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de Almeida CP, Barbosa RR, Ferraz CG, de Castro RD, Ribeiro PR. Genome-wide identification of the GDSL-type esterase/lipase protein (GELP) gene family in Ricinus communis and its transcriptional regulation during germination and seedling establishment under different abiotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108939. [PMID: 39029309 DOI: 10.1016/j.plaphy.2024.108939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 07/10/2024] [Accepted: 07/13/2024] [Indexed: 07/21/2024]
Abstract
GDSL-type esterase/lipase protein (GELP) genes are crucial in the specialized lipid metabolism, in the responses to abiotic stresses, and in the regulation of plant homeostasis. R. communis is an important oilseed crop species that can sustain growth and productivity when exposed to harsh environmental conditions. Herein, we raised the question of whether the GELP gene family could be involved in the acquisition of R. communis tolerance to abiotic stresses during seed germination and seedling establishment. Thus, we used bioinformatics and transcriptomics to characterize the R. communis GELP gene family. R. communis genome possesses 96 GELP genes that were characterized by extensive bioinformatics, including phylogenetic analysis, subcellular localization, exon-intron distribution, the analysis of regulatory cis-elements, tandem duplication, and physicochemical properties. Transcriptomics indicated that numerous RcGELP genes are readily responsive to high-temperature and salt stresses and might be potential candidates for genome editing techniques to develop abiotic stress-tolerant crops.
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Affiliation(s)
- Catherine P de Almeida
- Metabolomics Research Group, Instituto de Química, Universidade Federal da Bahia, Rua Barão de Jeremoabo s/n, 40170-115, Salvador, Brazil; Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal da Bahia, Rua Barão de Jeremoabo s/n, 40170-115, Salvador, Brazil
| | - Rhaissa R Barbosa
- Metabolomics Research Group, Instituto de Química, Universidade Federal da Bahia, Rua Barão de Jeremoabo s/n, 40170-115, Salvador, Brazil; Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal da Bahia, Rua Barão de Jeremoabo s/n, 40170-115, Salvador, Brazil
| | - Caline G Ferraz
- Metabolomics Research Group, Instituto de Química, Universidade Federal da Bahia, Rua Barão de Jeremoabo s/n, 40170-115, Salvador, Brazil; Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal da Bahia, Rua Barão de Jeremoabo s/n, 40170-115, Salvador, Brazil
| | - Renato D de Castro
- Metabolomics Research Group, Instituto de Química, Universidade Federal da Bahia, Rua Barão de Jeremoabo s/n, 40170-115, Salvador, Brazil
| | - Paulo R Ribeiro
- Metabolomics Research Group, Instituto de Química, Universidade Federal da Bahia, Rua Barão de Jeremoabo s/n, 40170-115, Salvador, Brazil; Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal da Bahia, Rua Barão de Jeremoabo s/n, 40170-115, Salvador, Brazil.
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Duan L, Wang F, Shen H, Xie S, Chen X, Xie Q, Li R, Cao A, Li H. Identification, evolution, and expression of GDSL-type Esterase/Lipase (GELP) gene family in three cotton species: a bioinformatic analysis. BMC Genomics 2023; 24:795. [PMID: 38129780 PMCID: PMC10734139 DOI: 10.1186/s12864-023-09717-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/04/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND GDSL esterase/lipases (GELPs) play important roles in plant growth, development, and response to biotic and abiotic stresses. Presently, an extensive and in-depth analysis of GELP family genes in cotton is still not clear enough, which greatly limits the further understanding of cotton GELP function and regulatory mechanism. RESULTS A total of 389 GELP family genes were identified in three cotton species of Gossypium hirsutum (193), G. arboreum (97), and G. raimondii (99). These GELPs could be classified into three groups and eight subgroups, with the GELPs in same group to have similar gene structures and conserved motifs. Evolutionary event analysis showed that the GELP family genes tend to be diversified at the spatial dimension and certain conservative at the time dimension, with a trend of potential continuous expansion in the future. The orthologous or paralogous GELPs among different genomes/subgenomes indicated the inheritance from genome-wide duplication during polyploidization, and the paralogous GELPs were derived from chromosomal segment duplication or tandem replication. GELP genes in the A/D subgenome underwent at least three large-scale replication events in the evolutionary process during the period of 0.6-3.2 MYA, with two large-scale evolutionary events between 0.6-1.8 MYA that were associated with tetraploidization, and the large-scale duplication between 2.6-9.1 MYA that occurred during diploidization. The cotton GELPs indicated diverse expression patterns in tissue development, ovule and fiber growth, and in response to biotic and abiotic stresses, combining the existing cis-elements in the promoter regions, suggesting the GELPs involvements of functions to be diversification and of the mechanisms to be a hormone-mediated manner. CONCLUSIONS Our results provide a systematic and comprehensive understanding the function and regulatory mechanism of cotton GELP family, and offer an effective reference for in-depth genetic improvement utilization of cotton GELPs.
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Affiliation(s)
- Lisheng Duan
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Fei Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Haitao Shen
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Shuangquan Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Xifeng Chen
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Quanliang Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Rong Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Aiping Cao
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Hongbin Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
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Ding Y, Xing L, Xu J, Jiang T, Tang X, Wang Y, Huang S, Hao W, Zhou X, Zhang Y, Xie CG. Genome-wide exploration of the GDSL-type esterase/lipase gene family in rapeseed reveals several BnGELP proteins active during early seedling development. FRONTIERS IN PLANT SCIENCE 2023; 14:1139972. [PMID: 37008509 PMCID: PMC10050346 DOI: 10.3389/fpls.2023.1139972] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
The Gly-Asp-Ser-Leu (GDSL)-type esterase/lipase proteins (GELP) are one of the most important families of lipolytic enzymes and play prominent roles in seed germination and early seedling establishment through mobilizing the lipids stored in seeds. However, there are no comprehensive studies systematically investigating the GELP gene family in Brassica napus (BnGELP), and their biological significance to these physiological processes are far from understood. In the present study, a total of 240 BnGELP genes were identified in B. napus cultivar "Zhongshuang 11" (ZS11), which is nearly 2.3-fold more GELP genes than in Arabidopsis thaliana. The BnGELP genes clustered into 5 clades based on phylogenetic analysis. Ten BnGELPs were identified through zymogram analysis of esterase activity followed by mass spectrometry, among which five clustered into the clade 5. Gene and protein architecture, gene expression, and cis-element analyses of BnGELP genes in clade 5 suggested that they may play different roles in different tissues and in response to different abiotic stresses. BnGELP99 and BnGELP159 were slightly induced by cold, which may be attributed to two low-temperature responsive cis-acting regulatory elements present in their promoters. An increased activity of esterase isozymes by cold was also observed, which may reflect other cold inducible esterases/lipases in addition to the ten identified BnGELPs. This study provides a systemic view of the BnGELP gene family and offers a strategy for researchers to identify candidate esterase/lipase genes responsible for lipid mobilization during seed germination and early seedling establishment.
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Affiliation(s)
- Yahui Ding
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Liwen Xing
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Jiamin Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Teng Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xiuhua Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Yaxuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Shuhua Huang
- Hybrid Rapeseed Research Centre of Shaanxi Province, Yangling, China
| | - Wenfang Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xiaona Zhou
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Yanfeng Zhang
- Hybrid Rapeseed Research Centre of Shaanxi Province, Yangling, China
| | - Chang Gen Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
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Wang J, Zhao H, Qu Y, Yang P, Huang J. The binding pocket properties were fundamental to functional diversification of the GDSL-type esterases/lipases gene family in cotton. FRONTIERS IN PLANT SCIENCE 2023; 13:1099673. [PMID: 36743561 PMCID: PMC9889996 DOI: 10.3389/fpls.2022.1099673] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Cotton is one of the most important crops in the world. GDSL-type esterases/lipases (GELPs) are widely present in all kingdoms and play an essential role in regulating plant growth, development, and responses to abiotic and biotic stresses. However, the molecular mechanisms underlying this functional diversity remain unclear. Here, based on the identification of the GELP gene family, we applied genetic evolution and molecular simulation techniques to explore molecular mechanisms in cotton species. A total of 1502 GELP genes were identified in 10 cotton species. Segmental duplication and differences in evolutionary rates are the leading causes of the increase in the number and diversity of GELP genes during evolution for ecological adaptation. Structural analysis revealed that the GELP family has high structural diversity. Moreover, molecular simulation studies have demonstrated significant differences in the properties of the binding pockets among cotton GELPs. In the process of adapting to the environment, GELPs not only have segmental duplication but also have different evolutionary rates, resulting in gene diversity. This diversity leads to significant differences in the 3D structure and binding pocket properties and, finally, to functional diversity. These findings provide a reference for further functional analyses of plant GELPs.
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Affiliation(s)
- Jianshe Wang
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, Henan, China
| | - Haiyan Zhao
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, Henan, China
| | - Yunfang Qu
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Peng Yang
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Jinling Huang
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China
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Xu Q, He H, He B, Li T, Liu Y, Zhu S, Zhang G. Nitrogen Allocation Tradeoffs Within-Leaf between Photosynthesis and High-Temperature Adaptation among Different Varieties of Pecan ( Carya illinoinensis [Wangenh.] K. Koch). PLANTS (BASEL, SWITZERLAND) 2022; 11:2828. [PMID: 36365281 PMCID: PMC9657520 DOI: 10.3390/plants11212828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/07/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Interpreting leaf nitrogen (N) allocation is essential to understanding leaf N cycling and the economy of plant adaptation to environmental fluctuations, yet the way these mechanisms shift in various varieties under high temperatures remains unclear. Here, eight varieties of pecan (Carya illinoinensis [Wangenh.] K. Koch), Mahan, YLC10, YLC12, YLC13, YLC29, YLC35, YLJ042, and YLJ5, were compared to investigate the effects of high temperatures on leaf N, photosynthesis, N allocation, osmolytes, and lipid peroxidation and their interrelations. Results showed that YLC35 had a higher maximum net photosynthetic rate (Pmax) and photosynthetic N-use efficiency (PNUE), while YLC29 had higher N content per area (Na) and lower PNUE. YLC35, with lower malondialdehyde (MDA), had the highest proportions of N allocation in rubisco (Pr), bioenergetics (Pb), and photosynthetic apparatus (Pp), while YLC29, with the highest MDA, had the lowest Pr, Pb, and Pp, implying more leaf N allocated to the photosynthetic apparatus for boosting PNUE or to non-photosynthetic apparatus for alleviating damage. Structural equation modeling (SEM) demonstrated that N allocation was affected negatively by leaf N and positively by photosynthesis, and their combination indirectly affected lipid peroxidation through the reverse regulation of N allocation. Our results indicate that different varieties of pecan employ different resource-utilization strategies and growth-defense tradeoffs for homeostatic balance under high temperatures.
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