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Qin J, Hou X, Wang H, Yuan T, Wei H, Liu G, Chen Y, Lian B, Zhong F, Zhang J, Yu C. Comparative genomic analysis reveals expansion of the DnaJ gene family in Lagerstroemia indica and its members response to salt stress. Genetica 2024; 152:101-117. [PMID: 38724749 DOI: 10.1007/s10709-024-00208-1] [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: 11/11/2023] [Accepted: 04/18/2024] [Indexed: 06/26/2024]
Abstract
DnaJs/Hsp40s/JPDs are obligate co-chaperones of heat shock proteins (Hsp70), performing crucial biological functions within organisms. A comparative genome analysis of four genomes (Vitis vinifera, Eucalyptus grandis, Lagerstroemia indica, and Punica granatum) revealed that the DnaJ gene family in L. indica has undergone expansion, although not to the extent observed in P. granatum. Inter-genome collinearity analysis of four plants indicates that members belonging to Class A and B are more conserved during evolution. In L. indica, the expanded members primarily belong to Class-C. Tissue expression patterns and the biochemical characterization of LiDnaJs further suggested that DnaJs may be involved in numerous biological processes in L. indica. Transcriptome and qPCR analyses of salt stressed leaves identified at least ten LiDnaJs that responded to salt stress. In summary, we have elucidated the expansion mechanism of the LiDnaJs, which is attributed to a recent whole-genome triplication. This research laid the foundation for functional analysis of LiDnaJs and provides gene resources for breeding salt-tolerant varieties of L. indica.
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Affiliation(s)
- Jin Qin
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Xiaoyu Hou
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Huanzhe Wang
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Tianyi Yuan
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Hui Wei
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong University, NO.9 Seyuan Road, Nantong, 226019, Jiangsu, China
| | - Guoyuan Liu
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong University, NO.9 Seyuan Road, Nantong, 226019, Jiangsu, China
| | - Yanhong Chen
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong University, NO.9 Seyuan Road, Nantong, 226019, Jiangsu, China
| | - Bolin Lian
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong University, NO.9 Seyuan Road, Nantong, 226019, Jiangsu, China
| | - Fei Zhong
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong University, NO.9 Seyuan Road, Nantong, 226019, Jiangsu, China
| | - Jian Zhang
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China.
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong University, NO.9 Seyuan Road, Nantong, 226019, Jiangsu, China.
| | - Chunmei Yu
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China.
- Key Laboratory of Landscape Plant Genetics and Breeding, Nantong University, NO.9 Seyuan Road, Nantong, 226019, Jiangsu, China.
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Wang J, Long W, Pan J, Zhang X, Luo L, Qian M, Chen W, Luo L, Xu W, Li Y, Cai Y, Xie H. DNAL7, a new allele of NAL11, has major pleiotropic effects on rice architecture. PLANTA 2024; 259:93. [PMID: 38509429 DOI: 10.1007/s00425-024-04376-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
MAIN CONCLUSION dnal7, a novel allelic variant of the OsHSP40, affects rice plant architecture and grain yield by coordinating auxins, cytokinins, and gibberellic acids. Plant height and leaf morphology are the most important traits of the ideal plant architecture (IPA), and discovering related genes is critical for breeding high-yield rice. Here, a dwarf and narrow leaf 7 (dnal7) mutant was identified from a γ-ray treated mutant population, which exhibits pleiotropic effects, including dwarfing, narrow leaves, small seeds, and low grain yield per plant compared to the wild type (WT). Histological analysis showed that the number of veins and the distance between adjacent small veins (SVs) were significantly reduced compared to the WT, indicating that DNAL7 controls leaf size by regulating the formation of veins. Map-based cloning and transgenic complementation revealed that DNAL7 is allelic to NAL11, which encodes OsHSP40, and the deletion of 2 codons in dnal7 destroyed the His-Pro-Asp (HPD) motif of OsHSP40. In addition, expression of DNAL7 in both WT and dnal7 gradually increased with the increase of temperature in the range of 27-31 °C. Heat stress significantly affected the seedling height and leaf width of the dnal7 mutant. A comparative transcriptome analysis of WT and dnal7 revealed that DNAL7 influenced multiple metabolic pathways, including plant hormone signal transduction, carbon metabolism, and biosynthesis of amino acids. Furthermore, the contents of the cytokinins in leaf blades were much higher in dnal7 than in the WT, whereas the contents of auxins were lower in dnal7. The contents of bioactive gibberellic acids (GAs) including GA1, GA3, and GA4 in shoots were decreased in dnal7. Thus, DNAL7 regulates rice plant architecture by coordinating the balance of auxins, cytokinins, and GAs. These results indicate that OsHSP40 is a pleiotropic gene, which plays an important role in improving rice yield and plant architecture.
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Affiliation(s)
- Jie Wang
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Center for Rice, Nanchang, 330200, Jiangxi, China
- Applied Biotechnology Research Center, Wuhan University of Bioengineering, Wuhan, 430415, Hubei, China
| | - Weixiong Long
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Center for Rice, Nanchang, 330200, Jiangxi, China
| | - Jintao Pan
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Center for Rice, Nanchang, 330200, Jiangxi, China
| | - Xiaolin Zhang
- Applied Biotechnology Research Center, Wuhan University of Bioengineering, Wuhan, 430415, Hubei, China
| | - Lihua Luo
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Center for Rice, Nanchang, 330200, Jiangxi, China
| | - Mingjuan Qian
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Center for Rice, Nanchang, 330200, Jiangxi, China
| | - Wei Chen
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Center for Rice, Nanchang, 330200, Jiangxi, China
| | - Laiyang Luo
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Center for Rice, Nanchang, 330200, Jiangxi, China
| | - Weibiao Xu
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Center for Rice, Nanchang, 330200, Jiangxi, China
| | - Yonghui Li
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Center for Rice, Nanchang, 330200, Jiangxi, China
| | - Yaohui Cai
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Center for Rice, Nanchang, 330200, Jiangxi, China
| | - Hongwei Xie
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Center for Rice, Nanchang, 330200, Jiangxi, China.
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Ren W, Ding B, Dong W, Yue Y, Long X, Zhou Z. Unveiling HSP40/60/70/90/100 gene families and abiotic stress response in Jerusalem artichoke. Gene 2024; 893:147912. [PMID: 37863300 DOI: 10.1016/j.gene.2023.147912] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/28/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
Heat shock proteins (HSPs) are essential for plant growth, development, and stress adaptation. However, their roles in Jerusalem artichoke are largely unexplored. Using bioinformatics, we classified 143 HSP genes into distinct families: HSP40 (82 genes), HSP60 (22 genes), HSP70 (29 genes), HSP90 (6 genes), and HSP100 (4 genes). Our analysis covered their traits, evolution, and structures. Using RNA-seq data, we uncovered unique expression patterns of these HSP genes across growth stages and tissues. Notably, HSP40, HSP60, HSP70, HSP90, and HSP100 families each had specific roles. We also studied how these gene families responded to various stresses, from extreme temperatures to drought and salinity, revealing intricate expression dynamics. Remarkably, HSP40 showed remarkable flexibility, while HSP60, HSP70, HSP90, and HSP100 responded specifically to stress types. Moreover, our analysis unveiled significant correlations between gene pairs under stress, implying cooperative interactions. qRT-PCR validation underscored the significance of particular genes such as HtHSP60-7, HtHSP90-5, HtHSP100-2, and HtHSP100-3 in responding to stress. In summary, our study advances the understanding of how HSP gene families collectively manage stresses in Jerusalem artichoke. This provides insights into specific gene functions and broader plant stress responses.
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Affiliation(s)
- Wencai Ren
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Baishui Ding
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenhan Dong
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Yue
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaohua Long
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaosheng Zhou
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Gao H, Lin X, Yuan X, Zou J, Zhang H, Zhang Y, Liu Z. The salivary chaperone protein NlDNAJB9 of Nilaparvata lugens activates plant immune responses. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6874-6888. [PMID: 37103882 DOI: 10.1093/jxb/erad154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/25/2023] [Indexed: 06/19/2023]
Abstract
The brown planthopper (BPH) Nilaparvata lugens (Stål) is a main pest on rice. It secretes saliva to regulate plant defense responses, when penetrating rice plant and sucking phloem sap through its stylet. However, the molecular mechanisms of BPH salivary proteins regulating plant defense responses remain poorly understood. A N. lugens DNAJ protein (NlDNAJB9) gene was highly expressed in salivary glands, and the knock down of NlDNAJB9 significantly enhanced honeydew excretion and fecundity of the BPH. NlDNAJB9 could induce plant cell death, and the overexpression of NlDNAJB9 gene in Nicotiana benthamiana induced calcium signaling, mitogen-activated protein kinase (MAPK) cascades, reactive oxygen species (ROS) accumulation, jasmonic acid (JA) hormone signaling and callose deposition. The results from different NlDNAJB9 deletion mutants indicated that the nuclear localization of NlDNAJB9 was not necessary to induce cell death. The DNAJ domain was the key region to induce cell death, and the overexpression of DNAJ domain in N. benthamiana significantly inhibited insect feeding and pathogenic infection. NlDNAJB9 might interact indirectly with NlHSC70-3 to regulate plant defense responses. NlDNAJB9 and its orthologs were highly conserved in three planthopper species, and could induce ROS burst and cell death in plants. Our study provides new insights into the molecular mechanisms of insect-plant interactions.
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Affiliation(s)
- Haoli Gao
- Key laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Xumin Lin
- Key laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Xiaowei Yuan
- Key laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Jianzheng Zou
- Key laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Huihui Zhang
- Key laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Yixi Zhang
- Key laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Zewen Liu
- Key laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
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Bekele-Alemu A, Ligaba-Osena A. Comprehensive in silico analysis of the underutilized crop tef (Eragrostis tef (Zucc.) Trotter) genome reveals drought tolerance signatures. BMC PLANT BIOLOGY 2023; 23:506. [PMID: 37865758 PMCID: PMC10589971 DOI: 10.1186/s12870-023-04515-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/05/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Tef (Eragrostis tef) is a C4 plant known for its tiny, nutritious, and gluten-free grains. It contains higher levels of protein, vitamins, and essential minerals like calcium (Ca), iron (Fe), copper (Cu), and zinc (Zn) than common cereals. Tef is cultivated in diverse ecological zones under diverse climatic conditions. Studies have shown that tef has great diversity in withstanding environmental challenges such as drought. Drought is a major abiotic stress severely affecting crop productivity and becoming a bottleneck to global food security. Here, we used in silico-based functional genomic analysis to identify drought-responsive genes in tef and validated their expression using quantitative RT-PCR. RESULTS We identified about 729 drought-responsive genes so far reported in six crop plants, including rice, wheat, maize, barley, sorghum, pearl millet, and the model plant Arabidopsis, and reported 20 genes having high-level of GO terms related to drought, and significantly enriched in several biological and molecular function categories. These genes were found to play diverse roles, including water and fluid transport, resistance to high salt, cold, and drought stress, abscisic acid (ABA) signaling, de novo DNA methylation, and transcriptional regulation in tef and other crops. Our analysis revealed substantial differences in the conserved domains of some tef genes from well-studied rice orthologs. We further analyzed the expression of sixteen tef orthologs using quantitative RT-PCR in response to PEG-induced osmotic stress. CONCLUSIONS The findings showed differential regulation of some drought-responsive genes in shoots, roots, or both tissues. Hence, the genes identified in this study may be promising candidates for trait improvement in crops via transgenic or gene-editing technologies.
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Affiliation(s)
- Abreham Bekele-Alemu
- Laboratory of Plant Molecular Biology and Biotechnology, Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Ayalew Ligaba-Osena
- Laboratory of Plant Molecular Biology and Biotechnology, Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA.
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Nidumolu LCM, Lorilla KM, Chakravarty I, Uhde-Stone C. Soybean Root Transcriptomics: Insights into Sucrose Signaling at the Crossroads of Nutrient Deficiency and Biotic Stress Responses. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112117. [PMID: 37299096 DOI: 10.3390/plants12112117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023]
Abstract
Soybean (Glycine max) is an important agricultural crop, but nutrient deficiencies frequently limit soybean production. While research has advanced our understanding of plant responses to long-term nutrient deficiencies, less is known about the signaling pathways and immediate responses to certain nutrient deficiencies, such as Pi and Fe deficiencies. Recent studies have shown that sucrose acts as a long-distance signal that is sent in increased concentrations from the shoot to the root in response to various nutrient deficiencies. Here, we mimicked nutrient deficiency-induced sucrose signaling by adding sucrose directly to the roots. To unravel transcriptomic responses to sucrose acting as a signal, we performed Illumina RNA-sequencing of soybean roots treated with sucrose for 20 min and 40 min, compared to non-sucrose-treated controls. We obtained a total of 260 million paired-end reads, mapping to 61,675 soybean genes, some of which are novel (not yet annotated) transcripts. Of these, 358 genes were upregulated after 20 min, and 2416 were upregulated after 40 min of sucrose exposure. GO (gene ontology) analysis revealed a high proportion of sucrose-induced genes involved in signal transduction, particularly hormone, ROS (reactive oxygen species), and calcium signaling, in addition to regulation of transcription. In addition, GO enrichment analysis indicates that sucrose triggers crosstalk between biotic and abiotic stress responses.
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Affiliation(s)
| | - Kristina Mae Lorilla
- Department of Biological Sciences, California State University, East Bay, Hayward, CA 94542, USA
| | - Indrani Chakravarty
- Department of Biological Sciences, California State University, East Bay, Hayward, CA 94542, USA
| | - Claudia Uhde-Stone
- Department of Biological Sciences, California State University, East Bay, Hayward, CA 94542, USA
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Zhao L, Jia T, Jiao Q, Hu X. Research Progress in J-Proteins in the Chloroplast. Genes (Basel) 2022; 13:1469. [PMID: 36011380 PMCID: PMC9407819 DOI: 10.3390/genes13081469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
The J-proteins, also called DNAJ-proteins or heat shock protein 40 (HSP40), are one of the famous molecular chaperones. J-proteins, HSP70s and other chaperones work together as constitute ubiquitous types of molecular chaperone complex, which function in a wide variety of physiological processes. J-proteins are widely distributed in major cellular compartments. In the chloroplast of higher plants, around 18 J-proteins and multiple J-like proteins are present; however, the functions of most of them remain unclear. During the last few years, important progress has been made in the research on their roles in plants. There is increasing evidence that the chloroplast J-proteins play essential roles in chloroplast development, photosynthesis, seed germination and stress response. Here, we summarize recent research advances on the roles of J-proteins in the chloroplast, and discuss the open questions that remain in this field.
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Affiliation(s)
- Lu Zhao
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Ting Jia
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Qingsong Jiao
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Xueyun Hu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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