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Chen R, Gu G, Zhang B, Du C, Lin X, Cai W, Zheng Y, Li T, Wang R, Xie X. Genome-wide identification and expression analysis of the U-box E3 ubiquitin ligase gene family related to bacterial wilt resistance in tobacco ( Nicotiana tabacum L.) and eggplant ( Solanum melongena L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1425651. [PMID: 39139726 PMCID: PMC11319268 DOI: 10.3389/fpls.2024.1425651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/12/2024] [Indexed: 08/15/2024]
Abstract
The E3 enzyme in the UPS pathway is a crucial factor for inhibiting substrate specificity. In Solanaceae, the U-box E3 ubiquitin ligase has a complex relationship with plant growth and development, and plays a pivotal role in responding to various biotic and abiotic stresses. The analysis of the U-box gene family in Solanaceae and its expression profile under different stresses holds significant implications. A total of 116 tobacco NtU-boxs and 56 eggplant SmU-boxs were identified based on their respective genome sequences. Phylogenetic analysis of U-box genes in tobacco, eggplant, tomato, Arabidopsis, pepper, and potato revealed five distinct subgroups (I-V). Gene structure and protein motifs analysis found a high degree of conservation in both exon/intron organization and protein motifs among tobacco and eggplant U-box genes especially the members within the same subfamily. A total of 15 pairs of segmental duplication and 1 gene pair of tandem duplication were identified in tobacco based on the analysis of gene duplication events, while 10 pairs of segmental duplication in eggplant. It is speculated that segmental duplication events are the primary driver for the expansion of the U-box gene family in both tobacco and eggplant. The promoters of NtU-box and SmU-box genes contained cis-regulatory elements associated with cellular development, phytohormones, environment stress, and photoresponsive elements. Transcriptomic data analysis shows that the expression levels of the tobacco and eggplant U-box genes in different tissues and various abiotic stress conditions. Using cultivar Hongda of tobacco and cultivar Yanzhi of eggplant as materials, qRT-PCR analysis has revealed that 15 selected NtU-box genes and 8 SmU-box may play important roles in response to pathogen Ras invasion both in tobacco and eggplant.
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Affiliation(s)
- Rui Chen
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Gang Gu
- Institute of Tobacco Science, Fujian Provincial Tobacco Company, Fuzhou, China
| | - Binghui Zhang
- Institute of Tobacco Science, Fujian Provincial Tobacco Company, Fuzhou, China
| | | | | | | | - Yan Zheng
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Tong Li
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Ruiqi Wang
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Xiaofang Xie
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture & Forestry University, Fuzhou, China
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Zhou X, Li Y, Wang J, Zhao Y, Wang H, Han Y, Lin X. Genome-wide identification of U-box gene family and expression analysis in response to saline-alkali stress in foxtail millet ( Setaria italica L. Beauv). Front Genet 2024; 15:1356807. [PMID: 38435060 PMCID: PMC10904469 DOI: 10.3389/fgene.2024.1356807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 01/22/2024] [Indexed: 03/05/2024] Open
Abstract
E3 ubiquitin ligases are central modifiers of plant signaling pathways that regulate protein function, localization, degradation, and other biological processes by linking ubiquitin to target proteins. E3 ubiquitin ligases include proteins with the U-box domain. However, there has been no report about the foxtail millet (Setaria italica L. Beauv) U-box gene family (SiPUB) to date. To explore the function of SiPUBs, this study performed genome-wide identification of SiPUBs and expression analysis of them in response to saline-alkali stress. A total of 70 SiPUBs were identified, which were unevenly distributed on eight chromosomes. Phylogenetic and conserved motif analysis demonstrated that SiPUBs could be clustered into six subfamilies (I-VI), and most SiPUBs were closely related to the homologues in rice. Twenty-eight types of cis-acting elements were identified in SiPUBs, most of which contained many light-responsive elements and plant hormone-responsive elements. Foxtail millet had 19, 78, 85, 18, and 89 collinear U-box gene pairs with Arabidopsis, rice, sorghum, tomato, and maize, respectively. Tissue specific expression analysis revealed great variations in SiPUB expression among different tissues, and most SiPUBs were relatively highly expressed in roots, indicating that SiPUBs may play important roles in root development or other growth and development processes of foxtail millet. Furthermore, the responses of 15 SiPUBs to saline-alkali stress were detected by qRT-PCR. The results showed that saline-alkali stress led to significantly differential expression of these 15 SiPUBs, and SiPUB20/48/70 may play important roles in the response mechanism against saline-alkali stress. Overall, this study provides important information for further exploration of the biological function of U-box genes.
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Affiliation(s)
- Xiaoke Zhou
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yun Li
- Research Center of Rural Vitalization, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jian Wang
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yuxue Zhao
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Huimin Wang
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yucui Han
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Xiaohu Lin
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
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Shao Y, Mu D, Zhou Y, Liu X, Huang X, Wilson IW, Qi Y, Lu Y, Zhu L, Zhang Y, Qiu D, Tang Q. Genome-Wide Mining of CULLIN E3 Ubiquitin Ligase Genes from Uncaria rhynchophylla. PLANTS (BASEL, SWITZERLAND) 2024; 13:532. [PMID: 38498523 PMCID: PMC10891735 DOI: 10.3390/plants13040532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/10/2024] [Accepted: 02/13/2024] [Indexed: 03/20/2024]
Abstract
CULLIN (CUL) protein is a subtype of E3 ubiquitin ligase that is involved in a variety of biological processes and responses to stress in plants. In Uncaria rhynchophylla, the CUL gene family has not been identified and its role in plant development, stress response and secondary metabolite synthesis has not been studied. In this study, 12 UrCUL gene members all contained the typical N-terminal domain and C-terminal domain identified from the U. rhynchophylla genome and were classified into four subfamilies based on the phylogenetic relationship with CULs in Arabidopsis thaliana. They were unevenly distributed on eight chromosomes but had a similar structural composition in the same subfamily, indicating that they were relatively conserved and potentially had similar gene functions. An interspecific and intraspecific collinearity analysis showed that fragment duplication played an important role in the evolution of the CUL gene family. The analysis of the cis-acting elements suggests that the UrCULs may play an important role in various biological processes, including the abscisic acid (ABA) response. To investigate this hypothesis, we treated the roots of U. rhynchophylla tissue-cultured seedlings with ABA. The expression pattern analysis showed that all the UrCUL genes were widely expressed in roots with various expression patterns. The co-expression association analysis of the UrCULs and key enzyme genes in the terpenoid indole alkaloid (TIA) synthesis pathway revealed the complex expression patterns of 12 UrCUL genes and some key TIA enzyme genes, especially UrCUL1, UrCUL1-likeA, UrCUL2-likeA and UrCUL2-likeB, which might be involved in the biosynthesis of TIAs. The results showed that the UrCULs were involved in the response to ABA hormones, providing important information for elucidating the function of UrCULs in U. rhynchophylla. The mining of UrCULs in the whole genome of U. rhynchophylla provided new information for understanding the CUL gene and its function in plant secondary metabolites, growth and development.
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Affiliation(s)
- Yingying Shao
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (D.M.); (Y.Z.); (X.L.); (Y.L.); (L.Z.); (Y.Z.)
| | - Detian Mu
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (D.M.); (Y.Z.); (X.L.); (Y.L.); (L.Z.); (Y.Z.)
| | - Yu Zhou
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (D.M.); (Y.Z.); (X.L.); (Y.L.); (L.Z.); (Y.Z.)
| | - Xinghui Liu
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (D.M.); (Y.Z.); (X.L.); (Y.L.); (L.Z.); (Y.Z.)
| | - Xueshuang Huang
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua 410208, China;
| | - Iain W. Wilson
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Yuxin Qi
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua 410208, China;
| | - Ying Lu
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (D.M.); (Y.Z.); (X.L.); (Y.L.); (L.Z.); (Y.Z.)
| | - Lina Zhu
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (D.M.); (Y.Z.); (X.L.); (Y.L.); (L.Z.); (Y.Z.)
| | - Yao Zhang
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (D.M.); (Y.Z.); (X.L.); (Y.L.); (L.Z.); (Y.Z.)
| | - Deyou Qiu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
| | - Qi Tang
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (D.M.); (Y.Z.); (X.L.); (Y.L.); (L.Z.); (Y.Z.)
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Liu Y, Li C, Qin A, Deng W, Chen R, Yu H, Wang Y, Song J, Zeng L. Genome-wide identification and transcriptome profiling expression analysis of the U-box E3 ubiquitin ligase gene family related to abiotic stress in maize (Zea mays L.). BMC Genomics 2024; 25:132. [PMID: 38302871 PMCID: PMC10832145 DOI: 10.1186/s12864-024-10040-8] [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: 09/15/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND The U-box gene family encodes E3 ubiquitin ligases involved in plant hormone signaling pathways and abiotic stress responses. However, there has yet to be a comprehensive analysis of the U-box gene family in maize (Zea mays L.) and its responses to abiotic stress. RESULTS In this study, 85 U-box family proteins were identified in maize and were classified into four subfamilies based on phylogenetic analysis. In addition to the conserved U-box domain, we identified additional functional domains, including Pkinase, ARM, KAP and Tyr domains, by analyzing the conserved motifs and gene structures. Chromosomal localization and collinearity analysis revealed that gene duplications may have contributed to the expansion and evolution of the U-box gene family. GO annotation and KEGG pathway enrichment analysis identified a total of 105 GO terms and 21 KEGG pathways that were notably enriched, including ubiquitin-protein transferase activity, ubiquitin conjugating enzyme activity and ubiquitin-mediated proteolysis pathway. Tissue expression analysis showed that some ZmPUB genes were specifically expressed in certain tissues and that this could be due to their functions. In addition, RNA-seq data for maize seedlings under salt stress revealed 16 stress-inducible plant U-box genes, of which 10 genes were upregulated and 6 genes were downregulated. The qRT-PCR results for genes responding to abiotic stress were consistent with the transcriptome analysis. Among them, ZmPUB13, ZmPUB18, ZmPUB19 and ZmPUB68 were upregulated under all three abiotic stress conditions. Subcellular localization analysis showed that ZmPUB19 and ZmPUB59 were located in the nucleus. CONCLUSIONS Overall, our study provides a comprehensive analysis of the U-box gene family in maize and its responses to abiotic stress, suggesting that U-box genes play an important role in the stress response and providing insights into the regulatory mechanisms underlying the response to abiotic stress in maize.
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Affiliation(s)
- Yongle Liu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
- College of Life Sciences, Nanjing University, Nanjing, 210095, People's Republic of China
| | - Changgen Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Aokang Qin
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Wenli Deng
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Rongrong Chen
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Hongyang Yu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Yihua Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Jianbo Song
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
- Jiangxi Provincial Key Laboratory of Conservation Biology, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
| | - Liming Zeng
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
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Tang X, Sun F, Zhang N, Rana BB, Kharel R, Luo P, Si H. RNA-seq provides insights into potato deubiquitinase responses to drought stress in seedling stage. FRONTIERS IN PLANT SCIENCE 2023; 14:1268448. [PMID: 37780518 PMCID: PMC10539648 DOI: 10.3389/fpls.2023.1268448] [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: 07/28/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023]
Abstract
Ubiquitination is a specific protein degradation and reversible post-translational modification process that can be reversed by deubiquitinase (DUBs). DUBs can hydrolyze and release ubiquitin in the substrate protein so that the substrate can avoid degradation or change its activity, and it has an impact on plant growth and development, cell cycle, abiotic stress response, and other biological processes. Transcript sequences of potato varieties "DM1-3", "Atlantic" and "Cooperation-88" downloaded from Potato Genome Resources were used for genome-wide identification of the DUB gene family using Hidden Markov Models and verified in the NCBI CD-Search tool. The characteristics of DUB genes from different potato varieties were analyzed including subcellular localization, gene structural motifs, phylogenetic tree, and sequence homology. Polyethylene glycol 6000 (PEG6000) induced drought stress transcriptome analysis was performed on the "Atlantic", and differentially expressed genes were screened, with emphasis on the characterization of deubiquitinase. DUB genes have a complex gene structure, often with a large number of exons and alternative splicing. Their promoters contain abundant abiotic stress-responsive elements, such as 425 MYC, 325 ABRE, and 320 MYB. There are also a large number of orthologous genes in the DUBs of the three potato varieties, and these genes are often clustered in similar regions on the genome. We performed transcriptome sequencing of the potato under PEG-induced drought stress and analyzed it for the first time using the Atlantic as a reference genome. We identified a total of 6067 down-regulated differentially expressed genes (DEGs) and 4950 up-regulated DEGs under PEG-induced drought stress. We screened the expression of DUBs and observed that 120 DUBs were up-regulated where most of them functioned in the nucleus, and the interacting proteins of DUBs were also localized in the nucleus. We have comprehensively identified and analyzed potato DUBs, and the accurately aligned transcriptome data which will further deepen the understanding of DUBs involved in the regulation of osmotic stress.
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Affiliation(s)
- Xun Tang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fujun Sun
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Birendra Bahadur Rana
- Nepal Agricultural Research Council, National Potato Research Program, Lalitpur, Nepal
| | - Raju Kharel
- Department of Genetics and Plant Breeding, Agricultural and Forestry University, Chitwan, Nepal
| | - Pan Luo
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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Zizelski Valenci G, Raveh D, Bar-Zvi D. The activity of the stress modulated Arabidopsis ubiquitin ligases PUB46 and PUB48 is partially redundant. PLANT SIGNALING & BEHAVIOR 2022; 17:2072111. [PMID: 35546519 PMCID: PMC9116408 DOI: 10.1080/15592324.2022.2072111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
The Arabidopsis ubiquitin ligases PUB46, PUB47 and PUB48 are encoded by paralogus genes. Single gene pub46 and pub48 mutants display increased drought sensitivity compared to wild type (WT) suggesting that each has specific biological activity. The high sequence homology between PUB46 and PUB48 activity suggested that they may also share some aspects of their activity. Unfortunately, the close proximity of the PUB46 and PUB48 gene loci precludes obtaining a double mutant required to study if they are partially redundant by crossing the available single mutants. We thus applied microRNA technology to reduce the activity of all three gene products of the PUB46-48 subfamily by constructing an artificial microRNA (aMIR) targeted to this subfamily. Expressing aMIR46-48 in WT plants resulted in increased drought-sensitivity, a phenotype resembling that of each of the single pub46 and pub48 mutants, and enhanced sensitivity to methyl viologen, similar to that observed for the pub46 mutant. The WT plants expressing aMIR46-48 plants also revealed reduced inhibition by ABA at seed germination, a phenotype not evident in the single mutants. Expressing aMIR46-48 in pub46 and pub48 mutants further enhanced the drought sensitivity of each parental single mutant and of WT expressing aMIR46-48. These results suggest that the biological activities of PUB46 and PUB48 in abiotic stress response are partially redundant.
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Affiliation(s)
- Gal Zizelski Valenci
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Dina Raveh
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Dudy Bar-Zvi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Black Center for Bioenergetics in Life Sciences, Ben-Gurion University of the NegevThe Doris and Bertie I. , Beer-Sheva, Israel
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Comprehensive Analysis of StSRO Gene Family and Its Expression in Response to Different Abiotic Stresses in Potato. Int J Mol Sci 2022; 23:ijms232113518. [DOI: 10.3390/ijms232113518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/19/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022] Open
Abstract
As a highly conserved family of plant-specific proteins, SIMILAR-TO-RCD-ONE (SROs) play an essential role in plant growth, development and response to abiotic stresses. In this study, six StSRO genes were identified by searching the PARP, RST and WWE domains based on the genome-wide data of potato database DM v6.1, and they were named StSRO1–6 according to their locations on chromosomes. StSRO genes were comprehensively analyzed using bioinformatics methods. The results showed that six StSRO genes were irregularly distributed on five chromosomes. Phylogenetic analysis showed that 30 SRO genes of four species were distributed in three groups, while StSRO genes were distributed in groups II and III. The promoter sequence of StSRO genes contained many cis-acting elements related to hormones and stress responses. In addition, the expression level of StSRO genes in different tissues of doubled monoploid (DM) potato, as well as under salt, drought stresses and hormone treatments, was analyzed by RNA-seq data from the online database and quantitative real-time polymerase chain reaction (qRT-PCR) analysis. Furthermore, the expression level of StSRO genes was analyzed by transcriptome analysis under mild, moderate and severe salt stress. It was concluded that StSRO genes could respond to different abiotic conditions, but their expression level was significantly different. This study lays a foundation for further studies on the biological functions of the StSRO gene family.
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Liu H, Wang Q, Wang J, Liu Y, Renzeng W, Zhao G, Niu K. Key factors for differential drought tolerance in two contrasting wild materials of Artemisia wellbyi identified using comparative transcriptomics. BMC PLANT BIOLOGY 2022; 22:445. [PMID: 36114467 PMCID: PMC9482295 DOI: 10.1186/s12870-022-03830-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Drought is a significant condition that restricts vegetation growth on the Tibetan Plateau. Artemisia wellbyi is a unique semi-shrub-like herb in the family Compositae, which distributed in northern and northwest of Tibetan Plateau. It is a dominant species in the community that can well adapt to virous environment stress, such as drought and low temperature. Therefore, A. wellbyi. has a potential ecological value for soil and water conservation of drought areas. Understanding the molecular mechanisms of A. wellbyi. that defense drought stress can acquire the key genes for drought resistance breeding of A. wellbyi. and provide a theoretical basis for vegetation restoration of desertification area. However, they remain unclear. Thus, our study compared the transcriptomic characteristics of drought-tolerant "11" and drought-sensitive "6" material of A. wellbyi under drought stress. RESULTS A total of 4875 upregulated and 4381 downregulated differentially expressed genes (DEGs) were induced by drought in the tolerant material; however, only 1931 upregulated and 4174 downregulated DEGs were induced by drought in the sensitive material. The photosynthesis and transcriptional regulation differed significantly with respect to the DEGs number and expression level. We found that CDPKs (calmodulin-like domain protein kinases), SOS3 (salt overly sensitive3), MAPKs (mitogen-activated protein kinase cascades), RLKs (receptor like kinase), and LRR-RLKs (repeat leucine-rich receptor kinase) were firstly involved in response to drought stress in drought tolerant A. wellbyi. Positive regulation of genes associated with the metabolism of ABA (abscisic acid), ET (ethylene), and IAA (indole acetic acid) could play a crucial role in the interaction with other transcriptional regulatory factors, such as MYBs (v-myb avian myeloblastosis viral oncogene homolog), AP2/EREBPs (APETALA2/ethylene-responsive element binding protein family), WRKYs, and bHLHs (basic helix-loop-helix family members) and receptor kinases, and regulate downstream genes for defense against drought stress. In addition, HSP70 (heat shock protein70) and MYB73 were considered as the hub genes because of their strong association with other DEGs. CONCLUSIONS Positive transcriptional regulation and negative regulation of photosynthesis could be associated with better growth performance under drought stress in the drought-tolerant material. In addition, the degradation of sucrose and starch in the tolerant A. wellbyi to alleviate osmotic stress and balance excess ROS. These results highlight the candidate genes that are involved in enhancing the performance of drought-tolerant A. wellbyi and provide a theoretical basis for improving the performance of drought-resistant A. wellbyi.
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Affiliation(s)
- Huan Liu
- Key Laboratory of Grassland Ecosystems, College of Grassland Science, Ministry of Education, Gansu Agricultural University, Lanzhou, 730070 China
| | - Qiyu Wang
- Key Laboratory of Grassland Ecosystems, College of Grassland Science, Ministry of Education, Gansu Agricultural University, Lanzhou, 730070 China
| | - Jinglong Wang
- Tibet Grassland Science Research Institute, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850000 China
| | - Yunfei Liu
- Tibet Grassland Science Research Institute, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850000 China
| | - Wangdui Renzeng
- Tibet Grassland Science Research Institute, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850000 China
| | - Guiqin Zhao
- Key Laboratory of Grassland Ecosystems, College of Grassland Science, Ministry of Education, Gansu Agricultural University, Lanzhou, 730070 China
| | - Kuiju Niu
- Key Laboratory of Grassland Ecosystems, College of Grassland Science, Ministry of Education, Gansu Agricultural University, Lanzhou, 730070 China
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Fang Y, Du Q, Yang Q, Jiang J, Hou X, Yang Z, Zhao D, Li X, Xie X. Identification, characterization, and expression profiling of the putative U-box E3 ubiquitin ligase gene family in Sorghum bicolor. Front Microbiol 2022; 13:942302. [PMID: 36187972 PMCID: PMC9520534 DOI: 10.3389/fmicb.2022.942302] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022] Open
Abstract
The U-box family is one of the main E3 ubiquitin ligase families in plants. The U-box family has been characterized in several species. However, genome-wide gene identification and expression profiling of the U-box family in response to abiotic stress in Sorghum bicolor remain unclear. In this study, we broadly identified 68 U-box genes in the sorghum genome, including 2 CHIP genes, and 1 typical UFD2 (Ub fusion degradation 2) gene. The U-box gene family was divided into eight subclasses based on homology and conserved domain characteristics. Evolutionary analysis identified 14, 66, and 82 U-box collinear gene pairs in sorghum compared with arabidopsis, rice, and maize, respectively, and a unique tandem repeat pair (SbPUB26/SbPUB27) is present in the sorghum genome. Gene Ontology (GO) enrichment analysis showed that U-box proteins were mainly related to ubiquitination and modification, and various stress responses. Comprehensive analysis of promoters, expression profiling, and gene co-regulation networks also revealed that many sorghum U-box genes may be correlated with multiple stress responses. In summary, our results showed that sorghum contains 68 U-box genes, which may be involved in multiple abiotic stress responses. The findings will support future gene functional studies related to ubiquitination in sorghum.
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Affiliation(s)
- Yuanpeng Fang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Qiaoli Du
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Qian Yang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Junmei Jiang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Xiaolong Hou
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Zaifu Yang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Degang Zhao
- College of Life Sciences, Ministry of Education, Institute of Agricultural Bioengineering, Key Laboratory of Mountain Plant Resources Protection and Germplasm Innovation, Guizhou University, Guiyang, China
- Guizhou Academy of Agricultural Sciences, Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture, Guizhou Institute of Biotechnology, Guiyang, China
| | - Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Xin Xie
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Academy of Agricultural Sciences, Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture, Guizhou Institute of Biotechnology, Guiyang, China
- *Correspondence: Xin Xie,
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Zhou J, Qi A, Wang B, Zhang X, Dong Q, Liu J. Integrated Analyses of Transcriptome and Chlorophyll Fluorescence Characteristics Reveal the Mechanism Underlying Saline-Alkali Stress Tolerance in Kosteletzkya pentacarpos. FRONTIERS IN PLANT SCIENCE 2022; 13:865572. [PMID: 35599866 PMCID: PMC9122486 DOI: 10.3389/fpls.2022.865572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
In recent years, soil salinization has become increasingly severe, and the ecological functions of saline-alkali soils have deteriorated because of the lack of plants. Therefore, understanding the tolerance mechanisms of saline-alkali-tolerant plants has become crucial to restore the ecological functions of saline-alkali soils. In this study, we evaluated the molecular mechanism underlying the tolerance of Kosteletzkya pentacarpos L. (seashore mallow) seedlings treated with 0.05 or 0.5% saline-alkali solution (NaCl: NaHCO3 = 4:1 mass ratio) for 1 and 7 days. We identified the key genes involved in tolerance to saline-alkali stress using orthogonal partial least squares regression analysis (OPLS-RA) based on both chlorophyll fluorescence indexes and stress-responsive genes using transcriptome analysis, and, finally, validated their expression using qRT-PCR. We observed minor changes in the maximum photochemical efficiency of the stressed seedlings, whose photosynthetic performance remained stable. Moreover, compared to the control, other indicators varied more evidently on day 7 of 0.5% saline-alkali treatment, but no variations were observed in other treatments. Transcriptome analysis revealed a total of 54,601 full-length sequences, with predominantly downregulated differentially expressed gene (DEG) expression. In the high concentration treatment, the expression of 89.11 and 88.38% of DEGs was downregulated on days 1 and 7, respectively. Furthermore, nine key genes, including KpAGO4, KpLARP1C, and KpPUB33, were involved in negative regulatory pathways, such as siRNA-mediated DNA methylation, inhibition of 5'-terminal oligopyrimidine mRNA translation, ubiquitin/proteasome degradation, and other pathways, including programmed cell death. Finally, quantitative analysis suggested that the expression of key genes was essentially downregulated. Thus, these genes can be used in plant molecular breeding in the future to generate efficient saline-alkali-tolerant plant germplasm resources to improve the ecological functions of saline-alkali landscapes.
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Affiliation(s)
- Jian Zhou
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Center of Horticulture Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Anguo Qi
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Center of Horticulture Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Baoquan Wang
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Center of Horticulture Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Xiaojing Zhang
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
| | - Qidi Dong
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
| | - Jinxiu Liu
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
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11
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Singh AK, Gupta KJ, Singla-Pareek SL, Foyer CH, Pareek A. Raising crops for dry and saline lands: Challenges and the way forward. PHYSIOLOGIA PLANTARUM 2022; 174:e13730. [PMID: 35762125 DOI: 10.1111/ppl.13730] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Anil Kumar Singh
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, Delhi, India
| | | | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, Delhi, India
| | - Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
- National Agri-Food Biotechnology Institute, Sahibzada Ajit Singh Nagar, Punjab, India
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