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Antonietta M, Martinez D, Guiamet JJ. Delayed senescence and crop performance under stress: always a functional couple? JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4244-4257. [PMID: 38635775 DOI: 10.1093/jxb/erae174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/17/2024] [Indexed: 04/20/2024]
Abstract
Exposure to abiotic stresses accelerates leaf senescence in most crop plant species, thereby reducing photosynthesis and other assimilatory processes. In some cases, genotypes with delayed leaf senescence (i.e. 'stay-green') show stress resistance, particularly in cases of water deficit, and this has led to the proposal that senescence delay improves crop performance under some abiotic stresses. In this review, we summarize the evidence for increased resistance to abiotic stress, mostly water deficit, in genotypes with delayed senescence, and specifically focus on the physiological mechanisms and agronomic conditions under which the stay-green trait may ameliorate grain yield under stress.
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Affiliation(s)
| | - Dana Martinez
- Instituto de Fisiología Vegetal, CONICET-UNLP, Argentina
| | - Juan J Guiamet
- Instituto de Fisiología Vegetal, CONICET-UNLP, Argentina
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Eshaghi M, Rashidi-Monfared S. Co-regulatory network analysis of the main secondary metabolite (SM) biosynthesis in Crocus sativus L. Sci Rep 2024; 14:15839. [PMID: 38982154 PMCID: PMC11233700 DOI: 10.1038/s41598-024-65870-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 06/25/2024] [Indexed: 07/11/2024] Open
Abstract
Saffron (Crocus sativus L.) is being embraced as the most important medicinal plant and the commercial source of saffron spice. Despite the beneficial economic and medicinal properties of saffron, the regulatory mechanism of the correlation of TFs and genes related to the biosynthesis of the apocarotenoids pathway is less obvious. Realizing these regulatory hierarchies of gene expression networks related to secondary metabolites production events is the main challenge owing to the complex and extensive interactions between the genetic behaviors. Recently, high throughput expression data have been highly feasible for constructing co-regulation networks to reveal the regulated processes and identifying novel candidate hub genes in response to complex processes of the biosynthesis of secondary metabolites. Herein, we performed Weighted Gene Co-expression Network Analysis (WGCNA), a systems biology method, to identify 11 regulated modules and hub TFs related to secondary metabolites. Three specialized modules were found in the apocarotenoids pathway. Several hub TFs were identified in notable modules, including MADS, C2H2, ERF, bZIP, HD-ZIP, and zinc finger protein MYB and HB, which were potentially associated with apocarotenoid biosynthesis. Furthermore, the expression levels of six hub TFs and six co-regulated genes of apocarotenoids were validated with RT-qPCR. The results confirmed that hub TFs specially MADS, C2H2, and ERF had a high correlation (P < 0.05) and a positive effect on genes under their control in apocarotenoid biosynthesis (CCD2, GLT2, and ADH) among different C. sativus ecotypes in which the metabolite contents were assayed. Promoter analysis of the co-expressed genes of the modules involved in apocarotenoids biosynthesis pathway suggested that not only are the genes co-expressed, but also share common regulatory motifs specially related to hub TFs of each module and that they may describe their common regulation. The result can be used to engineer valuable secondary metabolites of C. sativus by manipulating the hub regulatory TFs.
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Affiliation(s)
- Mahsa Eshaghi
- Department of Plant Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Sajad Rashidi-Monfared
- Department of Plant Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
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Zhou R, Song Y, Xue X, Xue R, Jiang H, Zhou Y, Qi X, Wang Y. Differential Transcription Profiling Reveals the MicroRNAs Involved in Alleviating Damage to Photosynthesis under Drought Stress during the Grain Filling Stage in Wheat. Int J Mol Sci 2024; 25:5518. [PMID: 38791558 PMCID: PMC11122533 DOI: 10.3390/ijms25105518] [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: 04/04/2024] [Revised: 05/09/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
To explore the possible novel microRNA (miRNA) regulatory pathways in Zhengmai 1860, a newly cultivated drought-tolerant wheat (Triticum aestivum L.) cultivar, miRNA transcriptome sequencing of the flag leaves of Zhengmai 1860, drought-sensitive variety Zhoumai 18, and drought-resistant variety Bainong 207 was performed during the grain filling stage. We also observed changes in the chloroplast ultrastructure, phytohormone levels, and antioxidant- and photosynthesis-related physiological indicators in three wheat varieties. The results showed that the flag leaves of the drought-tolerant variety Zhengmai 1860 had higher chlorophyll contents and net photosynthetic rates than those of Zhoumai 18 under drought stress during the grain filling stage; in addition, the chloroplast structure was more complete. However, there was no significant difference between Zhengmai 1860 and Bainong 207. MiRNA transcriptome analysis revealed that the differential expression of the miRNAs and mRNAs exhibited variable specificity. The KEGG pathway enrichment results indicated that most of the genes were enriched in the MAPK signaling pathway, plant hormone signal transduction, photosynthetic antennae protein, and amino acid and carbohydrate metabolism. In the drought-tolerant cultivar Zhengmai 1860, tae-miR408 was targeted to regulate the allene oxide synthase (AOS) gene, inhibit its expression, reduce the AOS content, and decrease the synthesis of jasmonic acid (JA) and abscisic acid (ABA). The results of this study suggest that Zhengmai 1860 could improve the photosynthetic performance of flag leaves by inhibiting the expression of genes involved in the JA pathway through miRNAs under drought conditions. Moreover, multiple miRNAs may target chlorophyll, antioxidant enzymes, phytohormone signal transduction, and other related pathways; thus, it is possible to provide a more theoretical basis for wheat molecular breeding.
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Affiliation(s)
- Ruixiang Zhou
- College of Life Sciences, Henan Agricultural University, 218 Ping’an Avenue, Zhengzhou 450046, China
| | - Yuhang Song
- College of Life Sciences, Henan Agricultural University, 218 Ping’an Avenue, Zhengzhou 450046, China
| | - Xinyu Xue
- College of Life Sciences, Henan Agricultural University, 218 Ping’an Avenue, Zhengzhou 450046, China
| | - Ruili Xue
- College of Life Sciences, Henan Agricultural University, 218 Ping’an Avenue, Zhengzhou 450046, China
| | - Haifang Jiang
- College of Life Sciences, Henan Agricultural University, 218 Ping’an Avenue, Zhengzhou 450046, China
| | - Yi Zhou
- College of Life Sciences, Henan Agricultural University, 218 Ping’an Avenue, Zhengzhou 450046, China
| | - Xueli Qi
- Henan Academy of Crop Molecular Breeding, Zhengzhou 450002, China
| | - Yuexia Wang
- College of Life Sciences, Henan Agricultural University, 218 Ping’an Avenue, Zhengzhou 450046, China
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Yang Y, Sun J, Qiu C, Jiao P, Wang H, Wu Z, Li Z. Comparative genomic analysis of the Growth-Regulating Factors-Interacting Factors (GIFs) in six Salicaceae species and functional analysis of PeGIF3 reveals their regulatory role in Populus heteromorphic leaves. BMC Genomics 2024; 25:317. [PMID: 38549059 PMCID: PMC10976704 DOI: 10.1186/s12864-024-10221-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 03/13/2024] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND The growth-regulating factor-interacting factor (GIF) gene family plays a vital role in regulating plant growth and development, particularly in controlling leaf, seed, and root meristem homeostasis. However, the regulatory mechanism of heteromorphic leaves by GIF genes in Populus euphratica as an important adaptative trait of heteromorphic leaves in response to desert environment remains unknown. RESULTS This study aimed to identify and characterize the GIF genes in P. euphratica and other five Salicaceae species to investigate their role in regulating heteromorphic leaf development. A total of 27 GIF genes were identified and characterized across six Salicaceae species (P. euphratica, Populus pruinose, Populus deltoides, Populus trichocarpa, Salix sinopurpurea, and Salix suchowensis) at the genome-wide level. Comparative genomic analysis among these species suggested that the expansion of GIFs may be derived from the specific Salicaceae whole-genome duplication event after their divergence from Arabidopsis thaliana. Furthermore, the expression data of PeGIFs in heteromorphic leaves, combined with functional information on GIF genes in Arabidopsis, indicated the role of PeGIFs in regulating the leaf development of P. euphratica, especially PeGIFs containing several cis-acting elements associated with plant growth and development. By heterologous expression of the PeGIF3 gene in wild-type plants (Col-0) and atgif1 mutant of A. thaliana, a significant difference in leaf expansion along the medial-lateral axis, and an increased number of leaf cells, were observed between the overexpressed plants and the wild type. CONCLUSION PeGIF3 enhances leaf cell proliferation, thereby resulting in the expansion of the central-lateral region of the leaf. The findings not only provide global insights into the evolutionary features of Salicaceae GIFs but also reveal the regulatory mechanism of PeGIF3 in heteromorphic leaves of P. euphratica.
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Affiliation(s)
- Yuqi Yang
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, 843300, Alar, China
- College of Life Science and Technology, Tarim University, 843300, Alar, China
- Desert Poplar Research Center of Tarim University, 843300, Alar, China
| | - Jianhao Sun
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, 843300, Alar, China
- College of Life Science and Technology, Tarim University, 843300, Alar, China
- Desert Poplar Research Center of Tarim University, 843300, Alar, China
| | - Chen Qiu
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, 843300, Alar, China
- College of Life Science and Technology, Tarim University, 843300, Alar, China
- Desert Poplar Research Center of Tarim University, 843300, Alar, China
| | - Peipei Jiao
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, 843300, Alar, China
- College of Life Science and Technology, Tarim University, 843300, Alar, China
- Desert Poplar Research Center of Tarim University, 843300, Alar, China
| | - Houling Wang
- College of Biological Sciences and Technology, Beijing Forestry University, 100083, Beijing, China
| | - Zhihua Wu
- College of Life Sciences, Zhejiang Normal University, 321004, Jinhua, China.
| | - Zhijun Li
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, 843300, Alar, China.
- College of Life Science and Technology, Tarim University, 843300, Alar, China.
- Desert Poplar Research Center of Tarim University, 843300, Alar, China.
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Wang G, Liu X, Gan SS. The ABA-AtNAP-SAG113 PP2C module regulates leaf senescence by dephoshorylating SAG114 SnRK3.25 in Arabidopsis. MOLECULAR HORTICULTURE 2023; 3:22. [PMID: 37899482 PMCID: PMC10614403 DOI: 10.1186/s43897-023-00072-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 10/16/2023] [Indexed: 10/31/2023]
Abstract
We previously reported that ABA inhibits stomatal closure through AtNAP-SAG113 PP2C regulatory module during leaf senescence. The mechanism by which this module exerts its function is unknown. Here we report the identification and functional analysis of SAG114, a direct target of the regulatory module. SAG114 encodes SnRK3.25. Both bimolecular fluorescence complementation (BiFC) and yeast two-hybrid assays show that SAG113 PP2C physically interacts with SAG114 SnRK3.25. Biochemically the SAG113 PP2C dephosphorylates SAG114 in vitro and in planta. RT-PCR and GUS reporter analyses show that SAG114 is specifically expressed in senescing leaves in Arabidopsis. Functionally, the SAG114 knockout mutant plants have a significantly bigger stomatal aperture and a much faster water loss rate in senescing leaves than those of wild type, and display a precocious senescence phenotype. The premature senescence phenotype of sag114 is epistatic to sag113 (that exhibits a remarkable delay in leaf senescence) because the sag113 sag114 double mutant plants show an early leaf senescence phenotype, similar to that of sag114. These results not only demonstrate that the ABA-AtNAP-SAG113 PP2C regulatory module controls leaf longevity by dephosphorylating SAG114 kinase, but also reveal the involvement of the SnRK3 family gene in stomatal movement and water loss during leaf senescence.
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Affiliation(s)
- Gaopeng Wang
- Present Address: Shanghai Institute of Technology, Shanghai, 201418, China
| | - Xingwang Liu
- Present Address: Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Su-Sheng Gan
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
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Yao P, Zhang C, Qin T, Liu Y, Liu Z, Xie X, Bai J, Sun C, Bi Z. Comprehensive Analysis of GH3 Gene Family in Potato and Functional Characterization of StGH3.3 under Drought Stress. Int J Mol Sci 2023; 24:15122. [PMID: 37894803 PMCID: PMC10606756 DOI: 10.3390/ijms242015122] [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: 08/23/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
As an important hormone response gene, Gretchen Hagen 3 (GH3) maintains hormonal homeostasis by conjugating excess auxin with amino acids during plant stress-related signaling pathways. GH3 genes have been characterized in many plant species, but they are rarely reported in potato. Here, 19 StGH3 genes were isolated and characterized. Phylogenetic analysis indicated that StGH3s were divided into two categories (group I and group III). Analyses of gene structure and motif composition showed that the members of a specific StGH3 subfamily are relatively conserved. Collinearity analysis of StGH3 genes in potato and other plants laid a foundation for further exploring the evolutionary characteristics of the StGH3 genes. Promoter analysis showed that most StGH3 promoters contained hormone and abiotic stress response elements. Multiple transcriptome studies indicated that some StGH3 genes were responsive to ABA, water deficits, and salt treatments. Moreover, qRT-PCR analysis indicated that StGH3 genes could be induced by phytohormones (ABA, SA, and MeJA) and abiotic stresses (water deficit, high salt, and low temperature), although with different patterns. Furthermore, transgenic tobacco with transient overexpression of the StGH3.3 gene showed positive regulation in response to water deficits by increasing proline accumulation and reducing the leaf water loss rate. These results suggested that StGH3 genes may be involved in the response to abiotic stress through hormonal signal pathways. Overall, this study provides useful insights into the evolution and function of StGH3s and lays a foundation for further study on the molecular mechanisms of StGH3s in the regulation of potato drought resistance.
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Affiliation(s)
- Panfeng Yao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
| | - Chunli Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Tianyuan Qin
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
| | - Zhen Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
| | - Xiaofei Xie
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (P.Y.); (C.Z.); (T.Q.); (Y.L.); (Z.L.); (X.X.); (J.B.); (C.S.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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Liu J, Li G, Wang R, Wang G, Wan Y. Genome-Wide Analysis of WRKY Transcription Factors Involved in Abiotic Stress and ABA Response in Caragana korshinskii. Int J Mol Sci 2023; 24:ijms24119519. [PMID: 37298467 DOI: 10.3390/ijms24119519] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
The WRKY transcription factor family plays a vital role in plant development and environmental response. However, the information of WRKY genes at the genome-wide level is rarely reported in Caragana korshinskii. In this study, we identified and renamed 86 CkWRKY genes, which were further classified into three groups through phylogenetic analysis. Most of these WRKY genes were clustered and distributed on eight chromosomes. Multiple sequence alignment revealed that the conserved domain (WRKYGQK) of the CkWRKYs was basically consistent, but there were also six variation types (WRKYGKK, GRKYGQK, WRMYGQK, WRKYGHK, WKKYEEK and RRKYGQK) that appeared. The motif composition of the CkWRKYs was quite conservative in each group. In general, the number of WRKY genes gradually increased from lower to higher plant species in the evolutionary analysis of 28 species, with some exceptions. Transcriptomics data and RT-qPCR analysis showed that the CkWRKYs in different groups were involved in abiotic stresses and ABA response. Our results provided a basis for the functional characterization of the CkWRKYs involved in stress resistance in C. korshinskii.
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Affiliation(s)
- Jinhua Liu
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Guojing Li
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Ruigang Wang
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Guangxia Wang
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yongqing Wan
- Key Laboratory of Plants Adversity Adaptation and Genetic Improvement in Cold and Arid Regions of Inner Mongolia, Inner Mongolia Agricultural University, Hohhot 010018, China
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Lin Y, Chen W, Yang Q, Zhang Y, Ma X, Li M. Genome-Wide Characterization and Gene Expression Analyses of Malate Dehydrogenase ( MDH) Genes in Low-Phosphorus Stress Tolerance of Chinese Fir ( Cunninghamia lanceolata). Int J Mol Sci 2023; 24:ijms24054414. [PMID: 36901845 PMCID: PMC10003207 DOI: 10.3390/ijms24054414] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/17/2023] [Accepted: 02/08/2023] [Indexed: 02/25/2023] Open
Abstract
Malate dehydrogenase (MDH) genes play vital roles in developmental control and environmental stress tolerance in sessile plants by modulating the organic acid-malic acid level. However, MDH genes have not yet been characterized in gymnosperm, and their roles in nutrient deficiency are largely unexplored. In this study, 12 MDH genes were identified in Chinese fir (Cunninghamia lanceolata), namely, ClMDH-1, -2, -3, …, and -12. Chinese fir is one of the most abundant commercial timber trees in China, and low phosphorus has limited its growth and production due to the acidic soil of southern China. According to the phylogenetic analysis, MDH genes were classified into five groups, and Group 2 genes (ClMDH-7, -8, -9, and 10) were only found to be present in Chinese fir but not in Arabidopsis thaliana and Populus trichocarpa. In particular, the Group 2 MDHs also had specific functional domains-Ldh_1_N (malidase NAD-binding functional domain) and Ldh_1_C (malate enzyme C-terminal functional domain)-indicating a specific function of ClMDHs in the accumulation of malate. All ClMDH genes contained the conserved MDH gene characteristic functional domains Ldh_1_N and Ldh_1_C, and all ClMDH proteins exhibited similar structures. Twelve ClMDH genes were identified from eight chromosomes, involving fifteen ClMDH homologous gene pairs, each with a Ka/Ks ratio of <1. The analysis of cis-elements, protein interactions, and transcription factor interactions of MDHs showed that the ClMDH gene might play a role in plant growth and development, and in response to stress mechanisms. The results of transcriptome data and qRT-PCR validation based on low-phosphorus stress showed that ClMDH1, ClMDH6, ClMDH7, ClMDH2, ClMDH4, ClMDH5, ClMDH10 and ClMDH11 were upregulated under low-phosphorus stress and played a role in the response of fir to low-phosphorus stress. In conclusion, these findings lay a foundation for further improving the genetic mechanism of the ClMDH gene family in response to low-phosphorus stress, exploring the potential function of this gene, promoting the improvement of fir genetics and breeding, and improving production efficiency.
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Affiliation(s)
- Yawen Lin
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wanting Chen
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qiang Yang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yajing Zhang
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiangqing Ma
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Colleges and University Engineering Research Center of Plantation Sustainable Management, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ming Li
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Colleges and University Engineering Research Center of Plantation Sustainable Management, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: ; Tel.: +86-591-8378-0261
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RNAseq-Based Working Model for Transcriptional Regulation of Crosstalk between Simultaneous Abiotic UV-B and Biotic Stresses in Plants. Genes (Basel) 2023; 14:genes14020240. [PMID: 36833168 PMCID: PMC9957429 DOI: 10.3390/genes14020240] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/10/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
Plants adjust their secondary metabolism by altering the expression of corresponding genes to cope with both abiotic and biotic stresses. In the case of UV-B radiation, plants produce protective flavonoids; however, this reaction is impeded during pattern-triggered immunity (PTI) induced by pathogens. Pathogen attack can be mimicked by the application of microbial associated molecular patterns (e.g., flg22) to study crosstalk between PTI and UV-B-induced signaling pathways. Switching from Arabidopsis cell cultures to in planta studies, we analyzed whole transcriptome changes to gain a deeper insight into crosstalk regulation. We performed a comparative transcriptomic analysis by RNAseq with four distinct mRNA libraries and identified 10778, 13620, and 11294 genes, which were differentially expressed after flg22, UV-B, and stress co-treatment, respectively. Focusing on genes being either co-regulated with the UV-B inducible marker gene chalcone synthase CHS or the flg22 inducible marker gene FRK1 identified a large set of transcription factors from diverse families, such as MYB, WRKY, or NAC. These data provide a global view of transcriptomic reprogramming during this crosstalk and constitute a valuable dataset for further deciphering the underlying regulatory mechanism(s), which appear to be much more complex than previously anticipated. The possible involvement of MBW complexes in this context is discussed.
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Comprehensive Analysis of Glutamate Receptor-like Genes in Rice ( Oryza sativa L.): Genome-Wide Identification, Characteristics, Evolution, Chromatin Accessibility, gcHap Diversity, Population Variation and Expression Analysis. Curr Issues Mol Biol 2022; 44:6404-6427. [PMID: 36547098 PMCID: PMC9777005 DOI: 10.3390/cimb44120437] [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: 11/14/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Glutamate receptors (GLR) are widely present in animals and plants, playing essential roles in regulating plant growth, development and stress response. At present, most studies of GLRs in plants are focused on Arabidopsis thaliana, while there have been few studies on rice. In this study, we identified 26 OsGLR genes in rice (Oryza sativa L.). Then, we analyzed the chromosomal location, physical and chemical properties, subcellular location, transmembrane (TM) helices, signal peptides, three-dimensional (3D) structure, cis-acting elements, evolution, chromatin accessibility, population variation, gene-coding sequence haplotype (gcHap) and gene expression under multiple abiotic stress and hormone treatments. The results showed that out of the 26 OsGLR genes, ten genes had the TM domain, signal peptides and similar 3D structures. Most OsGLRs exhibited high tissue specificity in expression under drought stress. In addition, several OsGLR genes were specifically responsive to certain hormones. The favorable gcHap of many OsGLR genes in modern varieties showed obvious differentiation between Xian/indica and Geng/japonica subspecies. This study, for the first time, comprehensively analyzes the OsGLR genes in rice, and provides an important reference for further research on their molecular function.
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Maqsood H, Munir F, Amir R, Gul A. Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum. FRONTIERS IN PLANT SCIENCE 2022; 13:1031679. [PMID: 36507398 PMCID: PMC9731513 DOI: 10.3389/fpls.2022.1031679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/25/2022] [Indexed: 06/12/2023]
Abstract
Tomato is a drought-sensitive crop which has high susceptibility to adverse climatic changes. Dehydration-responsive element-binding (DREB) are significant plant transcription factors that have a vital role in regulating plant abiotic stress tolerance by networking with DRE/CRT cis-regulatory elements in response to stresses. In this study, bioinformatics analysis was performed to conduct the genome-wide identification and characterization of DREB genes and promoter elements in Solanum lycopersicum. In genome-wide coverage, 58 SlDREB genes were discovered on 12 chromosomes that justified the criteria of the presence of AP2 domain as conserved motifs. Intron-exon organization and motif analysis showed consistency with phylogenetic analysis and confirmed the absence of the A3 class, thus dividing the SlDREB genes into five categories. Gene expansion was observed through tandem duplication and segmental duplication gene events in SlDREB genes. Ka/Ks values were calculated in ortholog pairs that indicated divergence time and occurrence of purification selection during the evolutionary period. Synteny analysis demonstrated that 32 out of 58 and 47 out of 58 SlDREB genes were orthologs to Arabidopsis and Solanum tuberosum, respectively. Subcellular localization predicted that SlDREB genes were present in the nucleus and performed primary functions in DNA binding to regulate the transcriptional processes according to gene ontology. Cis-acting regulatory element analysis revealed the presence of 103 motifs in 2.5-kbp upstream promoter sequences of 58 SlDREB genes. Five representative SlDREB proteins were selected from the resultant DREB subgroups for 3D protein modeling through the Phyre2 server. All models confirmed about 90% residues in the favorable region through Ramachandran plot analysis. Moreover, active catalytic sites and occurrence in disorder regions indicated the structural and functional flexibility of SlDREB proteins. Protein association networks through STRING software suggested the potential interactors that belong to different gene families and are involved in regulating similar functional and biological processes. Transcriptome data analysis has revealed that the SlDREB gene family is engaged in defense response against drought and heat stress conditions in tomato. Overall, this comprehensive research reveals the identification and characterization of SlDREB genes that provide potential knowledge for improving abiotic stress tolerance in tomato.
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Affiliation(s)
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
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Astigueta FH, Baigorria AH, García MN, Delfosse VC, González SA, Pérez de la Torre MC, Moschen S, Lia VV, Heinz RA, Fernández P, Trupkin SA. Characterization and expression analysis of WRKY genes during leaf and corolla senescence of Petunia hybrida plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1765-1784. [PMID: 36387973 PMCID: PMC9636358 DOI: 10.1007/s12298-022-01243-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Several families of transcription factors (TFs) control the progression of senescence. Many key TFs belonging to the WRKY family have been described to play crucial roles in the regulation of leaf senescence, mainly in Arabidopsis thaliana. However, little is known about senescence-associated WRKY members in floricultural species. Delay of senescence in leaves and petals of Petunia hybrida, a worldwide ornamental crop are highly appreciated traits. In this work, starting from 28 differentially expressed WRKY genes of A. thaliana during the progression of leaf senescence, we identified the orthologous in P. hybrida and explored the expression profiles of 20 PhWRKY genes during the progression of natural (age-related) leaf and corolla senescence as well as in the corollas of flowers undergoing pollination-induced senescence. Simultaneous visualization showed consistent and similar expression profiles of PhWRKYs during natural leaf and corolla senescence, although weak expression changes were observed during pollination-induced senescence. Comparable expression trends between PhWRKYs and the corresponding genes of A. thaliana were observed during leaf senescence, although more divergence was found in petals of pollinated petunia flowers. Integration of expression data with phylogenetics, conserved motif and cis-regulatory element analyses were used to establish a list of candidates that could regulate more than one senescence process. Our results suggest that several members of the WRKY family of TFs are tightly linked to the regulation of senescence in P. hybrida. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01243-y.
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Affiliation(s)
- Francisco H. Astigueta
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Escuela de Ciencia Y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires Argentina
| | - Amilcar H. Baigorria
- Escuela de Ciencia Y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires Argentina
| | - Martín N. García
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas Y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| | - Verónica C. Delfosse
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Escuela de Ciencia Y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires Argentina
| | - Sergio A. González
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
| | - Mariana C. Pérez de la Torre
- Instituto de Floricultura, Centro de Investigación de Recursos Naturales, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| | - Sebastián Moschen
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Famaillá, 4142 Tucumán, Argentina
| | - Verónica V. Lia
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas Y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
- Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, 1428 Buenos Aires, Argentina
| | - Ruth A. Heinz
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas Y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| | - Paula Fernández
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Escuela de Ciencia Y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas Y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| | - Santiago A. Trupkin
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto de Floricultura, Centro de Investigación de Recursos Naturales, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
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Yang Q, Li B, Rizwan HM, Sun K, Zeng J, Shi M, Guo T, Chen F. Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression analysis under Fusarium kyushuense and drought stress conditions in Passiflora edulis. FRONTIERS IN PLANT SCIENCE 2022; 13:972734. [PMID: 36092439 PMCID: PMC9453495 DOI: 10.3389/fpls.2022.972734] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 07/27/2022] [Indexed: 05/07/2023]
Abstract
The NAC gene family is one of the largest plant transcription factors (TFs) families and plays important roles in plant growth, development, metabolism, and biotic and abiotic stresses. However, NAC gene family has not been reported in passion fruit (Passiflora edulis). In this study, a total of 105 NAC genes were identified in the passion fruit genome and were unevenly distributed across all nine-passion fruit chromomere, with a maximum of 48 PeNAC genes on chromosome one. The physicochemical features of all 105 PeNAC genes varied including 120 to 3,052 amino acids, 3 to 8 conserved motifs, and 1 to 3 introns. The PeNAC genes were named (PeNAC001-PeNAC105) according to their chromosomal locations and phylogenetically grouped into 15 clades (NAC-a to NAC-o). Most PeNAC proteins were predicted to be localized in the nucleus. The cis-element analysis indicated the possible roles of PeNAC genes in plant growth, development, light, hormones, and stress responsiveness. Moreover, the PeNAC gene duplications including tandem (11 gene pairs) and segmental (12 gene pairs) were identified and subjected to purifying selection. All PeNAC proteins exhibited similar 3D structures, and a protein-protein interaction network analysis with known Arabidopsis proteins was predicted. Furthermore, 17 putative ped-miRNAs were identified to target 25 PeNAC genes. Potential TFs including ERF, BBR-BPC, Dof, and bZIP were identified in promoter region of all 105 PeNAC genes and visualized in a TF regulatory network. GO and KEGG annotation analysis exposed that PeNAC genes were related to different biological, molecular, and cellular terms. The qRT-PCR expression analysis discovered that most of the PeNAC genes including PeNAC001, PeNAC003, PeNAC008, PeNAC028, PeNAC033, PeNAC058, PeNAC063, and PeNAC077 were significantly upregulated under Fusarium kyushuense and drought stress conditions compared to controls. In conclusion, these findings lay the foundation for further functional studies of PeNAC genes to facilitate the genetic improvement of plants to stress resistance.
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Affiliation(s)
| | | | | | | | | | | | | | - Faxing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
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Zhang Y, Li Y, Zhang Y, Zhang Z, Zhang D, Wang X, Lai B, Huang D, Gu L, Xie Y, Miao Y. Genome-wide H3K9 acetylation level increases with age-dependent senescence of flag leaf in rice. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4696-4715. [PMID: 35429161 DOI: 10.1093/jxb/erac155] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and histone modification, but the precise mechanism is as yet unclear. Here, we analysed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac with gene expression and transcript elongation. During flag leaf aging, we observed 1249 up-regulated differentially expressed genes (DEGs) and 996 down-regulated DEGs, showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac. We produced a landscape of H3K9 acetylation-modified gene expression targets that include known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis-related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac, and elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice.
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Affiliation(s)
- Yu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanyun Li
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyu Zhang
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Deyu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaonan Wang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Binfan Lai
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dandan Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yakun Xie
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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Ahmar S, Gruszka D. In-Silico Study of Brassinosteroid Signaling Genes in Rice Provides Insight Into Mechanisms Which Regulate Their Expression. Front Genet 2022; 13:953458. [PMID: 35873468 PMCID: PMC9299959 DOI: 10.3389/fgene.2022.953458] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/14/2022] [Indexed: 12/14/2022] Open
Abstract
Brassinosteroids (BRs) regulate a diverse spectrum of processes during plant growth and development and modulate plant physiology in response to environmental fluctuations and stress factors. Thus, the BR signaling regulators have the potential to be targeted for gene editing to optimize the architecture of plants and make them more resilient to environmental stress. Our understanding of the BR signaling mechanism in monocot crop species is limited compared to our knowledge of this process accumulated in the model dicot species - Arabidopsis thaliana. A deeper understanding of the BR signaling and response during plant growth and adaptation to continually changing environmental conditions will provide insight into mechanisms that govern the coordinated expression of the BR signaling genes in rice (Oryza sativa) which is a model for cereal crops. Therefore, in this study a comprehensive and detailed in silico analysis of promoter sequences of rice BR signaling genes was performed. Moreover, expression profiles of these genes during various developmental stages and reactions to several stress conditions were analyzed. Additionally, a model of interactions between the encoded proteins was also established. The obtained results revealed that promoters of the 39 BR signaling genes are involved in various regulatory mechanisms and interdependent processes that influence growth, development, and stress response in rice. Different transcription factor-binding sites and cis-regulatory elements in the gene promoters were identified which are involved in regulation of the genes’ expression during plant development and reactions to stress conditions. The in-silico analysis of BR signaling genes in O. sativa provides information about mechanisms which regulate the coordinated expression of these genes during rice development and in response to other phytohormones and environmental factors. Since rice is both an important crop and the model species for other cereals, this information may be important for understanding the regulatory mechanisms that modulate the BR signaling in monocot species. It can also provide new ways for the plant genetic engineering technology by providing novel potential targets, either cis-elements or transcriptional factors, to create elite genotypes with desirable traits.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Damian Gruszka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
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Rizwan HM, Waheed A, Ma S, Li J, Arshad MB, Irshad M, Li B, Yang X, Ali A, Ahmed MAA, Shaheen N, Scholz SS, Oelmüller R, Lin Z, Chen F. Comprehensive Genome-Wide Identification and Expression Profiling of Eceriferum ( CER) Gene Family in Passion Fruit ( Passiflora edulis) Under Fusarium kyushuense and Drought Stress Conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:898307. [PMID: 35832215 PMCID: PMC9272567 DOI: 10.3389/fpls.2022.898307] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Plant surfaces are covered with cuticle wax and are the first barrier between a plant and environmental stresses. Eceriferum (CER) is an important gene family involved in wax biosynthesis and stress resistance. In this study, for the first time, 34 CER genes were identified in the passion fruit (Passiflora edulis) genome, and PeCER proteins varied in physicochemical properties. A phylogenetic tree was constructed and divided into seven clades to identify the evolutionary relationship with other plant species. Gene structure analyses revealed that conserved motifs ranged from 1 to 24, and that exons ranged from 1 to 29. The cis-element analysis provides insight into possible roles of PeCER genes in plant growth, development and stress responses. The syntenic analysis revealed that segmental (six gene pairs) and tandem (six gene pairs) gene duplication played an important role in the expansion of PeCER genes and underwent a strong purifying selection. In addition, 12 putative ped-miRNAs were identified to be targeting 16 PeCER genes, and PeCER6 was the most targeted by four miRNAs including ped-miR157a-5p, ped-miR164b-5p, ped-miR319b, and ped-miR319l. Potential transcription factors (TFs) such as ERF, AP2, MYB, and bZIP were predicted and visualized in a TF regulatory network interacting with PeCER genes. GO and KEGG annotation analysis revealed that PeCER genes were highly related to fatty acid, cutin, and wax biosynthesis, plant-pathogen interactions, and stress response pathways. The hypothesis that most PeCER proteins were predicted to localize to the plasma membrane was validated by transient expression assays of PeCER32 protein in onion epidermal cells. qRT-PCR expression results showed that most of the PeCER genes including PeCER1, PeCER11, PeCER15, PeCER17, and PeCER32 were upregulated under drought and Fusarium kyushuense stress conditions compared to controls. These findings provide a foundation for further studies on functions of PeCER genes to further facilitate the genetic modification of passion fruit wax biosynthesis and stress resistance.
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Affiliation(s)
| | - Abdul Waheed
- Key Laboratory for Bio Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Songfeng Ma
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiankun Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Muhammad Bilal Arshad
- Department of Plant Breeding and Genetics, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Muhammad Irshad
- College of Horticulture, The University of Agriculture, Peshawar, Pakistan
| | - Binqi Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuelian Yang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ahmad Ali
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohamed A. A. Ahmed
- Plant Production Department (Horticulture-Medicinal and Aromatic Plants), Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Nusrat Shaheen
- Department of Chemistry, Abbottabad University of Science and Technology, Abbottabad, Pakistan
| | - Sandra S. Scholz
- Matthias Schleiden Institute, Plant Physiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Ralf Oelmüller
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Matthias Schleiden Institute, Plant Physiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Zhimin Lin
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Faxing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
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Ngo V, Fleischmann BK, Jung M, Hein L, Lother A. Histone Deacetylase 6 Inhibitor JS28 Prevents Pathological Gene Expression in Cardiac Myocytes. J Am Heart Assoc 2022; 11:e025857. [PMID: 35699165 PMCID: PMC9238633 DOI: 10.1161/jaha.122.025857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022]
Abstract
Background Epigenetic modulators have been proposed as promising new drug targets to treat adverse remodeling in heart failure. Here, we evaluated the potential of 4 epigenetic drugs, including the recently developed histone deacetylase 6 (HDAC6) inhibitor JS28, to prevent endothelin-1 induced pathological gene expression in cardiac myocytes and analyzed the chromatin binding profile of the respective inhibitor targets. Methods and Results Cardiac myocytes were differentiated and puromycin-selected from mouse embryonic stem cells and treated with endothelin-1 to induce pathological gene expression (938 differentially expressed genes, q<0.05). Dysregulation of gene expression was at least in part prevented by epigenetic inhibitors, including the pan-BRD (bromodomain-containing protein) inhibitor bromosporine (290/938 genes), the BET (bromodomain and extraterminal) inhibitor JQ1 (288/938), the broad-spectrum HDAC inhibitor suberoylanilide hydroxamic acid (227/938), and the HDAC6 inhibitor JS28 (210/938). Although the 4 compounds were similarly effective toward pathological gene expression, JS28 demonstrated the least adverse effects on physiological gene expression. Genome-wide chromatin binding profiles revealed that HDAC6 binding sites were preferentially associated with promoters of genes involved in RNA processing. In contrast, BRD4 binding was associated with genes involved in core cardiac myocyte functions, for example, myocyte contractility, and showed enrichment at enhancers and intronic regions. These distinct chromatin binding profiles of HDAC6 and BRD4 might explain the different effects of their inhibitors on pathological versus physiological gene expression. Conclusions In summary, we demonstrated, that the HDAC6 inhibitor JS28 effectively prevented the adverse effects of endothelin-1 on gene expression with minor impact on physiological gene expression in cardiac myocytes. Selective HDAC6 inhibition by JS28 appears to be a promising strategy for future evaluation in vivo and potential translation into clinical application.
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Affiliation(s)
- Vivien Ngo
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of MedicineUniversity of FreiburgGermany
| | - Bernd K. Fleischmann
- Institute of Physiology I, Life & Brain Center, Medical FacultyUniversity of BonnGermany
| | - Manfred Jung
- Institute of Pharmaceutical SciencesUniversity of FreiburgGermany
| | - Lutz Hein
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of MedicineUniversity of FreiburgGermany
- BIOSS Centre for Biological Signaling StudiesUniversity of FreiburgGermany
| | - Achim Lother
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of MedicineUniversity of FreiburgGermany
- Interdisciplinary Medical Intensive Care (IMIT), Medical Center – University of Freiburg, Faculty of MedicineUniversity of FreiburgGermany
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Ayoub Khan M, Dongru K, Yifei W, Ying W, Penghui A, Zicheng W. Characterization of WRKY Gene Family in Whole-Genome and Exploration of Flowering Improvement Genes in Chrysanthemum lavandulifolium. FRONTIERS IN PLANT SCIENCE 2022; 13:861193. [PMID: 35557735 PMCID: PMC9087852 DOI: 10.3389/fpls.2022.861193] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/02/2022] [Indexed: 05/27/2023]
Abstract
Chrysanthemum is a well-known ornamental plant with numerous uses. WRKY is a large family of transcription factors known for a variety of functions ranging from stress resistance to plant growth and development. Due to the limited research on the WRKY family in chrysanthemums, we examined them for the first time in Chrysanthemum lavandulifolium. A total of 138 ClWRKY genes were identified, which were classified into three groups. Group III in C. lavandulifolium contains 53 members, which is larger than group III of Arabidopsis. The number of introns varied from one to nine in the ClWRKY gene family. The "WRKYGQK" motif is conserved in 118 members, while other members showed slight variations. AuR and GRE responsive cis-acting elements were located in the promoter region of WRKY members, which are important for plant development and flowering induction. In addition, the W box was present in most genes; the recognition site for the WRKY gene may play a role in autoregulation and cross-regulation. The expression of the most variable 19 genes in terms of different parameters was observed at different stages. Among them, 10 genes were selected due to the presence of CpG islands, while nine genes were selected based on their close association with important Arabidopsis genes related to floral traits. ClWRKY36 and ClWRKY45 exhibit differential expression at flowering stages in the capitulum, while methylation is detected in three genes, including ClWRKY31, ClWRKY100, and ClWRKY129. Our results provide a basis for further exploration of WRKY members to find their functions in plant growth and development, especially in flowering traits.
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Liu J, Wang R, Li G, Wan Y. Cloning and prokaryotic expression of WRKY48 from Caragana intermedia. Open Life Sci 2022; 17:131-138. [PMID: 35350447 PMCID: PMC8919828 DOI: 10.1515/biol-2022-0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/30/2021] [Accepted: 01/03/2022] [Indexed: 12/03/2022] Open
Abstract
Caragana intermedia (C. intermedia) is a kind of drought-tolerant leguminous shrub. WRKY transcription factors are one of the largest family of transcription factors in plants and play critical regulatory roles in stress tolerance and the development of plants. In our study, CiWRKY48 was cloned from C. intermedia, analyzed using bioinformatics software, and expressed with a prokaryotic expression system. The results showed that the open reading frame (ORF) of CiWRKY48 was 1158bp, the molecular weight (MW) was 42 kDa, and its subcellular localization was in the nucleus. Additionally, fusion protein was obtained, and confirmed by western blotting. The stress resistance of the pET30a-His-MBP-CiWRKY48 transformed Escherichia coli expression strain was reduced under mannitol and salt treatment, compared with the control. Overall, our findings provided a foundation for uncovering the function of CiWRKY48.
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Affiliation(s)
- Jinhua Liu
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University , Hohhot , 010018 , P. R. China
| | - Ruigang Wang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University , Hohhot , 010018 , P. R. China
- Inner Mongolia Enterprise Key Laboratory of Tree Breeding, Mengshu Ecological Construction Group Co., Ltd. , Hohhot , 011517 , P. R. China
- Inner Mongolia Engineering Research Center for Plant Gene Resources Mining and Molecular Breeding, Inner Mongolia Agricultural University , Hohhot , 010021 , P. R. China
| | - Guojing Li
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University , Hohhot , 010018 , P. R. China
| | - Yongqing Wan
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University , Hohhot , 010018 , P. R. China
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Tomar S, Subba A, Bala M, Singh AK, Pareek A, Singla-Pareek SL. Genetic Conservation of CBS Domain Containing Protein Family in Oryza Species and Their Association with Abiotic Stress Responses. Int J Mol Sci 2022; 23:ijms23031687. [PMID: 35163610 PMCID: PMC8836131 DOI: 10.3390/ijms23031687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 01/27/2023] Open
Abstract
Crop Wild Relatives (CWRs) form a comprehensive gene pool that can answer the queries related to plant domestication, speciation, and ecological adaptation. The genus ‘Oryza’ comprises about 27 species, of which two are cultivated, while the remaining are wild. Here, we have attempted to understand the conservation and diversification of the genes encoding Cystathionine β-synthase (CBS) domain-containing proteins (CDCPs) in domesticated and CWRs of rice. Few members of CDCPs were previously identified to be stress-responsive and associated with multiple stress tolerance in rice. Through genome-wide analysis of eleven rice genomes, we identified a total of 36 genes encoding CDCPs in O. longistaminata, 38 in O. glaberrima, 39 each in O. rufipogon, O. glumaepatula, O. brachyantha, O. punctata, and O. sativa subsp. japonica, 40 each in O. barthii and O. meridionalis, 41 in O. nivara, and 42 in O. sativa subsp. indica. Gene duplication analysis as well as non-synonymous and synonymous substitutions in the duplicated gene pairs indicated that this family is shaped majorly by the negative or purifying selection pressure through the long-term evolution process. We identified the presence of two additional hetero-domains, namely TerCH and CoatomerE (specifically in O. sativa subsp. indica), which were not reported previously in plant CDCPs. The in silico expression analysis revealed some of the members to be responsive to various abiotic stresses. Furthermore, the qRT-PCR based analysis identified some members to be highly inducive specifically in salt-tolerant genotype in response to salinity. The cis-regulatory element analysis predicted the presence of numerous stress as well as a few phytohormone-responsive elements in their promoter region. The data presented in this study would be helpful in the characterization of these CDCPs from rice, particularly in relation to abiotic stress tolerance.
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Affiliation(s)
- Surabhi Tomar
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
| | - Ashish Subba
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
| | - Meenu Bala
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834010, India; (M.B.); (A.K.S.)
| | - Anil Kumar Singh
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834010, India; (M.B.); (A.K.S.)
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi 110012, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India;
- National Agri-Food Biotechnology Institute, Mohali 140306, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
- Correspondence:
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Xie W, Li X, Wang S, Yuan M. OsWRKY53 Promotes Abscisic Acid Accumulation to Accelerate Leaf Senescence and Inhibit Seed Germination by Downregulating Abscisic Acid Catabolic Genes in Rice. FRONTIERS IN PLANT SCIENCE 2022; 12:816156. [PMID: 35154213 PMCID: PMC8828546 DOI: 10.3389/fpls.2021.816156] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/29/2021] [Indexed: 05/29/2023]
Abstract
Abscisic acid (ABA) largely promotes leaf senescence and inhibits seed germination in plants. Endogenous ABA content is finely tuned by many transcription factors. In this study, we showed that OsWRKY53 is a positive regulator of leaf senescence and a negative regulator of seed germination in rice. OsWRKY53 expression was induced in leaves under aging, dark, and ABA treatment. The OsWRKY53-overexpressing (OsWRKY53-oe) plants showed early yellowing leaves, while the OsWRKY53 (oswrky53) knockout mutants maintained green leaves than the wild type under natural, dark-induced, and ABA-induced senescence conditions. Transcriptional analysis revealed that ABA catabolic genes, namely, OsABA8ox1 and OsABA8ox2, two key genes participating in ABA catabolism harboring ABA 8'-hydroxylase activity, were markedly downregulated in OsWRKY53-oe leaves. Chromatin immunoprecipitation and protoplast transient assays revealed that OsWRKY53 directly bound to the promoters of OsABA8ox1 and OsABA8ox2 to repress their transcription, resulting in elevated endogenous ABA contents that promoted premature leaf senescence in the OsWRKY53-oe plants. It indicates that OsWRKY53 is a positive regulator through regulating ABA accumulation to promote leaf senescence. In addition, accumulated ABA simultaneously inhibited seed germination and post-germination growth in OsWRKY53-oe plants. Taken together, OsWRKY53 suppresses the transcript of ABA catabolic genes to promote ABA accumulation to modulate ABA-induced leaf senescence and ABA-mediated inhibition of seed germination.
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Mehla S, Kumar U, Kapoor P, Singh Y, Sihag P, Sagwal V, Balyan P, Kumar A, Ahalawat N, Lakra N, Singh KP, Pesic V, Djalovic I, Mir RR, Dhankher OP. Structural and functional insights into the candidate genes associated with different developmental stages of flag leaf in bread wheat ( Triticum aestivum L.). Front Genet 2022; 13:933560. [PMID: 36092892 PMCID: PMC9449350 DOI: 10.3389/fgene.2022.933560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/04/2022] [Indexed: 02/05/2023] Open
Abstract
Grain yield is one of the most important aims for combating the needs of the growing world population. The role of development and nutrient transfer in flag leaf for higher yields at the grain level is well known. It is a great challenge to properly exploit this knowledge because all the processes, starting from the emergence of the flag leaf to the grain filling stages of wheat (Triticum aestivum L.), are very complex biochemical and physiological processes to address. This study was conducted with the primary goal of functionally and structurally annotating the candidate genes associated with different developmental stages of flag leaf in a comprehensive manner using a plethora of in silico tools. Flag leaf-associated genes were analyzed for their structural and functional impacts using a set of bioinformatics tools and algorithms. The results revealed the association of 17 candidate genes with different stages of flag leaf development in wheat crop. Of these 17 candidate genes, the expression analysis results revealed the upregulation of genes such as TaSRT1-5D, TaPNH1-7B, and TaNfl1-2B and the downregulation of genes such as TaNAP1-7B, TaNOL-4D, and TaOsl2-2B can be utilized for the generation of high-yielding wheat varieties. Through MD simulation and other in silico analyses, all these proteins were found to be stable. Based on the outcome of bioinformatics and molecular analysis, the identified candidate genes were found to play principal roles in the flag leaf development process and can be utilized for higher-yield wheat production.
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Affiliation(s)
- Sheetal Mehla
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Upendra Kumar
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Prexha Kapoor
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Yogita Singh
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Pooja Sihag
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Vijeta Sagwal
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Priyanka Balyan
- Department of Botany, Deva Nagri P. G. College, CCS University, Meerut, India
| | - Anuj Kumar
- Shantou University Medical College, Shantou, China
- Dalhousie University, Halifax, NS, Canada
| | - Navjeet Ahalawat
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Nita Lakra
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Krishna Pal Singh
- Biophysics Unit, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, India
- Vice-Chancellor’s Secretariat, Mahatma Jyotiba Phule Rohilkhand University, Bareilly, India
| | - Vladan Pesic
- Department of Genetics and Plant Breeding, Faculty of Agriculture, University of Belgrade, Belgrade, Serbia
| | - Ivica Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maxim Gorki 30, Novi Sad, Serbia
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-Kashmir), Srinagar, India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, MA, United States
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23
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Rizwan HM, Shaozhong F, Li X, Bilal Arshad M, Yousef AF, Chenglong Y, Shi M, Jaber MYM, Anwar M, Hu SY, Yang Q, Sun K, Ahmed MAA, Min Z, Oelmüller R, Zhimin L, Chen F. Genome-Wide Identification and Expression Profiling of KCS Gene Family in Passion Fruit ( Passiflora edulis) Under Fusarium kyushuense and Drought Stress Conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:872263. [PMID: 35548275 PMCID: PMC9081883 DOI: 10.3389/fpls.2022.872263] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/03/2022] [Indexed: 05/02/2023]
Abstract
Plant and fruit surfaces are covered with cuticle wax and provide a protective barrier against biotic and abiotic stresses. Cuticle wax consists of very-long-chain fatty acids (VLCFAs) and their derivatives. β-Ketoacyl-CoA synthase (KCS) is a key enzyme in the synthesis of VLCFAs and provides a precursor for the synthesis of cuticle wax, but the KCS gene family was yet to be reported in the passion fruit (Passiflora edulis). In this study, thirty-two KCS genes were identified in the passion fruit genome and phylogenetically grouped as KCS1-like, FAE1-like, FDH-like, and CER6-like. Furthermore, thirty-one PeKCS genes were positioned on seven chromosomes, while one PeKCS was localized to the unassembled genomic scaffold. The cis-element analysis provides insight into the possible role of PeKCS genes in phytohormones and stress responses. Syntenic analysis revealed that gene duplication played a crucial role in the expansion of the PeKCS gene family and underwent a strong purifying selection. All PeKCS proteins shared similar 3D structures, and a protein-protein interaction network was predicted with known Arabidopsis proteins. There were twenty putative ped-miRNAs which were also predicted that belong to nine families targeting thirteen PeKCS genes. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation results were highly associated with fatty acid synthase and elongase activity, lipid metabolism, stress responses, and plant-pathogen interaction. The highly enriched transcription factors (TFs) including ERF, MYB, Dof, C2H2, TCP, LBD, NAC, and bHLH were predicted in PeKCS genes. qRT-PCR expression analysis revealed that most PeKCS genes were highly upregulated in leaves including PeKCS2, PeKCS4, PeKCS8, PeKCS13, and PeKCS9 but not in stem and roots tissues under drought stress conditions compared with controls. Notably, most PeKCS genes were upregulated at 9th dpi under Fusarium kyushuense biotic stress condition compared to controls. This study provides a basis for further understanding the functions of KCS genes, improving wax and VLCFA biosynthesis, and improvement of passion fruit resistance.
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Affiliation(s)
| | - Fang Shaozhong
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Xiaoting Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Muhammad Bilal Arshad
- Department of Plant Breeding and Genetics, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Ahmed Fathy Yousef
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Horticulture, College of Agriculture, University of Al-Azhar, Assiut, Egypt
| | - Yang Chenglong
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Meng Shi
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohammed Y. M. Jaber
- Department of Plant Production and Protection, Faculty of Agriculture and Veterinary Medicine, An-Najah National University, Nablus, Palestine
| | - Muhammad Anwar
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Shuai-Ya Hu
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agriculture University, Nanjing, China
| | - Qiang Yang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kaiwei Sun
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohamed A. A. Ahmed
- Plant Production Department (Horticulture-Medicinal and Aromatic Plants), Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Zheng Min
- Department of Horticulture, Fujian Agricultural Vocational College, Fuzhou, China
| | - Ralf Oelmüller
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Matthias Schleiden Institute, Plant Physiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Lin Zhimin
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, China
- *Correspondence: Lin Zhimin,
| | - Faxing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Faxing Chen,
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ain-Ali QU, Mushtaq N, Amir R, Gul A, Tahir M, Munir F. Genome-wide promoter analysis, homology modeling and protein interaction network of Dehydration Responsive Element Binding (DREB) gene family in Solanum tuberosum. PLoS One 2021; 16:e0261215. [PMID: 34914734 PMCID: PMC8675703 DOI: 10.1371/journal.pone.0261215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/27/2021] [Indexed: 12/24/2022] Open
Abstract
Dehydration Responsive Element Binding (DREB) regulates the expression of numerous stress-responsive genes, and hence plays a pivotal role in abiotic stress responses and tolerance in plants. The study aimed to develop a complete overview of the cis-acting regulatory elements (CAREs) present in S. tuberosum DREB gene promoters. A total of one hundred and four (104) cis-regulatory elements (CREs) were identified from 2.5kbp upstream of the start codon (ATG). The in-silico promoter analysis revealed variable sets of cis-elements and functional diversity with the predominance of light-responsive (30%), development-related (20%), abiotic stress-responsive (14%), and hormone-responsive (12%) elements in StDREBs. Among them, two light-responsive elements (Box-4 and G-box) were predicted in 64 and 61 StDREB genes, respectively. Two development-related motifs (AAGAA-motif and as-1) were abundant in StDREB gene promoters. Most of the DREB genes contained one or more Myeloblastosis (MYB) and Myelocytometosis (MYC) elements associated with abiotic stress responses. Hormone-responsive element i.e. ABRE was found in 59 out of 66 StDREB genes, which implied their role in dehydration and salinity stress. Moreover, six proteins were chosen corresponding to A1-A6 StDREB subgroups for secondary structure analysis and three-dimensional protein modeling followed by model validation through PROCHECK server by Ramachandran Plot. The predicted models demonstrated >90% of the residues in the favorable region, which further ensured their reliability. The present study also anticipated pocket binding sites and disordered regions (DRs) to gain insights into the structural flexibility and functional annotation of StDREB proteins. The protein association network determined the interaction of six selected StDREB proteins with potato proteins encoded by other gene families such as MYB and NAC, suggesting their similar functional roles in biological and molecular pathways. Overall, our results provide fundamental information for future functional analysis to understand the precise molecular mechanisms of the DREB gene family in S. tuberosum.
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Affiliation(s)
- Qurat-ul ain-Ali
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Nida Mushtaq
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rabia Amir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Alvina Gul
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhammad Tahir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
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Iqbal Z, Iqbal MS, Sangpong L, Khaksar G, Sirikantaramas S, Buaboocha T. Comprehensive genome-wide analysis of calmodulin-binding transcription activator (CAMTA) in Durio zibethinus and identification of fruit ripening-associated DzCAMTAs. BMC Genomics 2021; 22:743. [PMID: 34649525 PMCID: PMC8518175 DOI: 10.1186/s12864-021-08022-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/13/2021] [Indexed: 12/11/2022] Open
Abstract
Background Fruit ripening is an intricate developmental process driven by a highly coordinated action of complex hormonal networks. Ethylene is considered as the main phytohormone that regulates the ripening of climacteric fruits. Concomitantly, several ethylene-responsive transcription factors (TFs) are pivotal components of the regulatory network underlying fruit ripening. Calmodulin-binding transcription activator (CAMTA) is one such ethylene-induced TF implicated in various stress and plant developmental processes. Results Our comprehensive analysis of the CAMTA gene family in Durio zibethinus (durian, Dz) identified 10 CAMTAs with conserved domains. Phylogenetic analysis of DzCAMTAs, positioned DzCAMTA3 with its tomato ortholog that has already been validated for its role in the fruit ripening process through ethylene-mediated signaling. Furthermore, the transcriptome-wide analysis revealed DzCAMTA3 and DzCAMTA8 as the highest expressing durian CAMTA genes. These two DzCAMTAs possessed a distinct ripening-associated expression pattern during post-harvest ripening in Monthong, a durian cultivar native to Thailand. The expression profiling of DzCAMTA3 and DzCAMTA8 under natural ripening conditions and ethylene-induced/delayed ripening conditions substantiated their roles as ethylene-induced transcriptional activators of ripening. Similarly, auxin-suppressed expression of DzCAMTA3 and DzCAMTA8 confirmed their responsiveness to exogenous auxin treatment in a time-dependent manner. Accordingly, we propose that DzCAMTA3 and DzCAMTA8 synergistically crosstalk with ethylene during durian fruit ripening. In contrast, DzCAMTA3 and DzCAMTA8 antagonistically with auxin could affect the post-harvest ripening process in durian. Furthermore, DzCAMTA3 and DzCAMTA8 interacting genes contain significant CAMTA recognition motifs and regulated several pivotal fruit-ripening-associated pathways. Conclusion Taken together, the present study contributes to an in-depth understanding of the structure and probable function of CAMTA genes in the post-harvest ripening of durian. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08022-1.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
| | - Mohammed Shariq Iqbal
- Amity Institute of Biotechnology, Amity University, Lucknow Campus, Lucknow, Uttar Pradesh, India
| | - Lalida Sangpong
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
| | - Gholamreza Khaksar
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
| | - Supaart Sirikantaramas
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand.,Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Teerapong Buaboocha
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand. .,Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
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Xu J, Gad AG, Luo Y, Fan C, Uddin JBG, ul Ain N, Huang C, Zhang Y, Miao Y, Zheng X. Five OsS40 Family Members Are Identified as Senescence-Related Genes in Rice by Reverse Genetics Approach. FRONTIERS IN PLANT SCIENCE 2021; 12:701529. [PMID: 34539694 PMCID: PMC8446524 DOI: 10.3389/fpls.2021.701529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/09/2021] [Indexed: 05/30/2023]
Abstract
A total of 16 OsS40 genes of Oryza sativa were identified in our previous work, but their functions remain unclear. In this study, 13 OsS40 members were knocked out using the CRISPR/cas9 gene-editing technology. After screening phenotype characterization of CRISPR/Cas9 mutants compared to WT, five oss40s mutants exhibited a stay-green phenotype at 30 days after heading. Moreover, increased grain size and grain weight occurred in the oss40-1, oss40-12, and oss40-14 lines, while declined grain weight appeared in the oss40-7 and oss40-13 mutants. The transcript levels of several senescence-associated genes (SAGs), chlorophyll degradation-related genes (CDGs), as well as WRKY members were differentially decreased in the five stay-green oss40s mutants compared to WT. Five oss40 mutants also exhibited a stay-green phenotype when the detached leaves were incubated under darkness for 4 days. OsSWEET4 and OsSWEET1b were significantly upregulated, while OsSWEET1a and OsSWEET13 were significantly downregulated in both oss40-7 and oss40-14 compared to WT. Furthermore, these five OsS40 displayed strong transcriptional activation activity and were located in the nucleus. Most of the OsS40 genes were downregulated in the oss40-1, oss40-7, and oss40-12 mutants, but upregulated in the oss40-13 and oss40-14 mutants, indicating coordinated regulation among OsS40 members. These results suggest that OsS40-1, OsS40-7, OsS40-12, OsS40-13, and OsS40-14 are senescence-associated genes, involved in the senescence and carbon allocation network by modulating other OsS40 members, SWEET member genes, and senescence-related gene expression.
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Qiao H, Liu Y, Cheng L, Gu X, Yin P, Li K, Zhou S, Wang G, Zhou C. TaWRKY13-A Serves as a Mediator of Jasmonic Acid-Related Leaf Senescence by Modulating Jasmonic Acid Biosynthesis. FRONTIERS IN PLANT SCIENCE 2021; 12:717233. [PMID: 34539711 PMCID: PMC8442999 DOI: 10.3389/fpls.2021.717233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Leaf senescence is crucial for crop yield and quality. Transcriptional regulation is a key step for integrating various senescence-related signals into the nucleus. However, few regulators of senescence implicating transcriptional events have been functionally characterized in wheat. Based on our RNA-seq data, we identified a WRKY transcription factor, TaWRKY13-A, that predominately expresses at senescent stages. By using the virus-induced gene silencing (VIGS) method, we manifested impaired transcription of TaWRKY13-A leading to a delayed leaf senescence phenotype in wheat. Moreover, the overexpression (OE) of TaWRKY13-A accelerated the onset of leaf senescence under both natural growth condition and darkness in Brachypodium distachyon and Arabidopsis thaliana. Furthermore, by physiological and molecular investigations, we verified that TaWRKY13-A participates in the regulation of leaf senescence via jasmonic acid (JA) pathway. The expression of JA biosynthetic genes, including AtLOX6, was altered in TaWRKY13-A-overexpressing Arabidopsis. We also demonstrated that TaWRKY13-A can interact with the promoter of AtLOX6 and TaLOX6 by using the electrophoretic mobility shift assay (EMSA) and luciferase reporter system. Consistently, we detected a higher JA level in TaWRKY13-A-overexpressing lines than that in Col-0. Moreover, our data suggested that TaWRKY13-A is partially functional conserved with AtWRKY53 in age-dependent leaf senescence. Collectively, this study manifests TaWRKY13-A as a positive regulator of JA-related leaf senescence, which could be a new clue for molecular breeding in wheat.
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Affiliation(s)
- Hualiang Qiao
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, China
| | - Yongwei Liu
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, China
| | - Lingling Cheng
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Xuelin Gu
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Pengcheng Yin
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ke Li
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Shuo Zhou
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, China
| | - Geng Wang
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Chunjiang Zhou
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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Hussain A, Noman A, Arif M, Farooq S, Khan MI, Cheng P, Qari SH, Anwar M, Hashem M, Ashraf MF, Alamri S, Adnan M, Khalofah A, Al-Zoubi OM, Ansari MJ, Khan KA, Sun Y. A basic helix-loop-helix transcription factor CabHLH113 positively regulate pepper immunity against Ralstonia solanacearum. Microb Pathog 2021; 156:104909. [PMID: 33964418 DOI: 10.1016/j.micpath.2021.104909] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/26/2021] [Accepted: 04/15/2021] [Indexed: 11/26/2022]
Abstract
Pepper's (Capsicum annum) response to bacterial pathogen Ralstonia solanacearm inoculation (RSI) and abiotic stresses is known to be synchronized by transcriptional network; however, related molecular mechanisms need extensive experimentation. We identified and characterized functions of CabHLH113 -a basic helix-loop-helix transcription factor-in pepper immunity to R. solanacearum infection. The RSI and foliar spray of phytohormones, including salicylic acid (SA), methyl jasmonate (MeJA), ethylene (ETH), and absicic acid (ABA) induced transcription of CabHLH113 in pepper. Loss of function of CabHLH113 by virus-induced-gene-silencing (VIGS) compromised defense of pepper plants against RSI and suppressed relative expression levels of immunity-associated marker genes, i.e., CaPR1, CaNPR1, CaDEF1, CaHIR1 and CaABR1. Pathogen growth was significantly increased after loss of function of CabHLH113 compared with un-silenced plants with remarkable increase in pepper susceptibility. Besides, transiently over-expression of CabHLH113 induced HR-like cell death, H2O2 accumulation and up-regulation of defense-associated marker genes, e.g. CaPR1, CaNPR1, CaDEF1, CaHIR1 and CaABR1. Additionally, transient over-expression of CabHLH113 enhanced the transcriptional levels of CaWRKY6, CaWRKY27 and CaWRKY40. Conversely, transient over-expression of CaWRKY6, CaWRKY27 and CaWRKY40 enhanced the transcriptional levels of CabHLH113. Collectively, our results indicate that newly characterized CabHLH113 has novel defense functions in pepper immunity against RSI via triggering HR-like cell death and cellular levels of defense linked genes.
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Affiliation(s)
- Ansar Hussain
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China; Department of Plant Breeding and Genetics, Ghazi University, Dera Ghazi Khan, Pakistan.
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad, Pakistan.
| | - Muhammad Arif
- Department of Plant Protection, Ghazi University, Dera Ghazi Khan, Pakistan
| | - Shahid Farooq
- Department of Agronomy, Ghazi University, Dera Ghazi Khan, Pakistan
| | - Muhammad Ifnan Khan
- Department of Plant Breeding and Genetics, Ghazi University, Dera Ghazi Khan, Pakistan
| | - Ping Cheng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China
| | - Sameer H Qari
- Biology Department, Aljumum University College, Umm Al - Qura University, Makkah, Saudi Arabia
| | - Muhammad Anwar
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, People's Republic of China
| | - Mohamed Hashem
- King Khalid University, College of Science, Department of Biology, Abha, 61413, Saudi Arabia; Assiut University, Faculty of Science, Botany and Microbiology Department, Assiut, 71516, Egypt
| | - Muhammad Furqan Ashraf
- College of Life Sciences, South China Agricultural University, No.483 Wushan Road, Tianhe District, Guangzhou, 510642, China
| | - Saad Alamri
- King Khalid University, College of Science, Department of Biology, Abha, 61413, Saudi Arabia
| | - Muhammad Adnan
- College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Ahlam Khalofah
- King Khalid University, College of Science, Department of Biology, Abha, 61413, Saudi Arabia; Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
| | | | - Mohammad Javed Ansari
- Department of Botany, Hindu College Moradabad (MJP Rohilkhand University Bareilly), 244001, India
| | - Khalid Ali Khan
- King Khalid University, College of Science, Department of Biology, Abha, 61413, Saudi Arabia; Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia; Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
| | - Yunhao Sun
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China.
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Current Understanding of Leaf Senescence in Rice. Int J Mol Sci 2021; 22:ijms22094515. [PMID: 33925978 PMCID: PMC8123611 DOI: 10.3390/ijms22094515] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/24/2021] [Indexed: 11/17/2022] Open
Abstract
Leaf senescence, which is the last developmental phase of plant growth, is controlled by multiple genetic and environmental factors. Leaf yellowing is a visual indicator of senescence due to the loss of the green pigment chlorophyll. During senescence, the methodical disassembly of macromolecules occurs, facilitating nutrient recycling and translocation from the sink to the source organs, which is critical for plant fitness and productivity. Leaf senescence is a complex and tightly regulated process, with coordinated actions of multiple pathways, responding to a sophisticated integration of leaf age and various environmental signals. Many studies have been carried out to understand the leaf senescence-associated molecular mechanisms including the chlorophyll breakdown, phytohormonal and transcriptional regulation, interaction with environmental signals, and associated metabolic changes. The metabolic reprogramming and nutrient recycling occurring during leaf senescence highlight the fundamental role of this developmental stage for the nutrient economy at the whole plant level. The strong impact of the senescence-associated nutrient remobilization on cereal productivity and grain quality is of interest in many breeding programs. This review summarizes our current knowledge in rice on (i) the actors of chlorophyll degradation, (ii) the identification of stay-green genotypes, (iii) the identification of transcription factors involved in the regulation of leaf senescence, (iv) the roles of leaf-senescence-associated nitrogen enzymes on plant performance, and (v) stress-induced senescence. Compiling the different advances obtained on rice leaf senescence will provide a framework for future rice breeding strategies to improve grain yield.
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Bhattacharjee A, Srivastava PL, Nath O, Jain M. Genome-wide discovery of OsHOX24-binding sites and regulation of desiccation stress response in rice. PLANT MOLECULAR BIOLOGY 2021; 105:205-214. [PMID: 33025523 DOI: 10.1007/s11103-020-01078-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
OsHOX24 mediates regulation of desiccation stress response via complex regulatory network as indicated by its binding to several target genes including transcription factors in rice. HD-ZIP I subfamily of homeobox transcription factors (TFs) are involved in abiotic stress responses and plant development. Previously, we demonstrated the role of OsHOX24, a member of HD-ZIP I subfamily, in abiotic stress responses. In this study, we identified downstream targets of OsHOX24 under control and desiccation stress conditions via chromatin immunoprecipitation-sequencing (ChIP-seq) approach in wild-type and OsHOX24 over-expression transgenic in rice. OsHOX24-binding sites in each sample and differential binding sites between the samples were detected at various genomic locations, including genic and intergenic regions. Gene ontology enrichment analysis revealed that OsHOX24 direct target genes were involved in several biological processes, including plant development, ABA-mediated signalling pathway, ubiquitin-dependent protein catabolic process, ion transport, abiotic and biotic stress responses besides transcriptional and translational regulation. The enrichment of several cis-regulatory motifs representing binding sites of other TFs, such as ABFs, ERF1, MYB1, LTREs and SORLIP2, suggested the involvement of OsHOX24 in a complex regulatory network. These findings indicate that OsHOX24-mediated desiccation stress regulation involves modulation of a plethora of target genes, which participate in diverse pathways in rice.
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Affiliation(s)
- Annapurna Bhattacharjee
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Prabhakar Lal Srivastava
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Onkar Nath
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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López CM, Pineda M, Alamillo JM. Differential Regulation of Drought Responses in Two Phaseolus vulgaris Genotypes. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9121815. [PMID: 33371446 PMCID: PMC7768404 DOI: 10.3390/plants9121815] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/11/2020] [Accepted: 12/20/2020] [Indexed: 05/29/2023]
Abstract
Drought is probably the most harmful stress affecting common bean crops. Domestication, worldwide spread and local farming practices has entailed the development of a wide variety of common bean genotypes with different degrees of resistance to water stress. In this work, physiological and molecular responses to water stress have been compared in two common bean accessions, PHA-0683 and PMB-0220, previously identified as highly and moderately resistant to water stress, respectively. Our hypothesis was that only quantitative differences in the expression patterns of key genes should be found if molecular mechanisms regulating drought resistance are similar in the two accessions. However, results presented here indicate that the resistance to drought in PMB-0220 and PHA-0683 common bean accessions is regulated by different molecular mechanisms. Differential regulation of ABA synthesis and ABA signaling related genes among the two genotypes, and the control of the drought-induced senescence have a relevant contribution to the higher resistance level of PHA-0683 accession. Our results also suggest that expression patterns of key senescence-related transcription factors could be considered in the screening for drought resistance in common bean germplasm collections.
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Genome-Wide Characterization and Expression Analysis of NHX Gene Family under Salinity Stress in Gossypium barbadense and Its Comparison with Gossypium hirsutum. Genes (Basel) 2020; 11:genes11070803. [PMID: 32708576 PMCID: PMC7397021 DOI: 10.3390/genes11070803] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/06/2020] [Accepted: 07/14/2020] [Indexed: 12/13/2022] Open
Abstract
Cotton is an important economic crop affected by different abiotic stresses at different developmental stages. Salinity limits the growth and productivity of crops worldwide. Na+/H+ antiporters play a key role during the plant development and in its tolerance to salt stress. The aim of the present study was a genome-wide characterization and expression pattern analysis under the salinity stress of the sodium-proton antiporter (NHX) of Gossypium barbadense in comparison with Gossypium hirsutum. In G. barbadense, 25 NHX genes were identified on the basis of the Na+_H+ exchanger domain. All except one of the G. barbadense NHX transporters have an Amiloride motif that is a known inhibitor of Na+ ions in plants. A phylogenetic analysis inferred three classes of GbNHX genes-viz., Vac (GbNHX1, 2 and 4), Endo (GbNHX6), and PM (GbNHX7). A high number of the stress-related cis-acting elements observed in promoters show their role in tolerance against abiotic stresses. The Ka/Ks values show that the majority of GbNHX genes are subjected to strong purifying selection under the course of evolution. To study the functional divergence of G. barbadense NHX transporters, the real-time gene expression was analyzed under salt stress in the root, stem, and leaf tissues. In G. barbadense, the expression was higher in the stem, while in G. hirsutum the leaf and root showed a high expression. Moreover, our results revealed that NHX2 homologues in both species have a high expression under salinity stress at higher time intervals, followed by NHX7. The protein-protein prediction study revealed that GbNHX7 is involved in the CBL-CIPK protein interaction pathway. Our study also provided valuable information explaining the molecular mechanism of Na+ transport for the further functional study of Gossypium NHX genes.
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Nabi RBS, Tayade R, Imran QM, Hussain A, Shahid M, Yun BW. Functional Insight of Nitric-Oxide Induced DUF Genes in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2020; 11:1041. [PMID: 32765550 PMCID: PMC7378322 DOI: 10.3389/fpls.2020.01041] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/24/2020] [Indexed: 05/30/2023]
Abstract
Advances in next-generation sequencing technologies facilitate the study of plant molecular functions in detail and with precision. Plant genome and proteome databases are continually being updated with large transcriptomic or genomic datasets. With the ever-increasing amount of sequencing data, several thousands of genes or proteins in public databases remain uncharacterized, and their domain functions are largely unknown. Such proteins contain domains of unknown function (DUF). In the present study, we identified 231 upregulated and 206 downregulated DUF genes from the available RNA-Seq-based transcriptome profiling datasets of Arabidopsis leaves exposed to a nitric oxide donor, S-nitroso-L-cysteine (CysNO). In addition, we performed extensive in silico and biological experiments to determine the potential functions of AtDUF569 and to elucidate its role in plant growth, development, and defense. We validated the expression pattern of the most upregulated and the most downregulated DUF genes from the transcriptomic data. In addition, a loss-of AtDUF569 function mutant was evaluated for growth, development, and defense against biotic and abiotic stresses. According to the results of the study, AtDUF569 negatively regulates biotic stress responses and differentially regulates plant growth under nitro-oxidative stress conditions.
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Affiliation(s)
- Rizwana Begum Syed Nabi
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, South Korea
| | - Rupesh Tayade
- Laboratory of Plant Breeding, School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Qari Muhammad Imran
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Adil Hussain
- Department of Agriculture, Abdul Wali Khan University, Mardan, Pakistan
| | - Muhammad Shahid
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Byung-Wook Yun
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
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Villano C, Esposito S, D'Amelia V, Garramone R, Alioto D, Zoina A, Aversano R, Carputo D. WRKY genes family study reveals tissue-specific and stress-responsive TFs in wild potato species. Sci Rep 2020; 10:7196. [PMID: 32346026 PMCID: PMC7188836 DOI: 10.1038/s41598-020-63823-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/06/2020] [Indexed: 01/30/2023] Open
Abstract
Wild potatoes, as dynamic resource adapted to various environmental conditions, represent a powerful and informative reservoir of genes useful for breeding efforts. WRKY transcription factors (TFs) are encoded by one of the largest families in plants and are involved in several biological processes such as growth and development, signal transduction, and plant defence against stress. In this study, 79 and 84 genes encoding putative WRKY TFs have been identified in two wild potato relatives, Solanum commersonii and S. chacoense. Phylogenetic analysis of WRKY proteins divided ScWRKYs and SchWRKYs into three Groups and seven subGroups. Structural and phylogenetic comparative analyses suggested an interspecific variability of WRKYs. Analysis of gene expression profiles in different tissues and under various stresses allowed to select ScWRKY045 as a good candidate in wounding-response, ScWRKY055 as a bacterial infection triggered WRKY and ScWRKY023 as a multiple stress-responsive WRKY gene. Those WRKYs were further studied through interactome analysis allowing the identification of potential co-expression relationships between ScWRKYs/SchWRKYs and genes of various pathways. Overall, this study enabled the discrimination of WRKY genes that could be considered as potential candidates in both breeding programs and functional studies.
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Affiliation(s)
- Clizia Villano
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy
| | - Salvatore Esposito
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy.,CREA Via Cavalleggeri 25, 84098, Pontecagnano-Faiano, Italy
| | - Vincenzo D'Amelia
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy.,National Research Council of Italy, Institute of Biosciences and Bioresources (CNR-IBBR), Via Università 133, Portici, NA, Italy
| | - Raffaele Garramone
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy
| | - Daniela Alioto
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy
| | | | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy.
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy.
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35
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Sun H, Hao P, Gu L, Cheng S, Wang H, Wu A, Ma L, Wei H, Yu S. Pectate lyase-like Gene GhPEL76 regulates organ elongation in Arabidopsis and fiber elongation in cotton. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 293:110395. [PMID: 32081256 DOI: 10.1016/j.plantsci.2019.110395] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/02/2019] [Accepted: 12/27/2019] [Indexed: 05/08/2023]
Abstract
Pectate lyases (PELs) play important roles in plant growth and development, mainly by degrading the pectin in primary cell walls. However, the role of PELs in cotton fiber elongation, which also involves changes in cellular structure and components, is poorly understood. Therefore, we aimed to isolate and characterize GhPEL76, as we suspected it to contribute to the regulation of fiber elongation. Expression analysis (qRT-PCR) revealed that GhPEL76 is predominately expressed in cotton fiber, with significantly different expression levels in long- and short-fiber cultivars, and that GhPEL76 expression is responsive to gibberellic acid and indoleacetic acid treatment. Furthermore, GhPEL76 promoter-driven β-glucuronidase activity was detected in the roots, hypocotyls, and leaves of transgenic Arabidopsis plants, and the overexpression of GhPEL76 in transgenic Arabidopsis promoted the elongation of several organs, including petioles, hypocotyls, primary roots, and trichomes. Additionally, the virus-induced silencing of GhPEL76 in cotton reduced fiber length, and both yeast one-hybrid and transient dual-luciferase assays suggested that GhbHLH13, a bHLH transcription factor that is up-regulated during fiber elongation, activates GhPEL76 expression by binding to the G-box of the GhPEL76 promoter region. Therefore, these results suggest GhPEL76 positively regulates fiber elongation and provide a basis for future studies of cotton fiber development.
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Affiliation(s)
- Huiru Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China; College of Life Science, Yan'an University, Yan'an, 716000, China; College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Pengbo Hao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China; College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Lijiao Gu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Shuaishuai Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China; College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Aimin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China; College of Life Science, Yan'an University, Yan'an, 716000, China.
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36
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Joly-Lopez Z, Platts AE, Gulko B, Choi JY, Groen SC, Zhong X, Siepel A, Purugganan MD. An inferred fitness consequence map of the rice genome. NATURE PLANTS 2020; 6:119-130. [PMID: 32042156 PMCID: PMC7446671 DOI: 10.1038/s41477-019-0589-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 12/20/2019] [Indexed: 05/04/2023]
Abstract
The extent to which sequence variation impacts plant fitness is poorly understood. High-resolution maps detailing the constraint acting on the genome, especially in regulatory sites, would be beneficial as functional annotation of noncoding sequences remains sparse. Here, we present a fitness consequence (fitCons) map for rice (Oryza sativa). We inferred fitCons scores (ρ) for 246 inferred genome classes derived from nine functional genomic and epigenomic datasets, including chromatin accessibility, messenger RNA/small RNA transcription, DNA methylation, histone modifications and engaged RNA polymerase activity. These were integrated with genome-wide polymorphism and divergence data from 1,477 rice accessions and 11 reference genome sequences in the Oryzeae. We found ρ to be multimodal, with ~9% of the rice genome falling into classes where more than half of the bases would probably have a fitness consequence if mutated. Around 2% of the rice genome showed evidence of weak negative selection, frequently at candidate regulatory sites, including a novel set of 1,000 potentially active enhancer elements. This fitCons map provides perspective on the evolutionary forces associated with genome diversity, aids in genome annotation and can guide crop breeding programs.
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Affiliation(s)
- Zoé Joly-Lopez
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Adrian E Platts
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Brad Gulko
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Simon C Groen
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Xuehua Zhong
- Laboratory of Genetics and Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA.
- Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates.
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Xu W, Tang W, Wang C, Ge L, Sun J, Qi X, He Z, Zhou Y, Chen J, Xu Z, Ma YZ, Chen M. SiMYB56 Confers Drought Stress Tolerance in Transgenic Rice by Regulating Lignin Biosynthesis and ABA Signaling Pathway. FRONTIERS IN PLANT SCIENCE 2020; 11:785. [PMID: 32625221 PMCID: PMC7314972 DOI: 10.3389/fpls.2020.00785] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/18/2020] [Indexed: 05/19/2023]
Abstract
Foxtail millet (Setaria italica) originated in China and is generally cultivated in arid and barren soil. Through long-term harsh environmental selection, foxtail millet has acquired significant drought resistance. However, the molecular mechanism of foxtail millet drought resistance is still unknown. Here, we identified a drought-induced R2R3-MYB transcription factor SiMYB56 in foxtail millet. Overexpression of SiMYB56 significantly enhances tolerance to drought stress in transgenic rice plants at both the vegetative and the reproductive stage and has no adverse effect on its normal growth. Compared with wild-type controls, SiMYB56-overexpressing rice plants had lower MDA content and higher lignin content under drought conditions. Quantitative real-time PCR and Transcriptional activity assays demonstrated that SiMYB56 could activate expression of lignin biosynthesis genes under drought conditions. Also, we found that overexpression of SiMYB56 can led to ABA accumulation in the seeds transgenic rice plants. Further experiments showed that Overexpression of SiMYB56 can upregulate the expression of ABA synthesis and response related genes under drought conditions. In conclusion, SiMYB56 may enhance the drought resistance of transgenic rice plants by regulating lignin biosynthesis and ABA signaling pathway, making SiMYB56 a candidate gene for drought resistance improvement in gramineous crops.
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Affiliation(s)
- Weiya Xu
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wensi Tang
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunxiao Wang
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Linhao Ge
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianchang Sun
- Institute of Crop Sciences, Ningxia Academy of Agriculture and Forestry Sciences, Yongning, China
| | - Xin Qi
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhang He
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongbin Zhou
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Chen
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhaoshi Xu
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - You-Zhi Ma
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: You-Zhi Ma,
| | - Ming Chen
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Ming Chen,
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Zentgraf U, Doll J. Arabidopsis WRKY53, a Node of Multi-Layer Regulation in the Network of Senescence. PLANTS (BASEL, SWITZERLAND) 2019; 8:E578. [PMID: 31817659 PMCID: PMC6963213 DOI: 10.3390/plants8120578] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 12/24/2022]
Abstract
Leaf senescence is an integral part of plant development aiming at the remobilization of nutrients and minerals out of the senescing tissue into developing parts of the plant. Sequential as well as monocarpic senescence maximize the usage of nitrogen, mineral, and carbon resources for plant growth and the sake of the next generation. However, stress-induced premature senescence functions as an exit strategy to guarantee offspring under long-lasting unfavorable conditions. In order to coordinate this complex developmental program with all kinds of environmental input signals, complex regulatory cues have to be in place. Major changes in the transcriptome imply important roles for transcription factors. Among all transcription factor families in plants, the NAC and WRKY factors appear to play central roles in senescence regulation. In this review, we summarize the current knowledge on the role of WRKY factors with a special focus on WRKY53. In contrast to a holistic multi-omics view we want to exemplify the complexity of the network structure by summarizing the multilayer regulation of WRKY53 of Arabidopsis.
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Affiliation(s)
- Ulrike Zentgraf
- Center for Plant Molecular Biology (ZMBP), University of Tuebingen, Auf der Morgenstelle 32, 72076 Tuebingen, Germany;
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Liu H, Cao M, Chen X, Ye M, Zhao P, Nan Y, Li W, Zhang C, Kong L, Kong N, Yang C, Chen Y, Wang D, Chen Q. Genome-Wide Analysis of the Lateral Organ Boundaries Domain (LBD) Gene Family in Solanum tuberosum. Int J Mol Sci 2019; 20:ijms20215360. [PMID: 31661866 PMCID: PMC6861928 DOI: 10.3390/ijms20215360] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/13/2019] [Accepted: 10/22/2019] [Indexed: 11/16/2022] Open
Abstract
Lateral organ boundaries domain (LBD) proteins belong to a particular class of transcription factors of lateral organ boundary (LOB) specific domains that play essential roles in plant growth and development. However, a potato phylogenetic analysis of the LBD family has not been fully studied by scholars and researchers. In this research, bioinformatics methods and the growth of potatoes were used to identify 43 StLBD proteins. We separated them into seven subfamilies: Ia, Ib, Ic, Id, Ie, IIa and IIb. The number of amino acids encoded by the potato LBD family ranged from 94 to 327. The theoretical isoelectric point distribution ranged from 4.16 to 9.12 Kda, and they were distributed among 10 chromosomes. The results of qRT-PCR showed that the expression levels of StLBD2-6 and StLBD3-5 were up-regulated under drought stress in the stem. The expression levels of StLBD1-5 and StLBD2-6 were down-regulated in leaves. We hypothesized that StLBD1-5 was down-regulated under drought stress, and that StLBD2-6 and StLBD3-5 up-regulation might help to maintain the normal metabolism of potato and enhance the potatoes’ resistance to drought.
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Affiliation(s)
- Hengzhi Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Minxuan Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Xiaoli Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Minghui Ye
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Peng Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Yunyou Nan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Wan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Chao Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Lingshuang Kong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Nana Kong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Chenghui Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Yue Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Dongdong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Qin Chen
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China.
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OsWRKY5 Promotes Rice Leaf Senescence via Senescence-Associated NAC and Abscisic Acid Biosynthesis Pathway. Int J Mol Sci 2019; 20:ijms20184437. [PMID: 31505875 PMCID: PMC6770167 DOI: 10.3390/ijms20184437] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/07/2019] [Accepted: 09/08/2019] [Indexed: 01/31/2023] Open
Abstract
The onset of leaf senescence is triggered by external cues and internal factors such as phytohormones and signaling pathways involving transcription factors (TFs). Abscisic acid (ABA) strongly induces senescence and endogenous ABA levels are finely tuned by many senescence-associated TFs. Here, we report on the regulatory function of the senescence-induced TF OsWRKY5 TF in rice (Oryza sativa). OsWRKY5 expression was rapidly upregulated in senescing leaves, especially in yellowing sectors initiated by aging or dark treatment. A T-DNA insertion activation-tagged OsWRKY5-overexpressing mutant (termed oswrky5-D) promoted leaf senescence under natural and dark-induced senescence (DIS) conditions. By contrast, a T-DNA insertion oswrky5-knockdown mutant (termed oswrky5) retained leaf greenness during DIS. Reverse-transcription quantitative PCR (RT-qPCR) showed that OsWRKY5 upregulates the expression of genes controlling chlorophyll degradation and leaf senescence. Furthermore, RT-qPCR and yeast one-hybrid analysis demonstrated that OsWRKY5 indirectly upregulates the expression of senescence-associated NAM/ATAF1/2/CUC2 (NAC) genes including OsNAP and OsNAC2. Precocious leaf yellowing in the oswrky5-D mutant might be caused by elevated endogenous ABA concentrations resulting from upregulated expression of ABA biosynthesis genes OsNCED3, OsNCED4, and OsNCED5, indicating that OsWRKY is a positive regulator of ABA biosynthesis during leaf senescence. Furthermore, OsWRKY5 expression was suppressed by ABA treatment. Taken together, OsWRKY5 is a positive regulator of leaf senescence that upregulates senescence-induced NAC, ABA biosynthesis, and chlorophyll degradation genes.
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Zheng X, Jehanzeb M, Zhang Y, Li L, Miao Y. Characterization of S40-like proteins and their roles in response to environmental cues and leaf senescence in rice. BMC PLANT BIOLOGY 2019; 19:174. [PMID: 31046677 PMCID: PMC6498481 DOI: 10.1186/s12870-019-1767-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/09/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND Senescence affects the quality and yield of plants by regulating different traits of plants. A few members of S40 gene family, the barley HvS40 and the Arabidopsis AtS40-3, have been shown to play a role in leaf senescence in Barley and Arabidopsis. Although we previously reported that S40 family exist in most of plants, up to now, no more function of S40 members in plant has been demonstrated. The aim of this study was to provide the senescence related information of S40 gene family in rice as rice is a major crop that feeds about half of the human population in the world. RESULTS A total of 16 OsS40 genes were identified from the genome database of Oryza sativa L. japonica by bioinformatics analysis. Phylogenetic analysis reveals that the 16 OsS40 proteins are classified into five groups, and 4 of the 16 members belong to group I to which also the HvS40 and AtS40-3 is assigned. S40 genes of rice show high structural similarities, as 13 out of the 16 genes have no intron and the other 3 genes have only 1 or 2 introns. The expression patterns of OsS40 genes were analyzed during natural as well as stress-induced leaf senescence in correspondence with senescence marker genes. We found that 6 of them displayed differential but clearly up-regulated transcript profiles under diverse situations of senescence, including darkness, nitrogen deficiency, hormone treatments as well as pathogen infection. Furthermore, three OsS40 proteins were identified as nuclear located proteins by transient protoplast transformation assay. CONCLUSIONS Taking all findings together, we concluded that OsS40-1, OsS40-2, OsS40-12 and OsS40-14 genes have potential regulatory function of crosstalk among abiotic, biotic and developmental senescence in rice. Our results provide valuable baseline for functional validation studies of the rice S40 genes in rice leaf senescence.
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Affiliation(s)
- Xiangzi Zheng
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Muhammad Jehanzeb
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Yuanyuan Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Li Li
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China.
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Gu L, Dou L, Guo Y, Wang H, Li L, Wang C, Ma L, Wei H, Yu S. The WRKY transcription factor GhWRKY27 coordinates the senescence regulatory pathway in upland cotton (Gossypium hirsutum L.). BMC PLANT BIOLOGY 2019; 19:116. [PMID: 30922232 PMCID: PMC6440019 DOI: 10.1186/s12870-019-1688-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 02/19/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Premature senescence can reduce the yield and quality of crops. WRKY transcription factors (TFs) play important roles during leaf senescence, but little is known about their ageing mechanisms in cotton. RESULTS In this study, a group III WRKY TF, GhWRKY27, was isolated and characterized. The expression of GhWRKY27 was induced by leaf senescence and was higher in an early-ageing cotton variety than in a non-early-ageing cotton variety. Overexpression of GhWRKY27 in Arabidopsis promoted leaf senescence, as determined by reduced chlorophyll content and elevated expression of senescence-associated genes (SAGs). Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that GhWRKY27 interacted with an MYB TF, GhTT2. Putative target genes of GhWRKY27 were identified via chromatin immunoprecipitation followed by sequencing (ChIP-seq). Yeast one-hybrid (Y1H) assay and electrophoretic mobility shift assay (EMSA) revealed that GhWRKY27 binds directly to the promoters of cytochrome P450 94C1 (GhCYP94C1) and ripening-related protein 2 (GhRipen2-2). In addition, the expression patterns of GhTT2, GhCYP94C1 and GhRipen2-2 were identified during leaf senescence. Transient dual-luciferase reporter assay indicated that GhWRKY27 could activate the expression of GhCYP94C1 and GhRipen2-2. CONCLUSIONS Our work lays the foundation for further study of the functional roles of WRKY genes during leaf senescence in cotton. In addition, our data provide new insights into the senescence-associated mechanisms of WRKY genes in cotton.
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Affiliation(s)
- Lijiao Gu
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Lingling Dou
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Yaning Guo
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Libei Li
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Congcong Wang
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
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Wang Y, Zhang N, Li T, Yang J, Zhu X, Fang C, Li S, Si H. Genome-wide identification and expression analysis of StTCP transcription factors of potato (Solanum tuberosum L.). Comput Biol Chem 2018; 78:53-63. [PMID: 30497020 DOI: 10.1016/j.compbiolchem.2018.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 11/06/2018] [Accepted: 11/15/2018] [Indexed: 12/19/2022]
Abstract
The plant-specific TCP transcription factors, which play critical roles in diverse aspects of biological processes, have been identified and analyzed in various plant species. However, no systematical study of TCP family genes in potato (Solanum tuberosum L.) has been undertaken. In this study, a total of 31 non-redundant TCP transcription factors of potato were identified and divided into two subfamilies including three distinct subclades. The various orthologous TCP genes in Arabidopsis, rice, potato and tomato were identified using synteny and phylogenetic analysis. Protein motif analysis demonstrated that StTCPs in the same subclade shared similar conserved motif structures. Gene structure analysis showed that almost all StTCPs displayed highly conserved exon-intron organization. The analysis of StTCP gene promoter regions revealed that multiple cis-acting elements were involved in plant growth, development, hormone responses as well as stress responses. The result of StTCP gene expression profiles showed they had tissue-specific expression patterns which implied their differentiated functions. According to the results of quantitative RT-PCR (qRT-PCR), 7 StTCP genes were dramatically up-regulated during the release of tuber dormancy and some specific StTCP genes were strongly responding to different abiotic stresses and multiple hormones, which suggested they had important roles in potato growth and development processes. The results of our findings could provide comprehensive insights in StTCP family genes of potato for further functional investigations.
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Affiliation(s)
- Yapeng Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science/Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, China; College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
| | - Ning Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Ting Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Jiangwei Yang
- Gansu Provincial Key Laboratory of Aridland Crop Science/Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Xi Zhu
- Gansu Provincial Key Laboratory of Aridland Crop Science/Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, China; College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
| | - Chenxi Fang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Shigui Li
- Gansu Provincial Key Laboratory of Aridland Crop Science/Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Huaijun Si
- Gansu Provincial Key Laboratory of Aridland Crop Science/Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
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Wang W, Guo X, Li YM, Wang XY, Yang XJ, Wang YF, Wang TY. Enhanced transgene expression using cis-acting elements combined with the EF1 promoter in a mammalian expression system. Eur J Pharm Sci 2018; 123:539-545. [DOI: 10.1016/j.ejps.2018.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/12/2018] [Accepted: 08/11/2018] [Indexed: 10/28/2022]
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Gu L, Wei H, Wang H, Su J, Yu S. Characterization and functional analysis of GhWRKY42, a group IId WRKY gene, in upland cotton (Gossypium hirsutum L.). BMC Genet 2018; 19:48. [PMID: 30060731 PMCID: PMC6065155 DOI: 10.1186/s12863-018-0653-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 07/11/2018] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND WRKY transcription factors (TFs) participate in various physiological processes of plants. Although WRKY genes have been well studied in model plants, knowledge of the functional roles of these genes is still extremely limited in cotton. RESULTS In this study, a group IId WRKY gene from cotton, GhWRKY42, was isolated and characterized. Our data showed that GhWRKY42 localized to the nucleus. A transactivation assay in yeast demonstrated that GhWRKY42 was not a transcriptional activator. A β-glucuronidase (GUS) activity assay revealed that the promoter of GhWRKY42 showed fragment deletion activity in Nicotiana tabacum and was mainly expressed in the roots, stems and leaves of ProGhWRKY42::GUS transgenic Arabidopsis plants. Quantitative real-time PCR (qRT-PCR) analysis indicated that GhWRKY42 was up-regulated during leaf senescence and was induced after exposure to abiotic stresses. Constitutive expression of GhWRKY42 in Arabidopsis led to a premature aging phenotype, which was correlated with an increased number of senescent leaves, reduced chlorophyll content and elevated expression of senescence-associated genes (SAGs). In addition, virus-induced gene silencing (VIGS) was used to silence the endogenous GhWRKY42 gene in cotton, and this silencing reduced plant height. CONCLUSIONS Our findings indicate that GhWRKY42 is involved in abiotic stress responses, premature leaf senescence and stem development. This work establishes a solid foundation for further functional analysis of the GhWRKY42 gene in cotton.
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Affiliation(s)
- Lijiao Gu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
| | - Junji Su
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, People's Republic of China.
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Hima Kumari P, Anil Kumar S, Ramesh K, Sudhakar Reddy P, Nagaraju M, Bhanu Prakash A, Shah T, Henderson A, Srivastava RK, Rajasheker G, Chitikineni A, Varshney RK, Rathnagiri P, Lakshmi Narasu M, Kavi Kishor PB. Genome-Wide Identification and Analysis of Arabidopsis Sodium Proton Antiporter (NHX) and Human Sodium Proton Exchanger (NHE) Homologs in Sorghum bicolor. Genes (Basel) 2018; 9:genes9050236. [PMID: 29751546 PMCID: PMC5977176 DOI: 10.3390/genes9050236] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 11/16/2022] Open
Abstract
Na⁺ transporters play an important role during salt stress and development. The present study is aimed at genome-wide identification, in silico analysis of sodium-proton antiporter (NHX) and sodium-proton exchanger (NHE)-type transporters in Sorghum bicolor and their expression patterns under varied abiotic stress conditions. In Sorghum, seven NHX and nine NHE homologs were identified. Amiloride (a known inhibitor of Na⁺/H⁺ exchanger activity) binding motif was noticed in both types of the transporters. Chromosome 2 was found to be a hotspot region with five sodium transporters. Phylogenetic analysis inferred six ortholog and three paralog groups. To gain an insight into functional divergence of SbNHX/NHE transporters, real-time gene expression was performed under salt, drought, heat, and cold stresses in embryo, root, stem, and leaf tissues. Expression patterns revealed that both SbNHXs and SbNHEs are responsive either to single or multiple abiotic stresses. The predicted protein⁻protein interaction networks revealed that only SbNHX7 is involved in the calcineurin B-like proteins (CBL)- CBL interacting protein kinases (CIPK) pathway. The study provides insights into the functional divergence of SbNHX/NHE transporter genes with tissue specific expressions in Sorghum under different abiotic stress conditions.
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Affiliation(s)
- P Hima Kumari
- Department of Genetics, Osmania University, Hyderabad 500 007, India.
- Centre for Biotechnology, Institute of Science & Technology, JNT University, Hyderabad 500 085, India.
| | - S Anil Kumar
- Department of Genetics, Osmania University, Hyderabad 500 007, India.
- Centre for Biotechnology, Institute of Science & Technology, JNT University, Hyderabad 500 085, India.
| | - Katam Ramesh
- Department of Biological Sciences, Florida A&M University, Tallahassee, FL 32307, USA.
| | - Palakolanu Sudhakar Reddy
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India.
| | - M Nagaraju
- Department of Genetics, Osmania University, Hyderabad 500 007, India.
| | - A Bhanu Prakash
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India.
| | - Trushar Shah
- IITA-Kenya c/o International Livestock Research Institute (ILRI), PO Box 30709, Nairobi 00100, Kenya.
| | - Ashley Henderson
- Department of Biological Sciences, Florida A&M University, Tallahassee, FL 32307, USA.
- Ottawa University, Ottawa, KS 66067, USA.
| | - Rakesh K Srivastava
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India.
| | - G Rajasheker
- Department of Genetics, Osmania University, Hyderabad 500 007, India.
| | - A Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India.
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India.
| | - P Rathnagiri
- Genomix CARL Pvt. Ltd. Rayalapuram Road, Pulivendula, 516 390, Kadapa, Andhra Pradesh, India.
| | - M Lakshmi Narasu
- Centre for Biotechnology, Institute of Science & Technology, JNT University, Hyderabad 500 085, India.
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad 500 007, India.
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Abedini D, Rashidi Monfared S. Co-regulation analysis of co-expressed modules under cold and pathogen stress conditions in tomato. Mol Biol Rep 2018; 45:335-345. [PMID: 29551007 DOI: 10.1007/s11033-018-4166-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/13/2018] [Indexed: 11/28/2022]
Abstract
A primary mechanism for controlling the development of multicellular organisms is transcriptional regulation, which carried out by transcription factors (TFs) that recognize and bind to their binding sites on promoter region. The distance from translation start site, order, orientation, and spacing between cis elements are key factors in the concentration of active nuclear TFs and transcriptional regulation of target genes. In this study, overrepresented motifs in cold and pathogenesis responsive genes were scanned via Gibbs sampling method, this method is based on detection of overrepresented motifs by means of a stochastic optimization strategy that searches for all possible sets of short DNA segments. Then, identified motifs were checked by TRANSFAC, PLACE and Soft Berry databases in order to identify putative TFs which, interact to the motifs. Several cis/trans regulatory elements were found using these databases. Moreover, cross-talk between cold and pathogenesis responsive genes were confirmed. Statistical analysis was used to determine distribution of identified motifs on promoter region. In addition, co-regulation analysis results, illustrated genes in pathogenesis responsive module are divided into two main groups. Also, promoter region was crunched to six subareas in order to draw the pattern of distribution of motifs in promoter subareas. The result showed the majority of motifs are concentrated on 700 nucleotides upstream of the translational start site (ATG). In contrast, this result isn't true in another group. In other words, there was no difference between total and compartmentalized regions in cold responsive genes.
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Affiliation(s)
- Davar Abedini
- Department of Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Sajad Rashidi Monfared
- Department of Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
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Li N, Wei S, Chen J, Yang F, Kong L, Chen C, Ding X, Chu Z. OsASR2 regulates the expression of a defence-related gene, Os2H16, by targeting the GT-1 cis-element. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:771-783. [PMID: 28869785 PMCID: PMC5814579 DOI: 10.1111/pbi.12827] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 08/23/2017] [Indexed: 05/11/2023]
Abstract
The GT-1 cis-element widely exists in many plant gene promoters. However, the molecular mechanism that underlies the response of the GT-1 cis-element to abiotic and biotic stresses remains elusive in rice. We previously isolated a rice short-chain peptide-encoding gene, Os2H16, and demonstrated that it plays important roles in both disease resistance and drought tolerance. Here, we conducted a promoter assay of Os2H16 and identified GT-1 as an important cis-element that mediates Os2H16 expression in response to pathogen attack and osmotic stress. Using the repeated GT-1 as bait, we characterized an abscisic acid, stress and ripening 2 (ASR2) protein from yeast-one hybridization screening. Sequence alignments showed that the carboxy-terminal domain of OsASR2 containing residues 80-138 was the DNA-binding domain. Furthermore, we identified that OsASR2 was specifically bound to GT-1 and activated the expression of the target gene Os2H16, as well as GFP driven by the chimeric promoter of 2 × GT-1-35S mini construct. Additionally, the expression of OsASR2 was elevated by pathogens and osmotic stress challenges. Overexpression of OsASR2 enhanced the resistance against Xanthomonas oryzae pv. oryzae and Rhizoctonia solani, and tolerance to drought in rice. These results suggest that the interaction between OsASR2 and GT-1 plays an important role in the crosstalk of the response of rice to biotic and abiotic stresses.
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Affiliation(s)
- Ning Li
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTaianShandongChina
| | - Shutong Wei
- Shandong Provincial Key Laboratory for Biology of Vegetable Disease and Insect PestsCollege of Plant ProtectionShandong Agricultural UniversityTaianShandongChina
| | - Jing Chen
- Shandong Provincial Key Laboratory for Biology of Vegetable Disease and Insect PestsCollege of Plant ProtectionShandong Agricultural UniversityTaianShandongChina
| | - Fangfang Yang
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTaianShandongChina
| | - Lingguang Kong
- Shandong Provincial Key Laboratory for Biology of Vegetable Disease and Insect PestsCollege of Plant ProtectionShandong Agricultural UniversityTaianShandongChina
| | - Cuixia Chen
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTaianShandongChina
| | - Xinhua Ding
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTaianShandongChina
- Shandong Provincial Key Laboratory for Biology of Vegetable Disease and Insect PestsCollege of Plant ProtectionShandong Agricultural UniversityTaianShandongChina
| | - Zhaohui Chu
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTaianShandongChina
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Leng Y, Ye G, Zeng D. Genetic Dissection of Leaf Senescence in Rice. Int J Mol Sci 2017; 18:E2686. [PMID: 29232920 PMCID: PMC5751288 DOI: 10.3390/ijms18122686] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/28/2017] [Accepted: 12/01/2017] [Indexed: 12/04/2022] Open
Abstract
Leaf senescence, the final stage of leaf development, is a complex and highly regulated process that involves a series of coordinated actions at the cellular, tissue, organ, and organism levels under the control of a highly regulated genetic program. In the last decade, the use of mutants with different levels of leaf senescence phenotypes has led to the cloning and functional characterizations of a few genes, which has greatly improved the understanding of genetic mechanisms underlying leaf senescence. In this review, we summarize the recent achievements in the genetic mechanisms in rice leaf senescence.
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Affiliation(s)
- Yujia Leng
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
- CAAS-IRRI Joint Laboratory for Genomics-assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| | - Guoyou Ye
- CAAS-IRRI Joint Laboratory for Genomics-assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| | - Dali Zeng
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
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50
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Liu B, Zhao S, Wu X, Wang X, Nan Y, Wang D, Chen Q. Identification and characterization of phosphate transporter genes in potato. J Biotechnol 2017; 264:17-28. [DOI: 10.1016/j.jbiotec.2017.10.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 10/17/2017] [Accepted: 10/17/2017] [Indexed: 10/18/2022]
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