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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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Zeng J, Wu C, Ye X, Zhou J, Chen Y, Li L, Lin M, Wang S, Liu S, Yan Y, Tie W, Yang J, Yan F, Zeng L, Liu Y, Hu W. MePP2C24, a cassava (Manihot esculenta) gene encoding protein phosphatase 2C, negatively regulates drought stress and abscisic acid responses in transgenic Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108291. [PMID: 38141400 DOI: 10.1016/j.plaphy.2023.108291] [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: 06/13/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
Abscisic acid (ABA) signaling plays a crucial role in plant development and response to abiotic/biotic stress. However, the function and regulation of protein phosphatase 2C (PP2C), a key component of abscisic acid signaling, under abiotic stress are still unknown in cassava, a drought-tolerant crop. In this study, a cassava PP2C gene (MePP2C24) was cloned and characterized. The MePP2C24 transcripts increased in response to mannitol, NaCl, and ABA. Overexpression of MePP2C24 in Arabidopsis resulted in increased sensitivity to drought stress and decreased sensitivity to exogenous ABA. This was demonstrated by transgenic lines having higher levels of malondialdehyde (MDA), ion leakage (IL), and reactive oxygen species (ROS), lower activities of catalase (CAT) and peroxidase (POD), and lower proline content than wild type (WT) under drought stress. Moreover, MePP2C24 overexpression caused decrease in expression of drought-responsive genes related to ABA signaling pathway. In addition, MePP2C24 was localized in the cell nucleus and showed self-activation. Furthermore, many MePYLs (MePYL1, MePYL4, MePYL7-9, and MePYL11-13) could interact with MePP2C24 in the presence of ABA, and MePYL1 interacted with MePP2C24 in both the presence and absence of ABA. Additionally, MebZIP11 interacted with the promoter of MePP2C24 and exerted a suppressive effect. Taken together, our results suggest that MePP2C24 acts as a negative regulator of drought tolerance and ABA response.
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Affiliation(s)
- Jian Zeng
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China.
| | - Chunlai Wu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China; The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, 430074, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China
| | - Xiaoxue Ye
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China
| | - Jiewei Zhou
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China
| | - Yingtong Chen
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China
| | - Lizhen Li
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China
| | - Man Lin
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China
| | - Shuting Wang
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China
| | - Siwen Liu
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Yan Yan
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China
| | - Weiwei Tie
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China
| | - Jinghao Yang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China
| | - Fei Yan
- Shaanxi Provincial Bioresource Key Laboratory, College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723000, China
| | - Liwang Zeng
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China.
| | - Yujia Liu
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong, China.
| | - Wei Hu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Institute of Scientific and Technical Information, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 517101, China.
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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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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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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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Sheng H, Zhang J, Pan C, Wang S, Gu S, Li F, Ma Y, Ma Y. Genome-wide identification of bovine ADAMTS gene family and analysis of its expression profile in the inflammatory process of mammary epithelial cells. Int J Biol Macromol 2023:125304. [PMID: 37315674 DOI: 10.1016/j.ijbiomac.2023.125304] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/29/2023] [Accepted: 06/04/2023] [Indexed: 06/16/2023]
Abstract
ADAM metallopeptidase with thrombospondin type 1 motif (ADAMTS) are secreted, multi-domain matrix-related zinc endopeptidases that play a role in organogenesis, assembly and degradation of extracellular matrix (ECM), cancer and inflammation. Genome-wide identification and analysis of the bovine ADAMTS gene family has not yet been carried out. In this study, 19 ADAMTS family genes were identified in Bos taurus by genome-wide bioinformatics analysis, and they were unevenly distributed on 12 chromosomes. Phylogenetic analysis shows that the Bos taurus ADAMTS are divided into eight subfamilies, with highly consistent gene structures and motifs within the same subfamily. Collinearity analysis showed that the Bos taurus ADAMTS gene family is homologous to other bovine subfamily species, and many ADAMTS genes may be derived from tandem replication and segmental replication. In addition, based on the analysis of RNA-seq data, we found the expression pattern of ADAMTS gene in different tissues. Meanwhile, we also analyzed the expression profile of ADAMTS gene in the inflammatory response of bovine mammary epithelial cells (BMECs) stimulated by LPS by qRT-PCR. The results can provide ideas for understanding the evolutionary relationship and expression pattern of ADAMTS gene in Bovidae, and clarify the theoretical basis of the function of ADAMTS in inflammation.
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Affiliation(s)
- Hui Sheng
- School of Agriculture, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Junxing Zhang
- School of Agriculture, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Cuili Pan
- School of Agriculture, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Shuzhe Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Shuaifeng Gu
- School of Agriculture, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Fen Li
- School of Agriculture, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Yanfen Ma
- School of Agriculture, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Yun Ma
- School of Agriculture, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan 750021, China.
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Genome-Wide Identification of Strawberry Metal Tolerance Proteins and Their Expression under Cadmium Toxicity. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8060477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Metal tolerance proteins (MTPs) are divalent cation transporters, known to upkeep the mineral nutrition of plants and heavy metal transport at cell, tissue, or whole plant levels. However, information related to evolutionary relationships and biological functions of MTP genes in strawberry (Fragaria vesca L.) remain elusive. Herein, we identified 12 MTP genes from the strawberry genome and divided them into three main groups (i.e., Zn-MTP, Fe/Zn MTP, and Mn-MTP), which is similar to MTP grouping in Arabidopsis and rice. The strawberry MTPs (FvMTPs) are predicted to be localized in the vacuole, while open reading frame (ORF) length ranged from 1113 to 2589 bp with 370 to 862 amino acids, and possess 4 to 6 transmembrane domains (TMDs), except for FvMTP12 that possessed 16 TMDs. All the FvMTP genes had putative cation efflux and cation diffusion facilitator domains along with a zinc dimerization (ZT-dimer) domain in Mn-MTPs. The collinear analysis suggested their conservation between strawberry and Arabidopsis MTPs. Promoter analysis also demonstrated that some of them might possibly be regulated by hormones and abiotic stress factors. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis proposed that FvMTP genes are involved in cation transport and homeostasis. The expression analysis showed that FvMTP1, FvMTP1.1, and FvMTP4 were significantly induced in leaf samples, while FvMTP1.1 and FvMTP4 were significantly regulated in roots of cadmium (Cd)-treated strawberry plants during progressive stress duration. The findings of Cd accumulation depicted that Cd contents were significantly higher in root tissues than that of leaf tissues of strawberry. These results are indicative of their response during the specific duration in Cd detoxification, while further functional studies can accurately verify their specific role.
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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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Dhillon MK, Jaba J, Mishra P, Iquebal MA, Jaiswal S, Tanwar AK, Bharat N, Arora N, Mishra SP, Gogineni SP, Hasan F, Rai A, Kumar D, Sharma HC. Whole genome sequencing of spotted stem borer, Chilo partellus, reveals multiple genes encoding enzymes for detoxification of insecticides. Funct Integr Genomics 2022; 22:611-624. [PMID: 35426546 DOI: 10.1007/s10142-022-00852-w] [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: 11/24/2021] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 11/24/2022]
Abstract
Spotted stem borer, Chilo partellus, is the most important constraint for increasing the production and productivity of maize and sorghum, the two major coarse cereals in Asia and Africa. The levels of resistance to this pest in the cultivated germplasm are low to moderate, and hence, farmers have to use insecticides for effective control of this pest. However, there is no information on the detoxification mechanisms in C. partellus, which is one of the constraints for deployment of appropriate insecticides to control this pest. The ability to detoxify insecticides varies across insect populations, and hence, we sequenced different populations of C. partellus to identify and understand detoxification mechanisms to devise appropriate strategies for deployment of different insecticides for controlling this pest. Larval samples were sequenced from three different cohorts of C. partellus using the Illumina HiSeq 2500 platform. The data were subjected to identify putative genes that are involved in detoxification on insecticides in our cohort insect species. These studies resulted in identification of 64 cytochrome P450 genes (CYP450s), and 36 glutathione S-transferases genes (GSTs) encoding metabolic detoxification enzymes, primarily responsible for xenobiotic metabolism in insects. A total of 183 circadian genes with > 80% homolog and 11 olfactory receptor genes that mediate chemical cues were found in the C. partellus genome. Also, target receptors related to insecticide action, 4 acetylcholinesterase (AChE), 14 γ-aminobutyric acid (GABA), and 15 nicotinic acetylcholine (nAChR) receptors were detected. This is the first report of whole genome sequencing of C. partellus useful for understanding mode of action of different insecticides, and mechanisms of detoxification and designing target-specific insecticides to develop appropriate strategies to control C. partellus for sustainable crop production.
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Affiliation(s)
- Mukesh K Dhillon
- Division of Entomology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jagdish Jaba
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad, 502324, Telangana, India
| | - Pallavi Mishra
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Aditya K Tanwar
- Division of Entomology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Nareshkumar Bharat
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad, 502324, Telangana, India
| | - Naveen Arora
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad, 502324, Telangana, India
| | - Suraj Prasad Mishra
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad, 502324, Telangana, India
| | - Shyam Prasad Gogineni
- ICAR-Indian Institute of Millets Research, Rajendranagar, Hyderabad, 500030, Telangana, India
| | - Fazil Hasan
- Division of Entomology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India. .,Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, 123031, Haryana, India.
| | - Hari C Sharma
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad, 502324, Telangana, India
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11
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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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12
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Nie L, Xu Z, Wu L, Chen X, Cui Y, Wang Y, Song J, Yao H. Genome-wide identification of protein phosphatase 2C family members in Glycyrrhiza uralensis Fisch. and their response to abscisic acid and polyethylene glycol stress. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2022. [DOI: 10.1080/16583655.2022.2027650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Liping Nie
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, People’s Republic of China
| | - Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, People’s Republic of China
| | - Liwei Wu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, People’s Republic of China
| | - Xinlian Chen
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, People’s Republic of China
| | - Yingxian Cui
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, People’s Republic of China
| | - Yu Wang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, People’s Republic of China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, People’s Republic of China
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, People’s Republic of China
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Zhang P, Yuan Z, Wei L, Qiu X, Wang G, Liu Z, Fu J, Cao L, Wang T. Overexpression of ZmPP2C55 positively enhances tolerance to drought stress in transgenic maize plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 314:111127. [PMID: 34895535 DOI: 10.1016/j.plantsci.2021.111127] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 06/14/2023]
Abstract
Serine/threonine protein phosphatases play essential roles in plants. PP2C has diverse functions related to development and stress response, while little is known about the functions of PP2C genes with respect to a variety of stresses in maize. In the present study, three ZmPP2C genes, ZmPP2C55, ZmPP2C28, and ZmPP2C71, were identified. Subcellular localization demonstrated that ZmPP2C28 and ZmPP2C71 were nuclear proteins, and ZmPP2C55 was located in both the nucleus and cytoplasm. qRT-PCR analysis showed that ZmPP2C55, ZmPP2C28, and ZmPP2C71 were expressed in roots, leaves and stems, and the three genes were responsive to drought, salt, high-temperature stress and exogenous ABA treatment. To explore the function of the ZmPP2C gene, ZmPP2C55-overexpressing transgenic lines were generated. The transgenic plants exhibited higher RWC, proline content, POD and SOD activities, GSH content and GSH/GSSG ratio and lower MDA content, electrolyte leakage and GSSG content compared with WT plants under natural stress treatment when seedlings were at the three-leaf. Our results illustrated that the overexpression of ZmPP2C55 positively enhanced tolerance to drought stress.
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Affiliation(s)
- Pengyu Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - Zhen Yuan
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - Li Wei
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - Xiao Qiu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - Guorui Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - Zhixue Liu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - Jiaxu Fu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - Liru Cao
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - Tongchao Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, 450046, China.
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Wang G, Sun X, Guo Z, Joldersma D, Guo L, Qiao X, Qi K, Gu C, Zhang S. Genome-wide Identification and Evolution of the PP2C Gene Family in Eight Rosaceae Species and Expression Analysis Under Stress in Pyrus bretschneideri. Front Genet 2021; 12:770014. [PMID: 34858482 PMCID: PMC8632025 DOI: 10.3389/fgene.2021.770014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/11/2021] [Indexed: 11/23/2022] Open
Abstract
Type 2C protein phosphatase (PP2C) plays an essential role in abscisic acid (ABA) signaling transduction processes. In the current study, we identify 719 putative PP2C genes in eight Rosaceae species, including 118 in Chinese white pear, 110 in European pear, 73 in Japanese apricot, 128 in apple, 74 in peach, 65 in strawberry, 78 in sweet cherry, and 73 in black raspberry. Further, the phylogenetic analysis categorized PbrPP2C genes of Chinese white pear into twelve subgroups based on the phylogenic analysis. We observed that whole-genome duplication (WGD) and dispersed gene duplication (DSD) have expanded the Rosaceae PP2C family despite simultaneous purifying selection. Expression analysis finds that PbrPP2C genes have organ-specific functions. QRT-PCR validation of nine PbrPP2C genes of subgroup A indicates a role in ABA-mediated response to abiotic stress. Finally, we find that five PbrPP2C genes of subgroup A function in the nucleus. In summary, our research suggests that the PP2C family functions to modulate ABA signals and responds to abiotic stress.
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Affiliation(s)
- Guoming Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China
| | - Xun Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China
| | - Zhihua Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China
| | - Dirk Joldersma
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
| | - Lei Guo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
| | - Xin Qiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China
| | - Kaijie Qi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China
| | - Chao Gu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China
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Zubair M, Farzand A, Mumtaz F, Khan AR, Sheikh TMM, Haider MS, Yu C, Wang Y, Ayaz M, Gu Q, Gao X, Wu H. Novel Genetic Dysregulations and Oxidative Damage in Fusarium graminearum Induced by Plant Defense Eliciting Psychrophilic Bacillus atrophaeus TS1. Int J Mol Sci 2021; 22:ijms222212094. [PMID: 34829976 PMCID: PMC8622878 DOI: 10.3390/ijms222212094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 11/27/2022] Open
Abstract
This study elaborates inter-kingdom signaling mechanisms, presenting a sustainable and eco-friendly approach to combat biotic as well as abiotic stress in wheat. Fusarium graminearum is a devastating pathogen causing head and seedling blight in wheat, leading to huge yield and economic losses. Psychrophilic Bacillus atrophaeus strain TS1 was found as a potential biocontrol agent for suppression of F. graminearum under low temperature by carrying out extensive biochemical and molecular studies in comparison with a temperate biocontrol model strain Bacillus amyloliquefaciens FZB42 at 15 and 25 °C. TS1 was able to produce hydrolytic extracellular enzymes as well as antimicrobial lipopeptides, i.e., surfactin, bacillomycin, and fengycin, efficiently at low temperatures. The Bacillus strain-induced oxidative cellular damage, ultrastructural deformities, and novel genetic dysregulations in the fungal pathogen as the bacterial treatment at low temperature were able to downregulate the expression of newly predicted novel fungal genes potentially belonging to necrosis inducing protein families (fgHCE and fgNPP1). The wheat pot experiments conducted at 15 and 25 °C revealed the potential of TS1 to elicit sudden induction of plant defense, namely, H2O2 and callose enhanced activity of plant defense-related enzymes and induced over-expression of defense-related genes which accumulatively lead to the suppression of F. graminearum and decreased diseased leaf area.
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Affiliation(s)
- Muhammad Zubair
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China; (M.Z.); (A.F.); (A.R.K.); (T.M.M.S.); (C.Y.); (Y.W.); (M.A.); (Q.G.); (X.G.)
| | - Ayaz Farzand
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China; (M.Z.); (A.F.); (A.R.K.); (T.M.M.S.); (C.Y.); (Y.W.); (M.A.); (Q.G.); (X.G.)
- Department of Plant Pathology, University of Agriculture, Faisalabad 38040, Pakistan
| | - Faiza Mumtaz
- Department of Pharmacology, School of Medicine, Tehran University of Medical Sciences, P.O. Box 13145-784, Tehran 13145-784, Iran;
| | - Abdur Rashid Khan
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China; (M.Z.); (A.F.); (A.R.K.); (T.M.M.S.); (C.Y.); (Y.W.); (M.A.); (Q.G.); (X.G.)
| | - Taha Majid Mahmood Sheikh
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China; (M.Z.); (A.F.); (A.R.K.); (T.M.M.S.); (C.Y.); (Y.W.); (M.A.); (Q.G.); (X.G.)
| | | | - Chenjie Yu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China; (M.Z.); (A.F.); (A.R.K.); (T.M.M.S.); (C.Y.); (Y.W.); (M.A.); (Q.G.); (X.G.)
| | - Yujie Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China; (M.Z.); (A.F.); (A.R.K.); (T.M.M.S.); (C.Y.); (Y.W.); (M.A.); (Q.G.); (X.G.)
| | - Muhammad Ayaz
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China; (M.Z.); (A.F.); (A.R.K.); (T.M.M.S.); (C.Y.); (Y.W.); (M.A.); (Q.G.); (X.G.)
| | - Qin Gu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China; (M.Z.); (A.F.); (A.R.K.); (T.M.M.S.); (C.Y.); (Y.W.); (M.A.); (Q.G.); (X.G.)
| | - Xuewen Gao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China; (M.Z.); (A.F.); (A.R.K.); (T.M.M.S.); (C.Y.); (Y.W.); (M.A.); (Q.G.); (X.G.)
| | - Huijun Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China; (M.Z.); (A.F.); (A.R.K.); (T.M.M.S.); (C.Y.); (Y.W.); (M.A.); (Q.G.); (X.G.)
- Correspondence: ; Tel./Fax: +86-25-84395268
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16
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Paediatric Antimicrobial Stewardship for Respiratory Infections in the Emergency Setting: A Systematic Review. Antibiotics (Basel) 2021; 10:antibiotics10111366. [PMID: 34827304 PMCID: PMC8615165 DOI: 10.3390/antibiotics10111366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial resistance occurs due to the propensity of microbial pathogens to develop resistance to antibiotics over time. Antimicrobial stewardship programs (ASPs) have been developed in response to this growing crisis, to limit unnecessary antibiotic prescription through initiatives such as education-based seminars, prescribing guidelines, and rapid respiratory pathogen (RRP) testing. Paediatric patients who present to the emergency setting with respiratory symptoms are a particularly high-risk population susceptible to inappropriate antibiotic prescribing behaviours and are therefore an ideal cohort for focused ASPs. The purpose of this systematic review was to assess the efficacy and safety of ASPs in this clinical context. A systematic search of PubMed, Medline, EMBASE and the Cochrane Database of Systematic Reviews was conducted to review the current evidence. Thirteen studies were included in the review and these studies assessed a range of stewardship interventions and outcome measures. Overall, ASPs reduced the rates of antibiotic prescription, increased the prescription of narrow-spectrum antibiotics, and shortened the duration of antibiotic therapy. Multimodal interventions that were education-based and those that used RRP testing were found to be the most effective. Whilst we found strong evidence that ASPs are effective in reducing antibiotic prescribing, further studies are required to assess whether they translate to equivalent clinical outcomes.
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Pervaiz T, Liu SW, Uddin S, Amjid MW, Niu SH, Wu HX. The Transcriptional Landscape and Hub Genes Associated with Physiological Responses to Drought Stress in Pinus tabuliformis. Int J Mol Sci 2021; 22:ijms22179604. [PMID: 34502511 PMCID: PMC8431770 DOI: 10.3390/ijms22179604] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/11/2021] [Accepted: 09/01/2021] [Indexed: 01/18/2023] Open
Abstract
Drought stress has an extensive impact on regulating various physiological, metabolic, and molecular responses. In the present study, the Pinus tabuliformis transcriptome was studied to evaluate the drought-responsive genes using RNA- Sequencing approache. The results depicted that photosynthetic rate and H2O conductance started to decline under drought but recovered 24 h after re-watering; however, the intercellular CO2 concentration (Ci) increased with the onset of drought. We identified 84 drought-responsive transcription factors, 62 protein kinases, 17 transcriptional regulators, and 10 network hub genes. Additionally, we observed the expression patterns of several important gene families, including 2192 genes positively expressed in all 48 samples, and 40 genes were commonly co-expressed in all drought and recovery stages compared with the control samples. The drought-responsive transcriptome was conserved mainly between P. tabuliformis and A. thaliana, as 70% (6163) genes had a homologous in arabidopsis, out of which 52% homologous (3178 genes corresponding to 2086 genes in Arabidopsis) were also drought response genes in arabidopsis. The collaborative network exhibited 10 core hub genes integrating with ABA-dependent and independent pathways closely conserved with the ABA signaling pathway in the transcription factors module. PtNCED3 from the ABA family genes had shown significantly different expression patterns under control, mild, prolonged drought, and recovery stages. We found the expression pattern was considerably increased with the prolonged drought condition. PtNCED3 highly expressed in all drought-tested samples; more interestingly, expression pattern was higher under mild and prolonged drought. PtNCED3 is reported as one of the important regulating enzymes in ABA synthesis. The continuous accumulation of ABA in leaves increased resistance against drought was due to accumulation of PtNCED3 under drought stress in the pine needles.
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Affiliation(s)
- Tariq Pervaiz
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (T.P.); (S.-W.L.); (S.U.)
| | - Shuang-Wei Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (T.P.); (S.-W.L.); (S.U.)
| | - Saleem Uddin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (T.P.); (S.-W.L.); (S.U.)
| | - Muhammad Waqas Amjid
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China;
| | - Shi-Hui Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (T.P.); (S.-W.L.); (S.U.)
- Correspondence: (S.-H.N.); (H.X.W.)
| | - Harry X. Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (T.P.); (S.-W.L.); (S.U.)
- Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Linnaeus vag 6, SE-901 83 Umea, Sweden
- CSIRO National Research Collection Australia, Black Mountain Laboratory, Canberra, ACT 2601, Australia
- Correspondence: (S.-H.N.); (H.X.W.)
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Haider MS, De Britto S, Nagaraj G, Gurulingaiah B, Shekhar R, Ito SI, Jogaiah S. Genome-Wide Identification, Diversification, and Expression Analysis of Lectin Receptor-Like Kinase (LecRLK) Gene Family in Cucumber under Biotic Stress. Int J Mol Sci 2021; 22:6585. [PMID: 34205396 PMCID: PMC8234520 DOI: 10.3390/ijms22126585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 12/27/2022] Open
Abstract
Members of the lectin receptor-like kinase (LecRLKs) family play a vital role in innate plant immunity. Few members of the LecRLKs family have been characterized in rice and Arabidopsis, respectively. However, little literature is available about LecRLKs and their role against fungal infection in cucumber. In this study, 60 putative cucumber LecRLK (CsLecRLK) proteins were identified using genome-wide analysis and further characterized into L-type LecRLKs (24) and G-type LecRLKs (36) based on domain composition and phylogenetic analysis. These proteins were allocated to seven cucumber chromosomes and found to be involved in the expansion of the CsLecRLK gene family. Subcellular localization of CsaLecRLK9 and CsaLecRLK12 showed green fluorescence signals in the plasma membrane of leaves. The transcriptional profiling of CsLecRLK genes showed that L-type LecRLKs exhibited functional redundancy as compared to G-type LecRLKs. The qRT-PCR results indicated that both L- and G-type LecRLKs showed significant response against plant growth-promoting fungi (PGPF-Trichoderma harzianum Rifai), powdery mildew pathogen (PPM-Golovinomyces orontii (Castagne) V.P. Heluta), and combined (PGPF+PPM) treatments. The findings of this study contribute to a better understanding of the role of cucumber CsLecRLK genes in response to PGPF, PPM, and PGPF+PPM treatments and lay the basis for the characterization of this important functional gene family.
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Affiliation(s)
- Muhammad Salman Haider
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China;
| | - Savitha De Britto
- Laboratory of Plant Healthcare and Diagnostics, P.G. Department of Biotechnology and Microbiology, Karnatak University, Dharwad 580003, India;
- Division of Biological Sciences, School of Science and Technology, University of Goroka, Goroka 441, Papua New Guinea
| | - Geetha Nagaraj
- Nanobiotechnology Laboratory, Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570006, India; (G.N.); (B.G.); (R.S.)
| | - Bhavya Gurulingaiah
- Nanobiotechnology Laboratory, Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570006, India; (G.N.); (B.G.); (R.S.)
| | - Ravikant Shekhar
- Nanobiotechnology Laboratory, Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570006, India; (G.N.); (B.G.); (R.S.)
| | - Shin-ichi Ito
- Laboratory of Molecular Plant Pathology, Department of Biological and Environmental Sciences, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan
- Research Center for Thermotolerant Microbial Resources (RCTMR), Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Sudisha Jogaiah
- Laboratory of Plant Healthcare and Diagnostics, P.G. Department of Biotechnology and Microbiology, Karnatak University, Dharwad 580003, India;
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Khan N, Fatima F, Haider MS, Shazadee H, Liu Z, Zheng T, Fang J. Genome-Wide Identification and Expression Profiling of the Polygalacturonase ( PG) and Pectin Methylesterase ( PME) Genes in Grapevine ( Vitis vinifera L.). Int J Mol Sci 2019; 20:ijms20133180. [PMID: 31261768 PMCID: PMC6651664 DOI: 10.3390/ijms20133180] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/21/2019] [Accepted: 06/27/2019] [Indexed: 01/07/2023] Open
Abstract
In pectin regulation, polygalacturonases (PGs) and pectin methylesterases (PMEs) are critical components in the transformation, disassembly network, and remodeling of plant primary cell walls. In the current study, we identified 36 PG and 47 PME genes using the available genomic resources of grapevine. Herein, we provide a comprehensive overview of PGs and PMEs, including phylogenetic and collinearity relationships, motif and gene structure compositions, gene duplications, principal component analysis, and expression profiling during developmental stages. Phylogenetic analysis of PGs and PMEs revealed similar domain composition patterns with Arabidopsis. The collinearity analysis showed high conservation and gene duplications with purifying selection. The type of duplications also varied in terms of gene numbers in PGs (10 dispersed, 1 proximal, 12 tandem, and 13 segmental, respectively) and PMEs (23 dispersed, 1 proximal, 16 tandem, and 7 segmental, respectively). The tissue-specific response of PG and PME genes based on the reported transcriptomic data exhibited diverged expression patterns in various organs during different developmental stages. Among PGs, VvPG8, VvPG10, VvPG13, VvPG17, VvPG18, VvPG19, VvPG20, VvPG22, and VvPG23 showed tissue- or organ-specific expression in majority of the tissues during development. Similarly, in PMEs, VvPME3, VvPME4, VvPME5, VvPME6, VvPME19, VvPME21, VvPME23, VvPME29, VvPME31, and VvPME32 suggested high tissue-specific response. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomics (KEGG) enrichment, and cis-elements prediction analysis also suggested the putative functions of PGs and PMEs in plant development, such as pectin and carbohydrate metabolism, and stress activities. Moreover, qRT-PCR validation of 32 PG and PME genes revealed their role in various organs of grapevines (i.e., root, stem, tendril, inflorescence, flesh, skins, and leaves). Therefore, these findings will lead to novel insights and encourage cutting-edge research on functional characterization of PGs and PMEs in fruit crop species.
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Affiliation(s)
- Nadeem Khan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Fizza Fatima
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Muhammad Salman Haider
- Key laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hamna Shazadee
- College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhongjie Liu
- Key laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Zheng
- Key laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinggui Fang
- Key laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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