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Qi C, Xv L, Xia W, Zhu Y, Wang Y, Zhang Z, Dai H, Miao M. Genome-Wide Identification and Expression Patterns of Cucumber Invertases and Their Inhibitor Genes. Int J Mol Sci 2023; 24:13421. [PMID: 37686228 PMCID: PMC10487868 DOI: 10.3390/ijms241713421] [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: 08/08/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Invertases and their inhibitors play important roles in sucrose metabolism, growth and development, signal transduction, and biotic and abiotic stress tolerance in many plant species. However, in cucumber, both the gene members and functions of invertase and its inhibitor families remain largely unclear. In this study, in comparison with the orthologues of Citrullus lanatus (watermelon), Cucumis melo (melon), and Arabidopsis thaliana (Arabidopsis), 12 invertase genes and 12 invertase inhibitor genes were identified from the genome of Cucumis sativus (cucumber). Among them, the 12 invertase genes were classified as 4 cell wall invertases, 6 cytoplasmic invertases, and 2 vacuolar invertases. Most invertase genes were conserved in cucumber, melon, and watermelon, with several duplicate genes in melon and watermelon. Transcriptome analysis distinguished these genes into various expression patterns, which included genes CsaV3_2G025540 and CsaV3_2G007220, which were significantly expressed in different tissues, organs, and development stages, and genes CsaV3_7G034730 and CsaV3_5G005910, which might be involved in biotic and abiotic stress. Six genes were further validated in cucumber based on quantitative real-time PCR (qRT-PCR), and three of them showed consistent expression patterns as revealed in the transcriptome. These results provide important information for further studies on the physiological functions of cucumber invertases (CSINVs) and their inhibitors (CSINHs).
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Affiliation(s)
- Chenze Qi
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (C.Q.); (L.X.); (W.X.); (Y.Z.); (Y.W.); (Z.Z.); (H.D.)
| | - Liyun Xv
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (C.Q.); (L.X.); (W.X.); (Y.Z.); (Y.W.); (Z.Z.); (H.D.)
| | - Wenhao Xia
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (C.Q.); (L.X.); (W.X.); (Y.Z.); (Y.W.); (Z.Z.); (H.D.)
| | - Yunyi Zhu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (C.Q.); (L.X.); (W.X.); (Y.Z.); (Y.W.); (Z.Z.); (H.D.)
| | - Yudan Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (C.Q.); (L.X.); (W.X.); (Y.Z.); (Y.W.); (Z.Z.); (H.D.)
| | - Zhiping Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (C.Q.); (L.X.); (W.X.); (Y.Z.); (Y.W.); (Z.Z.); (H.D.)
| | - Haibo Dai
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (C.Q.); (L.X.); (W.X.); (Y.Z.); (Y.W.); (Z.Z.); (H.D.)
| | - Minmin Miao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (C.Q.); (L.X.); (W.X.); (Y.Z.); (Y.W.); (Z.Z.); (H.D.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics, The Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
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Li Z, Rao MJ, Li J, Wang Y, Chen P, Yu H, Ma C, Wang L. CRISPR/Cas9 Mutant Rice Ospmei12 Involved in Growth, Cell Wall Development, and Response to Phytohormone and Heavy Metal Stress. Int J Mol Sci 2022; 23:ijms232416082. [PMID: 36555723 PMCID: PMC9784561 DOI: 10.3390/ijms232416082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Pectin is one of the constituents of the cell wall, distributed in the primary cell wall and middle lamella, affecting the rheological properties and the cell wall stickiness. Pectin methylesterase (PME) and pectin methylesterase inhibitor (PMEI) are the most important factors for modifying methyl esterification. In this study, 45 PMEI genes from rice (Oryza sativa L.) were screened by bioinformatics tools, and their structure, motifs, cis-acting elements in the promoter region, chromosomal distribution, gene duplication, and phylogenetic relationship were analyzed. Furthermore, CRISPR/Cas9 was used to edit the OsPMEI12 (LOC_Os03G01020) and two mutant pmei12 lines were obtained to explore the functions of OsPMEI in plant growth and development, and under cadmium (Cd) stress. Compared to wild type (WT) Nipponbare, the second inverted internodes of the mutant plants shortened significantly, resulting in the reduction in plant height at mature stage. The seed setting rate, and fresh and dry weights of the mutants were also decreased in mutant plants. In addition, the pectin methylation of pmei12 lines is decreased as expected, and the pectin content of the cell wall increased at both seedling and maturity stages; however, the cellulose and hemicellulose increased only at seedling stage. Interestingly, the growth of the pmei12 lines was better than the WT in both normal conditions and under two phytohormone (GA3 and NAA) treatments at seedling stage. Under Cd stress, the fresh and dry weights were increased in pmei12 lines. These results indicated that OsPMEI12 was involved in the regulation of methyl esterification during growth, affected cell wall composition and agronomic traits, and might play an important role in responses to phytohormones and stress.
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Affiliation(s)
- Zhaoyang Li
- College of Plant Science and Technology, Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Muhammad Junaid Rao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China
| | - Jiaying Li
- College of Plant Science and Technology, Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanting Wang
- College of Plant Science and Technology, Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Peng Chen
- College of Plant Science and Technology, Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Hua Yu
- College of Plant Science and Technology, Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Chongjian Ma
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China
- Correspondence: (C.M.); (L.W.)
| | - Lingqiang Wang
- College of Plant Science and Technology, Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China
- Correspondence: (C.M.); (L.W.)
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3
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Zhou Y, Li R, Wang S, Ding Z, Zhou Q, Liu J, Wang Y, Yao Y, Hu X, Guo J. Overexpression of MePMEI1 in Arabidopsis enhances Pb tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:996981. [PMID: 36186034 PMCID: PMC9523724 DOI: 10.3389/fpls.2022.996981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Pb is one of the most ubiquitously distributed heavy metal pollutants in soils and has serious negative effects on plant growth, food safety, and public health. Pectin methylesterase inhibitors (PMEIs) play a pivotal role in regulating the integrity of plant cell walls; however, the molecular basis by which PMEIs promote plant resistance to abiotic stress remains poorly understood. In this study, we identified a novel PMEI gene, MePMEI1, from Manihot esculenta, and determined its role in plant resistance to Pb stress. The expression of MePMEI1 was remarkably upregulated in the roots, stems, and leaves of cassava plants following exposure to Pb stress. An analysis of subcellular localization revealed that the MePMEI1 protein was localized in the cell wall. MePMEI1 inhibited commercial orange peel pectin methyltransferase (PME), and the expression of MePMEI1 in Arabidopsis decreased the PME activity, indicating that MePMEI1 can inhibit PME activity in the cell wall. Additionally, the overexpression of MePMEI1 in Arabidopsis reduced oxidative damage and induced the thickening of cell walls, thus contributing to Pb tolerance. Altogether, the study reports a novel mechanism by which the MePMEI1 gene, which encodes the PMEI protein in cassava, plays an essential role in promoting tolerance to Pb toxicity by regulating the thickness of cell walls. These results provide a theoretical basis for the MePMEI1-mediated plant breeding for increasing heavy metal tolerance and provide insights into controlling Pb pollution in soils through phytoremediation in future studies.
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Affiliation(s)
- Yangjiao Zhou
- School of Life Sciences, Hainan University, Haikou, China
| | - Ruimei Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou, China
| | - Shijia Wang
- School of Life Sciences, Hainan University, Haikou, China
| | - Zhongping Ding
- School of Life Sciences, Hainan University, Haikou, China
| | - Qin Zhou
- School of Life Sciences, Hainan University, Haikou, China
| | - Jiao Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou, China
| | - Yajia Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou, China
| | - Yuan Yao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou, China
| | - Xinwen Hu
- School of Life Sciences, Hainan University, Haikou, China
| | - Jianchun Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou, China
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Wang D, Jin S, Chen Z, Shan Y, Li L. Genome-wide identification of the pectin methylesterase inhibitor genes in Brassica napus and expression analysis of selected members. FRONTIERS IN PLANT SCIENCE 2022; 13:940284. [PMID: 35937343 PMCID: PMC9354821 DOI: 10.3389/fpls.2022.940284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Pectin methylesterase inhibitors (PMEIs) modulate the status of pectin methylesterification by inhibiting the activity of pectin methylesterase (PME). Recent advances indicate PMEIs play an important role in regulating plant cell wall properties and defense responses. In this study, a genome-wide analysis of PMEI gene family in Brassica napus (B. napus) was conducted and the expression patterns of PMEI genes in response to Sclerotinia sclerotiorum (S. sclerotiorum) was investigated. A total of 190 PMEI proteins were identified from the genome of B. napus. Chromosomal location, gene structure and properties of the PMEI family were analyzed, and these features were compared with Arabidopsis thaliana (A. thaliana). A total of 123 syntenic ortholog pairs were detected from BnPMEI family by synteny analysis. Results showed the expansion of BnPMEI genes was likely predominately from whole-genome duplication (WGD) or segmental duplications. Multiple cis-elements related to plant growth and development, environmental stress responses, hormone responses were detected in the promoters of BnPMEI genes, implying they were regulated by both internal and external factors. Furthermore, expression analysis of transcriptome data combined with quantitative RT-PCR (qRT-PCR) validation identified several candidates that were strongly responsive to S. sclerotiorum infection. These BnPMEI genes are candidates for manipulation to breed novel and improved genotypes that are more resistant to sclerotinia stem rot (SSR). Extensive interactions were detected among 30 BnPMEI proteins, forming complex protein-protein interaction networks. Besides, 48 BnPMEIs showed interactions with other proteins including a range of cell wall structure-related enzymes. This study provides new insights into the evolution and function of PMEIs in B. napus and lays a foundation for breeding novel genotypes for crop improvement.
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Affiliation(s)
- Duoduo Wang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Shunda Jin
- Key Laboratory of Tropical Fruit Tree Biology of Hainan Province, Haikou, China
| | - Zhe Chen
- Key Laboratory of Tropical Fruit Tree Biology of Hainan Province, Haikou, China
| | - Yue Shan
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Lei Li
- School of Life Sciences, Jiangsu University, Zhenjiang, China
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Li B, Wang H, He S, Ding Z, Wang Y, Li N, Hao X, Wang L, Yang Y, Qian W. Genome-Wide Identification of the PMEI Gene Family in Tea Plant and Functional Analysis of CsPMEI2 and CsPMEI4 Through Ectopic Overexpression. FRONTIERS IN PLANT SCIENCE 2022; 12:807514. [PMID: 35154201 PMCID: PMC8829431 DOI: 10.3389/fpls.2021.807514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/14/2021] [Indexed: 05/26/2023]
Abstract
Pectin methylesterase inhibitor (PMEI) inhibits pectin methylesterase (PME) activity at post-translation level, which plays core roles in vegetative and reproductive processes and various stress responses of plants. However, the roles of PMEIs in tea plant are still undiscovered. Herein, a total of 51 CsPMEIs genes were identified from tea plant genome. CsPMEI1-4 transcripts were varied in different tea plant tissues and regulated by various treatments, including biotic and abiotic stresses, sugar treatments, cold acclimation and bud dormancy. Overexpression of CsPMEI4 slightly decreased cold tolerance of transgenic Arabidopsis associated with lower electrolyte leakage, soluble sugars contents and transcripts of many cold-induced genes as compared to wild type plants. Under long-day and short-day conditions, CsPMEI2/4 promoted early flowering phenotypes in transgenic Arabidopsis along with higher expression levels of many flowering-related genes. Moreover, overexpression of CsPMEI2/4 decreased PME activity, but increased sugars contents (sucrose, glucose, and fructose) in transgenic Arabidopsis as compared with wild type plants under short-day condition. These results indicate that CsPMEIs are widely involved in tea plant vegetative and reproductive processes, and also in various stress responses. Moreover, CsPMEI4 negatively regulated cold response, meanwhile, CsPMEI2/4 promoted early flowering of transgenic Arabidopsis via the autonomous pathway. Collectively, these results open new perspectives on the roles of PMEIs in tea plant.
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Affiliation(s)
- Bo Li
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao, China
| | - Huan Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao, China
| | - Shan He
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao, China
| | - Zhaotang Ding
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao, China
| | - Yu Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao, China
| | - Nana Li
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Xinyuan Hao
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Lu Wang
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Yajun Yang
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Wenjun Qian
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao, China
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Amplification, sequencing and characterization of pectin methyl esterase inhibitor 51 gene in Tectona grandis L.f. Saudi J Biol Sci 2021; 28:5451-5460. [PMID: 34588855 PMCID: PMC8459126 DOI: 10.1016/j.sjbs.2021.07.015] [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: 04/09/2021] [Revised: 06/25/2021] [Accepted: 07/04/2021] [Indexed: 11/25/2022] Open
Abstract
Tectona grandis L.f. (Teak), a very important source of incomparable timber, withstands a wide range of tropical deciduous conditions. We achieved partial amplification of pectin methylesterase inhibitor 51 (PMEI) gene in teak by E. pilularis cinnamoyl Co-A reductase (CCR) gene specific primer. The amplified teak gene was of 750 bp, 79% identity and 97% query cover with PMEI of Sesamum indicum. The phylogenetic tree clustered the amplified gene with PMEI of database plant species, Erythranthe guttata and Sesamum indicum (87% bootstrap value). On conversion to amino acid sequence, the obtained protein comprised 237 amino acids. However, PMEI region spanned from 24 to 171 amino acids, 15.94 kDa molecular weight, 8.97 pI value and C697H1117N199O211S9 molecular formula with four conserved cysteine residues as disulfide bridges. 25.9 % protein residues were hydrophilic, 42.7% hydrophobic and 31.2% neutral. Teak 3D PMEI protein structure corresponded well with Arabidopsis thaliana and Actinidia deliciosa PMEIs. The gene maintains integrity of pectin component of middle lamella of primary cell wall and confers tolerance against various kinds of stresses. Teak conferred with overexpression of PMEI may secure a wide adaptability as well as luxuriant timber productivity and quality in adverse/ fluctuating/ scarce climatic and environmental conditions of tropical forests.
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Zhu X, Tang C, Li Q, Qiao X, Li X, Cai Y, Wang P, Sun Y, Zhang H, Zhang S, Wu J. Characterization of the pectin methylesterase inhibitor gene family in Rosaceae and role of PbrPMEI23/39/41 in methylesterified pectin distribution in pear pollen tube. PLANTA 2021; 253:118. [PMID: 33961146 DOI: 10.1007/s00425-021-03638-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/01/2021] [Indexed: 05/02/2023]
Abstract
Pectin methylesterase inhibitor gene family in the seven Rosaceae species (including three pear cultivars) is characterized and three pectin methylesterase inhibitor genes are identified to regulate pollen tube growth in pear. Pectin methylesterase inhibitor (PMEI) participates in a variety of biological processes in plants. However, the information and function of PMEI genes in Rosaceae are largely unknown. In this study, a total of 423 PMEI genes are identified in the genomes of seven Rosaceae species. The PMEI genes in pear are categorized into five subfamilies based on structural analysis and evolutionary analysis. WGD and TD are the main duplication events in the PMEI gene family of pear. Quantitative real-time PCR analysis indicates that PbrPMEI23, PbrPMEI39, and PbrPMEI41 are increasingly expressed during pear pollen tube growth. Under the treatment of recombinant proteins PbrPMEI23, PbrPMEI39 or PbrPMEI41, the content of methylesterified pectin at the region 5-20 μm from the pollen tube tip significantly increases, and the growth of pear pollen tubes is promoted. These results indicate that PMEI regulates the growth of pollen tubes by changing the distribution of methylesterified pectin in the apex.
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Affiliation(s)
- Xiaoxuan Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chao Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qionghou Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin Qiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xian Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yilin Cai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yangyang Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hua Zhang
- Shanghai Vocational College of Agriculture and Forestry, Shanghai, 201699, China
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juyou Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China.
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, China.
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Chen G, Wang J, Wang H, Wang C, Tang X, Li J, Zhang L, Song J, Hou J, Yuan L. Genome-wide analysis of proline-rich extension-like receptor protein kinase (PERK) in Brassica rapa and its association with the pollen development. BMC Genomics 2020; 21:401. [PMID: 32539701 PMCID: PMC7296749 DOI: 10.1186/s12864-020-06802-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/02/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Proline-rich extension-like receptor protein kinases (PERKs) are an important class of receptor kinases located in the plasma membrane, most of which play a vital role in pollen development. RESULTS Our study identified 25 putative PERK genes from the whole Brassica rapa genome (AA). Phylogenetic analysis of PERK protein sequences from 16 Brassicaceae species divided them into four subfamilies. The biophysical properties of the BrPERKs were investigated. Gene duplication and synteny analyses and the calculation of Ka/Ks values suggested that all 80 orthologous/paralogous gene pairs between B. rapa and A. thaliana, B. nigra and B. oleracea have experienced strong purifying selection. RNA-Seq data and qRT-PCR analyses showed that several BrPERK genes were expressed in different tissues, while some BrPERKs exhibited high expression levels only in buds. Furthermore, comparative transcriptome analyses from six male-sterile lines of B. rapa indicated that 7 BrPERK genes were downregulated in all six male-sterile lines. Meanwhile, the interaction networks of the BrPERK genes were constructed and 13 PERK coexpressed genes were identified, most of which were downregulated in the male sterile buds. CONCLUSION Combined with interaction networks, coexpression and qRT-PCR analyses, these results demonstrated that two BrPERK genes, Bra001723.1 and Bra037558.1 (the orthologs of AtPERK6 (AT3G18810)), were downregulated beginning in the meiosis II period of male sterile lines and involved in anther development. Overall, this comprehensive analysis of some BrPERK genes elucidated their roles in male sterility.
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Affiliation(s)
- Guohu Chen
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China. .,Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei, 230036, China. .,Wanjiang Vegetable Industrial Technology Institute, Maanshan, 238200, China.
| | - Jian Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China.,Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei, 230036, China
| | - Hao Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Chenggang Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China. .,Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei, 230036, China. .,Wanjiang Vegetable Industrial Technology Institute, Maanshan, 238200, China.
| | - Xiaoyan Tang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China.,Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei, 230036, China
| | - Jie Li
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Lei Zhang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Jianghua Song
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Jinfeng Hou
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Lingyun Yuan
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
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Miao L, Gao Y, Zhao K, Kong L, Yu S, Li R, Liu K, Yu X. Comparative analysis of basic helix-loop-helix gene family among Brassica oleracea, Brassica rapa, and Brassica napus. BMC Genomics 2020; 21:178. [PMID: 32093614 PMCID: PMC7041300 DOI: 10.1186/s12864-020-6572-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 02/10/2020] [Indexed: 01/24/2024] Open
Abstract
Background The basic helix–loop–helix (bHLH) is the second largest gene family in the plant, some members play important roles in pistil development and response to drought, waterlogging, cold stress and salt stress. The bHLH gene family has been identified in many species, except for Brassica oleracea and B. napus thus far. This study aims to identify the bHLH family members in B. oleracea, B. rapa and B. napus, and elucidate the expression, duplication, phylogeny and evolution characters of them. Result A total of 268 bHLH genes in B. oleracea, 440 genes in B. napus, and 251 genes in B. rapa, including 21 new bHLH members, have been identified. Subsequently, the analyses of the phylogenetic trees, conserved motifs and gene structures showed that the members in the same subfamily were highly conserved. Most Ka/Ks values of homologous gene were < 1, which indicated that these genes suffered from strong purifying selection for retention. The retention rates of BrabHLH and BolbHLH genes were 51.6 and 55.1%, respectively. The comparative expression patterns between B. rapa and B. napus showed that they had similar expression patterns in the root and contrasting patterns in the stems, leaves, and reproductive tissues. In addition, there were 41 and 30 differential expression bHLH genes under the treatments of ABA and JA, respectively, and the number of down regulation genes was significantly more than up regulation genes. Conclusion In the present study, we identified and performed the comparative genomics analysis of bHLH gene family among B. oleracea, B. rapa and B. napus, and also investigated their diversity. The expression patterns between B. rapa and B. napus shows that they have the similar expression pattern in the root and opposite patterns in the stems, leaves, and reproduction tissues. Further analysis demonstrated that some bHLH gene members may play crucial roles under the abiotic and biotic stress conditions. This is the first to report on the bHLH gene family analysis in B. oleracea and B. napus, which can offer useful information on the functional analysis of the bHLH gene in plants.
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Affiliation(s)
- Liming Miao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang, 310058, Hangzhou, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang, 310058, Hangzhou, China
| | - Yingying Gao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang, 310058, Hangzhou, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang, 310058, Hangzhou, China
| | - Kun Zhao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang, 310058, Hangzhou, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang, 310058, Hangzhou, China
| | - Lijun Kong
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang, 310058, Hangzhou, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang, 310058, Hangzhou, China
| | - Shubo Yu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang, 310058, Hangzhou, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang, 310058, Hangzhou, China
| | - Rongrong Li
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang, 310058, Hangzhou, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang, 310058, Hangzhou, China
| | - Kaiwen Liu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang, 310058, Hangzhou, China.,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang, 310058, Hangzhou, China
| | - Xiaolin Yu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Zhejiang, 310058, Hangzhou, China. .,Key Laboratory of Horticultural Plant Growth, Development, and Quality Improvement, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang, 310058, Hangzhou, China.
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10
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Zhang P, Wang H, Qin X, Chen K, Zhao J, Zhao Y, Yue B. Genome-wide identification, phylogeny and expression analysis of the PME and PMEI gene families in maize. Sci Rep 2019; 9:19918. [PMID: 31882640 PMCID: PMC6934449 DOI: 10.1038/s41598-019-56254-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 12/05/2019] [Indexed: 01/09/2023] Open
Abstract
Pectins, the major components of cell walls in plants, are synthesized and secreted to cell walls as highly methyl-esterified polymers and then demethyl-esterified by pectin methylesterases (PMEs). The PMEs are spatially regulated by pectin methylesterase inhibitors (PMEIs). In this study, 43 and 49 putative PME and PMEI genes were identified in maize, respectively. Gene structure and motif analysis revealed that members in the same paralogous pairs or in the same subgroup generally had common motif compositions and gene structure patterns, which indicates functional similarity between the closely related ZmPME/PMEI genes. Gene ontology annotation analysis showed that most of the ZmPME/PMEI genes are involved in cell wall modification and pectin catabolic process with molecular functions of pectinesterase or pectinesterase inhibitor activities. There are 35 ZmPME/PMEI genes expressed higher in anthers than in other tissues from the NimbleGen maize microarray data, and the semiq-RT-PCR assay revealed most of these ZmPME/PMEIs specially expressed in anthers and pollens, indicating they possibly had role in anther and pollen development. In addition, these ZmPME/PMEI genes were highly expressed in the fertile anthers, while lowly or no expressed in sterile anthers. This further indicated these genes might be involved in the development of anther and pollen.
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Affiliation(s)
- Panpan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiner Qin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kuan Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiuran Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yanxin Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Bing Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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11
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Ren A, Ahmed RI, Chen H, Han L, Sun J, Ding A, Guo Y, Kong Y. Genome-Wide Identification, Characterization and Expression Patterns of the Pectin Methylesterase Inhibitor Genes in Sorghum bicolor. Genes (Basel) 2019; 10:E755. [PMID: 31561536 PMCID: PMC6826626 DOI: 10.3390/genes10100755] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/21/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023] Open
Abstract
Cell walls are basically complex with dynamic structures that are being involved in several growth and developmental processes, as well as responses to environmental stresses and the defense mechanism. Pectin is secreted into the cell wall in a highly methylesterified form. It is able to perform function after the de-methylesterification by pectin methylesterase (PME). Whereas, the pectin methylesterase inhibitor (PMEI) plays a key role in plant cell wall modification through inhibiting the PME activity. It provides pectin with different levels of degree of methylesterification to affect the cell wall structures and properties. The PME activity was analyzed in six tissues of Sorghum bicolor, and found a high level in the leaf and leaf sheath. PMEI families have been identified in many plant species. Here, a total of 55 pectin methylesterase inhibitor genes (PMEIs) were identified from S. bicolor whole genome, a more detailed annotation of this crop plant as compared to the previous study. Chromosomal localization, gene structures and sequence characterization of the PMEI family were analyzed. Moreover, cis-acting elements analysis revealed that each PMEI gene was regulated by both internal and environmental factors. The expression patterns of each PMEI gene were also clustered according to expression pattern analyzed in 47 tissues under different developmental stages. Furthermore, some SbPMEIs were induced when treated with hormonal and abiotic stress. Taken together, these results laid a strong foundation for further study of the functions of SbPMEIs and pectin modification during plant growth and stress responses of cereal.
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Affiliation(s)
- Angyan Ren
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Rana Imtiaz Ahmed
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Ayub Agricultural Research Institute, Faisalabad 38850, Pakistan.
| | - Huanyu Chen
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Shijiazhuang 050021, China.
| | - Linhe Han
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Jinhao Sun
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Anming Ding
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Yongfeng Guo
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Yingzhen Kong
- College of Agronomy of Qing Dao Agricultural University, Qingdao 266108, China.
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The Multifaceted Role of Pectin Methylesterase Inhibitors (PMEIs). Int J Mol Sci 2018; 19:ijms19102878. [PMID: 30248977 PMCID: PMC6213510 DOI: 10.3390/ijms19102878] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 09/04/2018] [Accepted: 09/05/2018] [Indexed: 01/30/2023] Open
Abstract
Plant cell walls are complex and dynamic structures that play important roles in growth and development, as well as in response to stresses. Pectin is a major polysaccharide of cell walls rich in galacturonic acid (GalA). Homogalacturonan (HG) is considered the most abundant pectic polymer in plant cell walls and is partially methylesterified at the C6 atom of galacturonic acid. Its degree (and pattern) of methylation (DM) has been shown to affect biomechanical properties of the cell wall by making pectin susceptible for enzymatic de-polymerization and enabling gel formation. Pectin methylesterases (PMEs) catalyze the removal of methyl-groups from the HG backbone and their activity is modulated by a family of proteinaceous inhibitors known as pectin methylesterase inhibitors (PMEIs). As such, the interplay between PME and PMEI can be considered as a determinant of cell adhesion, cell wall porosity and elasticity, as well as a source of signaling molecules released upon cell wall stress. This review aims to highlight recent updates in our understanding of the PMEI gene family, their regulation and structure, interaction with PMEs, as well as their function in response to stress and during development.
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