has been observed that the PP2C genes in A. venetum and A. hendersonii exhibit different expression patterns. Specifically, AvPP2C2, 6, 24, 27, 41 and AhPP2C2, 6, 24, 27, 42 have shown significant differences in expression under salt stress. This indicates that these genes may play a crucial role in the salt tolerance mechanism of A. venetum and A. hendersonii. CONCLUSIONS In this study, we conducted a genome-wide analysis of the AvPP2C and AhPP2C gene families in Apocynum, which provided a reference for further understanding the functional characteristics of these genes.
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Affiliation(s)
- Jiayi Chen
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, Changsha, 410219, China
| | - Yue Wang
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, Changsha, 410219, China
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Yongmei Wu
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, Changsha, 410219, China
| | - Xiaoyu Huang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Xiaojun Qiu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Jikang Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
- Yuelushan Laboratory, Changsha, 410082, P.R. China
| | - Qian Lin
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, Changsha, 410219, China
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Haohan Zhao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
- Yuelushan Laboratory, Changsha, 410082, P.R. China
| | - Fengming Chen
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, Changsha, 410219, China.
| | - Gang Gao
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, Changsha, 410219, China.
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
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Zhai Z, Ao Q, Yang L, Lu F, Cheng H, Fang Q, Li C, Chen Q, Yan J, Wei Y, Jiang YQ, Yang B. Rapeseed PP2C37 Interacts with PYR/PYL Abscisic Acid Receptors and Negatively Regulates Drought Tolerance. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12445-12458. [PMID: 38771652 DOI: 10.1021/acs.jafc.4c00385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Global water deficit is a severe abiotic stress threatening the yielding and quality of crops. Abscisic acid (ABA) is a phytohormone that mediates drought tolerance. Protein kinases and phosphatases function as molecular switches in eukaryotes. Protein phosphatases type 2C (PP2Cs) are a major family that play essential roles in ABA signaling and stress responses. However, the role and underlying mechanism of PP2C in rapeseed (Brassica napus L.) mediating drought response has not been reported yet. Here, we characterized a PP2C family member, BnaPP2C37, and its expression level was highly induced by ABA and dehydration treatments. It negatively regulates drought tolerance in rapeseed. We further identified that BnaPP2C37 interacted with multiple PYR/PYL receptors and a drought regulator BnaCPK5 (calcium-dependent protein kinase 5) through yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. Specifically, BnaPYL1 and BnaPYL9 repress BnaPP2C37 phosphatase activity. Moreover, the pull-down assay and phosphatase assays show BnaPP2C37 interacts with BnaCPK5 to dephosphorylate BnaCPK5 and its downstream BnaABF3. Furthermore, a dual-luciferase assay revealed BnaPP2C37 transcript level was enhanced by BnaABF3 and BnaABF4, forming a negative feedback regulation to ABA response. In summary, we identified that BnaPP2C37 functions negatively in drought tolerance of rapeseed, and its phosphatase activity is repressed by BnaPYL1/9 whereas its transcriptional level is upregulated by BnaABF3/4.
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Affiliation(s)
- Zengkang Zhai
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Qianqian Ao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Liuqing Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Fangxiao Lu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Haokun Cheng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Qinxin Fang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Chun Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Qinqin Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Jingli Yan
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, Henan Province, People's Republic of China
| | - Yongsheng Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Yuan-Qing Jiang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Bo Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of 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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Gao Y, Qu D, Zhou M, Tang R, Ye J, Li X, Wang Y. Rhizobial-induced phosphatase GmPP2C61A positively regulates soybean nodulation. PHYSIOLOGIA PLANTARUM 2024; 176:e14341. [PMID: 38741264 DOI: 10.1111/ppl.14341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/16/2024]
Abstract
Symbiotic nitrogen fixation (SNF) is crucial for legumes, providing them with the nitrogen necessary for plant growth and development. Nodulation is the first step in the establishment of SNF. However, the determinant genes in soybean nodulation and the understanding of the underlying molecular mechanisms governing nodulation are still limited. Herein, we identified a phosphatase, GmPP2C61A, which was specifically induced by rhizobia inoculation. Using transgenic hairy roots harboring GmPP2C61A::GUS, we showed that GmPP2C61A was mainly induced in epidermal cells following rhizobia inoculation. Functional analysis revealed that knockdown or knock-out of GmPP2C61A significantly reduced the number of nodules, while overexpression of GmPP2C61A promoted nodule formation. Additionally, GmPP2C61A protein was mainly localized in the cytoplasm and exhibited conserved phosphatase activity in vitro. Our findings suggest that phosphatase GmPP2C61A serves as a critical regulator in soybean nodulation, highlighting its potential significance in enhancing symbiotic nitrogen fixation.
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Affiliation(s)
- Yongkang Gao
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P.R. China
| | - Dejie Qu
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P.R. China
| | - Miaomiao Zhou
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P.R. China
| | - Ruiheng Tang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P.R. China
| | - Junjie Ye
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P.R. China
| | - Xia Li
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P.R. China
| | - Youning Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, P.R. China
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University Yangling, Shaanxi Province, P.R. China
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Kaur S, Seem K, Duhan N, Kumar S, Kaundal R, Mohapatra T. Comparative miRNome and transcriptome analyses reveal the expression of novel miRNAs in the panicle of rice implicated in sustained agronomic performance under terminal drought stress. PLANTA 2024; 259:128. [PMID: 38639776 DOI: 10.1007/s00425-024-04399-x] [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: 11/21/2023] [Accepted: 03/27/2024] [Indexed: 04/20/2024]
Abstract
MAIN CONCLUSION Differential expression of 128 known and 111 novel miRNAs in the panicle of Nagina 22 under terminal drought stress targeting transcription factors, stress-associated genes, etc., enhances drought tolerance and helps sustain agronomic performance under terminal drought stress. Drought tolerance is a complex multigenic trait, wherein the genes are fine-tuned by coding and non-coding components in mitigating deleterious effects. MicroRNA (miRNA) controls gene expression at post-transcriptional level either by cleaving mRNA (transcript) or by suppressing its translation. miRNAs are known to control developmental processes and abiotic stress tolerance in plants. To identify terminal drought-responsive novel miRNA in contrasting rice cultivars, we constructed small RNA (sRNA) libraries from immature panicles of drought-tolerant rice [Nagina 22 (N 22)] and drought-sensitive (IR 64) cultivars grown under control and terminal drought stress. Our analysis of sRNA-seq data resulted in the identification of 169 known and 148 novel miRNAs in the rice cultivars. Among the novel miRNAs, 68 were up-regulated while 43 were down-regulated in the panicle of N 22 under stress. Interestingly, 31 novel miRNAs up-regulated in N 22 were down-regulated in IR 64, whereas 4 miRNAs down-regulated in N 22 were up-regulated in IR 64 under stress. To detect the effects of miRNA on mRNA expression level, transcriptome analysis was performed, while differential expression of miRNAs and their target genes was validated by RT-qPCR. Targets of the differentially expressed miRNAs include transcription factors and stress-associated genes involved in cellular/metabolic/developmental processes, response to abiotic stress, programmed cell death, photosynthesis, panicle/seed development, and grain yield. Differential expression of the miRNAs could be validated in an independent set of the samples. The findings might be useful in genetic improvement of drought-tolerant rice.
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Affiliation(s)
- Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA
- ICAR-Research Complex for North Eastern Hill Region (NEH), Umiam, Meghalaya, 793103, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Naveen Duhan
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA.
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA.
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
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Ndathe R, Kato N. Phosphatidic acid produced by phospholipase Dα1 and Dδ is incorporated into the internal membranes but not involved in the gene expression of RD29A in the abscisic acid signaling network in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2024; 15:1356699. [PMID: 38681216 PMCID: PMC11045897 DOI: 10.3389/fpls.2024.1356699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/21/2024] [Indexed: 05/01/2024]
Abstract
Core protein components of the abscisic acid (ABA) signaling network, pyrabactin resistance (PYR), protein phosphatases 2C (PP2C), and SNF1-related protein kinase 2 (SnRK2) are involved in the regulation of stomatal closure and gene expression downstream responses in Arabidopsis thaliana. Phosphatidic acid (PA) produced by the phospholipases Dα1 and Dδ (PLDs) in the plasma membrane has been identified as a necessary molecule in ABA-inducible stomatal closure. On the other hand, the involvement of PA in ABA-inducible gene expression has been suggested but remains a question. In this study, the involvement of PA in the ABA-inducible gene expression was examined in the model plant Arabidopsis thaliana and the canonical RD29A ABA-inducible gene that possesses a single ABA-responsive element (ABRE) in the promoter. The promoter activity and accumulation of the RD29A mRNA during ABA exposure to the plants were analyzed under conditions in which the production of PA by PLDs is abrogated through chemical and genetic modification. Changes in the subcellular localization of PA during the signal transduction were analyzed with confocal microscopy. The results obtained in this study suggest that inhibition of PA production by the PLDs does not affect the promoter activity of RD29A. PA produced by the PLDs and exogenously added PA in the plasma membrane are effectively incorporated into internal membranes to transduce the signal. However, exogenously added PA induces stomatal closure but not RD29A expression. This is because PA produced by the PLDs most likely inhibits the activity of not all but only the selected PP2C family members, the negative regulators of the RD29A promoter. This finding underscores the necessity for experimental verifications to adapt previous knowledge into a signaling network model before its construction.
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Affiliation(s)
| | - Naohiro Kato
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States
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9
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Akter N, Islam MSU, Rahman MS, Zohra FT, Rahman SM, Manirujjaman M, Sarkar MAR. Genome-wide identification and characterization of protein phosphatase 2C (PP2C) gene family in sunflower (Helianthus annuus L.) and their expression profiles in response to multiple abiotic stresses. PLoS One 2024; 19:e0298543. [PMID: 38507444 PMCID: PMC10954154 DOI: 10.1371/journal.pone.0298543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 01/25/2024] [Indexed: 03/22/2024] Open
Abstract
Plant protein phosphatase 2C (PP2C) plays vital roles in responding to various stresses, stimulating growth factors, phytohormones, and metabolic activities in many important plant species. However, the PP2C gene family has not been investigated in the economically valuable plant species sunflower (Helianthus annuus L.). This study used comprehensive bioinformatics tools to identify and characterize the PP2C gene family members in the sunflower genome (H. annuus r1.2). Additionally, we analyzed the expression profiles of these genes using RNA-seq data under four different stress conditions in both leaf and root tissues. A total of 121 PP2C genes were identified in the sunflower genome distributed unevenly across the 17 chromosomes, all containing the Type-2C phosphatase domain. HanPP2C genes are divided into 15 subgroups (A-L) based on phylogenetic tree analysis. Analyses of conserved domains, gene structures, and motifs revealed higher structural and functional similarities within various subgroups. Gene duplication and collinearity analysis showed that among the 53 HanPP2C gene pairs, 48 demonstrated segmental duplications under strong purifying selection pressure, with only five gene pairs showing tandem duplications. The abundant segmental duplication was observed compared to tandem duplication, which was the major factor underlying the dispersion of the PP2C gene family in sunflowers. Most HanPP2C proteins were localized in the nucleus, cytoplasm, and chloroplast. Among the 121 HanPP2C genes, we identified 71 miRNAs targeting 86 HanPP2C genes involved in plant developmental processes and response to abiotic stresses. By analyzing cis-elements, we identified 63 cis-regulatory elements in the promoter regions of HanPP2C genes associated with light responsiveness, tissue-specificity, phytohormone, and stress responses. Based on RNA-seq data from two sunflower tissues (leaf and root), 47 HanPP2C genes exhibited varying expression levels in leaf tissue, while 49 HanPP2C genes showed differential expression patterns in root tissue across all stress conditions. Transcriptome profiling revealed that nine HanPP2C genes (HanPP2C12, HanPP2C36, HanPP2C38, HanPP2C47, HanPP2C48, HanPP2C53, HanPP2C54, HanPP2C59, and HanPP2C73) exhibited higher expression in leaf tissue, and five HanPP2C genes (HanPP2C13, HanPP2C47, HanPP2C48, HanPP2C54, and HanPP2C95) showed enhanced expression in root tissue in response to the four stress treatments, compared to the control conditions. These results suggest that these HanPP2C genes may be potential candidates for conferring tolerance to multiple stresses and further detailed characterization to elucidate their functions. From these candidates, 3D structures were predicted for six HanPP2C proteins (HanPP2C47, HanPP2C48, HanPP2C53, HanPP2C54, HanPP2C59, and HanPP2C73), which provided satisfactory models. Our findings provide valuable insights into the PP2C gene family in the sunflower genome, which could play a crucial role in responding to various stresses. This information can be exploited in sunflower breeding programs to develop improved cultivars with increased abiotic stress tolerance.
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Affiliation(s)
- Nasrin Akter
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Shohel Ul Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Fatema Tuz Zohra
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Shaikh Mizanur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - M. Manirujjaman
- Department of Structural and Cellular Biology, Tulane University School of Medicine, New Orleans, Louisiana, LA, United States of America
| | - Md. Abdur Rauf Sarkar
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
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Iglesias-Moya J, Benítez Á, Segura M, Alonso S, Garrido D, Martínez C, Jamilena M. Structural and functional characterization of genes PYL-PP2C-SnRK2s in the ABA signalling pathway of Cucurbita pepo. BMC Genomics 2024; 25:268. [PMID: 38468207 PMCID: PMC10926676 DOI: 10.1186/s12864-024-10158-9] [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: 09/27/2023] [Accepted: 02/24/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND The core regulation of the abscisic acid (ABA) signalling pathway comprises the multigenic families PYL, PP2C, and SnRK2. In this work, we conducted a genome-wide study of the components of these families in Cucurbita pepo. RESULTS The bioinformatic analysis of the C. pepo genome resulted in the identification of 19 CpPYL, 102 CpPP2C and 10 CpSnRK2 genes. The investigation of gene structure and protein motifs allowed to define 4 PYL, 13 PP2C and 3 SnRK2 subfamilies. RNA-seq analysis was used to determine the expression of these gene families in different plant organs, as well as to detect their differential gene expression during germination, and in response to ABA and cold stress in leaves. The specific tissue expression of some gene members indicated the relevant role of some ABA signalling genes in plant development. Moreover, their differential expression under ABA treatment or cold stress revealed those ABA signalling genes that responded to ABA, and those that were up- or down-regulated in response to cold stress. A reduced number of genes responded to both treatments. Specific PYL-PP2C-SnRK2 genes that had potential roles in germination were also detected, including those regulated early during the imbibition phase, those regulated later during the embryo extension and radicle emergence phase, and those induced or repressed during the whole germination process. CONCLUSIONS The outcomes of this research open new research lines for agriculture and for assessing gene function in future studies.
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Affiliation(s)
- Jessica Iglesias-Moya
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120, Almería, Spain
| | - Álvaro Benítez
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120, Almería, Spain
| | - María Segura
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120, Almería, Spain
| | - Sonsoles Alonso
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120, Almería, Spain
| | - Dolores Garrido
- Department of Plant Physiology. Faculty of Science, University of Granada, 18021, Granada, Spain
| | - Cecilia Martínez
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120, Almería, Spain.
| | - Manuel Jamilena
- Department of Biology and Geology. Agri-food Campus of International Excellence (CeiA3) and Research Center CIAIMBITAL, University of Almería, 04120, Almería, Spain.
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Satasiya P, Patel S, Patel R, Raigar OP, Modha K, Parekh V, Joshi H, Patel V, Chaudhary A, Sharma D, Prajapati M. Meta-analysis of identified genomic regions and candidate genes underlying salinity tolerance in rice (Oryza sativa L.). Sci Rep 2024; 14:5730. [PMID: 38459066 PMCID: PMC10923909 DOI: 10.1038/s41598-024-54764-9] [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: 02/13/2023] [Accepted: 02/16/2024] [Indexed: 03/10/2024] Open
Abstract
Rice output has grown globally, yet abiotic factors are still a key cause for worry. Salinity stress seems to have the more impact on crop production out of all abiotic stresses. Currently one of the most significant challenges in paddy breeding for salinity tolerance with the help of QTLs, is to determine the QTLs having the best chance of improving salinity tolerance with the least amount of background noise from the tolerant parent. Minimizing the size of the QTL confidence interval (CI) is essential in order to primarily include the genes responsible for salinity stress tolerance. By considering that, a genome-wide meta-QTL analysis on 768 QTLs from 35 rice populations published from 2001 to 2022 was conducted to identify consensus regions and the candidate genes underlying those regions responsible for the salinity tolerance, as it reduces the confidence interval (CI) to many folds from the initial QTL studies. In the present investigation, a total of 65 MQTLs were extracted with an average CI reduced from 17.35 to 1.66 cM including the smallest of 0.01 cM. Identification of the MQTLs for individual traits and then classifying the target traits into correlated morphological, physiological and biochemical aspects, resulted in more efficient interpretation of the salinity tolerance, identifying the candidate genes and to understand the salinity tolerance mechanism as a whole. The results of this study have a huge potential to improve the rice genotypes for salinity tolerance with the help of MAS and MABC.
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Affiliation(s)
- Pratik Satasiya
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
| | - Sanyam Patel
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
| | - Ritesh Patel
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
| | - Om Prakash Raigar
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Kaushal Modha
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
| | - Vipul Parekh
- Department of Biotechnology, College of Forestry, Navsari Agricultural University, Navsari, Gujarat, India
| | - Haimil Joshi
- Coastal Soil Salinity Research Station Danti-Umbharat, Navsari Agricultural University, Navsari, Gujarat, India
| | - Vipul Patel
- Regional Rice Research Station, Vyara, Navsari Agricultural University, Navsari, Gujarat, India
| | - Ankit Chaudhary
- Kishorbhai Institute of Agriculture Sciences and Research Centre, Uka Tarsadia University, Bardoli, Gujarat, India.
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
| | - Maulik Prajapati
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
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Zheng H, Xie Y, Mu C, Cheng W, Bai Y, Gao J. Deciphering the regulatory role of PheSnRK genes in Moso bamboo: insights into hormonal, energy, and stress responses. BMC Genomics 2024; 25:252. [PMID: 38448813 PMCID: PMC10916206 DOI: 10.1186/s12864-024-10176-7] [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: 11/09/2023] [Accepted: 03/01/2024] [Indexed: 03/08/2024] Open
Abstract
The SnRK (sucrose non-fermentation-related protein kinase) plays an important role in regulating various signals in plants. However, as an important bamboo shoot and wood species, the response mechanism of PheSnRK in Phyllostachys edulis to hormones, low energy and stress remains unclear. In this paper, we focused on the structure, expression, and response of SnRK to hormones and sugars. In this study, we identified 75 PheSnRK genes from the Moso bamboo genome, which can be divided into three groups according to the evolutionary relationship. Cis-element analysis has shown that the PheSnRK gene can respond to various hormones, light, and stress. The PheSnRK2.9 proteins were localized in the nucleus and cytoplasm. Transgenic experiments showed that overexpression of PheSnRK2.9 inhibited root development, the plants were salt-tolerant and exhibited slowed starch consumption in Arabidopsis in the dark. The results of yeast one-hybrid and dual luciferase assay showed that PheIAAs and PheNACs can regulate PheSnRK2.9 gene expression by binding to the promoter of PheSnRK2.9. This study provided a comprehensive understanding of PheSnRK genes of Moso bamboo, which provides valuable information for further research on energy regulation mechanism and stress response during the growth and development of Moso bamboo.
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Affiliation(s)
- Huifang Zheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China
- College of Life Science, Leshan Normal University, Leshan, China
| | - Yali Xie
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China
| | - Changhong Mu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China
| | - Wenlong Cheng
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China
| | - Yucong Bai
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China
| | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, 100102, Beijing, China.
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Chandran AEJ, Finkler A, Hait TA, Kiere Y, David S, Pasmanik-Chor M, Shkolnik D. Calcium regulation of the Arabidopsis Na+/K+ transporter HKT1;1 improves seed germination under salt stress. PLANT PHYSIOLOGY 2024; 194:1834-1852. [PMID: 38057162 PMCID: PMC10904324 DOI: 10.1093/plphys/kiad651] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/02/2023] [Accepted: 11/09/2023] [Indexed: 12/08/2023]
Abstract
Calcium is known to improve seed-germination rates under salt stress. We investigated the involvement of calcium ions (Ca2+) in regulating HIGH-AFFINITY K+ TRANSPORTER 1 (HKT1; 1), which encodes a Na+/K+ transporter, and its post-translational regulator TYPE 2C PROTEIN PHOSPHATASE 49 (PP2C49), in germinating Arabidopsis (Arabidopsis thaliana) seedlings. Germination rates of hkt1 mutant seeds under salt stress remained unchanged by CaCl2 treatment in wild-type Arabidopsis, whereas pp2c49 mutant seeds displayed improved salt-stress tolerance in the absence of CaCl2 supplementation. Analysis of HKT1;1 and PP2C49 promoter activity revealed that CaCl2 treatment results in radicle-focused expression of HKT1;1 and reduction of the native radicle-exclusive expression of PP2C49. Ion-content analysis indicated that CaCl2 treatment improves K+ retention in germinating wild-type seedlings under salt stress, but not in hkt1 seedlings. Transgenic seedlings designed to exclusively express HKT1;1 in the radicle during germination displayed higher germination rates under salt stress than the wild type in the absence of CaCl2 treatment. Transcriptome analysis of germinating seedlings treated with CaCl2, NaCl, or both revealed 118 upregulated and 94 downregulated genes as responsive to the combined treatment. Bioinformatics analysis of the upstream sequences of CaCl2-NaCl-treatment-responsive upregulated genes revealed the abscisic acid response element CACGTGTC, a potential CaM-binding transcription activator-binding motif, as most prominent. Our findings suggest a key role for Ca2+ in mediating salt-stress responses during germination by regulating genes that function to maintain Na+ and K+ homeostasis, which is vital for seed germination under salt stress.
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Affiliation(s)
- Ancy E J Chandran
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Aliza Finkler
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tom Aharon Hait
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yvonne Kiere
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Sivan David
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Metsada Pasmanik-Chor
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Doron Shkolnik
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel
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Qian L, Yin S, Lu N, Yue E, Yan J. Full-length transcriptome reveals the pivotal role of ABA and ethylene in the cold stress response of Tetrastigma hemsleyanum. FRONTIERS IN PLANT SCIENCE 2024; 15:1285879. [PMID: 38357266 PMCID: PMC10864657 DOI: 10.3389/fpls.2024.1285879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
Tetrastigma hemsleyanum is a valuable herb widely used in Chinese traditional and modern medicine. Winter cold severely limits the artificial cultivation of this plant, but the physiological and molecular mechanisms upon exposure to cold stress in T. hemsleyanum are unclear. T. hemsleyanum plants with different geographical origins exhibit large differences in response to cold stress. In this research study, using T. hemsleyanum ecotypes that exhibit frost tolerance (FR) and frost sensitivity (FS), we analyzed the response of cottage seedlings to a simulated frost treatment; plant hormones were induced with both short (2 h) and long (9 h) frost treatments, which were used to construct the full-length transcriptome and obtained 76,750 transcripts with all transcripts mapped to 28,805 genes, and 27,215 genes, respectively, annotated to databases. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed enrichment in plant hormone signaling pathways. Further analysis shows that differently expressed genes (DEGs) concentrated on calcium signaling, ABA biosynthesis and signal transduction, and ethylene in response to cold stress. We also found that endogenous ABA and ethylene content were increased after cold treatment, and exogenous ABA and ethylene significantly improved cold tolerance in both ecotypes. Our results elucidated the pivotal role of ABA and ethylene in response to cold stress in T. hemsleyanum and identified key genes.
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Affiliation(s)
- Lihua Qian
- Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Shuya Yin
- Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Na Lu
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Erkui Yue
- Institute of Crop Science and Ecology, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Jianli Yan
- Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
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15
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Zhang P, Liu D, Ma J, Sun C, Wang Z, Zhu Y, Zhang X, Liu Y. Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe. BMC Genomics 2024; 25:83. [PMID: 38245685 PMCID: PMC10799369 DOI: 10.1186/s12864-024-09966-w] [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: 11/19/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Protein phosphatases type 2C (PP2C) are heavily involved in plant growth and development, hormone-related signaling pathways and the response of various biotic and abiotic stresses. However, a comprehensive report identifying the genome-scale of PP2C gene family in ginger is yet to be published. RESULTS In this study, 97 ZoPP2C genes were identified based on the ginger genome. These genes were classified into 15 branches (A-O) according to the phylogenetic analysis and distributed unevenly on 11 ginger chromosomes. The proteins mainly functioned in the nucleus. Similar motif patterns and exon/intron arrangement structures were identified in the same subfamily of ZoPP2Cs. Collinearity analysis indicated that ZoPP2Cs had 33 pairs of fragment duplicated events uniformly distributed on the corresponding chromosomes. Furthermore, ZoPP2Cs showed greater evolutionary proximity to banana's PP2Cs. The forecast of cis-regulatory elements and transcription factor binding sites demonstrated that ZoPP2Cs participate in ginger growth, development, and responses to hormones and stresses. ZoERFs have plenty of binding sites of ZoPP2Cs, suggesting a potential synergistic contribution between ZoERFs and ZoPP2Cs towards regulating growth/development and adverse conditions. The protein-protein interaction network displayed that five ZoPP2Cs (9/23/26/49/92) proteins have robust interaction relationship and potential function as hub proteins. Furthermore, the RNA-Seq and qRT-PCR analyses have shown that ZoPP2Cs exhibit various expression patterns during ginger maturation and responses to environmental stresses such as chilling, drought, flooding, salt, and Fusarium solani. Notably, exogenous application of melatonin led to notable up-regulation of ZoPP2Cs (17/59/11/72/43) under chilling stress. CONCLUSIONS Taken together, our investigation provides significant insights of the ginger PP2C gene family and establishes the groundwork for its functional validation and genetic engineering applications.
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Affiliation(s)
- Pan Zhang
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Deqi Liu
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Jiawei Ma
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Chong Sun
- Special Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Zhaofei Wang
- Special Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Yongxing Zhu
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Xuemei Zhang
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Yiqing Liu
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China.
- Special Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China.
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Yang D, Zhang X, Cao M, Yin L, Gao A, An K, Gao S, Guo S, Yin H. Genome-Wide Identification, Expression and Interaction Analyses of PP2C Family Genes in Chenopodium quinoa. Genes (Basel) 2023; 15:41. [PMID: 38254931 PMCID: PMC10815568 DOI: 10.3390/genes15010041] [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: 11/03/2023] [Revised: 12/19/2023] [Accepted: 12/24/2023] [Indexed: 01/24/2024] Open
Abstract
Plant protein phosphatase 2Cs (PP2Cs) function as inhibitors in protein kinase cascades involved in various processes and are crucial participants in both plant development and signaling pathways activated by abiotic stress. In this study, a genome-wide study was conducted on the CqPP2C gene family. A total of putative 117 CqPP2C genes were identified. Comprehensive analyses of physicochemical properties, chromosome localization and subcellular localization were conducted. According to phylogenetic analysis, CqPP2Cs were divided into 13 subfamilies. CqPP2Cs in the same subfamily had similar gene structures, and conserved motifs and all the CqPP2C proteins had the type 2C phosphatase domains. The expansion of CqPP2Cs through gene duplication was primarily driven by segmental duplication, and all duplicated CqPP2Cs underwent evolutionary changes guided by purifying selection. The expression of CqPP2Cs in various tissues under different abiotic stresses was analyzed using RNA-seq data. The findings indicated that CqPP2C genes played a role in regulating both the developmental processes and stress responses of quinoa. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis of six CqPP2C genes in subfamily A revealed that they were up-regulated or down-regulated under salt and drought treatments. Furthermore, the results of yeast two-hybrid assays revealed that subfamily A CqPP2Cs interacted not only with subclass III CqSnRK2s but also with subclass II CqSnRK2s. Subfamily A CqPP2Cs could interact with CqSnRK2s in different combinations and intensities in a variety of biological processes and biological threats. Overall, our results will be useful for understanding the functions of CqPP2C in regulating ABA signals and responding to abiotic stress.
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Affiliation(s)
- Dongdong Yang
- College of Life Sciences, Yantai University, Yantai 264005, China; (D.Y.); (X.Z.); (M.C.); (L.Y.); (A.G.); (K.A.); (S.G.)
| | - Xia Zhang
- College of Life Sciences, Yantai University, Yantai 264005, China; (D.Y.); (X.Z.); (M.C.); (L.Y.); (A.G.); (K.A.); (S.G.)
| | - Meng Cao
- College of Life Sciences, Yantai University, Yantai 264005, China; (D.Y.); (X.Z.); (M.C.); (L.Y.); (A.G.); (K.A.); (S.G.)
| | - Lu Yin
- College of Life Sciences, Yantai University, Yantai 264005, China; (D.Y.); (X.Z.); (M.C.); (L.Y.); (A.G.); (K.A.); (S.G.)
| | - Aihong Gao
- College of Life Sciences, Yantai University, Yantai 264005, China; (D.Y.); (X.Z.); (M.C.); (L.Y.); (A.G.); (K.A.); (S.G.)
| | - Kexin An
- College of Life Sciences, Yantai University, Yantai 264005, China; (D.Y.); (X.Z.); (M.C.); (L.Y.); (A.G.); (K.A.); (S.G.)
| | - Songmei Gao
- College of Life Sciences, Yantai University, Yantai 264005, China; (D.Y.); (X.Z.); (M.C.); (L.Y.); (A.G.); (K.A.); (S.G.)
| | - Shanli Guo
- College of Grassland Sciences, Qingdao Agricultural University, Qingdao 266109, China
- High-Efficiency Agricultural Technology Industry Research Institute of Saline and Alkaline Land of Dongying, Qingdao Agricultural University, Dongying 257300, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao Agricultural University, Qingdao 266109, China
| | - Haibo Yin
- College of Life Sciences, Yantai University, Yantai 264005, China; (D.Y.); (X.Z.); (M.C.); (L.Y.); (A.G.); (K.A.); (S.G.)
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17
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Wang R, Li C, Jia Z, Su Y, Ai Y, Li Q, Guo X, Tao Z, Lin F, Liang Y. Reversible phosphorylation of a lectin-receptor-like kinase controls xylem immunity. Cell Host Microbe 2023; 31:2051-2066.e7. [PMID: 37977141 DOI: 10.1016/j.chom.2023.10.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/23/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023]
Abstract
Pattern-recognition receptors (PRRs) mediate basal resistance to most phytopathogens. However, plant responses can be cell type specific, and the mechanisms governing xylem immunity remain largely unknown. We show that the lectin-receptor-like kinase LORE contributes to xylem basal resistance in Arabidopsis upon infection with Ralstonia solanacearum, a destructive plant pathogen that colonizes the xylem to cause bacterial wilt. Following R. solanacearum infection, LORE is activated by phosphorylation at residue S761, initiating a phosphorelay that activates reactive oxygen species production and cell wall lignification. To prevent prolonged activation of immune signaling, LORE recruits and phosphorylates type 2C protein phosphatase LOPP, which dephosphorylates LORE and attenuates LORE-mediated xylem immunity to maintain immune homeostasis. A LOPP knockout confers resistance against bacterial wilt disease in Arabidopsis and tomatoes without impacting plant growth. Thus, our study reveals a regulatory mechanism in xylem immunity involving the reversible phosphorylation of receptor-like kinases.
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Affiliation(s)
- Ran Wang
- Zhejiang Xianghu Laboratory, Department of Plant Protection, Zhejiang University, Hangzhou 310058, China
| | - Chenying Li
- Zhejiang Xianghu Laboratory, Department of Plant Protection, Zhejiang University, Hangzhou 310058, China
| | - Zhiyi Jia
- Zhejiang Xianghu Laboratory, Department of Plant Protection, Zhejiang University, Hangzhou 310058, China
| | - Yaxing Su
- Zhejiang Xianghu Laboratory, Department of Plant Protection, Zhejiang University, Hangzhou 310058, China
| | - Yingfei Ai
- Zhejiang Xianghu Laboratory, Department of Plant Protection, Zhejiang University, Hangzhou 310058, China
| | - Qinghong Li
- Zhejiang Xianghu Laboratory, Department of Plant Protection, Zhejiang University, Hangzhou 310058, China
| | - Xijie Guo
- Zhejiang Xianghu Laboratory, Department of Plant Protection, Zhejiang University, Hangzhou 310058, China
| | - Zeng Tao
- Zhejiang Xianghu Laboratory, Department of Plant Protection, Zhejiang University, Hangzhou 310058, China
| | - Fucheng Lin
- Zhejiang Xianghu Laboratory, Department of Plant Protection, Zhejiang University, Hangzhou 310058, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Hangzhou 311200, China.
| | - Yan Liang
- Zhejiang Xianghu Laboratory, Department of Plant Protection, Zhejiang University, Hangzhou 310058, China.
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18
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Chen C, Cheng D, Li L, Sun X, He S, Li M, Chen J. Physiological Characteristics and Transcriptome Analysis of Exogenous Brassinosteroid-Treated Kiwifruit. Int J Mol Sci 2023; 24:17252. [PMID: 38139080 PMCID: PMC10744020 DOI: 10.3390/ijms242417252] [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: 10/18/2023] [Revised: 11/24/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Brassinosteroids (BRs) play pivotal roles in improving plant stress tolerance. To investigate the mechanism of BR regulation of salt tolerance in kiwifruit, we used 'Hongyang' kiwifruit as the test material. We exposed the plants to 150 mmol/L NaCl stress and irrigated them with exogenous BR (2,4-epibrassinolide). The phenotypic analysis showed that salt stress significantly inhibited photosynthesis in kiwifruit, leading to a significant increase in the H2O2 content of leaves and roots and a significant increase in Na+/K+, resulting in oxidative damage and an ion imbalance. BR treatment resulted in enhanced photosynthesis, reduced H2O2 content, and reduced Na+/K+ in leaves, alleviating the salt stress injury. Furthermore, transcriptome enrichment analysis showed that the differentially expressed genes (DEGs) related to BR treatment are involved in pathways such as starch and sucrose metabolism, pentose and glucuronate interconversions, and plant hormone signal transduction, among others. Among the DEGs involved in plant hormone signal transduction, those with the highest expression were involved in abscisic acid signal transduction. Moreover, there was a significant increase in the expression of the AcHKT1 gene, which regulates ion transduction, and the antioxidant enzyme AcFSD2 gene, which is a key gene for improving salt tolerance. The data suggest that BRs can improve salt tolerance by regulating ion homeostasis and reducing oxidative stress.
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Affiliation(s)
- Chen Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Dawei Cheng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Lan Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Xiaoxu Sun
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Shasha He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Ming Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
- Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang 453514, China
| | - Jinyong Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
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19
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Liu Q, Qin B, Zhang D, Liang X, Yang Y, Wang L, Wang M, Zhang Y. Identification and Characterization of the HbPP2C Gene Family and Its Expression in Response to Biotic and Abiotic Stresses in Rubber Tree. Int J Mol Sci 2023; 24:16061. [PMID: 38003251 PMCID: PMC10671201 DOI: 10.3390/ijms242216061] [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: 09/29/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Plant PP2C genes are crucial for various biological processes. To elucidate the potential functions of these genes in rubber tree (Hevea brasiliensis), we conducted a comprehensive analysis of these genes using bioinformatics methods. The 60 members of the PP2C family in rubber tree were identified and categorized into 13 subfamilies. The PP2C proteins were conserved across different plant species. The results revealed that the HbPP2C genes contained multiple elements responsive to phytohormones and stresses in their promoters, suggesting their involvement in these pathways. Expression analysis indicated that 40 HbPP2C genes exhibited the highest expression levels in branches and the lowest expression in latex. Additionally, the expression of A subfamily members significantly increased in response to abscisic acid, drought, and glyphosate treatments, whereas the expression of A, B, D, and F1 subfamily members notably increased under temperature stress conditions. Furthermore, the expression of A and F1 subfamily members was significantly upregulated upon powdery mildew infection, with the expression of the HbPP2C6 gene displaying a remarkable 33-fold increase. These findings suggest that different HbPP2C subgroups may have distinct roles in the regulation of phytohormones and the response to abiotic and biotic stresses in rubber tree. This study provides a valuable reference for further investigations into the functions of the HbPP2C gene family in rubber tree.
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Affiliation(s)
- Qifeng Liu
- Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Q.L.); (D.Z.); (X.L.); (Y.Y.)
| | - Bi Qin
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (B.Q.); (L.W.)
- Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture and Rural Affairs, Danzhou 571737, China
| | - Dong Zhang
- Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Q.L.); (D.Z.); (X.L.); (Y.Y.)
| | - Xiaoyu Liang
- Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Q.L.); (D.Z.); (X.L.); (Y.Y.)
| | - Ye Yang
- Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Q.L.); (D.Z.); (X.L.); (Y.Y.)
| | - Lifeng Wang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (B.Q.); (L.W.)
- Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture and Rural Affairs, Danzhou 571737, China
| | - Meng Wang
- Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Q.L.); (D.Z.); (X.L.); (Y.Y.)
| | - Yu Zhang
- Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Q.L.); (D.Z.); (X.L.); (Y.Y.)
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20
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Jardim-Messeder D, Cassol D, Souza-Vieira Y, Ehlers Loureiro M, Girke T, Boroni M, Lopes Corrêa R, Coelho A, Sachetto-Martins G. Genome-wide identification of core components of ABA signaling and transcriptome analysis reveals gene circuits involved in castor bean (Ricinus communis L.) response to drought. Gene 2023; 883:147668. [PMID: 37500024 DOI: 10.1016/j.gene.2023.147668] [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: 04/12/2023] [Revised: 07/06/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
Castor bean (Ricinus communis L.) can withstand long periods of water deficit and high temperatures, and therefore has been recognized as a drought-resistant plant species, allowing the study of gene networks involved in drought response and tolerance. The identification of genes networks related to drought response in this plant may yield important information in the characterization of molecular mechanisms correlating changes in the gene expression with the physiological adaptation processes. In this context, gene families related to abscisic acid (ABA) signaling play a crucial role in developmental and environmental adaptation processes of plants to drought stress. However, the families that function as the core components of ABA signaling, as well as genes networks related to drought response, are not well understood in castor bean. In this study 7 RcPYL, 63 RcPP2C, and 6 RcSnRK2 genes were identified in castor bean genome, which was further supported by chromosomal distribution, gene structure, evolutionary relationships, and conserved motif analyses. The castor bean general expression profile was investigated by RNAseq in root and leaf tissues in response to drought stress. These analyses allowed the identification of genes differentially expressed, including genes from the ABA signaling core, genes related to photosynthesis, cell wall, energy transduction, antioxidant response, and transcription factors. These analyses provide new insights into the core components of ABA signaling in castor bean, allow the identification of several molecular responses associated with the high physiological adaptation of castor bean to drought stress, and contribute to the identification of candidate genes for genetic improvement.
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Affiliation(s)
- Douglas Jardim-Messeder
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Daniela Cassol
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Institute for Integrative Genome Biology, Genomics Building, University of California, Riverside, CA 92521, USA
| | - Ygor Souza-Vieira
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Thomas Girke
- Institute for Integrative Genome Biology, Genomics Building, University of California, Riverside, CA 92521, USA
| | - Mariana Boroni
- Bioinformatics and Computational Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva, Rio de Janeiro, Brazil
| | - Régis Lopes Corrêa
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Coelho
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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21
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Chen Y, Zhao H, Wang Y, Qiu X, Gao G, Zhu A, Chen P, Wang X, Chen K, Chen J, Chen P, Chen J. Genome-Wide Identification and Expression Analysis of BnPP2C Gene Family in Response to Multiple Stresses in Ramie ( Boehmeria nivea L.). Int J Mol Sci 2023; 24:15282. [PMID: 37894962 PMCID: PMC10607689 DOI: 10.3390/ijms242015282] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/04/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
The protein phosphatase 2C (PP2C), a key regulator of the ABA signaling pathway, plays important roles in plant growth and development, hormone signaling, and abiotic stress response. Although the PP2C gene family has been identified in many species, systematic analysis was still relatively lacking in ramie (Boehmeria nivea L.). In the present study, we identified 63 BnPP2C genes from the ramie genome, using bioinformatics analysis, and classified them into 12 subfamilies, and this classification was consistently supported by their gene structures and conserved motifs. In addition, we observed that the functional differentiation of the BnPP2C family of genes was restricted and that fragment replication played a major role in the amplification of the BnPP2C gene family. The promoter cis-regulatory elements of BnPP2C genes were mainly involved in light response regulation, phytohormone synthesis, transport and signaling, environmental stress response and plant growth and development regulation. We identified BnPP2C genes with tissue specificity, using ramie transcriptome data from different tissues, in rhizome leaves and bast fibers. The qRT-PCR results showed that the BnPP2C1, BnPP2C26 and BnPP2C27 genes had a strong response to drought, high salt and ABA, and there were a large number of stress-responsive elements in the promoter region of BnPP2C1 and BnPP2C26. The results suggested that BnPP2C1 and BnPP2C26 could be used as the candidate genes for drought and salt tolerance in ramie. These results provide a reference for further studies on the function of the PP2C gene and advance the development of the mechanism of ramie stress response, with a view to providing candidate genes for the molecular breeding of ramie for drought and salt tolerance.
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Affiliation(s)
- Yu Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China; (Y.C.); (H.Z.); (Y.W.); (X.Q.); (G.G.); (A.Z.); (P.C.); (X.W.); (K.C.); (J.C.)
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Haohan Zhao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China; (Y.C.); (H.Z.); (Y.W.); (X.Q.); (G.G.); (A.Z.); (P.C.); (X.W.); (K.C.); (J.C.)
| | - Yue Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China; (Y.C.); (H.Z.); (Y.W.); (X.Q.); (G.G.); (A.Z.); (P.C.); (X.W.); (K.C.); (J.C.)
| | - Xiaojun Qiu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China; (Y.C.); (H.Z.); (Y.W.); (X.Q.); (G.G.); (A.Z.); (P.C.); (X.W.); (K.C.); (J.C.)
| | - Gang Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China; (Y.C.); (H.Z.); (Y.W.); (X.Q.); (G.G.); (A.Z.); (P.C.); (X.W.); (K.C.); (J.C.)
| | - Aiguo Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China; (Y.C.); (H.Z.); (Y.W.); (X.Q.); (G.G.); (A.Z.); (P.C.); (X.W.); (K.C.); (J.C.)
| | - Ping Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China; (Y.C.); (H.Z.); (Y.W.); (X.Q.); (G.G.); (A.Z.); (P.C.); (X.W.); (K.C.); (J.C.)
| | - Xiaofei Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China; (Y.C.); (H.Z.); (Y.W.); (X.Q.); (G.G.); (A.Z.); (P.C.); (X.W.); (K.C.); (J.C.)
| | - Kunmei Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China; (Y.C.); (H.Z.); (Y.W.); (X.Q.); (G.G.); (A.Z.); (P.C.); (X.W.); (K.C.); (J.C.)
| | - Jia Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China; (Y.C.); (H.Z.); (Y.W.); (X.Q.); (G.G.); (A.Z.); (P.C.); (X.W.); (K.C.); (J.C.)
| | - Peng Chen
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Jikang Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China; (Y.C.); (H.Z.); (Y.W.); (X.Q.); (G.G.); (A.Z.); (P.C.); (X.W.); (K.C.); (J.C.)
- National Breeding Center or Bast Fiber Crops, MARA, Changsha 410221, China
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22
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Liu Z, Zhang M, Wang L, Sun W, Li M, Feng C, Yang X. Genome-wide identification and expression analysis of PYL family genes and functional characterization of GhPYL8D2 under drought stress in Gossypium hirsutum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108072. [PMID: 37827043 DOI: 10.1016/j.plaphy.2023.108072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 09/05/2023] [Accepted: 09/29/2023] [Indexed: 10/14/2023]
Abstract
Cotton is a crucial economic crop, serving as a natural fiber source for the textile industry. However, drought stress poses a significant threat to cotton fiber quality and productivity worldwide. Pyrabactin Resistance 1-Like (PYL) proteins, as abscisic acid (ABA) receptors, play a crucial role in adverse stress responses, but knowledge about the PYLs in cotton remains limited. In our study, we identified 40 GhPYL genes in Gossypium hirsutum through a genome-wide analysis of the cotton genome database. Our analysis revealed that the PYL family formed three distinct subfamilies with typical family characteristics in G. hirsutum. Additionally, through quantitative expression analysis, including transcriptome dataset and qRT-PCR, we found that all GhPYLs were expressed in all tissues of G. hirsutum, and all GhPYLs were differentially expressed under drought stress. Among them, GhPYL4A1, GhPY5D1, GhPY8D2, and a member of the type 2C protein phosphatases clade A family in Gossypium hirsutum (GhPP2CA), GhHAI2D, showed significant differences in expression levels within 12 h after stress treatment. Our protein interaction analysis and BiFC demonstrated the complex regulatory network between GhPYL family proteins and GhPP2CA proteins. We also found that there is an interaction between GhPYL8D2 and GhHAI2D, and through drought treatment of transgenic cotton, we found that GhPYL8D2 played a vital role in the response of G. hirsutum to drought through stomatal control via co-regulation with GhHAI2D. Our findings provide useful insights into the regulation of GhPYL family genes that occur in response to abiotic stresses in cotton.
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Affiliation(s)
- Zhilin Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Mengmeng Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Lichen Wang
- College of Life Science, Linyi University, Linyi, 276000, Shandong, PR China.
| | - Weinan Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Meng Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Cheng Feng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, PR China.
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23
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Wu H, Zhu L, Cai G, Lv C, Yang H, Ren X, Hu B, Zhou X, Jiang T, Xiang Y, Wei R, Li L, Liu H, Muhammad I, Xia C, Lan H. Genome-Wide Identification and Characterization of the PP2C Family from Zea mays and Its Role in Long-Distance Signaling. PLANTS (BASEL, SWITZERLAND) 2023; 12:3153. [PMID: 37687398 PMCID: PMC10490008 DOI: 10.3390/plants12173153] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/25/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023]
Abstract
The protein phosphatase 2C (PP2C) constitutes a large gene family that plays crucial roles in regulating stress responses and plant development. A recent study has shown the involvement of an AtPP2C family member in long-distance nitrogen signaling in Arabidopsis. However, it remains unclear whether maize adopts a similar mechanism. In this study, we conducted a genome-wide survey and expression analysis of the PP2C family in maize. We identified 103 ZmPP2C genes distributed across 10 chromosomes, which were further classified into 11 subgroups based on an evolutionary tree. Notably, cis-acting element analysis revealed the presence of abundant hormone and stress-related, as well as nitrogen-related, cis-elements in the promoter regions of ZmPP2Cs. Expression analysis demonstrated the distinct expression patterns of nine genes under two nitrogen treatments. Notably, the expression of ZmPP2C54 and ZmPP2C85 in the roots was found to be regulated by long-distance signals from the shoots. These findings provide valuable insights into understanding the roles of ZmPP2Cs in long-distance nitrogen signaling in maize.
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Affiliation(s)
- Huan Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (H.W.)
| | - Ling Zhu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (H.W.)
| | - Guiping Cai
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (H.W.)
| | - Chenxi Lv
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (H.W.)
| | - Huan Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (H.W.)
| | - Xiaoli Ren
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (H.W.)
| | - Bo Hu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (H.W.)
| | - Xuemei Zhou
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (H.W.)
| | - Tingting Jiang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (H.W.)
| | - Yong Xiang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (H.W.)
| | - Rujun Wei
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (H.W.)
| | - Lujiang Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (H.W.)
| | - Hailan Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (H.W.)
| | - Imran Muhammad
- Department of Chemistry, Punjab College of Science, Faisalabad 54000, Pakistan
| | - Chao Xia
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (H.W.)
| | - Hai Lan
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (H.W.)
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
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24
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Huang Y, Yang R, Luo H, Yuan Y, Diao Z, Li J, Gong S, Yu G, Yao H, Zhang H, Cai Y. Arabidopsis Protein Phosphatase PIA1 Impairs Plant Drought Tolerance by Serving as a Common Negative Regulator in ABA Signaling Pathway. PLANTS (BASEL, SWITZERLAND) 2023; 12:2716. [PMID: 37514328 PMCID: PMC10384177 DOI: 10.3390/plants12142716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/16/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023]
Abstract
Reversible phosphorylation of proteins is a ubiquitous regulatory mechanism in vivo that can respond to external changes, and plays an extremely important role in cell signal transduction. Protein phosphatase 2C is the largest protein phosphatase family in higher plants. Recently, it has been found that some clade A members can negatively regulate ABA signaling pathways. However, the functions of several subgroups of Arabidopsis PP2C other than clade A have not been reported, and whether other members of the PP2C family also participate in the regulation of ABA signaling pathways remains to be studied. In this study, based on the previous screening and identification work of PP2C involved in the ABA pathway, the clade F member PIA1 encoding a gene of the PP2C family, which was down-regulated after ABA treatment during the screening, was selected as the target. Overexpression of PIA1 significantly down-regulated the expression of ABA marker gene RD29A in Arabidopsis protoplasts, and ABA-responsive elements have been found in the cis-regulatory elements of PIA1 by promoter analysis. When compared to Col-0, transgenic plants overexpressing PIA1 were less sensitive to ABA, whereas pia1 showed the opposite trait in seed germination, root growth, and stomatal opening experiments. Under drought stress, SOD, POD, CAT, and APX activities of PIA1 overexpression lines were lower than Col-0 and pia1, while the content of H2O2 was higher, leading to its lowest survival rate in test plants, which were consistent with the significant inhibition of the expression of ABA-dependent stress-responsive genes RD29B, ABI5, ABF3, and ABF4 in the PIA1 transgenic background after ABA treatment. Using yeast two-hybrid and luciferase complementation assays, PIA1 was found to interact with multiple ABA key signaling elements, including 2 RCARs and 6 SnRK2s. Our results indicate that PIA1 may reduce plant drought tolerance by functioning as a common negative regulator involved in ABA signaling pathway.
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Affiliation(s)
- Yan Huang
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Rongqian Yang
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Huiling Luo
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Yuan Yuan
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Zhihong Diao
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Junhao Li
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Shihe Gong
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Guozhi Yu
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Huipeng Yao
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Huaiyu Zhang
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
| | - Yi Cai
- College of Life Sciences, Sichuan Agricultural University, Ya'an 625000, China
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Huang X, Liang Y, Zhang R, Zhang B, Song X, Liu J, Lu M, Qin Z, Li D, Li S, Li Y. Genome-Wide Identification of the PP2C Gene Family and Analyses with Their Expression Profiling in Response to Cold Stress in Wild Sugarcane. PLANTS (BASEL, SWITZERLAND) 2023; 12:2418. [PMID: 37446979 DOI: 10.3390/plants12132418] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/09/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023]
Abstract
Type 2C protein phosphatases (PP2Cs) represent a major group of protein phosphatases in plants, some of which have already been confirmed to play important roles in diverse plant processes. In this study, analyses of the phylogenetics, gene structure, protein domain, chromosome localization, and collinearity, as well as an identification of the expression profile, protein-protein interaction, and subcellular location, were carried out on the PP2C family in wild sugarcane (Saccharum spontaneum). The results showed that 145 PP2C proteins were classified into 13 clades. Phylogenetic analysis suggested that SsPP2Cs are evolutionarily closer to those of sorghum, and the number of SsPP2Cs is the highest. There were 124 pairs of SsPP2C genes expanding via segmental duplications. Half of the SsPP2C proteins were predicted to be localized in the chloroplast (73), with the next most common predicted localizations being in the cytoplasm (37) and nucleus (17). Analysis of the promoter revealed that SsPP2Cs might be photosensitive, responsive to abiotic stresses, and hormone-stimulated. A total of 27 SsPP2Cs showed cold-stress-induced expressions, and SsPP2C27 (Sspon.01G0007840-2D) and SsPP2C64 (Sspon.03G0002800-3D) were the potential hubs involved in ABA signal transduction. Our study presents a comprehensive analysis of the SsPP2C gene family, which can play a vital role in the further study of phosphatases in wild sugarcane. The results suggest that the PP2C family is evolutionarily conserved, and that it functions in various developmental processes in wild sugarcane.
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Affiliation(s)
- Xing Huang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Yongsheng Liang
- Nanning Institute of Agricultural Sciences, Nanning 530021, China
| | - Ronghua Zhang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Baoqing Zhang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Xiupeng Song
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Junxian Liu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Manman Lu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Zhenqiang Qin
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Dewei Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Song Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
| | - Yangrui Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agicultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning 530007, China
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26
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Xie W, Liu S, Gao H, Wu J, Liu D, Kinoshita T, Huang CF. PP2C.D phosphatase SAL1 positively regulates aluminum resistance via restriction of aluminum uptake in rice. PLANT PHYSIOLOGY 2023; 192:1498-1516. [PMID: 36823690 PMCID: PMC10231357 DOI: 10.1093/plphys/kiad122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 06/01/2023]
Abstract
Aluminum (Al) toxicity represents a primary constraint for crop production in acidic soils. Rice (Oryza sativa) is a highly Al-resistant species; however, the molecular mechanisms underlying its high Al resistance are still not fully understood. Here, we identified SAL1 (SENSITIVE TO ALUMINUM 1), which encodes a plasma membrane (PM)-localized PP2C.D phosphatase, as a crucial regulator of Al resistance using a forward genetic screen. SAL1 was found to interact with and inhibit the activity of PM H+-ATPases, and mutation of SAL1 increased PM H+-ATPase activity and Al uptake, causing hypersensitivity to internal Al toxicity. Furthermore, knockout of NRAT1 (NRAMP ALUMINUM TRANSPORTER 1) encoding an Al uptake transporter in a sal1 background rescued the Al-sensitive phenotype of sal1, revealing that coordination of Al accumulation in the cell, wall and symplasm is critical for Al resistance in rice. By contrast, we found that mutations of PP2C.D phosphatase-encoding genes in Arabidopsis (Arabidopsis thaliana) enhanced Al resistance, which was attributed to increased malate secretion. Our results reveal the importance of PP2C.D phosphatases in Al resistance and the different strategies used by rice and Arabidopsis to defend against Al toxicity.
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Affiliation(s)
- Wenxiang Xie
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shuo Liu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Huiling Gao
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jun Wu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Dilin Liu
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Toshinori Kinoshita
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Chao-Feng Huang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
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27
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Wang D, Wei L, Liu T, Ma J, Huang K, Guo H, Huang Y, Zhang L, Zhao J, Tsuda K, Wang Y. Suppression of ETI by PTI priming to balance plant growth and defense through an MPK3/MPK6-WRKYs-PP2Cs module. MOLECULAR PLANT 2023; 16:903-918. [PMID: 37041748 DOI: 10.1016/j.molp.2023.04.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 05/04/2023]
Abstract
Pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) are required for host defense against pathogens. Although PTI and ETI are intimately connected, the underlying molecular mechanisms remain elusive. In this study, we demonstrate that flg22 priming attenuates Pseudomonas syringae pv. tomato DC3000 (Pst) AvrRpt2-induced hypersensitive cell death, resistance, and biomass reduction in Arabidopsis. Mitogen-activated protein kinases (MAPKs) are key signaling regulators of PTI and ETI. The absence of MPK3 and MPK6 significantly reduces pre-PTI-mediated ETI suppression (PES). We found that MPK3/MPK6 interact with and phosphorylate the downstream transcription factor WRKY18, which regulates the expression of AP2C1 and PP2C5, two genes encoding protein phosphatases. Furthermore, we observed that the PTI-suppressed ETI-triggered cell death, MAPK activation, and growth retardation are significantly attenuated in wrky18/40/60 and ap2c1 pp2c5 mutants. Taken together, our results suggest that the MPK3/MPK6-WRKYs-PP2Cs module underlies PES and is essential for the maintenance of plant fitness during ETI.
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Affiliation(s)
- Dacheng Wang
- Key Laboratory of Biological Interactions and Crop Health, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Lirong Wei
- Key Laboratory of Biological Interactions and Crop Health, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Ting Liu
- Key Laboratory of Biological Interactions and Crop Health, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Jinbiao Ma
- Key Laboratory of Biological Interactions and Crop Health, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Keyi Huang
- Key Laboratory of Biological Interactions and Crop Health, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Huimin Guo
- Key Laboratory of Biological Interactions and Crop Health, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Yufen Huang
- Key Laboratory of Biological Interactions and Crop Health, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Lei Zhang
- Key Laboratory of Biological Interactions and Crop Health, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Jing Zhao
- Key Laboratory of Biological Interactions and Crop Health, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Kenichi Tsuda
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yiming Wang
- Key Laboratory of Biological Interactions and Crop Health, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China.
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28
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Cui C, Feng L, Zhou C, Wan H, Zhou B. Transcriptome Revealed GhPP2C43-A Negatively Regulates Salinity Tolerance in an Introgression Line from a Semi-wild Upland Cotton. PLANT & CELL PHYSIOLOGY 2023:pcad036. [PMID: 37115634 DOI: 10.1093/pcp/pcad036] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 04/22/2023] [Accepted: 04/27/2023] [Indexed: 06/19/2023]
Abstract
Salt damage is one of the major threats to sustainable cotton production owing to the limited arable land in China mainly occupied by the production of staple food crops. Salt-stress tolerant cotton varieties are lacking in production and, the mechanisms underpinning salt-stress tolerance in cotton remain enigmatic. Here, DM37, an intraspecific introgression line from G. hirsutum race yucatanense acc TX-1046 into the G. hirsutum acc TM-1 background, was found to be highly tolerant to salt stress. Its seed germination rate and germination potential were significantly higher than the recipient TM-1 under salt stress. Physiological analysis showed DM37 had higher proline content and Peroxidase activity, as well as lower Na+/K+ ratios at the seedling stage, consistent with higher seedling survival rate after durable salt stress. Furthermore, comparative transcriptome analysis revealed that responsive patterns to salt stress in DM37 were different from TM-1. Weighted Correlation Network Analysis (WGCNA) demonstrated that co-expression modules associated with salt stress in DM37 also differed from TM-1. Out of them, GhPP2C43-A, a phosphatase gene, exhibited negative regulation of salt-stress tolerance verified by VIGS and transgenic Arabidopsis. Gene expression showed GhPP2C43-A in TM-1 was induced by durable salt stress but not in DM37 probably attributing to the variation of cis-element in its promoter, thereby being conferred different salt-stress tolerance. Our result would provide new genes/germplasms from semi-wild cotton in salt-stress tolerant cotton breeding. This study would give us new insights into the mechanisms underpinning the salt-stress tolerance in cotton.
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Affiliation(s)
- Changjiang Cui
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Liuchun Feng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Chenhui Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
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29
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Sharma E, Bhatnagar A, Bhaskar A, Majee SM, Kieffer M, Kepinski S, Khurana P, Khurana JP. Stress-induced F-Box protein-coding gene OsFBX257 modulates drought stress adaptations and ABA responses in rice. PLANT, CELL & ENVIRONMENT 2023; 46:1207-1231. [PMID: 36404527 DOI: 10.1111/pce.14496] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 10/15/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
F-box (FB) proteins that form part of SKP1-CUL1-F-box (SCF) type of E3 ubiquitin ligases are important components of plant growth and development. Here we characterized OsFBX257, a rice FB protein-coding gene that is differentially expressed under drought conditions and other abiotic stresses. Population genomics analysis suggest that OsFBX257 shows high allelic diversity in aus accessions and has been under positive selection in some japonica, aromatic and indica cultivars. Interestingly, allelic variation at OsFBX257 in aus cultivar Nagina22 is associated with an alternatively spliced transcript. Conserved among land plants, OsFBX257 is a component of the SCF complex, can form homomers and interact molecularly with the 14-3-3 rice proteins GF14b and GF14c. OsFBX257 is co-expressed in a network involving protein kinases and phosphatases. We show that OsFBX257 can bind the kinases OsCDPK1 and OsSAPK2, and that its phosphorylation can be reversed by phosphatase OsPP2C08. OsFBX257 expression level modulates root architecture and drought stress tolerance in rice. OsFBX257 knockdown (OsFBX257KD ) lines show reduced total root length and depth, crown root number, panicle size and survival under stress. In contrast, its overexpression (OsFBX257OE ) increases root depth, leaf and grain length, number of panicles, and grain yield in rice. OsFBX257 is a promising breeding target for alleviating drought stress-induced damage in rice.
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Affiliation(s)
- Eshan Sharma
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Akanksha Bhatnagar
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Avantika Bhaskar
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Susmita M Majee
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Martin Kieffer
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Stefan Kepinski
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Global Food and Environment Institute, University of Leeds, Leeds, UK
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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30
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Liu H, Chen S, Wu X, Li J, Xu C, Huang M, Wang H, Liu H, Zhao Z. Identification of the NAC Transcription Factor Family during Early Seed Development in Akebia trifoliata ( Thunb.) Koidz. PLANTS (BASEL, SWITZERLAND) 2023; 12:1518. [PMID: 37050144 PMCID: PMC10096588 DOI: 10.3390/plants12071518] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
This study aimed to gain an understanding of the possible function of NACs by examining their physicochemical properties, structure, chromosomal location, and expression. Being a family of plant-specific transcription factors, NAC (petunia no apical meristem and Arabidopsis thaliana ATAF1, ATAF2, and CUC2) is involved in plant growth and development. None of the NAC genes has been reported in Akebia trifoliata (Thunb.) Koidz (A. trifoliata). In this study, we identified 101 NAC proteins (AktNACs) in the A. trifoliata genome by bioinformatic analysis. One hundred one AktNACs were classified into the following twelve categories based on the phylogenetic analysis of NAC protein: NAC-a, NAC-b, NAC-c, NAC-d, NAC-e, NAC-f, NAC-g, NAC-h, NAC-i, NAC-j, NAC-k, and NAC-l. The accuracy of the clustering results was demonstrated based on the gene structure and conserved motif analysis of AktNACs. In addition, we identified 44 pairs of duplication genes, confirming the importance of purifying selection in the evolution of AktNACs. The morphology and microstructure of early A. trifoliata seed development showed that it mainly underwent rapid cell division, seed enlargement, embryo formation and endosperm development. We constructed AktNACs co-expression network and metabolite correlation network based on transcriptomic and metabolomic data of A. trifoliata seeds. The results of the co-expression network showed that 25 AtNAC genes were co-expressed with 233 transcription factors. Metabolite correlation analysis showed that 23 AktNACs were highly correlated with 28 upregulated metabolites. Additionally, 25 AktNACs and 235 transcription factors formed co-expression networks with 141 metabolites, based on correlation analysis involving AktNACs, transcription factors, and metabolites. Notably, AktNAC095 participates in the synthesis of 35 distinct metabolites. Eight of these metabolites, strongly correlated with AktNAC095, were upregulated during early seed development. These studies may provide insight into the evolution, possible function, and expression of AktNACs genes.
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Affiliation(s)
- Huijuan Liu
- College of Life Sciences, Guizhou University, Guiyang 550025, China
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Songshu Chen
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Xiaomao Wu
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Jinling Li
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Cunbin Xu
- College of Life Sciences, Guizhou University, Guiyang 550025, China
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Mingjin Huang
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Hualei Wang
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Hongchang Liu
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Zhi Zhao
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
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31
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Guo Y, Shi Y, Wang Y, Liu F, Li Z, Qi J, Wang Y, Zhang J, Yang S, Wang Y, Gong Z. The clade F PP2C phosphatase ZmPP84 negatively regulates drought tolerance by repressing stomatal closure in maize. THE NEW PHYTOLOGIST 2023; 237:1728-1744. [PMID: 36444538 DOI: 10.1111/nph.18647] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
Drought is a major environmental stress that threatens crop production. Therefore, identification of genes involved in drought stress response is of vital importance to decipher the molecular mechanism of stress signal transduction and breed drought tolerance crops, especially for maize. Clade A PP2C phosphatases are core abscisic acid (ABA) signaling components, regulating ABA signal transduction and drought response. However, the roles of other clade PP2Cs in drought resistance remain largely unknown. Here, we discovered a clade F PP2C, ZmPP84, that negatively regulates drought tolerance by screening a transgenic overexpression maize library. Quantitative RT-PCR indicates that the transcription of ZmPP84 is suppressed by drought stress. We identified that ZmMEK1, a member of the MAPKK family, interacts with ZmPP84 by immunoprecipitation and mass spectrometry analysis. Additionally, we found that ZmPP84 can dephosphorylate ZmMEK1 and repress its kinase activity on the downstream substrate kinase ZmSIMK1, while ZmSIMK1 is able to phosphorylate S-type anion channel ZmSLAC1 at S146 and T520 in vitro. Mutations of S146 and T520 to phosphomimetic aspartate could activate ZmSLAC1 currents in Xenopus oocytes. Taken together, our study suggests that ZmPP84 is a negative regulator of drought stress response that inhibits stomatal closure through dephosphorylating ZmMEK1, thereby repressing ZmMEK1-ZmSIMK1 signaling pathway.
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Affiliation(s)
- Yazhen Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yabo Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yalin Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Fang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Junsheng Qi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jingbo Zhang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yu Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Institute of Life Science and Green Development, School of Life Sciences, Hebei University, Baoding, 071002, China
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Beye A, Billot C, Ronfort J, McNally KL, Diouf D, Glaszmann JC. Traces of Introgression from cAus into Tropical Japonica Observed in African Upland Rice Varieties. RICE (NEW YORK, N.Y.) 2023; 16:12. [PMID: 36853402 PMCID: PMC9975138 DOI: 10.1186/s12284-023-00625-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Asian rice Oryza sativa, first domesticated in East Asia, has considerable success in African fields. When and where this introduction occurred is unclear. Rice varieties of Asian origin may have evolved locally during and after migration to Africa, resulting in unique adaptations, particularly in relation to upland cultivation as frequently practiced in Africa. METHODS We investigated the genetic differentiation between Asian and African varieties using the 3000 Rice Genomes SNP dataset. African upland cultivars were first characterized using principal component analysis among 292 tropical Japonica accessions from Africa and Asia. The particularities of African accessions were then explored using two inference techniques, PCA-KDE for supervised classification and chromosome painting, and ELAI for individual allelic dosage monitoring. KEY RESULTS Ambiguities of local differentiation between Japonica and other groups pointed at genomic segments that potentially resulted from genetic exchange. Those specific to West African upland accessions were concentrated on chromosome 6 and featured several cAus introgression signals, including a large one between 17.9 and 21.7 Mb. We found iHS statistics in support of positive selection in this region and we provide a list of candidate genes enriched in GO terms that have regulatory functions involved in stress responses that could have facilitated adaptation to harsh upland growing conditions.
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Affiliation(s)
- Abdoulaye Beye
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, 34398, Montpellier, France
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté Des Sciences Et Techniques, Université Cheikh Anta Diop, 10700, Dakar-Fann, Dakar, Senegal
| | - Claire Billot
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, 34398, Montpellier, France
| | - Joëlle Ronfort
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, 34398, Montpellier, France
| | - Kenneth L McNally
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, The Philippines
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté Des Sciences Et Techniques, Université Cheikh Anta Diop, 10700, Dakar-Fann, Dakar, Senegal
| | - Jean Christophe Glaszmann
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France.
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, 34398, Montpellier, France.
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Guo L, Lu S, Liu T, Nai G, Ren J, Gou H, Chen B, Mao J. Genome-Wide Identification and Abiotic Stress Response Analysis of PP2C Gene Family in Woodland and Pineapple Strawberries. Int J Mol Sci 2023; 24:ijms24044049. [PMID: 36835472 PMCID: PMC9961684 DOI: 10.3390/ijms24044049] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 02/22/2023] Open
Abstract
Protein phosphatase 2C (PP2C) is a negative regulator of serine/threonine residue protein phosphatase and plays an important role in abscisic acid (ABA) and abiotic-stress-mediated signaling pathways in plants. The genome complexity of woodland strawberry and pineapple strawberry is different due to the difference in chromosome ploidy. This study conducted a genome-wide investigation of the FvPP2C (Fragaria vesca) and FaPP2C (Fragaria ananassa) gene family. Fifty-six FvPP2C genes and 228 FaPP2C genes were identified from the woodland strawberry and pineapple strawberry genomes, respectively. FvPP2Cs were distributed on seven chromosomes, and FaPP2Cs were distributed on 28 chromosomes. The size of the FaPP2C gene family was significantly different from that of the FvPP2C gene family, but both FaPP2Cs and FvPP2Cs were localized in the nucleus, cytoplasm, and chloroplast. Phylogenetic analysis revealed that 56 FvPP2Cs and 228 FaPP2Cs could be divided into 11 subfamilies. Collinearity analysis showed that both FvPP2Cs and FaPP2Cs had fragment duplication, and the whole genome duplication was the main cause of PP2C gene abundance in pineapple strawberry. FvPP2Cs mainly underwent purification selection, and there were both purification selection and positive selection effects in the evolution of FaPP2Cs. Cis-acting element analysis found that the PP2C family genes of woodland and pineapple strawberries mainly contained light responsive elements, hormone responsive elements, defense and stress responsive elements, and growth and development-related elements. The results of quantitative real-time PCR (qRT-PCR) showed that the FvPP2C genes showed different expression patterns under ABA, salt, and drought treatment. The expression level of FvPP2C18 was upregulated after stress treatment, which may play a positive regulatory role in ABA signaling and abiotic stress response mechanisms. This study lays a foundation for further investigation on the function of the PP2C gene family.
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Wu Z, Luo L, Wan Y, Liu F. Genome-wide characterization of the PP2C gene family in peanut ( Arachis hypogaea L.) and the identification of candidate genes involved in salinity-stress response. FRONTIERS IN PLANT SCIENCE 2023; 14:1093913. [PMID: 36778706 PMCID: PMC9911800 DOI: 10.3389/fpls.2023.1093913] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Plant protein phosphatase 2C (PP2C) play important roles in response to salt stress by influencing metabolic processes, hormone levels, growth factors, etc. Members of the PP2C family have been identified in many plant species. However, they are rarely reported in peanut. In this study, 178 PP2C genes were identified in peanut, which were unevenly distributed across the 20 chromosomes, with segmental duplication in 78 gene pairs. AhPP2Cs could be divided into 10 clades (A-J) by phylogenetic analysis. AhPP2Cs had experienced segmental duplications and strong purifying selection pressure. 22 miRNAs from 14 different families were identified, targeting 57 AhPP2C genes. Gene structures and motifs analysis exhibited PP2Cs in subclades AI and AII had high structural and functional similarities. Phosphorylation sites of AhPP2C45/59/134/150/35/121 were predicted in motifs 2 and 4, which located within the catalytic site at the C-terminus. We discovered multiple MYB binding factors and ABA response elements in the promoter regions of the six genes (AhPP2C45/59/134/150/35/121) by cis-elements analysis. GO and KEGG enrichment analysis confirmed AhPP2C-A genes in protein binding, signal transduction, protein modification process response to abiotic stimulus through environmental information processing. Based on RNA-Seq data of 22 peanut tissues, clade A AhPP2Cs showed a varying degree of tissue specificity, of which, AhPP2C35 and AhPP2C121 specifically expressed in seeds, while AhPP2C45/59/134/150 expressed in leaves and roots. qRT-PCR indicated that AhPP2C45 and AhPP2C134 displayed significantly up-regulated expression in response to salt stress. These results indicated that AhPP2C45 and AhPP2C134 could be candidate PP2Cs conferring salt tolerance. These results provide further insights into the peanut PP2C gene family and indicate PP2Cs potentially involved in the response to salt stress, which can now be further investigated in peanut breeding efforts to obtain cultivars with improved salt tolerance.
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Affiliation(s)
- Zhanwei Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Lu Luo
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Yongshan Wan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Fengzhen Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
- College of Agronomy, Shandong Agricultural University, Tai’an, China
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Ahmed B, Hasan F, Tabassum A, Ahmed R, Hassan R, Amin MR, Alam M. Genome-wide investigation of SnRK2 gene family in two jute species: Corchorus olitorius and Corchorus capsularis. J Genet Eng Biotechnol 2023; 21:5. [PMID: 36652035 PMCID: PMC9849630 DOI: 10.1186/s43141-022-00453-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/15/2022] [Indexed: 01/19/2023]
Abstract
BACKGROUND Sucrose non-fermenting-1 (SNF1)-related protein kinase 2 (SnRK2), a plant-specific serine/threonine kinase family, is associated with metabolic responses, including abscisic acid signaling under biotic and abiotic stresses. So far, no information on a genome-wide investigation and stress-mediated expression profiling of jute SnRK2 is available. Recent whole-genome sequencing of two Corchorus species prompted to identify and characterize this SnRK2 gene family. RESULT We identified seven SnRK2 genes of each of Corchorus olitorius (Co) and C. capsularis (Cc) genomes, with similar physico-molecular properties and sub-group patterns of other models and related crops. In both species, the SnRK2 gene family showed an evolutionarily distinct trend. Highly variable C-terminal and conserved N-terminal regions were observed. Co- and CcSnRK2.3, Co- and CcSnRk2.5, Co- and CcSnRk2.7, and Co- and CcSnRK2.8 were upregulated in response to drought and salinity stresses. In waterlogging conditions, Co- and CcSnRk2.6 and Co- and CcSnRK2.8 showed higher activity when exposed to hypoxic conditions. Expression analysis in different plant parts showed that SnRK2.5 in both Corchorus species is highly expressed in fiber cells providing evidence of the role of fiber formation. CONCLUSION This is the first comprehensive study of SnRK2 genes in both Corchorus species. All seven genes identified in this study showed an almost similar pattern of gene structures and molecular properties. Gene expression patterns of these genes varied depending on the plant parts and in response to abiotic stresses.
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Affiliation(s)
- Borhan Ahmed
- grid.482525.c0000 0001 0699 8850Basic and Applied Research On Jute Project, Bangladesh Jute Research Institute, Dhaka, 1207 Bangladesh
| | - Fakhrul Hasan
- grid.443108.a0000 0000 8550 5526Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Salna, Gazipur, 1706 Bangladesh
| | - Anika Tabassum
- grid.442972.e0000 0001 2218 5390American International University of Bangladesh, Dhaka, 1229 Bangladesh
| | - Rasel Ahmed
- grid.482525.c0000 0001 0699 8850Basic and Applied Research On Jute Project, Bangladesh Jute Research Institute, Dhaka, 1207 Bangladesh
| | - Rajnee Hassan
- grid.24434.350000 0004 1937 0060Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE USA
| | - Md. Ruhul Amin
- grid.482525.c0000 0001 0699 8850Basic and Applied Research On Jute Project, Bangladesh Jute Research Institute, Dhaka, 1207 Bangladesh
| | - Mobashwer Alam
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, 47 Mayers Rd, Nambour, QLD 4560 Australia
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Saini LK, Bheri M, Pandey GK. Protein phosphatases and their targets: Comprehending the interactions in plant signaling pathways. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 134:307-370. [PMID: 36858740 DOI: 10.1016/bs.apcsb.2022.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Protein phosphorylation is a vital reversible post-translational modification. This process is established by two classes of enzymes: protein kinases and protein phosphatases. Protein kinases phosphorylate proteins while protein phosphatases dephosphorylate phosphorylated proteins, thus, functioning as 'critical regulators' in signaling pathways. The eukaryotic protein phosphatases are classified as phosphoprotein phosphatases (PPP), metallo-dependent protein phosphatases (PPM), protein tyrosine (Tyr) phosphatases (PTP), and aspartate (Asp)-dependent phosphatases. The PPP and PPM families are serine (Ser)/threonine (Thr) specific phosphatases (STPs) that dephosphorylate Ser and Thr residues. The PTP family dephosphorylates Tyr residues while dual-specificity phosphatases (DsPTPs/DSPs) dephosphorylate Ser, Thr, and Tyr residues. The composition of these enzymes as well as their substrate specificity are important determinants of their functional significance in a number of cellular processes and stress responses. Their role in animal systems is well-understood and characterized. The functional characterization of protein phosphatases has been extensively covered in plants, although the comprehension of their mechanistic basis is an ongoing pursuit. The nature of their interactions with other key players in the signaling process is vital to our understanding. The substrates or targets determine their potential as well as magnitude of the impact they have on signaling pathways. In this article, we exclusively overview the various substrates of protein phosphatases in plant signaling pathways, which are a critical determinant of the outcome of various developmental and stress stimuli.
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Affiliation(s)
- Lokesh K Saini
- Department of Plant Molecular Biology, University of Delhi South Campus, Dhaula Kuan, New Delhi, India
| | - Malathi Bheri
- Department of Plant Molecular Biology, University of Delhi South Campus, Dhaula Kuan, New Delhi, India
| | - Girdhar K Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, Dhaula Kuan, New Delhi, India.
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Cao Y, Dou D, Zhang D, Zheng Y, Ren Z, Su H, Sun C, Hu X, Bao M, Zhu B, Liu T, Chen Y, Ku L. ZmDWF1 regulates leaf angle in maize. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111459. [PMID: 36113675 DOI: 10.1016/j.plantsci.2022.111459] [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: 06/23/2022] [Revised: 09/06/2022] [Accepted: 09/10/2022] [Indexed: 06/15/2023]
Abstract
Leaf angle (LA) is a critical agronomic trait enhancing grain yield under high-density planting in maize. A number of researches have been conducted in recent years to investigate the quantitative trait loci/genes responsible for LA variation, while only a few genes were identified through map-based cloning. Here we cloned the ZmDWF1 gene, which was previously reported to encode Δ24-sterol reductase in the brassinosteroids (BRs) biosynthesis pathway. Overexpression of ZmDWF1 resulted in enlarged LA, indicating that ZmDWF1 is a positive regulator of LA in maize. To reveal the regulatory framework of ZmDWF1, we conducted RNA-Sequencing and yeast-two hybrid (Y2H) screening analysis. RNA-Sequencing analyzing results indicate ZmDWF1 mainly affected expression level of genes involved in cell wall associated metabolism and hormone metabolism including BR, gibberellin, and auxin. Y2H screening with Bi-FC assay confirmed three proteins (ZmPP2C-1, ZmROF1, and ZmTWD1) interacting with ZmDWF1. We revealed a new regulatory network of ZmDWF1 gene in controlling plant architecture in maize.
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Affiliation(s)
- Yingying Cao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Dandan Dou
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China; Henan Academy of Agricultural Science, Zhengzhou, Henan 450002, China
| | - Dongling Zhang
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China
| | - Yaogang Zheng
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China
| | - Zhenzhen Ren
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China
| | - Huihui Su
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China
| | - Chongyu Sun
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China
| | - Xiaomeng Hu
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China
| | - Miaomiao Bao
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China
| | - Bingqi Zhu
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China
| | - Tianxue Liu
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China
| | - Yanhui Chen
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China
| | - Lixia Ku
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China.
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Ganz P, Porras-Murillo R, Ijato T, Menz J, Straub T, Stührwohldt N, Moradtalab N, Ludewig U, Neuhäuser B. Abscisic acid influences ammonium transport via regulation of kinase CIPK23 and ammonium transporters. PLANT PHYSIOLOGY 2022; 190:1275-1288. [PMID: 35762968 PMCID: PMC9516733 DOI: 10.1093/plphys/kiac315] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/10/2022] [Indexed: 06/12/2023]
Abstract
Ammonium uptake at plant roots is regulated at the transcriptional, posttranscriptional, and posttranslational levels. Phosphorylation by the protein kinase calcineurin B-like protein (CBL)-interacting protein kinase 23 (CIPK23) transiently inactivates ammonium transporters (AMT1s), but the phosphatases activating AMT1s remain unknown. Here, we identified the PP2C phosphatase abscisic acid (ABA) insensitive 1 (ABI1) as an activator of AMT1s in Arabidopsis (Arabidopsis thaliana). We showed that high external ammonium concentrations elevate the level of the stress phytohormone ABA, possibly by de-glycosylation. Active ABA was sensed by ABI1-PYR1-like () complexes followed by the inactivation of ABI1, in turn activating CIPK23. Under favorable growth conditions, ABI1 reduced AMT1;1 and AMT1;2 phosphorylation, both by binding and inactivating CIPK23. ABI1 further directly interacted with AMT1;1 and AMT1;2, which would be a prerequisite for dephosphorylation of the transporter by ABI1. Thus, ABI1 is a positive regulator of ammonium uptake, coupling nutrient acquisition to abiotic stress signaling. Elevated ABA reduces ammonium uptake during stress situations, such as ammonium toxicity, whereas ABI1 reactivates AMT1s under favorable growth conditions.
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Affiliation(s)
- Pascal Ganz
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart D-70593, Germany
| | - Romano Porras-Murillo
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart D-70593, Germany
| | - Toyosi Ijato
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart D-70593, Germany
| | - Jochen Menz
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart D-70593, Germany
| | - Tatsiana Straub
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart D-70593, Germany
| | - Nils Stührwohldt
- Institute of Biology, Plant Physiology and Biochemistry, University of Hohenheim, Stuttgart D-70593, Germany
| | - Narges Moradtalab
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart D-70593, Germany
| | - Uwe Ludewig
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart D-70593, Germany
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Sisi C, Jieru D, Peidong C, Zhaolong Z, Yihang W, Shuwen C, Yan T, Tianyu W, Guiyan Y. Transcriptome-wide identification of walnut PP2C family genes in response to external stimulus. BMC Genomics 2022; 23:640. [PMID: 36076184 PMCID: PMC9461273 DOI: 10.1186/s12864-022-08856-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/23/2022] [Indexed: 11/11/2022] Open
Abstract
Walnut is an important economic tree species while confronting with global environmental stress, resulting in decline in quality and yield. Therefore, it is urgent to elucidate the molecular mechanism for the regulation of walnut response to adversity. The protein phosphatase 2C (PP2C) gene family participates in cellular processes in eukaryotes through reversible phosphorylation of proteins and signal transduction regulation. However, the stress response function of PP2C genes was far to be clarified. Therefore, to understand the stress response mechanism of walnut tree, in this study, a total of 41 PP2C genes with complete ORFs were identified from Juglans regia, whose basic bio-information and expression patterns in response to multiple stresses and ABA were confirmed. The results showed that the ORFs of JrPP2Cs were 495 ~ 3231 bp in length, the predicted JrPP2C proteins contained 164 to 1076 amino acids and the molecular weights were 18,581.96 ~ 118,853.34 Da, the pI was 4.55 ~ 9.58. These JrPP2C genes were unevenly distributed on 14 chromosomes, among which Chr11 and Chr13 contained the most genes. Phylogenetic analysis found that these JrPP2C proteins were classed into 9 subfamilies, among which group F covered most JrPP2Cs. The JrPP2Cs in the same subfamily exhibited similarities in the composition of conserved domains, amino acid sequences of motifs and exon/intron organization in DNA sequences. Each JrPP2C includes 4 ~ 10 motifs and each motif contained 15 ~ 37 amino acids. Among the motifs, motif1, motif2, motif3 and motif8 were most abundant. Most of the JrPP2C genes diversely response to osmotic, cadmium, and Colletotrichum gloeosporioide stress as well as ABA treatments, among which JrPP2C28, JrPP2C17, JrPP2C09, JrPP2C36 were more obvious and deserves further attention. All these results indicated that JrPP2C genes play potential vital roles in plant response to multiple stimulus, and are possibly involved in ABA-dependent signaling pathway.
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Affiliation(s)
- Chen Sisi
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Deng Jieru
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Cheng Peidong
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Zhang Zhaolong
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Wang Yihang
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Chen Shuwen
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Tang Yan
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Wang Tianyu
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Yang Guiyan
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China. .,Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China.
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Sobol G, Chakraborty J, Martin GB, Sessa G. The Emerging Role of PP2C Phosphatases in Tomato Immunity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:737-747. [PMID: 35696659 DOI: 10.1094/mpmi-02-22-0037-cr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The antagonistic effect of plant immunity on growth likely drove evolution of molecular mechanisms that prevent accidental initiation and prolonged activation of plant immune responses. Signaling networks of pattern-triggered and effector-triggered immunity, the two main layers of plant immunity, are tightly regulated by the activity of protein phosphatases that dephosphorylate their protein substrates and reverse the action of protein kinases. Members of the PP2C class of protein phosphatases have emerged as key negative regulators of plant immunity, primarily from research in the model plant Arabidopsis thaliana, revealing the potential to employ PP2C proteins to enhance plant disease resistance. As a first step towards focusing on the PP2C family for both basic and translational research, we analyzed the tomato genome sequence to ascertain the complement of the tomato PP2C family, identify conserved protein domains and signals in PP2C amino acid sequences, and examine domain combinations in individual proteins. We then identified tomato PP2Cs that are candidate regulators of single or multiple layers of the immune signaling network by in-depth analysis of publicly available RNA-seq datasets. These included expression profiles of plants treated with fungal or bacterial pathogen-associated molecular patterns, with pathogenic, nonpathogenic, and disarmed bacteria, as well as pathogenic fungi and oomycetes. Finally, we discuss the possible use of immunity-associated PP2Cs to better understand the signaling networks of plant immunity and to engineer durable and broad disease resistance in crop plants. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Guy Sobol
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
| | - Joydeep Chakraborty
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
| | - Gregory B Martin
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Guido Sessa
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
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Liu S, Lu C, Jiang G, Zhou R, Chang Y, Wang S, Wang D, Niu J, Wang Z. Comprehensive functional analysis of the PYL-PP2C-SnRK2s family in Bletilla striata reveals that BsPP2C22 and BsPP2C38 interact with BsPYLs and BsSnRK2s in response to multiple abiotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:963069. [PMID: 36035678 PMCID: PMC9404246 DOI: 10.3389/fpls.2022.963069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
As the core regulation network for the abscisic acid (ABA) signaling pathway, the PYL-PP2C-SnRK2s family commonly exists in many species. For this study, a total of 9 BsPYLs, 66 BsPP2Cs, and 7 BsSnRK2s genes were identified based on the genomic databases of Bletilla striata, which were classified into 3, 10, and 3 subgroups, respectively. Basic bioinformatics analysis completed, including the physicochemical properties of proteins, gene structures, protein motifs and conserved domains. Multiple cis-acting elements related to stress responses and plant growth were found in promoter regions. Further, 73 genes were localized on 16 pseudochromosomes and 29 pairs of paralogous genes were found via intraspecific collinearity analysis. Furthermore, tissue-specific expression was found in different tissues and germination stages. There were two BsPYLs, 10 BsPP2Cs, and four BsSnRK2 genes that exhibited a difference in response to multiple abiotic stresses. Moreover, subcellular localization analysis revealed six important proteins BsPP2C22, BsPP2C38, BsPP2C64, BsPYL2, BsPYL8, and BsSnRK2.4 which were localized in the nucleus and plasma membrane. Finally, yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays suggested that BsPP2C22 and BsPP2C38 could interact with multiple BsPYLs and BsSnRK2s proteins. This study systematically reported on the identification and characterization of the PYL-PP2C-SnRK2s family in B. striata, which provided a conceptual basis for deep insights into the functionality of ABA core signal pathways in Orchidaceae.
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Zhang G, Zhang Z, Luo S, Li X, Lyu J, Liu Z, Wan Z, Yu J. Genome-wide identification and expression analysis of the cucumber PP2C gene family. BMC Genomics 2022; 23:563. [PMID: 35933381 PMCID: PMC9356470 DOI: 10.1186/s12864-022-08734-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Background Type 2C protein phosphatase (PP2C) is a negative regulator of ABA signaling pathway, which plays important roles in stress signal transduction in plants. However, little research on the PP2C genes family of cucumber (Cucumis sativus L.), as an important economic vegetable, has been conducted. Results This study conducted a genome-wide investigation of the CsPP2C gene family. Through bioinformatics analysis, 56 CsPP2C genes were identified in cucumber. Based on phylogenetic analysis, the PP2C genes of cucumber and Arabidopsis were divided into 13 groups. Gene structure and conserved motif analysis showed that CsPP2C genes in the same group had similar gene structure and conserved domains. Collinearity analysis showed that segmental duplication events played a key role in the expansion of the cucumber PP2C genes family. In addition, the expression of CsPP2Cs under different abiotic treatments was analyzed by qRT-PCR. The results reveal that CsPP2C family genes showed different expression patterns under ABA, drought, salt, and cold treatment, and that CsPP2C3, 11–17, 23, 45, 54 and 55 responded significantly to the four stresses. By predicting the cis-elements in the promoter, we found that all CsPP2C members contained ABA response elements and drought response elements. Additionally, the expression patterns of CsPP2C genes were specific in different tissues. Conclusions The results of this study provide a reference for the genome-wide identification of the PP2C gene family in other species and provide a basis for future studies on the function of PP2C genes in cucumber. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08734-y.
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Affiliation(s)
- Guobin Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.,College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zeyu Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Shilei Luo
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.,College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xia Li
- Gansu Institute of Geological and Natural Disaster Prevention, Lanzhou, 730000, China
| | - Jian Lyu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zeci Liu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zilong Wan
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jihua Yu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China. .,College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China.
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Sezen UU, Worthy SJ, Umaña MN, Davies SJ, McMahon SM, Swenson NG. Comparative transcriptomics of tropical woody plants supports fast and furious strategy along the leaf economics spectrum in lianas. Biol Open 2022; 11:276072. [PMID: 35876379 PMCID: PMC9346291 DOI: 10.1242/bio.059184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/19/2022] [Indexed: 12/03/2022] Open
Abstract
Lianas, climbing woody plants, influence the structure and function of tropical forests. Climbing traits have evolved multiple times, including ancestral groups such as gymnosperms and pteridophytes, but the genetic basis of the liana strategy is largely unknown. Here, we use a comparative transcriptomic approach for 47 tropical plant species, including ten lianas of diverse taxonomic origins, to identify genes that are consistently expressed or downregulated only in lianas. Our comparative analysis of full-length transcripts enabled the identification of a core interactomic network common to lianas. Sets of transcripts identified from our analysis reveal features related to functional traits pertinent to leaf economics spectrum in lianas, include upregulation of genes controlling epidermal cuticular properties, cell wall remodeling, carbon concentrating mechanism, cell cycle progression, DNA repair and a large suit of downregulated transcription factors and enzymes involved in ABA-mediated stress response as well as lignin and suberin synthesis. All together, these genes are known to be significant in shaping plant morphologies through responses such as gravitropism, phyllotaxy and shade avoidance. Summary: The full-length fraction of liana transcriptomes mapped on a protein–protein interactome revealed the nature of their convergence through distinct sets of expressed and downregulated genes not observed in free-standing plants.
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Affiliation(s)
- U Uzay Sezen
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD, 21037, USA
| | - Samantha J Worthy
- Department of Evolution and Ecology, University of California, Davis, CA, 95616USA
| | - Maria N Umaña
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Stuart J Davies
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Gamboa, Panama.,Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington DC, 20560, USA
| | - Sean M McMahon
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd, Edgewater, MD, 21037, USA
| | - Nathan G Swenson
- Department of Evolution and Ecology, University of California, Davis, CA, 95616USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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Ren C, Kuang Y, Lin Y, Guo Y, Li H, Fan P, Li S, Liang Z. Overexpression of grape ABA receptor gene VaPYL4 enhances tolerance to multiple abiotic stresses in Arabidopsis. BMC PLANT BIOLOGY 2022; 22:271. [PMID: 35655129 PMCID: PMC9161562 DOI: 10.1186/s12870-022-03663-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/27/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Abscisic acid (ABA) plays a crucial role in abiotic stress responses. The pyrabactin resistance (PYR)/PYR-like (PYL)/regulatory component of ABA receptor (RCAR) proteins that have been characterized as ABA receptors function as the core components in ABA signaling pathway. However, the functions of grape PYL genes in response to different abiotic stresses, particularly cold stress, remain less studied. RESULTS In this study, we investigated the expression profiles of grape PYL genes upon cold treatment and isolated the VaPYL4 gene from Vitis amurensis, a cold-hardy grape species. Overexpression of VaPYL4 gene in grape calli and Arabidopsis resulted in enhanced cold tolerance. Moreover, plant resistance to drought and salt stress was also improved by overexpressing VaPYL4 in Arabidopsis. More importantly, we evaluated the contribution of VaPYL4 to plant growth and development after the treatment with cold, salt and drought stress simultaneously. The transgenic plants showed higher survival rates, earlier flowering phenotype, and heavier fresh weight of seedlings and siliques when compared with wild-type plants. Physiological analyses showed that transgenic plants had much lower content of malondialdehyde (MDA) and higher peroxidase (POD) activity. Stress-responsive genes such as RD29A (Responsive to desiccation 29A), COR15A (Cold responsive 15A) and KIN2 (Kinase 2) were also significantly up-regulated in VaPYL4-overexpressing Arabidopsis plants. CONCLUSIONS Our results show that overexpression of VaPYL4 could improve plant performance upon different abiotic stresses, which therefore provides a useful strategy for engineering future crops to deal with adverse environments.
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Affiliation(s)
- Chong Ren
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
| | - Yangfu Kuang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Yanping Lin
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Yuchen Guo
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Huayang Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Peige Fan
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093 People’s Republic of China
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Panigrahy M, Panigrahi KCS, Poli Y, Ranga A, Majeed N. Integrated Expression Analysis of Small RNA, Degradome and Microarray Reveals Complex Regulatory Action of miRNA during Prolonged Shade in Swarnaprabha Rice. BIOLOGY 2022; 11:biology11050798. [PMID: 35625525 PMCID: PMC9138629 DOI: 10.3390/biology11050798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 12/22/2022]
Abstract
Prolonged shade during the reproductive stage can result in significant yield losses in rice. For this study, we elucidated the role of microRNAs in prolonged-shade tolerance (~20 days of shade) in a shade-tolerant rice variety, Swarnaprabha (SP), in its reproductive stage using small RNA and degradome sequencing with expression analysis using microarray and qRT-PCR. This study demonstrates that miRNA (miR) regulation for shade-tolerance predominately comprises the deactivation of the miR itself, leading to the upregulation of their targets. Up- and downregulated differentially expressed miRs (DEms) presented drastic differences in the category of targets based on the function and pathway in which they are involved. Moreover, neutrally regulated and uniquely expressed miRs also contributed to the shade-tolerance response by altering the differential expression of their targets, probably due to their differential binding affinities. The upregulated DEms mostly targeted the cell wall, membrane, cytoskeleton, and cellulose synthesis-related transcripts, and the downregulated DEms targeted the transcripts of photosynthesis, carbon and sugar metabolism, energy metabolism, and amino acid and protein metabolism. We identified 16 miRNAs with 21 target pairs, whose actions may significantly contribute to the shade-tolerance phenotype and sustainable yield of SP. The most notable among these were found to be miR5493-OsSLAC and miR5144-OsLOG1 for enhanced panicle size, miR5493-OsBRITTLE1-1 for grain formation, miR6245-OsCsIF9 for decreased stem mechanical strength, miR5487-OsGns9 and miR168b-OsCP1 for better pollen development, and miR172b-OsbHLH153 for hyponasty under shade.
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Affiliation(s)
- Madhusmita Panigrahy
- Biofuel & Bioprocessing Research Centre, Institute of Technical Education and Research, Siksha ‘O’ Anusandhan University, Bhubaneswar 751002, India
- National Institute of Science Education and Research, Homi Bhabha National Institute (HBNI), Khurda 752050, India; (A.R.); (N.M.)
- Correspondence: (M.P.); (K.C.S.P.); Tel.: +91-8762086581 (M.P.); +91-6742494139 (K.C.S.P.)
| | - Kishore Chandra Sekhar Panigrahi
- National Institute of Science Education and Research, Homi Bhabha National Institute (HBNI), Khurda 752050, India; (A.R.); (N.M.)
- Correspondence: (M.P.); (K.C.S.P.); Tel.: +91-8762086581 (M.P.); +91-6742494139 (K.C.S.P.)
| | - Yugandhar Poli
- ICAR-Indian Institute of Rice Research, Rajendra Nagar, Hyderabad 500030, India;
| | - Aman Ranga
- National Institute of Science Education and Research, Homi Bhabha National Institute (HBNI), Khurda 752050, India; (A.R.); (N.M.)
| | - Neelofar Majeed
- National Institute of Science Education and Research, Homi Bhabha National Institute (HBNI), Khurda 752050, India; (A.R.); (N.M.)
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Wu XT, Xiong ZP, Chen KX, Zhao GR, Feng KR, Li XH, Li XR, Tian Z, Huo FL, Wang MX, Song W. Genome-Wide Identification and Transcriptional Expression Profiles of PP2C in the Barley (Hordeum vulgare L.) Pan-Genome. Genes (Basel) 2022; 13:genes13050834. [PMID: 35627219 PMCID: PMC9140614 DOI: 10.3390/genes13050834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
The gene family protein phosphatase 2C (PP2C) is related to developmental processes and stress responses in plants. Barley (Hordeum vulgare L.) is a popular cereal crop that is primarily utilized for human consumption and nutrition. However, there is little knowledge regarding the PP2C gene family in barley. In this study, a total of 1635 PP2C genes were identified in 20 barley pan-genome accessions. Then, chromosome localization, physical and chemical feature predictions and subcellular localization were systematically analyzed. One wild barley accession (B1K-04-12) and one cultivated barley (Morex) were chosen as representatives to further analyze and compare the differences in HvPP2Cs between wild and cultivated barley. Phylogenetic analysis showed that these HvPP2Cs were divided into 12 subgroups. Additionally, gene structure, conserved domain and motif, gene duplication event detection, interaction networks and gene expression profiles were analyzed in accessions Morex and B1K-04-12. In addition, qRT-PCR experiments in Morex indicated that seven HvMorexPP2C genes were involved in the response to aluminum and low pH stresses. Finally, a series of positively selected homologous genes were identified between wild accession B1K-04-12 and another 14 cultivated materials, indicating that these genes are important during barley domestication. This work provides a global overview of the putative physiological and biological functions of PP2C genes in barley. We provide a broad framework for understanding the domestication- and evolutionary-induced changes in PP2C genes between wild and cultivated barley.
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Affiliation(s)
- Xiao-Tong Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Zhu-Pei Xiong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Kun-Xiang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Guo-Rong Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Ke-Ru Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Xiu-Hua Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Xi-Ran Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Zhao Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Fu-Lin Huo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
| | - Meng-Xing Wang
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
- Correspondence: (M.-X.W.); (W.S.)
| | - Weining Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China; (X.-T.W.); (Z.-P.X.); (K.-X.C.); (G.-R.Z.); (K.-R.F.); lxh (X.-H.L.); (X.-R.L.); (Z.T.); (F.-L.H.)
- Correspondence: (M.-X.W.); (W.S.)
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Lu F, Li W, Peng Y, Cao Y, Qu J, Sun F, Yang Q, Lu Y, Zhang X, Zheng L, Fu F, Yu H. ZmPP2C26 Alternative Splicing Variants Negatively Regulate Drought Tolerance in Maize. FRONTIERS IN PLANT SCIENCE 2022; 13:851531. [PMID: 35463404 PMCID: PMC9024303 DOI: 10.3389/fpls.2022.851531] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/08/2022] [Indexed: 06/09/2023]
Abstract
Serine/threonine protein phosphatase 2C (PP2C) dephosphorylates proteins and plays crucial roles in plant growth, development, and stress response. In this study, we characterized a clade B member of maize PP2C family, i.e., ZmPP2C26, that negatively regulated drought tolerance by dephosphorylating ZmMAPK3 and ZmMAPK7 in maize. The ZmPP2C26 gene generated ZmPP2C26L and ZmPP2C26S isoforms through untypical alternative splicing. ZmPP2C26S lost 71 amino acids including an MAPK interaction motif and showed higher phosphatase activity than ZmPP2C26L. ZmPP2C26L directly interacted with, dephosphorylated ZmMAPK3 and ZmMAPK7, and localized in chloroplast and nucleus, but ZmPP2C26S only dephosphorylated ZmMAPK3 and localized in cytosol and nucleus. The expression of ZmPP2C26L and ZmPP2C26 was significantly inhibited by drought stress. Meanwhile, the maize zmpp2c26 mutant exhibited enhancement of drought tolerance with higher root length, root weight, chlorophyll content, and photosynthetic rate compared with wild type. However, overexpression of ZmPP2C26L and ZmPP2C26S significantly decreased drought tolerance in Arabidopsis and rice with lower root length, chlorophyll content, and photosynthetic rate. Phosphoproteomic analysis revealed that the ZmPP2C26 protein also altered phosphorylation level of proteins involved in photosynthesis. This study provides insights into understanding the mechanism of PP2C in response to abiotic stress.
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Affiliation(s)
- Fengzhong Lu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wanchen Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yalin Peng
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Cao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jingtao Qu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Fuai Sun
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qingqing Yang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanli Lu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Lanjie Zheng
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Fengling Fu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Haoqiang Yu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
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Association mapping of autumn-seeded rye (Secale cereale L.) reveals genetic linkages between genes controlling winter hardiness and plant development. Sci Rep 2022; 12:5793. [PMID: 35388069 PMCID: PMC8986816 DOI: 10.1038/s41598-022-09582-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 03/25/2022] [Indexed: 12/23/2022] Open
Abstract
Winter field survival (WFS) in autumn-seeded winter cereals is a complex trait associated with low temperature tolerance (LTT), prostrate growth habit (PGH), and final leaf number (FLN). WFS and the three sub-traits were analyzed by a genome-wide association study of 96 rye (Secale cereal L.) genotypes of different origins and winter-hardiness levels. A total of 10,244 single nucleotide polymorphism (SNP) markers were identified by genotyping by sequencing and 259 marker-trait-associations (MTAs; p < 0.01) were revealed by association mapping. The ten most significant SNPs (p < 1.49e−04) associated with WFS corresponded to nine strong candidate genes: Inducer of CBF Expression 1 (ICE1), Cold-regulated 413-Plasma Membrane Protein 1 (COR413-PM1), Ice Recrystallization Inhibition Protein 1 (IRIP1), Jasmonate-resistant 1 (JAR1), BIPP2C1-like protein phosphatase, Chloroplast Unusual Positioning Protein-1 (CHUP1), FRIGIDA-like 4 (FRL4-like) protein, Chalcone Synthase 2 (CHS2), and Phenylalanine Ammonia-lyase 8 (PAL8). Seven of the candidate genes were also significant for one or several of the sub-traits supporting the hypothesis that WFS, LTT, FLN, and PGH are genetically interlinked. The winter-hardy rye genotypes generally carried additional allele variants for the strong candidate genes, which suggested allele diversity was a major contributor to cold acclimation efficiency and consistent high WFS under varying field conditions.
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Akiyama M, Sugimoto H, Inoue SI, Takahashi Y, Hayashi M, Hayashi Y, Mizutani M, Ogawa T, Kinoshita D, Ando E, Park M, Gray WM, Kinoshita T. Type 2C protein phosphatase clade D family members dephosphorylate guard cell plasma membrane H+-ATPase. PLANT PHYSIOLOGY 2022; 188:2228-2240. [PMID: 34894269 PMCID: PMC8968332 DOI: 10.1093/plphys/kiab571] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/05/2021] [Indexed: 05/27/2023]
Abstract
Plasma membrane (PM) H+-ATPase in guard cells is activated by phosphorylation of the penultimate residue, threonine (Thr), in response to blue and red light, promoting stomatal opening. Previous in vitro biochemical investigation suggested that Mg2+- and Mn2+-dependent membrane-localized type 2C protein phosphatase (PP2C)-like activity mediates the dephosphorylation of PM H+-ATPase in guard cells. PP2C clade D (PP2C.D) was later demonstrated to be involved in PM H+-ATPase dephosphorylation during auxin-induced cell expansion in Arabidopsis (Arabidopsis thaliana). However, it is unclear whether PP2C.D phosphatases are involved in PM H+-ATPase dephosphorylation in guard cells. Transient expression experiments using Arabidopsis mesophyll cell protoplasts revealed that all PP2C.D isoforms dephosphorylate the endogenous PM H+-ATPase. We further analyzed PP2C.D6/8/9, which display higher expression levels than other isoforms in guard cells, observing that pp2c.d6, pp2c.d8, and pp2c.d9 single mutants showed similar light-induced stomatal opening and phosphorylation status of PM H+-ATPase in guard cells as Col-0. In contrast, the pp2c.d6/9 double mutant displayed wider stomatal apertures and greater PM H+-ATPase phosphorylation in response to blue light, but delayed dephosphorylation of PM H+-ATPase in guard cells; the pp2c.d6/8/9 triple mutant showed similar phenotypes to those of the pp2c.d6/9 double mutant. Taken together, these results indicate that PP2C.D6 and PP2C.D9 redundantly mediate PM H+-ATPase dephosphorylation in guard cells. Curiously, unlike auxin-induced cell expansion in seedlings, auxin had no effect on the phosphorylation status of PM H+-ATPase in guard cells.
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Affiliation(s)
| | | | - Shin-ichiro Inoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Yohei Takahashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Maki Hayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Yuki Hayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Miya Mizutani
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Takumi Ogawa
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Daichi Kinoshita
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Eigo Ando
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Meeyeon Park
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108, USA
| | - William M Gray
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108, USA
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Qiu J, Ni L, Xia X, Chen S, Zhang Y, Lang M, Li M, Liu B, Pan Y, Li J, Zhang X. Genome-Wide Analysis of the Protein Phosphatase 2C Genes in Tomato. Genes (Basel) 2022; 13:genes13040604. [PMID: 35456410 PMCID: PMC9032827 DOI: 10.3390/genes13040604] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 01/27/2023] Open
Abstract
The plant protein phosphatase 2C (PP2C) plays an irreplaceable role in phytohormone signaling, developmental processes, and manifold stresses. However, information about the PP2C gene family in tomato (Solanum lycopersicum) is relatively restricted. In this study, a genome-wide investigation of the SlPP2C gene family was performed. A total of 92 SlPP2C genes were identified, they were distributed on 11 chromosomes, and all the SlPP2C proteins have the type 2C phosphatase domains. Based on phylogenetic analysis of PP2C genes in Arabidopsis, rice, and tomato, SlPP2C genes were divided into eight groups, designated A–H, which is also supported by the analyses of gene structures and protein motifs. Gene duplication analysis revealed that the duplication of whole genome and chromosome segments was the main cause of SLPP2Cs expansion. A total of 26 cis-elements related to stress, hormones, and development were identified in the 3 kb upstream region of these SlPP2C genes. Expression profile analysis revealed that the SlPP2C genes display diverse expression patterns in various tomato tissues. Furthermore, we investigated the expression patterns of SlPP2C genes in response to Ralstonia solanacearum infection. RNA-seq and qRT-PCR data reveal that nine SlPP2Cs are correlated with R. solanacearum. The above evidence hinted that SlPP2C genes play multiple roles in tomato and may contribute to tomato resistance to bacterial wilt. This study obtained here will give an impetus to the understanding of the potential function of SlPP2Cs and lay a solid foundation for tomato breeding and transgenic resistance to plant pathogens.
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Affiliation(s)
- Jianfang Qiu
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Lei Ni
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Xue Xia
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Shihao Chen
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Yan Zhang
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Min Lang
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
| | - Mengyu Li
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Binman Liu
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Yu Pan
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Jinhua Li
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Xingguo Zhang
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
- Correspondence: ; Tel.: +86-23-68250974; Fax: +86-23-68251274
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